diff --git a/app/assets/templates/experiment_422/experiment.json b/app/assets/templates/experiment_422/experiment.json
index 49fb8f5b3..580cd4f8b 100644
--- a/app/assets/templates/experiment_422/experiment.json
+++ b/app/assets/templates/experiment_422/experiment.json
@@ -1 +1 @@
-{"experiment":{"id":422,"name":"CRISPR transformations with Agrobacterium tumefaciens","description":"The clustered regularly interspaced short palindromic repeats(CRISPR) associated Cas9/sgRNA system is a novel targeted genome-editing technique derived from the bacterial immune system. 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\ No newline at end of file
diff --git a/app/assets/templates/experiment_423/experiment.json b/app/assets/templates/experiment_423/experiment.json
index 96b275a41..07302a29c 100644
--- a/app/assets/templates/experiment_423/experiment.json
+++ b/app/assets/templates/experiment_423/experiment.json
@@ -1 +1 @@
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For cell lysates, centrifuge at 40 000–50 000 x g for 30 minutes. Close and lock the lid and then start the centrifuge cycle. If excessive vibration occurs, or if a crack is heard or tube breakage is suspected, switch off the unit. Open the centrifuge only after the signal for the end of centrifugation is seen. Remove the sealed buckets (not tubes) slowly and carefully to prevent re-suspension. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-18T14:12:05.603Z","updated_at":"2019-02-11T12:51:42.964Z","last_modified_by_id":1,"protocol_id":3403},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2096,"name":"Capture","due_date":null,"description":null,"x":36,"y":0,"my_module_group_id":1190,"created_at":"2018-11-08T10:28:48.971Z","updated_at":"2018-12-21T13:25:20.382Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":1,"experiment_id":423,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":6023,"input_id":2097,"output_id":2096}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3405,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2096,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-08T10:28:49.025Z","updated_at":"2018-12-24T09:19:06.021Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4286,"name":"Preparation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the preparation guidelines for capture task.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:49.261Z","updated_at":"2018-12-24T09:19:05.983Z","last_modified_by_id":202,"protocol_id":3405},"checklists":[{"checklist":{"id":968,"name":"Guideline:","step_id":4286,"created_at":"2018-12-21T13:27:09.411Z","updated_at":"2018-12-21T13:27:09.411Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3984,"text":"Equilibrate all materials to the temperature at which the separation will be performed.","checked":false,"checklist_id":968,"created_at":"2018-12-21T13:27:09.413Z","updated_at":"2018-12-21T13:27:09.413Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3985,"text":"Eliminate air by flushing column end pieces with buffer. Ensure no air is trapped under the column net. Close column outlet leaving 1–2 cm of the buffer in the column.","checked":false,"checklist_id":968,"created_at":"2018-12-21T13:27:09.421Z","updated_at":"2018-12-21T13:27:09.421Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3986,"text":"Gently resuspend the medium. For media not supplied in suspension, use a medium: buffer ratio of approximately 1:2 to produce a suspension for mixing during rehydration. Avoid using magnetic stirrers since they may damage the matrix.","checked":false,"checklist_id":968,"created_at":"2018-12-21T13:27:09.427Z","updated_at":"2018-12-21T13:27:09.427Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4279,"name":"Stop the pump and close the column outlet.","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003eRemove the top piece and carefully fill the rest of the column with buffer to form an upward meniscus at the top. Insert the adaptor into the column at an angle, ensuring that no air is trapped under the net. Slide the adaptor slowly down the column (the outlet of the adaptor should be open) until the mark is reached. Lock the adaptor in position. Connect the column to the pump and begin equilibration. Re-position the adaptor if necessary.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:49.069Z","updated_at":"2018-12-21T13:29:08.411Z","last_modified_by_id":202,"protocol_id":3405},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4283,"name":"Column fill and setting the column outlet.","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003eEstimate the amount of resuspended medium required and our the required volume of the medium into the column. Pouring down a glass rod held against the wall of the column will minimize the introduction of air bubbles. \u003cstrong\u003eImmediately fill the column with buffer\u003c/strong\u003e. Mount the column top piece and connect to a pump. Open the column outlet and set the pump to the desired flow rate. If the recommended flow rate cannot be obtained, use the maximum flow rate the pump can deliver. \u003cstrong\u003eDo not exceed the maximum operating pressure of the medium or column.\u003c/strong\u003e Maintain the packing flow rate for at least 3 column volumes after a constant bed height is obtained. Mark the bed height on the column. Do not exceed 75% of the packing flow rate during any purification.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:49.179Z","updated_at":"2018-12-21T13:28:40.937Z","last_modified_by_id":202,"protocol_id":3405},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2097,"name":"Polishing","due_date":null,"description":null,"x":72,"y":0,"my_module_group_id":1190,"created_at":"2018-11-08T10:28:49.322Z","updated_at":"2018-12-21T13:25:20.391Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":423,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":6024,"input_id":2098,"output_id":2097}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3407,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2097,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-08T10:28:49.390Z","updated_at":"2018-12-24T09:51:46.809Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4287,"name":"Before applying a new sample","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eRe-equilibrate column with buffer until the baseline of the monitored signal is stable. Proteins can be monitored at\u003cstrong\u003e 280 nm.\u003c/strong\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:49.408Z","updated_at":"2018-12-21T13:31:50.804Z","last_modified_by_id":202,"protocol_id":3407},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4290,"name":"Polishing","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003e\u003cstrong\u003eEquilibrate with 2 column volumes of the buffer\u003c/strong\u003e at a recommended flow rate (See the table). Apply a sample volume equivalent to between 0.3% and 4% of the bed volume. For most applications, the sample volume should not exceed 2% to achieve high resolution. Smaller sample volumes generally lead to an improved resolution. \u003cbr\u003e\u003cstrong\u003eElute with 1 column volume of buffer solution\u003c/strong\u003e (10 to 50 mM sodium phosphate, 150 mM sodium chloride, pH 7.0 to 7.4, or select the buffer in which the sample should be stored or solubilized for the next step). The sample should be fully dissolved. 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Use a low flow rate to avoid gap formation. Perform a column performance test (see below) and \u003cstrong\u003edetermine the limit for maximum pressure over the packed bed is recommended.\u003c/strong\u003e If this has already been done, go to Step 2.\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eColumn efficiency test (the efficiency and peak asymmetry can be determined as follows): \u003c/strong\u003e\u003cbr\u003e\u003cbr\u003e\n\u003c/div\u003e\n\u003col\u003e\n\u003cli style=\"text-align: justify;\"\u003e\n\u003cdiv\u003eEquilibrate the packed column in distilled water or buffer at the flow rate recommended in the product instructions. \u003c/div\u003e\n\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003e\n\u003cdiv\u003eInject 2% acetone (20mg/mL in water) in a volume equivalent to 0.2% to 0.4% of the geometrical bed volume. \u003c/div\u003e\n\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003e\n\u003cdiv\u003eMonitor UV absorbance at 280 nm and determine the elution volume for acetone. \u003c/div\u003e\n\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003e\n\u003cdiv\u003e\n\u003cstrong\u003eCalculate column efficiency\u003c/strong\u003e, that is, the number of theoretical plates per meter (N/m). N/m= 5.54 x (\u003cspan style=\"color: inherit; font-size: inherit;\"\u003eVe x \u003c/span\u003eW\u003csub\u003e1/2\u003c/sub\u003e)\u003csup\u003e2\u003c/sup\u003e x 1/L ; where V\u003csub\u003ee\u003c/sub\u003e =peak elution (retention) volume; W\u003csub\u003e1/2\u003c/sub\u003e=peak width at half peak height; L= bed height (m)\u003c/div\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cdiv style=\"text-align: justify;\"\u003e\n\u003cstrong\u003eCalculate the asymmetry factor\u003c/strong\u003e A\u003csub\u003es\u003c/sub\u003e= b/a; where a=first half width at 10% peak height and b=second half width at 10% peak height\u003c/div\u003e\n\u003c/li\u003e\n\u003c/ol\u003e\n\u003cdiv\u003e[~tiny_mce_id:132]\u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-19T07:24:14.116Z","updated_at":"2018-12-24T09:51:46.772Z","last_modified_by_id":202,"protocol_id":3407},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2098,"name":"Analysis","due_date":null,"description":null,"x":105,"y":0,"my_module_group_id":1190,"created_at":"2018-11-08T10:28:49.665Z","updated_at":"2018-12-21T13:25:20.388Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":3,"experiment_id":423,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3409,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2098,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-08T10:28:49.719Z","updated_at":"2018-12-24T09:22:25.677Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5226,"name":"Purity analysis: SDS PAGE","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cem\u003e\u003cstrong\u003eSodium dodecyl \u003c/strong\u003e\u003c/em\u003esulfate polyacrylamide\u003cem\u003e\u003cstrong\u003e gel electrophoresis (SDS-PAGE) is a technology commonly used in protein purification and analysis.\u003c/strong\u003e \u003cstrong\u003eSDS-PAGE can separate proteins according to the differences in the charge and the different mobility due to different molecular sizes\u003c/strong\u003e\u003c/em\u003e. If the protein sample has been highly purified and contains only one protein, the results would show a single protein band after SDS-PAGE separation. However, when there are multiple proteins in the protein samples, different proteins can be separated into multiple protein bands through SDS-PAGE. Therefore, SDS-PAGE technology provides a direct way to analyze the purity of protein samples.\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-19T08:41:05.893Z","updated_at":"2018-12-24T09:22:25.629Z","last_modified_by_id":202,"protocol_id":3409},"checklists":[{"checklist":{"id":970,"name":"Guideline:","step_id":5226,"created_at":"2018-12-21T13:36:26.307Z","updated_at":"2018-12-21T13:36:26.307Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3994,"text":"Add 2 µL of 6X SDS loading buffer to 5–10 µL of supernatant from crude extracts, cell lysates or purified fractions as appropriate.","checked":false,"checklist_id":970,"created_at":"2018-12-21T13:36:26.308Z","updated_at":"2018-12-21T13:36:26.308Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3995,"text":"Vortex briefly and heat for 5 minutes at +90 to +100 °C.","checked":false,"checklist_id":970,"created_at":"2018-12-21T13:36:26.316Z","updated_at":"2018-12-21T13:36:26.316Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3996,"text":"Load the samples onto an SDS-polyacrylamide gel.","checked":false,"checklist_id":970,"created_at":"2018-12-21T13:36:26.323Z","updated_at":"2018-12-21T13:36:26.323Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3997,"text":"Run the gel and stain with Coomassie Blue or silver.","checked":false,"checklist_id":970,"created_at":"2018-12-21T13:36:26.329Z","updated_at":"2018-12-21T13:36:26.329Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5233,"name":"Protein Identity Analysis: Mass Spectromety","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv\u003eSelect the appropriate MS Instrument. Samples are measured according to Mass Spectrometer manual. After the MS data is collected, the next step is to\u003cstrong\u003e perform a database search to identify the proteins and/or peptides analyzed by MS\u003c/strong\u003e. A number of parameters can affect the outcome of a database search, and, ultimately, search parameters should consider the history of the sample, \u003cstrong\u003esuch as organism, enzymatic or chemical digestion, and reduction/alkylation steps\u003c/strong\u003e. Differences among search engines can include the scoring algorithm, whether it considers data quality, and whether it considers all fragment ion types or only a subset. Often, the best way to select an algorithm is to examine the details regarding data-format compatibility and necessary features, test it on a data set, and compare the results to what is expected. \u003c/div\u003e\n\u003cbr\u003e\n\u003cdiv class=\"row\" style=\"text-align: justify;\"\u003e\n\u003cdiv class=\"col-xs-12\"\u003e\n\u003cdiv class=\"ql-editor\"\u003e \u003c/div\u003e\n\u003c/div\u003e\n\u003c/div\u003e\n\u003cdiv class=\"row\" style=\"text-align: justify;\"\u003e \u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-19T09:32:37.616Z","updated_at":"2018-12-21T13:38:06.144Z","last_modified_by_id":202,"protocol_id":3409},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[{"id":539,"step_id":5233,"table_id":676}],"tables":[{"id":676,"created_at":"2018-12-19T09:32:37.619Z","updated_at":"2018-12-21T13:38:06.147Z","created_by_id":202,"last_modified_by_id":202,"name":"Commonly used mass spectrometers and their characteristics","team_id":1,"contents":"eyJkYXRhIjpbWyJJbnN0cnVtZW50IiwiTWFzcyByZXNvbHV0aW9uIiwiTWFz\ncyBhY2N1cmFjeSIsIlNlbnNpdGl2aXR5IiwibS96IHJhbmdlIiwiU2NhbiBy\nYXRlIiwiRHluYW1pYyByYW5nZSIsIk1TL01TIGNhcGFiaWxpdHkiLCJJb24g\nU291cmNlIiwiTWFpbiBhcHBsaWNhdGlvbnMiXSxbIlFJVCIsIjEwMDAiLCIx\nMDDigJMxMDAwIHBwbSIsInBpY29tb2xlIiwiNTDigJMyMDAwOyAyMDDigJM0\nMDAwIiwibW9kZXJhdGUiLCIxIEUzIiwiTVMiLCJFU0kiLCJwcm90ZWluIGlk\nZW50aWZpY2F0aW9uIG9mIGxvdyBjb21wbGV4IHNhbXBsZXM7IFBUTSBpZGVu\ndGlmaWNhdGlvbiJdLFsiVE9GIiwiMTAsMDAw4oCTMjAsMDAwIiwiMTDigJMy\nMCBwcG1iOyA8NSBwcG1jIiwiZmVtdG9tb2xlIiwibm8gdXBwZXIgbGltaXQi\nLCJmYXN0IiwiMSBFNCIsIm4vYWUiLCJNQUxESSIsInByb3RlaW4gaWRlbnRp\nZmljYXRpb24gZnJvbSBpbi1nZWwgZGlnZXN0aW9uIG9mIGdlbCBzZXBhcmF0\nZWQgcHJvdGVpbiBiYW5kIGJ5IHBlcHRpZGUgbWFzcyBmaW5nZXJwcmludGlu\nZyJdLFsiVE9GLVRPRiIsIjEwLDAwMOKAkzIwLDAwMCIsIjEw4oCTMjAgcHBt\nYjsgPDUgcHBtYyIsImZlbXRvbW9sZSIsIm5vIHVwcGVyIGxpbWl0IiwiZmFz\ndCIsIjEgRTQiLCJNUy9NUyIsIk1BTERJIiwicHJvdGVpbiBpZGVudGlmaWNh\ndGlvbiBmcm9tIGluLWdlbCBkaWdlc3Rpb24gb2YgZ2VsIHNlcGFyYXRlZCBw\ncm90ZWluIGJhbmQgYnkgcGVwdGlkZSBtYXNzIGZpbmdlcnByaW50aW5nIG9y\nIHNlcXVlbmNlIHRhZ2dpbmcgdmlhIENJRCBNUy9NUy4iXSxbIlEtcS1UT0Yi\nLCIxMCwwMDDigJMyMCwwMDAiLCIxMOKAkzIwIHBwbWI7IDw1IHBwbWMiLCJm\nZW10b21vbGUiLCJubyB1cHBlciBsaW1pdCIsIm1vZGVyYXRlIHRvIGZhc3Qi\nLCIxIEU0IiwiTVMvTVMiLCJNQUxESTsgRVNJIiwicHJvdGVpbiBpZGVudGlm\naWNhdGlvbiBmcm9tIGNvbXBsZXggcGVwdGlkZSBtaXh0dXJlczsgaW50YWN0\nIHByb3RlaW4gYW5hbHlzaXM7IFBUTSBpZGVudGlmaWNhdGlvbiJdXX0=\n","data_vector":"JzAwMCc6NTAsNTQsOTEsOTUsMTM5LDE0MyAnMSc6MzYsNjcsMTA4LDE1OCAn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\ndG9mJzo4NyAndXBwZXInOjY0LDEwNSwxNTMgJ3ZpYSc6MTMx\n"}]},{"step":{"id":4643,"name":"Quantity analysis: Bradford Assay","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow guidelines below to perform a Bradford assay. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-19T08:02:56.820Z","updated_at":"2018-12-24T09:20:53.287Z","last_modified_by_id":202,"protocol_id":3409},"checklists":[{"checklist":{"id":969,"name":"Guideline:","step_id":4643,"created_at":"2018-12-21T13:35:09.660Z","updated_at":"2018-12-21T13:35:09.660Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3987,"text":"Prepare five to eight dilutions of BSA standard with a range of 5 to 100 µg protein.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.662Z","updated_at":"2018-12-21T13:35:09.662Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3988,"text":"Dilute protein samples to obtain 5-100 µg protein/30 µL.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.669Z","updated_at":"2018-12-21T13:35:09.669Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3989,"text":"Set two blank tubes. For the standard curve, add 30 µL of water instead of the standard solution. For the unknown protein samples, add 30 µL protein preparation buffer instead. Protein solutions are normally assayed in duplicate or triplicate.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.675Z","updated_at":"2018-12-21T13:35:09.675Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3990,"text":"Add 1.5 mL of Bradford reagent to each tube and mix well.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.682Z","updated_at":"2018-12-21T13:35:09.682Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3991,"text":"Incubate at room temperature for at least 5 min.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.688Z","updated_at":"2018-12-21T13:35:09.688Z","created_by_id":null,"last_modified_by_id":null,"position":4},{"id":3992,"text":"Absorbance will increase over time; samples should incubate at RT for no more than 1 h.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.703Z","updated_at":"2018-12-21T13:35:09.703Z","created_by_id":null,"last_modified_by_id":null,"position":5},{"id":3993,"text":"Measure absorbance at 595 nm.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.710Z","updated_at":"2018-12-21T13:35:09.710Z","created_by_id":null,"last_modified_by_id":null,"position":6}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]}],"my_module_groups":[{"id":1190,"created_at":"2018-12-21T13:25:20.378Z","updated_at":"2018-12-21T13:25:20.378Z","created_by_id":202,"experiment_id":423}]}
\ No newline at end of file
+{"experiment":{"id":423,"name":"Antibody Purification","description":"Antibody purification involves selective enrichment or specific isolation of antibodies from serum, ascites fluid or cell culture supernatant of a hybridoma cell line. Purification methods range from very crude to highly specific.\r\nOnce they are purified (and possibly after labelling them with an enzyme or fluorescent tag), these antibodies can be used directly to probe the specific antigen in Western blotting, ELISA and other applications.","project_id":223,"created_by_id":202,"last_modified_by_id":202,"archived":false,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-08T10:28:48.389Z","updated_at":"2018-12-21T13:26:16.207Z","workflowimg_file_name":"wimg20181221-1-12rsihs.png","workflowimg_content_type":"image/png","workflowimg_file_size":1460,"workflowimg_updated_at":"2018-12-21T13:26:16.207Z","uuid":"289dac5b-9264-4c7c-8edf-845af442906b"},"my_modules":[{"my_module":{"id":2095,"name":"Buffer exchange and desalting","due_date":null,"description":null,"x":0,"y":0,"my_module_group_id":1190,"created_at":"2018-11-08T10:28:48.686Z","updated_at":"2018-12-21T13:25:20.385Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":0,"experiment_id":423,"state":"uncompleted","completed_on":null},"outputs":[{"id":6022,"input_id":2096,"output_id":2095}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3403,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2095,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-08T10:28:48.743Z","updated_at":"2019-02-11T12:51:43.301Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5209,"name":"Centrifuge set up","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow guidelines for centrifuge set up.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-18T14:10:46.319Z","updated_at":"2018-12-24T09:16:18.589Z","last_modified_by_id":202,"protocol_id":3403},"checklists":[{"checklist":{"id":934,"name":"Before use:","step_id":5209,"created_at":"2018-12-18T14:10:46.321Z","updated_at":"2018-12-18T14:10:46.321Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3838,"text":"Check the inside of the centrifuge and the rotors to ensure that everything is dry.","checked":false,"checklist_id":934,"created_at":"2018-12-18T14:10:46.323Z","updated_at":"2018-12-21T12:47:12.263Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3839,"text":"Check that shock-absorbing pads are in the bottom of the centrifuge buckets.","checked":false,"checklist_id":934,"created_at":"2018-12-18T14:10:46.331Z","updated_at":"2018-12-18T14:10:46.331Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3840,"text":"Balance the opposing buckets by weighing them with their tubes on an open two-pan balance.","checked":false,"checklist_id":934,"created_at":"2018-12-18T14:10:46.337Z","updated_at":"2018-12-18T14:10:46.337Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3841,"text":"Never fill centrifuge tubes to more than three-quarters capacity.","checked":false,"checklist_id":934,"created_at":"2018-12-18T14:10:46.344Z","updated_at":"2018-12-18T14:10:46.344Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3842,"text":"Symmetrically distribute balanced tubes in opposing buckets. Always operate the centrifuge with all buckets in place, even if two opposing buckets are empty.","checked":false,"checklist_id":934,"created_at":"2018-12-18T14:10:46.354Z","updated_at":"2018-12-18T14:10:46.354Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4273,"name":"Buffer exchange and desalting","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003e\u003cstrong\u003eFill the syringe with buffer.\u003c/strong\u003e To avoid introducing air into the column, connect the column \"drop to drop\" to the syringe (via the adapter). Wash the column. Use 25 mL buffer at 5 mL/min to remove completely the 20% ethanol (supplied as storage buffer). If air is trapped in the column, wash with degassed buffer until the air disappears. Air bubbles introduced onto the column by accident during sample application do not influence the separation.\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eApplying the sample.\u003c/strong\u003e Use a 2–5 mL syringe at a flow rate between 1–10 mL/min. Discard the liquid eluted from the column. If the sample volume is less than 1.5 mL, change to buffer and proceed with the injection until a total of 1.5 mL has been eluted. Discard the eluted liquid.pter). Elute the protein with the appropriate volume.\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eSelect volume from the table.\u003c/strong\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:48.761Z","updated_at":"2018-12-20T13:33:54.642Z","last_modified_by_id":202,"protocol_id":3403},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[{"id":438,"step_id":4273,"table_id":554}],"tables":[{"id":554,"created_at":"2018-11-08T10:28:48.787Z","updated_at":"2018-12-20T13:33:54.646Z","created_by_id":202,"last_modified_by_id":202,"name":"","team_id":1,"contents":"eyJkYXRhIjpbWyJTYW1wbGUgbG9hZCAobUwpIiwiQWRkIGJ1ZmZlciAobUwp\nIiwiRWx1dGUgYW5kIGNvbGxlY3QgKG1MKSIsIllpZWxkICglKSIsIlJlbWFp\nbmluZyBzYWx0ICglKSIsIkRpbHV0aW9uIGZhY3RvciAoJSkiXSxbIjAsMjUi\nLCIxLDI1IiwiMSwwIiwiPjk1IiwiMCwwIiwiNCwwIl0sWyIwLDUwIiwiMSww\nIiwiMSw1IiwiPjk1IiwiPDAsMSIsIjMsMCJdLFsiMSwwMCIsIjAsNSIsIjIs\nMCIsIj45NSIsIjwwLDIiLCIyLDAiXSxbIjEsNTAiLCIwIiwiMiwwIiwiPjk1\nIiwiPDAsMiIsIjEsMyJdXX0=\n","data_vector":"JzAnOjE2LDIxLDIzLDI0LDI2LDI3LDMwLDM0LDM3LDQwLDQzLDQ1LDQ4LDUx\nLDUzLDU1ICcwMCc6MzkgJzEnOjE4LDIwLDI5LDMxLDM1LDM4LDQ5LDU3ICcy\nJzo0Miw0Niw0Nyw1Miw1NiAnMjUnOjE3LDE5ICczJzozNiw1OCAnNCc6MjUg\nJzUnOjMyLDQxICc1MCc6MjgsNTAgJzk1JzoyMiwzMyw0NCw1NCAnYWRkJzo0\nICdhbmQnOjggJ2J1ZmZlcic6NSAnY29sbGVjdCc6OSAnZGlsdXRpb24nOjE0\nICdlbHV0ZSc6NyAnZmFjdG9yJzoxNSAnbG9hZCc6MiAnbWwnOjMsNiwxMCAn\ncmVtYWluaW5nJzoxMiAnc2FsdCc6MTMgJ3NhbXBsZSc6MSAneWllbGQnOjEx\n"}]},{"step":{"id":5210,"name":"Centrifugation of samples","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003eSwitch on and follow the manufacturer's instructions to set the centrifugation conditions.\u003cbr\u003eFor small sample volumes or proteins that adsorb non-specifically to filters, centrifuge at 10 000 x g for 15 minutes. For cell lysates, centrifuge at 40 000–50 000 x g for 30 minutes. Close and lock the lid and then start the centrifuge cycle. If excessive vibration occurs, or if a crack is heard or tube breakage is suspected, switch off the unit. Open the centrifuge only after the signal for the end of centrifugation is seen. Remove the sealed buckets (not tubes) slowly and carefully to prevent re-suspension. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-18T14:12:05.603Z","updated_at":"2019-02-11T12:51:42.964Z","last_modified_by_id":1,"protocol_id":3403},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2096,"name":"Capture","due_date":null,"description":null,"x":36,"y":0,"my_module_group_id":1190,"created_at":"2018-11-08T10:28:48.971Z","updated_at":"2018-12-21T13:25:20.382Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":1,"experiment_id":423,"state":"uncompleted","completed_on":null},"outputs":[{"id":6023,"input_id":2097,"output_id":2096}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3405,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2096,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-08T10:28:49.025Z","updated_at":"2018-12-24T09:19:06.021Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4286,"name":"Preparation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the preparation guidelines for capture task.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:49.261Z","updated_at":"2018-12-24T09:19:05.983Z","last_modified_by_id":202,"protocol_id":3405},"checklists":[{"checklist":{"id":968,"name":"Guideline:","step_id":4286,"created_at":"2018-12-21T13:27:09.411Z","updated_at":"2018-12-21T13:27:09.411Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3984,"text":"Equilibrate all materials to the temperature at which the separation will be performed.","checked":false,"checklist_id":968,"created_at":"2018-12-21T13:27:09.413Z","updated_at":"2018-12-21T13:27:09.413Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3985,"text":"Eliminate air by flushing column end pieces with buffer. Ensure no air is trapped under the column net. Close column outlet leaving 1–2 cm of the buffer in the column.","checked":false,"checklist_id":968,"created_at":"2018-12-21T13:27:09.421Z","updated_at":"2018-12-21T13:27:09.421Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3986,"text":"Gently resuspend the medium. For media not supplied in suspension, use a medium: buffer ratio of approximately 1:2 to produce a suspension for mixing during rehydration. 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Connect the column to the pump and begin equilibration. Re-position the adaptor if necessary.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:49.069Z","updated_at":"2018-12-21T13:29:08.411Z","last_modified_by_id":202,"protocol_id":3405},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4283,"name":"Column fill and setting the column outlet.","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003eEstimate the amount of resuspended medium required and our the required volume of the medium into the column. Pouring down a glass rod held against the wall of the column will minimize the introduction of air bubbles. \u003cstrong\u003eImmediately fill the column with buffer\u003c/strong\u003e. Mount the column top piece and connect to a pump. Open the column outlet and set the pump to the desired flow rate. If the recommended flow rate cannot be obtained, use the maximum flow rate the pump can deliver. \u003cstrong\u003eDo not exceed the maximum operating pressure of the medium or column.\u003c/strong\u003e Maintain the packing flow rate for at least 3 column volumes after a constant bed height is obtained. Mark the bed height on the column. Do not exceed 75% of the packing flow rate during any purification.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:49.179Z","updated_at":"2018-12-21T13:28:40.937Z","last_modified_by_id":202,"protocol_id":3405},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2097,"name":"Polishing","due_date":null,"description":null,"x":72,"y":0,"my_module_group_id":1190,"created_at":"2018-11-08T10:28:49.322Z","updated_at":"2018-12-21T13:25:20.391Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":423,"state":"uncompleted","completed_on":null},"outputs":[{"id":6024,"input_id":2098,"output_id":2097}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3407,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2097,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-08T10:28:49.390Z","updated_at":"2018-12-24T09:51:46.809Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4287,"name":"Before applying a new sample","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eRe-equilibrate column with buffer until the baseline of the monitored signal is stable. Proteins can be monitored at\u003cstrong\u003e 280 nm.\u003c/strong\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:49.408Z","updated_at":"2018-12-21T13:31:50.804Z","last_modified_by_id":202,"protocol_id":3407},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4290,"name":"Polishing","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003e\u003cstrong\u003eEquilibrate with 2 column volumes of the buffer\u003c/strong\u003e at a recommended flow rate (See the table). Apply a sample volume equivalent to between 0.3% and 4% of the bed volume. For most applications, the sample volume should not exceed 2% to achieve high resolution. Smaller sample volumes generally lead to an improved resolution. \u003cbr\u003e\u003cstrong\u003eElute with 1 column volume of buffer solution\u003c/strong\u003e (10 to 50 mM sodium phosphate, 150 mM sodium chloride, pH 7.0 to 7.4, or select the buffer in which the sample should be stored or solubilized for the next step). The sample should be fully dissolved. Centrifuge or filter to remove particulate matter.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-08T10:28:49.496Z","updated_at":"2018-12-21T13:31:21.770Z","last_modified_by_id":202,"protocol_id":3407},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[{"id":439,"step_id":4290,"table_id":555}],"tables":[{"id":555,"created_at":"2018-11-08T10:28:49.522Z","updated_at":"2018-12-21T13:31:21.773Z","created_by_id":202,"last_modified_by_id":202,"name":"Separation options","team_id":1,"contents":"eyJkYXRhIjpbWyJGcmFjdGlvbmF0aW9uIHJhbmdlLCBNciAoZ2xvYnVsYXIg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\nIDUwICIsIjIiLCIwLDA3NSJdXX0=\n","data_vector":"JzAnOjM3LDUyLDY3LDgyLDk3LDExMiwxMjcsMTQyICcwNzUnOjUzLDE0MyAn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\nLDExOCwxMjQsMTMzLDEzOSAndHlwaWNhbCc6MTEgJ3ZvbHVtZSc6Nw==\n"}]},{"step":{"id":5224,"name":"For the first time use","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv style=\"text-align: justify;\"\u003eRemove storage solution. Applying 2 column volume of distilled water at room temperature. Use a low flow rate to avoid gap formation. Perform a column performance test (see below) and \u003cstrong\u003edetermine the limit for maximum pressure over the packed bed is recommended.\u003c/strong\u003e If this has already been done, go to Step 2.\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eColumn efficiency test (the efficiency and peak asymmetry can be determined as follows): \u003c/strong\u003e\u003cbr\u003e\u003cbr\u003e\n\u003c/div\u003e\n\u003col\u003e\n\u003cli style=\"text-align: justify;\"\u003e\n\u003cdiv\u003eEquilibrate the packed column in distilled water or buffer at the flow rate recommended in the product instructions. \u003c/div\u003e\n\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003e\n\u003cdiv\u003eInject 2% acetone (20mg/mL in water) in a volume equivalent to 0.2% to 0.4% of the geometrical bed volume. \u003c/div\u003e\n\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003e\n\u003cdiv\u003eMonitor UV absorbance at 280 nm and determine the elution volume for acetone. \u003c/div\u003e\n\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003e\n\u003cdiv\u003e\n\u003cstrong\u003eCalculate column efficiency\u003c/strong\u003e, that is, the number of theoretical plates per meter (N/m). N/m= 5.54 x (\u003cspan style=\"color: inherit; font-size: inherit;\"\u003eVe x \u003c/span\u003eW\u003csub\u003e1/2\u003c/sub\u003e)\u003csup\u003e2\u003c/sup\u003e x 1/L ; where V\u003csub\u003ee\u003c/sub\u003e =peak elution (retention) volume; W\u003csub\u003e1/2\u003c/sub\u003e=peak width at half peak height; L= bed height (m)\u003c/div\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cdiv style=\"text-align: justify;\"\u003e\n\u003cstrong\u003eCalculate the asymmetry factor\u003c/strong\u003e A\u003csub\u003es\u003c/sub\u003e= b/a; where a=first half width at 10% peak height and b=second half width at 10% peak height\u003c/div\u003e\n\u003c/li\u003e\n\u003c/ol\u003e\n\u003cdiv\u003e[~tiny_mce_id:132]\u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-19T07:24:14.116Z","updated_at":"2018-12-24T09:51:46.772Z","last_modified_by_id":202,"protocol_id":3407},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2098,"name":"Analysis","due_date":null,"description":null,"x":105,"y":0,"my_module_group_id":1190,"created_at":"2018-11-08T10:28:49.665Z","updated_at":"2018-12-21T13:25:20.388Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":3,"experiment_id":423,"state":"uncompleted","completed_on":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3409,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2098,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-08T10:28:49.719Z","updated_at":"2018-12-24T09:22:25.677Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5226,"name":"Purity analysis: SDS PAGE","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cem\u003e\u003cstrong\u003eSodium dodecyl \u003c/strong\u003e\u003c/em\u003esulfate polyacrylamide\u003cem\u003e\u003cstrong\u003e gel electrophoresis (SDS-PAGE) is a technology commonly used in protein purification and analysis.\u003c/strong\u003e \u003cstrong\u003eSDS-PAGE can separate proteins according to the differences in the charge and the different mobility due to different molecular sizes\u003c/strong\u003e\u003c/em\u003e. If the protein sample has been highly purified and contains only one protein, the results would show a single protein band after SDS-PAGE separation. However, when there are multiple proteins in the protein samples, different proteins can be separated into multiple protein bands through SDS-PAGE. Therefore, SDS-PAGE technology provides a direct way to analyze the purity of protein samples.\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-19T08:41:05.893Z","updated_at":"2018-12-24T09:22:25.629Z","last_modified_by_id":202,"protocol_id":3409},"checklists":[{"checklist":{"id":970,"name":"Guideline:","step_id":5226,"created_at":"2018-12-21T13:36:26.307Z","updated_at":"2018-12-21T13:36:26.307Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3994,"text":"Add 2 µL of 6X SDS loading buffer to 5–10 µL of supernatant from crude extracts, cell lysates or purified fractions as appropriate.","checked":false,"checklist_id":970,"created_at":"2018-12-21T13:36:26.308Z","updated_at":"2018-12-21T13:36:26.308Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3995,"text":"Vortex briefly and heat for 5 minutes at +90 to +100 °C.","checked":false,"checklist_id":970,"created_at":"2018-12-21T13:36:26.316Z","updated_at":"2018-12-21T13:36:26.316Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3996,"text":"Load the samples onto an SDS-polyacrylamide gel.","checked":false,"checklist_id":970,"created_at":"2018-12-21T13:36:26.323Z","updated_at":"2018-12-21T13:36:26.323Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3997,"text":"Run the gel and stain with Coomassie Blue or silver.","checked":false,"checklist_id":970,"created_at":"2018-12-21T13:36:26.329Z","updated_at":"2018-12-21T13:36:26.329Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5233,"name":"Protein Identity Analysis: Mass Spectromety","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv\u003eSelect the appropriate MS Instrument. Samples are measured according to Mass Spectrometer manual. After the MS data is collected, the next step is to\u003cstrong\u003e perform a database search to identify the proteins and/or peptides analyzed by MS\u003c/strong\u003e. A number of parameters can affect the outcome of a database search, and, ultimately, search parameters should consider the history of the sample, \u003cstrong\u003esuch as organism, enzymatic or chemical digestion, and reduction/alkylation steps\u003c/strong\u003e. Differences among search engines can include the scoring algorithm, whether it considers data quality, and whether it considers all fragment ion types or only a subset. 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protein.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.662Z","updated_at":"2018-12-21T13:35:09.662Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3988,"text":"Dilute protein samples to obtain 5-100 µg protein/30 µL.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.669Z","updated_at":"2018-12-21T13:35:09.669Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3989,"text":"Set two blank tubes. For the standard curve, add 30 µL of water instead of the standard solution. For the unknown protein samples, add 30 µL protein preparation buffer instead. Protein solutions are normally assayed in duplicate or triplicate.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.675Z","updated_at":"2018-12-21T13:35:09.675Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3990,"text":"Add 1.5 mL of Bradford reagent to each tube and mix well.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.682Z","updated_at":"2018-12-21T13:35:09.682Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3991,"text":"Incubate at room temperature for at least 5 min.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.688Z","updated_at":"2018-12-21T13:35:09.688Z","created_by_id":null,"last_modified_by_id":null,"position":4},{"id":3992,"text":"Absorbance will increase over time; samples should incubate at RT for no more than 1 h.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.703Z","updated_at":"2018-12-21T13:35:09.703Z","created_by_id":null,"last_modified_by_id":null,"position":5},{"id":3993,"text":"Measure absorbance at 595 nm.","checked":false,"checklist_id":969,"created_at":"2018-12-21T13:35:09.710Z","updated_at":"2018-12-21T13:35:09.710Z","created_by_id":null,"last_modified_by_id":null,"position":6}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]}],"my_module_groups":[{"id":1190,"created_at":"2018-12-21T13:25:20.378Z","updated_at":"2018-12-21T13:25:20.378Z","created_by_id":202,"experiment_id":423}]}
\ No newline at end of file
diff --git a/app/assets/templates/experiment_430/experiment.json b/app/assets/templates/experiment_430/experiment.json
index dc3b6ce3b..35ad4814a 100644
--- a/app/assets/templates/experiment_430/experiment.json
+++ b/app/assets/templates/experiment_430/experiment.json
@@ -1 +1 @@
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antibiotic stock","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eDilute the 10 mg/mL antibiotic stock solution 1:10 in sterile broth or water to achieve a 1 mg/mL solution.\u003cbr\u003e Dilute the 1 mg/mL solution 1:10 in sterile broth or water to achieve a 0.1 mg/mL solution\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T12:10:09.672Z","updated_at":"2018-12-20T13:06:27.384Z","last_modified_by_id":202,"protocol_id":3453},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4370,"name":"Prepare agar plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003ePrepare agar plates following guidelines bellow.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T12:22:03.852Z","updated_at":"2018-12-24T09:08:20.489Z","last_modified_by_id":202,"protocol_id":3453},"checklists":[{"checklist":{"id":966,"name":"Guidelines:","step_id":4370,"created_at":"2018-12-21T11:52:37.302Z","updated_at":"2018-12-21T11:52:37.302Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3975,"text":"Dispense appropriate amounts of antibiotic solution into the respective containers. Follow table steps.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.304Z","updated_at":"2018-12-21T11:52:37.304Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3976,"text":"For each agar plate, add 25 mL agar (now at a temperature of 50°C) into the container, mix well (avoid bubbles) and pour 25 ml into a petri dish labelled with the respective antibiotic concentration.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.311Z","updated_at":"2018-12-21T11:52:37.311Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3977,"text":"Pour a control agar plate without any antibiotic. Adjust the number if necessary.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.317Z","updated_at":"2018-12-21T11:52:37.317Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3978,"text":"Allow agar to set.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.324Z","updated_at":"2018-12-21T11:52:37.324Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3979,"text":"Dry the surface of the agar plates either in an incubator or in a laminar airflow hood for 30 min. Leave the lid ajar.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.330Z","updated_at":"2018-12-21T11:52:37.330Z","created_by_id":null,"last_modified_by_id":null,"position":4},{"id":3980,"text":"Mark the bottom of the agar plates to define an orientation.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.336Z","updated_at":"2018-12-21T11:52:37.336Z","created_by_id":null,"last_modified_by_id":null,"position":5}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[{"id":545,"step_id":4370,"table_id":682}],"tables":[{"id":682,"created_at":"2018-12-20T13:07:47.021Z","updated_at":"2018-12-24T09:08:20.452Z","created_by_id":202,"last_modified_by_id":202,"name":"","team_id":1,"contents":"eyJkYXRhIjpbWyJBbnRpbWljcm9iaWFsIGNvbmNlbnRyYXRpb24gKG1nL0wp\nIiwiVm9sdW1lIG9mIGFudGliaW90aWMgc3RvY2sgc29sdXRpb24gKM68TCki\nLCJGaW5hbCBjb25jZW50cmF0aW9uIHdoZW4gYWRkaW5nIDI1bUwgb2YgYWdh\nciJdLFsiMTAiLCIzMjAiLCIxMjgiXSxbIjEwIiwiMTYwIiwiNjQiXSxbIjEw\nIiwiODAiLCIzMiJdLFsiMTAiLCI0MCIsIjE2Il0sWyIxIiwiMjAwIiwiOCJd\nLFsiMSIsIjEwMCIsIjQiXSxbIjEiLCI1MCIsIjIiXSxbIjAuMSIsIjI1MCIs\nIjEiXSxbIjAuMSIsIjEyNSIsIjAuNSJdLFsiMC4xIiwiNjIuNSIsIjAuMjUi\nXSxbIjAuMSIsIjMxLjI1IiwiMS4xMjUiXV19\n","data_vector":"JzAuMSc6MzksNDIsNDUsNDggJzAuMjUnOjQ3ICcwLjUnOjQ0ICcxJzozMCwz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\nZW4nOjEz\n"}]},{"step":{"id":4367,"name":"Calculate the amount of antibiotic solutions","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003eAs the medium cools down, calculate the amount of antibiotic solutions (10, 1 and 0.1 mg/L) needed. The table is an example of the volumes needed for a concentration range between 0.125 and 128 mg/L for one 25 mL agar plate per concentration. Adjust if a different concentration range is needed. The volumes of antibiotic and agar can also be varied depending on the number of plates to be poured. As each agar plate can be used for up to 48 tests, more than one plate might be necessary if a larger amount of isolates is going to be tested.\u003cbr\u003e\u003cbr\u003eLabel sterile containers appropriately (glass Erlenmeyer flasks closed with metal caps, tinfoil caps or cotton buds) with the final antibiotic concentration.\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T11:07:28.842Z","updated_at":"2018-12-21T11:50:54.557Z","last_modified_by_id":202,"protocol_id":3453},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[{"id":544,"step_id":4367,"table_id":681}],"tables":[{"id":681,"created_at":"2018-12-20T13:03:47.611Z","updated_at":"2018-12-21T11:50:54.563Z","created_by_id":202,"last_modified_by_id":202,"name":"","team_id":1,"contents":"eyJkYXRhIjpbWyJBbnRpbWljcm9iaWFsIGNvbmNlbnRyYXRpb24gKG1nL0wp\nIiwiVm9sdW1lIG9mIGFudGliaW90aWMgc3RvY2sgc29sdXRpb24gKM68TCki\nLCJGaW5hbCBjb25jZW50cmF0aW9uIHdoZW4gYWRkaW5nIDI1bUwgb2YgYWdh\nciJdLFsiMTAiLCIzMjAiLCIxMjgiXSxbIjEwIiwiMTYwIiwiNjQiXSxbIjEw\nIiwiODAiLCIzMiJdLFsiMTAiLCI0MCIsIjE2Il0sWyIxIiwiMjAwIiwiOCJd\nLFsiMSIsIjEwMCIsIjQiXSxbIjEiLCI1MCIsIjIiXSxbIjAuMSIsIjI1MCIs\nIjEiXSxbIjAuMSIsIjEyNSIsIjAuNSJdLFsiMC4xIiwiNjIuNSIsIjAuMjUi\nXSxbIjAuMSIsIjMxLjI1IiwiMS4xMjUiXV19\n","data_vector":"JzAuMSc6MzksNDIsNDUsNDggJzAuMjUnOjQ3ICcwLjUnOjQ0ICcxJzozMCwz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\nZW4nOjEz\n"}]},{"step":{"id":5197,"name":"Preparation and autoclaving of media","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv class=\"row\"\u003e\n\u003cdiv class=\"col-xs-12\"\u003e\n\u003cdiv class=\"ql-editor\"\u003e\n\u003cp\u003ePrepare MHA medium following manufacturer’s instructions. Autoclaving at 121.1°C for 15 minutes at 1 bar. Cool medium to 50°C after that. Around 25 mL is necessary to pour one 15 100 mm petri dish to produce the required depth of 3–4 mm. \u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\n\u003c/div\u003e\n\u003c/div\u003e\n\u003c/div\u003e\n\u003cdiv class=\"row\"\u003e \u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T14:00:24.509Z","updated_at":"2018-12-20T12:56:25.184Z","last_modified_by_id":202,"protocol_id":3453},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2126,"name":"Growth method","due_date":null,"description":null,"x":0,"y":17,"my_module_group_id":1185,"created_at":"2018-11-09T10:25:56.551Z","updated_at":"2018-12-19T13:28:00.808Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":430,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":6011,"input_id":2132,"output_id":2126}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3452,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2126,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-09T10:25:56.621Z","updated_at":"2018-12-24T09:01:33.704Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5201,"name":"Take samples for cell count","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eTake samples for cell count and follow protocol in \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#cou\"\u003e[#Cell count~tsk~YL]\u003c/span\u003e.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":5,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T14:33:52.646Z","updated_at":"2018-12-17T14:33:52.646Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4361,"name":"Assessment of turbidity","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cstrong\u003eTurbidity can be assessed visually by comparing the test and the McFarland Standard.\u003c/strong\u003e \u003cbr\u003e\u003cbr\u003eMix the McFarland 0.5 BaSO\u003csub\u003e4\u003c/sub\u003e standard vigorously using a vortex mixer. The turbidity is verified measuring the absorbance of the suspension spectrophotometrically. The absorbance should be in the same range as that of the McFarland standard 0.5 (OD625 nm should be at 0.08–0.13).\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:25:56.657Z","updated_at":"2018-12-21T11:15:08.233Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4360,"name":"Adjustment of suspension turbidity","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAdjust the suspension’s turbidity to that of a McFarland Standard 0.5 by adding sterile distilled water, saline or broth, if the turbidity is too high, or by adding more bacterial material if is too low.\u003cbr\u003e\u003cbr\u003eGo back to step 4.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":4,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:25:56.635Z","updated_at":"2018-12-21T11:15:35.763Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4362,"name":"Isolate preparation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow steps bellow for isolate preparation.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:25:56.680Z","updated_at":"2018-12-24T09:01:33.668Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[{"checklist":{"id":964,"name":"Guidelines:","step_id":4362,"created_at":"2018-12-21T11:14:19.776Z","updated_at":"2018-12-21T11:14:19.776Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3965,"text":"For each isolate, select three to five morphologically similar colonies from the fresh agar plate from task .","checked":false,"checklist_id":964,"created_at":"2018-12-21T11:14:19.778Z","updated_at":"2018-12-21T11:14:19.778Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3966,"text":"Plate preparation.","checked":false,"checklist_id":964,"created_at":"2018-12-21T11:14:19.785Z","updated_at":"2018-12-21T11:14:19.785Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3967,"text":"Touch the top of each selected colony using a sterile loop or cotton swab.","checked":false,"checklist_id":964,"created_at":"2018-12-21T11:14:19.791Z","updated_at":"2018-12-21T11:14:19.791Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3968,"text":"Transfer into a tube containing 3–4 mL of a suitable nutrient-rich medium.","checked":false,"checklist_id":964,"created_at":"2018-12-21T11:14:19.798Z","updated_at":"2018-12-21T11:14:19.798Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3969,"text":"Mix using a vortex mixer.","checked":false,"checklist_id":964,"created_at":"2018-12-21T11:14:19.805Z","updated_at":"2018-12-21T11:14:19.805Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4363,"name":"Pure cultures of bacterial isolates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollowing guidelines below will get you to obtain bacterial isolates.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:25:56.700Z","updated_at":"2018-12-24T09:00:48.862Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[{"checklist":{"id":963,"name":"Guidelines:","step_id":4363,"created_at":"2018-12-21T11:12:20.820Z","updated_at":"2018-12-21T11:12:20.820Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3962,"text":"Prepare media (store at 4°C).","checked":false,"checklist_id":963,"created_at":"2018-12-21T11:12:20.822Z","updated_at":"2018-12-21T11:12:20.822Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3963,"text":"Prepare antibiotic stock solutions.","checked":false,"checklist_id":963,"created_at":"2018-12-21T11:12:20.831Z","updated_at":"2018-12-21T11:12:20.831Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3964,"text":"Streak the bacterial isolates to be tested onto nutrient-rich agar plates without inhibitor to obtain single colonies","checked":false,"checklist_id":963,"created_at":"2018-12-21T11:12:20.838Z","updated_at":"2018-12-21T11:12:20.838Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[{"id":2788,"step_id":4363,"asset_id":3410}],"assets":[{"id":3410,"created_at":"2018-12-21T11:12:20.990Z","updated_at":"2018-12-24T09:00:48.810Z","file_file_name":"Streak_plate.PNG","file_content_type":"image/png","file_file_size":160488,"file_updated_at":"2018-12-21T15:31:42.468Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":176536,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]},{"step":{"id":4364,"name":"Incubate the broth","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eIncubation conditions:\u003cbr\u003e\n\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e35–37°C\u003c/li\u003e\n\u003cli\u003eShaker set at 225 r.p.m. until it reaches turbidity that is equal to or greater than the turbidity of a McFarland Standard 0.5.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003eCulture growth will require 2–6 h depending on the growth rate of the bacteria to be tested. This pause period can be used to prepare the antibiotic or peptide dilutions.\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:35:37.405Z","updated_at":"2018-12-21T11:35:00.293Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2125,"name":"Colony 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samples for cell count","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the protocol in \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#coun\"\u003e[#Cell count~tsk~YL]\u003c/span\u003e \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":4,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T14:34:48.930Z","updated_at":"2018-12-17T14:34:48.930Z","last_modified_by_id":202,"protocol_id":3450},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4357,"name":"Isolate preparation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines below to prepare an isolate.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T09:26:34.638Z","updated_at":"2018-12-24T08:59:10.687Z","last_modified_by_id":202,"protocol_id":3450},"checklists":[{"checklist":{"id":962,"name":"Guidelines","step_id":4357,"created_at":"2018-12-21T11:09:29.266Z","updated_at":"2018-12-21T11:09:29.266Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3957,"text":"For each isolate, select three to five morphologically similar colonies from the fresh agar plate from task","checked":false,"checklist_id":962,"created_at":"2018-12-21T11:09:29.268Z","updated_at":"2018-12-21T11:09:29.268Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3958,"text":"Plate preparation","checked":false,"checklist_id":962,"created_at":"2018-12-21T11:09:29.276Z","updated_at":"2018-12-21T11:09:29.276Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3959,"text":"Touch the top of each selected colony using a sterile loop or cotton swab.","checked":false,"checklist_id":962,"created_at":"2018-12-21T11:09:29.287Z","updated_at":"2018-12-21T11:09:29.287Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3960,"text":"Transfer the growth into a sterile capped glass tube containing sterile broth or saline solution.","checked":false,"checklist_id":962,"created_at":"2018-12-21T11:09:29.300Z","updated_at":"2018-12-21T11:09:29.300Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3961,"text":"Mix using a vortex mixer.","checked":false,"checklist_id":962,"created_at":"2018-12-21T11:09:29.307Z","updated_at":"2018-12-21T11:09:29.307Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5195,"name":"Pure cultures of bacterial isolates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eGrowth conditions:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e37°C\u003c/li\u003e\n\u003cli\u003e18-24h\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T13:07:04.214Z","updated_at":"2018-12-24T08:55:09.983Z","last_modified_by_id":202,"protocol_id":3450},"checklists":[{"checklist":{"id":961,"name":"Guidelines:","step_id":5195,"created_at":"2018-12-21T10:50:36.576Z","updated_at":"2018-12-21T10:50:36.576Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3954,"text":"Prepare media (store at 4°C)","checked":false,"checklist_id":961,"created_at":"2018-12-21T10:50:36.577Z","updated_at":"2018-12-21T10:50:36.577Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3955,"text":"Prepare antibiotic stock solutions","checked":false,"checklist_id":961,"created_at":"2018-12-21T10:50:36.584Z","updated_at":"2018-12-21T10:50:36.584Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3956,"text":"Streak the bacterial isolates to be tested onto nutrient-rich agar plates without inhibitor to obtain single colonies","checked":false,"checklist_id":961,"created_at":"2018-12-21T10:50:36.592Z","updated_at":"2018-12-21T10:50:36.592Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[{"id":2742,"step_id":5195,"asset_id":3358}],"assets":[{"id":3358,"created_at":"2018-12-17T13:09:17.744Z","updated_at":"2018-12-21T15:31:33.117Z","file_file_name":"Streaking_bacteria_method.png","file_content_type":"image/png","file_file_size":100610,"file_updated_at":"2018-12-21T15:31:32.844Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":110671,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]},{"step":{"id":4359,"name":"Adjustment of suspension turbidity","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAdjust the suspension’s turbidity to that of a McFarland Standard 0.5 by adding sterile distilled water, saline or broth, if the turbidity is too high, or by adding more bacterial material if is too low.\u003cbr\u003e\u003cbr\u003eGo back to step 3.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:13:32.396Z","updated_at":"2018-12-17T13:09:32.630Z","last_modified_by_id":202,"protocol_id":3450},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4358,"name":"Assessment of turbidity","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003e\u003cstrong\u003eTurbidity can be assessed visually by comparing the test and the McFarland Standard.\u003c/strong\u003e \u003cbr\u003e\u003cbr\u003eMix the McFarland 0.5 BaSO\u003csub\u003e4\u003c/sub\u003e standard vigorously using a vortex mixer. The turbidity is verified measuring the absorbance of the suspension spectrophotometrically. The absorbance should be in the same range as that of the McFarland standard 0.5 (OD625 nm should be at 0.08–0.13).\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:11:24.463Z","updated_at":"2018-12-21T11:10:10.216Z","last_modified_by_id":202,"protocol_id":3450},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2132,"name":"Antimicrobial susceptibility testing","due_date":null,"description":null,"x":34,"y":26,"my_module_group_id":1185,"created_at":"2018-11-09T14:20:10.098Z","updated_at":"2018-12-19T13:28:00.798Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":4,"experiment_id":430,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":6010,"input_id":2134,"output_id":2132}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3458,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2132,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-09T14:20:10.107Z","updated_at":"2018-12-24T09:38:55.415Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5198,"name":"Broth macrodilutions","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003e\u003cstrong\u003eBroth dilutions preparation:\u003c/strong\u003e Add 1 mL of each antibiotic dilution into one test tube for each isolate to be tested. Fill the control tubes with 1 mL sterile broth without an antimicrobial agent. Mix the bacterial suspension well. The suspension should be adjusted to 1x10\u003csup\u003e8\u003c/sup\u003e CFU mL/L from \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#grow\"\u003e[#Growth method~tsk~YI]\u003c/span\u003e  and \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#colo\"\u003e[#Colony suspension~tsk~YH]\u003c/span\u003e  by vortexing, and dilute it by a factor of 1:100 by adding 200 µL bacterial suspension to 19.8 mL sterile MHB in a sterile 50 mL Erlenmeyer flask to prepare a 20 mL inoculum. Adjust volumes if necessary. \u003cbr\u003e\u003cstrong\u003eInoculation:\u003c/strong\u003e Inoculate each test tube containing the antibiotic solution and one control test tube (growth control) with 1 mL of the bacterial suspension. This results in the final desired inoculum of 5x10\u003csup\u003e5\u003c/sup\u003e CFU mL/L.\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eIncubation:\u003c/strong\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e37°C\u003c/li\u003e\n\u003cli\u003e16-20h\u003c/li\u003e\n\u003cli\u003eShaking at 225 r.p.m.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cstrong\u003eCount colonies\u003c/strong\u003e the next day( \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#coun\"\u003e[#Cell count~tsk~YL]\u003c/span\u003e ).\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T14:06:59.583Z","updated_at":"2018-12-24T09:38:55.366Z","last_modified_by_id":202,"protocol_id":3458},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5200,"name":"Agar plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp style=\"text-align: justify;\"\u003e\u003cstrong\u003eBacterial suspension preparation:\u003c/strong\u003e Mix the bacterial suspension, adjusted to 1x10\u003csup\u003e8\u003c/sup\u003e CFU/mL from \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#grow\"\u003e[#Growth method~tsk~YI]\u003c/span\u003e  or  \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#colo\"\u003e[#Colony suspension~tsk~YH]\u003c/span\u003e  by vortexing and dilute it 1:10 into a cavity of a sterile 96-well microtiter plate by pipetting 10 mL into a well containing 90 ml of sterile broth or saline. Repeat for each bacterial isolate to be tested. Be sure to make a note of the content of each well and to inoculate the microtiter plate in a way that the inocula can be transferred to the agar plates using a 48-pin replicator. For up to 48 tests, inoculate only within rows A–H, columns 1–6 of the microtiter plate. As an alternative to the replicator, a multichannel micropipette set at 1µL can be used to deliver the spots. Make sure that the required number of bacterial cells is going to be transferred. A 48-pin replicator with 1.5 mm pins delivers 1 µL. The final inoculum for a spot with a size of 5–8 mm should deliver the desired cell density of around 10\u003csup\u003e4\u003c/sup\u003e CFU per spot. \u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eInoculation:\u003c/strong\u003e Sterilize the 48-pin replicator by soaking the pins in 95% ethanol and passing them through a Bunsen burner flame. Hold the pins in an upright position until the flame extinguishes. Let the pins cool in an inverted position to maintain sterility. Place the sterilized replicator into the microtiter plate to soak the pins and transfer it onto the agar plate. Start by inoculating a growth control plate without antibiotic. Make sure that each agar plate has the same orientation while inoculating and to make a note of the orientation so that spots on the agar plate can be assigned to the respective isolate tested. Inoculate the antibiotic-containing agar plates starting with the lowest concentration. Let the inoculum spots dry at room temperature before inverting the plates. Plate 100 µL of the last two 1:10 dilutions (10\u003csup\u003e–4\u003c/sup\u003e to 10\u003csup\u003e–5\u003c/sup\u003e) evenly onto antibiotic-free nutrient-rich agar plates using a sterile cell spreader.\u003c/p\u003e\n\u003cstrong\u003eIncubation:\u003cbr\u003e\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003e37°C\u003c/li\u003e\n\u003cli\u003e16-20h\u003c/li\u003e\n\u003c/ul\u003e\nCount colonies the next day ( \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#coun\"\u003e[#Cell count~tsk~YL]\u003c/span\u003e )\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T14:27:56.093Z","updated_at":"2018-12-21T12:02:30.778Z","last_modified_by_id":202,"protocol_id":3458},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2134,"name":"MIC agar dilutions","due_date":null,"description":null,"x":70,"y":26,"my_module_group_id":1185,"created_at":"2018-11-09T14:35:06.102Z","updated_at":"2018-12-19T13:28:00.795Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":5,"experiment_id":430,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3460,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2134,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-09T14:35:06.105Z","updated_at":"2018-12-21T12:03:19.161Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4387,"name":"Interpretation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eIn order for the test to be valid, the agar plates for the cell count have to be checked to verify that the right number of CFU were used. The presence of around 100–200 colonies on the lower of the two dilutions (10\u003csup\u003e-5\u003c/sup\u003e) of the initial bacterial suspension is expected when using the correct bacterial suspension density of 1–2x10\u003csup\u003e8\u003c/sup\u003e CFU/mL. If the cell numbers are within the desired range, the test can be analyzed to determine the MIC. Also check the antibiotic-free growth control plate. Visible growth needs to occur for the test to be valid.\u003cbr\u003e\u003cbr\u003e\u003cem\u003e\u003cstrong\u003eThe MIC is defined as the lowest concentration of the antimicrobial substance that inhibits visible growth of the tested isolate.\u003c/strong\u003e\u003c/em\u003e The growth of a single colony or faint film caused by the inoculum should be disregarded. When growth of the tested organism occurs on all agar plates with antimicrobial agent, the MIC is recorded as greater than the highest concentration tested. The MIC is recorded as less than or equal to the lowest concentration when no growth occurs on any of the agar plates but the growth control.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T14:42:15.692Z","updated_at":"2018-12-21T15:30:31.074Z","last_modified_by_id":202,"protocol_id":3460},"checklists":[],"step_comments":[],"step_assets":[{"id":2314,"step_id":4387,"asset_id":2839}],"assets":[{"id":2839,"created_at":"2018-11-09T14:42:15.835Z","updated_at":"2018-12-21T15:30:31.064Z","file_file_name":"Example.png","file_content_type":"image/png","file_file_size":159276,"file_updated_at":"2018-12-21T15:30:30.611Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":175203,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]}]}],"results":[]}],"my_module_groups":[{"id":1185,"created_at":"2018-12-19T13:28:00.792Z","updated_at":"2018-12-19T13:28:00.792Z","created_by_id":3,"experiment_id":430}]}
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antibiotic stock","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eDilute the 10 mg/mL antibiotic stock solution 1:10 in sterile broth or water to achieve a 1 mg/mL solution.\u003cbr\u003e Dilute the 1 mg/mL solution 1:10 in sterile broth or water to achieve a 0.1 mg/mL solution\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T12:10:09.672Z","updated_at":"2018-12-20T13:06:27.384Z","last_modified_by_id":202,"protocol_id":3453},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4370,"name":"Prepare agar plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003ePrepare agar plates following guidelines bellow.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T12:22:03.852Z","updated_at":"2018-12-24T09:08:20.489Z","last_modified_by_id":202,"protocol_id":3453},"checklists":[{"checklist":{"id":966,"name":"Guidelines:","step_id":4370,"created_at":"2018-12-21T11:52:37.302Z","updated_at":"2018-12-21T11:52:37.302Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3975,"text":"Dispense appropriate amounts of antibiotic solution into the respective containers. Follow table steps.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.304Z","updated_at":"2018-12-21T11:52:37.304Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3976,"text":"For each agar plate, add 25 mL agar (now at a temperature of 50°C) into the container, mix well (avoid bubbles) and pour 25 ml into a petri dish labelled with the respective antibiotic concentration.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.311Z","updated_at":"2018-12-21T11:52:37.311Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3977,"text":"Pour a control agar plate without any antibiotic. Adjust the number if necessary.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.317Z","updated_at":"2018-12-21T11:52:37.317Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3978,"text":"Allow agar to set.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.324Z","updated_at":"2018-12-21T11:52:37.324Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3979,"text":"Dry the surface of the agar plates either in an incubator or in a laminar airflow hood for 30 min. Leave the lid ajar.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.330Z","updated_at":"2018-12-21T11:52:37.330Z","created_by_id":null,"last_modified_by_id":null,"position":4},{"id":3980,"text":"Mark the bottom of the agar plates to define an orientation.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.336Z","updated_at":"2018-12-21T11:52:37.336Z","created_by_id":null,"last_modified_by_id":null,"position":5}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[{"id":545,"step_id":4370,"table_id":682}],"tables":[{"id":682,"created_at":"2018-12-20T13:07:47.021Z","updated_at":"2018-12-24T09:08:20.452Z","created_by_id":202,"last_modified_by_id":202,"name":"","team_id":1,"contents":"eyJkYXRhIjpbWyJBbnRpbWljcm9iaWFsIGNvbmNlbnRyYXRpb24gKG1nL0wp\nIiwiVm9sdW1lIG9mIGFudGliaW90aWMgc3RvY2sgc29sdXRpb24gKM68TCki\nLCJGaW5hbCBjb25jZW50cmF0aW9uIHdoZW4gYWRkaW5nIDI1bUwgb2YgYWdh\nciJdLFsiMTAiLCIzMjAiLCIxMjgiXSxbIjEwIiwiMTYwIiwiNjQiXSxbIjEw\nIiwiODAiLCIzMiJdLFsiMTAiLCI0MCIsIjE2Il0sWyIxIiwiMjAwIiwiOCJd\nLFsiMSIsIjEwMCIsIjQiXSxbIjEiLCI1MCIsIjIiXSxbIjAuMSIsIjI1MCIs\nIjEiXSxbIjAuMSIsIjEyNSIsIjAuNSJdLFsiMC4xIiwiNjIuNSIsIjAuMjUi\nXSxbIjAuMSIsIjMxLjI1IiwiMS4xMjUiXV19\n","data_vector":"JzAuMSc6MzksNDIsNDUsNDggJzAuMjUnOjQ3ICcwLjUnOjQ0ICcxJzozMCwz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\nZW4nOjEz\n"}]},{"step":{"id":4367,"name":"Calculate the amount of antibiotic solutions","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003eAs the medium cools down, calculate the amount of antibiotic solutions (10, 1 and 0.1 mg/L) needed. The table is an example of the volumes needed for a concentration range between 0.125 and 128 mg/L for one 25 mL agar plate per concentration. Adjust if a different concentration range is needed. The volumes of antibiotic and agar can also be varied depending on the number of plates to be poured. As each agar plate can be used for up to 48 tests, more than one plate might be necessary if a larger amount of isolates is going to be tested.\u003cbr\u003e\u003cbr\u003eLabel sterile containers appropriately (glass Erlenmeyer flasks closed with metal caps, tinfoil caps or cotton buds) with the final antibiotic concentration.\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T11:07:28.842Z","updated_at":"2018-12-21T11:50:54.557Z","last_modified_by_id":202,"protocol_id":3453},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[{"id":544,"step_id":4367,"table_id":681}],"tables":[{"id":681,"created_at":"2018-12-20T13:03:47.611Z","updated_at":"2018-12-21T11:50:54.563Z","created_by_id":202,"last_modified_by_id":202,"name":"","team_id":1,"contents":"eyJkYXRhIjpbWyJBbnRpbWljcm9iaWFsIGNvbmNlbnRyYXRpb24gKG1nL0wp\nIiwiVm9sdW1lIG9mIGFudGliaW90aWMgc3RvY2sgc29sdXRpb24gKM68TCki\nLCJGaW5hbCBjb25jZW50cmF0aW9uIHdoZW4gYWRkaW5nIDI1bUwgb2YgYWdh\nciJdLFsiMTAiLCIzMjAiLCIxMjgiXSxbIjEwIiwiMTYwIiwiNjQiXSxbIjEw\nIiwiODAiLCIzMiJdLFsiMTAiLCI0MCIsIjE2Il0sWyIxIiwiMjAwIiwiOCJd\nLFsiMSIsIjEwMCIsIjQiXSxbIjEiLCI1MCIsIjIiXSxbIjAuMSIsIjI1MCIs\nIjEiXSxbIjAuMSIsIjEyNSIsIjAuNSJdLFsiMC4xIiwiNjIuNSIsIjAuMjUi\nXSxbIjAuMSIsIjMxLjI1IiwiMS4xMjUiXV19\n","data_vector":"JzAuMSc6MzksNDIsNDUsNDggJzAuMjUnOjQ3ICcwLjUnOjQ0ICcxJzozMCwz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\nZW4nOjEz\n"}]},{"step":{"id":5197,"name":"Preparation and autoclaving of media","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv class=\"row\"\u003e\n\u003cdiv class=\"col-xs-12\"\u003e\n\u003cdiv class=\"ql-editor\"\u003e\n\u003cp\u003ePrepare MHA medium following manufacturer’s instructions. Autoclaving at 121.1°C for 15 minutes at 1 bar. Cool medium to 50°C after that. Around 25 mL is necessary to pour one 15 100 mm petri dish to produce the required depth of 3–4 mm. \u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\n\u003c/div\u003e\n\u003c/div\u003e\n\u003c/div\u003e\n\u003cdiv class=\"row\"\u003e \u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T14:00:24.509Z","updated_at":"2018-12-20T12:56:25.184Z","last_modified_by_id":202,"protocol_id":3453},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2126,"name":"Growth method","due_date":null,"description":null,"x":0,"y":17,"my_module_group_id":1185,"created_at":"2018-11-09T10:25:56.551Z","updated_at":"2018-12-19T13:28:00.808Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":430,"state":"uncompleted","completed_on":null},"outputs":[{"id":6011,"input_id":2132,"output_id":2126}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3452,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2126,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-09T10:25:56.621Z","updated_at":"2018-12-24T09:01:33.704Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5201,"name":"Take samples for cell count","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eTake samples for cell count and follow protocol in \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#cou\"\u003e[#Cell count~tsk~YL]\u003c/span\u003e.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":5,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T14:33:52.646Z","updated_at":"2018-12-17T14:33:52.646Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4361,"name":"Assessment of turbidity","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cstrong\u003eTurbidity can be assessed visually by comparing the test and the McFarland Standard.\u003c/strong\u003e \u003cbr\u003e\u003cbr\u003eMix the McFarland 0.5 BaSO\u003csub\u003e4\u003c/sub\u003e standard vigorously using a vortex mixer. The turbidity is verified measuring the absorbance of the suspension spectrophotometrically. The absorbance should be in the same range as that of the McFarland standard 0.5 (OD625 nm should be at 0.08–0.13).\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:25:56.657Z","updated_at":"2018-12-21T11:15:08.233Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4360,"name":"Adjustment of suspension turbidity","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAdjust the suspension’s turbidity to that of a McFarland Standard 0.5 by adding sterile distilled water, saline or broth, if the turbidity is too high, or by adding more bacterial material if is too low.\u003cbr\u003e\u003cbr\u003eGo back to step 4.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":4,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:25:56.635Z","updated_at":"2018-12-21T11:15:35.763Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4362,"name":"Isolate preparation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow steps bellow for isolate preparation.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:25:56.680Z","updated_at":"2018-12-24T09:01:33.668Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[{"checklist":{"id":964,"name":"Guidelines:","step_id":4362,"created_at":"2018-12-21T11:14:19.776Z","updated_at":"2018-12-21T11:14:19.776Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3965,"text":"For each isolate, select three to five morphologically similar colonies from the fresh agar plate from task .","checked":false,"checklist_id":964,"created_at":"2018-12-21T11:14:19.778Z","updated_at":"2018-12-21T11:14:19.778Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3966,"text":"Plate preparation.","checked":false,"checklist_id":964,"created_at":"2018-12-21T11:14:19.785Z","updated_at":"2018-12-21T11:14:19.785Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3967,"text":"Touch the top of each selected colony using a sterile loop or cotton swab.","checked":false,"checklist_id":964,"created_at":"2018-12-21T11:14:19.791Z","updated_at":"2018-12-21T11:14:19.791Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3968,"text":"Transfer into a tube containing 3–4 mL of a suitable nutrient-rich medium.","checked":false,"checklist_id":964,"created_at":"2018-12-21T11:14:19.798Z","updated_at":"2018-12-21T11:14:19.798Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3969,"text":"Mix using a vortex mixer.","checked":false,"checklist_id":964,"created_at":"2018-12-21T11:14:19.805Z","updated_at":"2018-12-21T11:14:19.805Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4363,"name":"Pure cultures of bacterial isolates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollowing guidelines below will get you to obtain bacterial isolates.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:25:56.700Z","updated_at":"2018-12-24T09:00:48.862Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[{"checklist":{"id":963,"name":"Guidelines:","step_id":4363,"created_at":"2018-12-21T11:12:20.820Z","updated_at":"2018-12-21T11:12:20.820Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3962,"text":"Prepare media (store at 4°C).","checked":false,"checklist_id":963,"created_at":"2018-12-21T11:12:20.822Z","updated_at":"2018-12-21T11:12:20.822Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3963,"text":"Prepare antibiotic stock solutions.","checked":false,"checklist_id":963,"created_at":"2018-12-21T11:12:20.831Z","updated_at":"2018-12-21T11:12:20.831Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3964,"text":"Streak the bacterial isolates to be tested onto nutrient-rich agar plates without inhibitor to obtain single colonies","checked":false,"checklist_id":963,"created_at":"2018-12-21T11:12:20.838Z","updated_at":"2018-12-21T11:12:20.838Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[{"id":2788,"step_id":4363,"asset_id":3410}],"assets":[{"id":3410,"created_at":"2018-12-21T11:12:20.990Z","updated_at":"2018-12-24T09:00:48.810Z","file_file_name":"Streak_plate.PNG","file_content_type":"image/png","file_file_size":160488,"file_updated_at":"2018-12-21T15:31:42.468Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":176536,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]},{"step":{"id":4364,"name":"Incubate the broth","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eIncubation conditions:\u003cbr\u003e\n\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e35–37°C\u003c/li\u003e\n\u003cli\u003eShaker set at 225 r.p.m. until it reaches turbidity that is equal to or greater than the turbidity of a McFarland Standard 0.5.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003eCulture growth will require 2–6 h depending on the growth rate of the bacteria to be tested. This pause period can be used to prepare the antibiotic or peptide dilutions.\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:35:37.405Z","updated_at":"2018-12-21T11:35:00.293Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2125,"name":"Colony 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samples for cell count","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the protocol in \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#coun\"\u003e[#Cell count~tsk~YL]\u003c/span\u003e \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":4,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T14:34:48.930Z","updated_at":"2018-12-17T14:34:48.930Z","last_modified_by_id":202,"protocol_id":3450},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4357,"name":"Isolate preparation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines below to prepare an isolate.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T09:26:34.638Z","updated_at":"2018-12-24T08:59:10.687Z","last_modified_by_id":202,"protocol_id":3450},"checklists":[{"checklist":{"id":962,"name":"Guidelines","step_id":4357,"created_at":"2018-12-21T11:09:29.266Z","updated_at":"2018-12-21T11:09:29.266Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3957,"text":"For each isolate, select three to five morphologically similar colonies from the fresh agar plate from task","checked":false,"checklist_id":962,"created_at":"2018-12-21T11:09:29.268Z","updated_at":"2018-12-21T11:09:29.268Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3958,"text":"Plate preparation","checked":false,"checklist_id":962,"created_at":"2018-12-21T11:09:29.276Z","updated_at":"2018-12-21T11:09:29.276Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3959,"text":"Touch the top of each selected colony using a sterile loop or cotton swab.","checked":false,"checklist_id":962,"created_at":"2018-12-21T11:09:29.287Z","updated_at":"2018-12-21T11:09:29.287Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3960,"text":"Transfer the growth into a sterile capped glass tube containing sterile broth or saline solution.","checked":false,"checklist_id":962,"created_at":"2018-12-21T11:09:29.300Z","updated_at":"2018-12-21T11:09:29.300Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3961,"text":"Mix using a vortex mixer.","checked":false,"checklist_id":962,"created_at":"2018-12-21T11:09:29.307Z","updated_at":"2018-12-21T11:09:29.307Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5195,"name":"Pure cultures of bacterial isolates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eGrowth 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solutions","checked":false,"checklist_id":961,"created_at":"2018-12-21T10:50:36.584Z","updated_at":"2018-12-21T10:50:36.584Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3956,"text":"Streak the bacterial isolates to be tested onto nutrient-rich agar plates without inhibitor to obtain single colonies","checked":false,"checklist_id":961,"created_at":"2018-12-21T10:50:36.592Z","updated_at":"2018-12-21T10:50:36.592Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[{"id":2742,"step_id":5195,"asset_id":3358}],"assets":[{"id":3358,"created_at":"2018-12-17T13:09:17.744Z","updated_at":"2018-12-21T15:31:33.117Z","file_file_name":"Streaking_bacteria_method.png","file_content_type":"image/png","file_file_size":100610,"file_updated_at":"2018-12-21T15:31:32.844Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":110671,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]},{"step":{"id":4359,"name":"Adjustment of suspension turbidity","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAdjust the suspension’s turbidity to 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Repeat for each bacterial isolate to be tested. Be sure to make a note of the content of each well and to inoculate the microtiter plate in a way that the inocula can be transferred to the agar plates using a 48-pin replicator. For up to 48 tests, inoculate only within rows A–H, columns 1–6 of the microtiter plate. As an alternative to the replicator, a multichannel micropipette set at 1µL can be used to deliver the spots. Make sure that the required number of bacterial cells is going to be transferred. A 48-pin replicator with 1.5 mm pins delivers 1 µL. The final inoculum for a spot with a size of 5–8 mm should deliver the desired cell density of around 10\u003csup\u003e4\u003c/sup\u003e CFU per spot. \u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eInoculation:\u003c/strong\u003e Sterilize the 48-pin replicator by soaking the pins in 95% ethanol and passing them through a Bunsen burner flame. Hold the pins in an upright position until the flame extinguishes. 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The presence of around 100–200 colonies on the lower of the two dilutions (10\u003csup\u003e-5\u003c/sup\u003e) of the initial bacterial suspension is expected when using the correct bacterial suspension density of 1–2x10\u003csup\u003e8\u003c/sup\u003e CFU/mL. If the cell numbers are within the desired range, the test can be analyzed to determine the MIC. Also check the antibiotic-free growth control plate. Visible growth needs to occur for the test to be valid.\u003cbr\u003e\u003cbr\u003e\u003cem\u003e\u003cstrong\u003eThe MIC is defined as the lowest concentration of the antimicrobial substance that inhibits visible growth of the tested isolate.\u003c/strong\u003e\u003c/em\u003e The growth of a single colony or faint film caused by the inoculum should be disregarded. When growth of the tested organism occurs on all agar plates with antimicrobial agent, the MIC is recorded as greater than the highest concentration tested. The MIC is recorded as less than or equal to the lowest concentration when no growth occurs on any of the agar plates but the growth control.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T14:42:15.692Z","updated_at":"2018-12-21T15:30:31.074Z","last_modified_by_id":202,"protocol_id":3460},"checklists":[],"step_comments":[],"step_assets":[{"id":2314,"step_id":4387,"asset_id":2839}],"assets":[{"id":2839,"created_at":"2018-11-09T14:42:15.835Z","updated_at":"2018-12-21T15:30:31.064Z","file_file_name":"Example.png","file_content_type":"image/png","file_file_size":159276,"file_updated_at":"2018-12-21T15:30:30.611Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":175203,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]}]}],"results":[]}],"my_module_groups":[{"id":1185,"created_at":"2018-12-19T13:28:00.792Z","updated_at":"2018-12-19T13:28:00.792Z","created_by_id":3,"experiment_id":430}]}
\ No newline at end of file
diff --git a/app/assets/templates/experiment_433/experiment.json b/app/assets/templates/experiment_433/experiment.json
index 2360f62cc..bbecf4ec0 100644
--- a/app/assets/templates/experiment_433/experiment.json
+++ b/app/assets/templates/experiment_433/experiment.json
@@ -1 +1 @@
-{"experiment":{"id":433,"name":"Development of SNP markers panel","description":"Single nucleotide polymorphisms (SNPs) markers are widely used for genomic research and breeding. 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You can chill it (in liquid nitrogen or at –80°C) to accelerate the precipitation without the risk of precipitating excess salt. 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Once dried, suspend DNA in 200 μL of TE buffer.","checked":false,"checklist_id":959,"created_at":"2018-12-21T09:54:21.535Z","updated_at":"2018-12-21T09:54:21.535Z","created_by_id":null,"last_modified_by_id":null,"position":6}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2150,"name":"RAD library preparation and sequencing","due_date":null,"description":null,"x":34,"y":0,"my_module_group_id":1167,"created_at":"2018-11-12T08:39:44.221Z","updated_at":"2018-12-17T07:51:25.145Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":1,"experiment_id":433,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":5924,"input_id":2151,"output_id":2150}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3488,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2150,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-12T08:39:44.225Z","updated_at":"2018-12-21T10:23:18.928Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4422,"name":"Shearing and size selection","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eLibraries can be quantified by fluorimetry and calibrated by sequencing. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-12T14:41:18.099Z","updated_at":"2018-12-21T10:23:18.771Z","last_modified_by_id":202,"protocol_id":3488},"checklists":[{"checklist":{"id":960,"name":"Guidelines:","step_id":4422,"created_at":"2018-12-21T10:22:55.963Z","updated_at":"2018-12-21T10:22:55.963Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3950,"text":"Size selection (100 to 800 bp) by agarose gel electrophoresis.","checked":false,"checklist_id":960,"created_at":"2018-12-21T10:22:55.965Z","updated_at":"2018-12-21T10:22:55.965Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3951,"text":"Gel purification, end repair, dA overhang addition, P2 paired-end adapter ligation and library amplification.","checked":false,"checklist_id":960,"created_at":"2018-12-21T10:22:55.972Z","updated_at":"2018-12-21T10:22:55.972Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3952,"text":"120 μL of each amplified library is size-selected (about 250 to 500 bp) by gel electrophoresis.","checked":false,"checklist_id":960,"created_at":"2018-12-21T10:22:55.981Z","updated_at":"2018-12-21T10:22:55.981Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3953,"text":"Final libraries are put through quality control and high-throughput sequencing.","checked":false,"checklist_id":960,"created_at":"2018-12-21T10:22:55.989Z","updated_at":"2018-12-21T10:23:18.774Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5192,"name":"PCR genotyping","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003ePCR conditions: \u003cbr\u003e\n\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e95°C for 1 min\u003c/li\u003e\n\u003cli\u003e35 cycles: 95°C for 15 s\u003c/li\u003e\n\u003cli\u003e56°C for 15 s\u003c/li\u003e\n\u003cli\u003e72°C for 22s\u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003ePCR products run at 60 V for 40 mins on a 2% agarose gel (0.5× TAE, stained with 100 ng/μL EtBr).\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T07:34:16.845Z","updated_at":"2018-12-21T10:18:46.189Z","last_modified_by_id":202,"protocol_id":3488},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[{"id":531,"step_id":5192,"table_id":668}],"tables":[{"id":668,"created_at":"2018-12-17T07:35:02.552Z","updated_at":"2018-12-21T10:18:46.191Z","created_by_id":202,"last_modified_by_id":202,"name":"PCR Mastermix","team_id":1,"contents":"eyJkYXRhIjpbWyJDb21wb25lbnQiLCJWb2x1bWUgKMK1bCkiLCJGaW5hbCBD\nb25jLiJdLFsiTXlUYXEgbWl4IiwiMyIsIjF4Il0sWyJGb3J3YXJkIHByaW1l\nciIsIjAsNCIsIjEwIM68TSJdLFsiUmV2ZXJzZSBwcmltZXIiLCIwLDQiLCIx\nMCDOvE0iXSxbIlRlbXBsYXRlIEROQSIsIjAsNSIsIjXigJM1MCBuZy/OvEwi\nXSxbIlVsdHJhcHVyZSB3YXRlciIsIjEsNyIsIiJdXX0=\n","data_vector":"JzAnOjEzLDIwLDI3ICcxJzozOCAnMTAnOjE1LDIyICcxeCc6MTAgJzIwMCc6\nMzEgJzIyMzUwJzozMiAnMjY1bCc6NCAnMjc0bCc6MzUgJzI3NG0nOjE3LDI0\nICczJzo5ICczMDInOjMgJzMxNic6MTYsMjMsMzQgJzM0Mic6MzAgJzQnOjE0\nLDIxICc1JzoyOCwyOSAnNyc6MzkgJ2NvbXBvbmVudCc6MSAnY29uYyc6NiAn\nZG5hJzoyNiAnZmluYWwnOjUgJ2ZvcndhcmQnOjExICdtaXgnOjggJ215dGFx\nJzo3ICduZyc6MzMgJ3ByaW1lcic6MTIsMTkgJ3JldmVyc2UnOjE4ICd0ZW1w\nbGF0ZSc6MjUgJ3VsdHJhcHVyZSc6MzYgJ3ZvbHVtZSc6MiAnd2F0ZXInOjM3\n"}]},{"step":{"id":4420,"name":"RAD library preparation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003e The RAD library was prepared as originally described in \u003ca href=\"https://www.ncbi.nlm.nih.gov/pubmed/18852878/\" target=\"_blank\" rel=\"noopener\"\u003earticle\u003c/a\u003e.\u003cbr\u003e\u003cbr\u003eAt least 30 specimens need to be chosen.\u003cbr\u003e\u003cbr\u003eEach sample is digested at 37°C for 40 min with restriction enzyme:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e6 U \u003cem\u003erestriction enzyme\u003c/em\u003e per μg genomic DNA in 1× Reaction Buffer 4 at a final concentration of about 1 μg DNA per 50 μL reaction volume\u003c/li\u003e\n\u003cli\u003eThe samples are heat-inactivated at 65°C for 20 min.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003eIndividual-specific P1 adapters, each with a unique 5 or 7 bp barcode is ligated to the digested DNA at 22°C for 15 min by adding:\u003cbr\u003e\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003e0.6 μL (DNA samples) 100 nmol/L P1 adapter\u003c/li\u003e\n\u003cli\u003e0.15 μL 100 mmol/L rATP \u003c/li\u003e\n\u003cli\u003e0.25 μL 10× Reaction Buffer 2\u003c/li\u003e\n\u003cli\u003e0.125 μL T4 ligase \u003c/li\u003e\n\u003cli\u003ereaction volumes made up to 15 μL with nuclease-free water \u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003eAfter heat-inactivation, the ligation reactions are slowly cooled to room temperature then combined in appropriate multiplex pools.\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-12T14:34:29.463Z","updated_at":"2018-12-21T10:21:18.478Z","last_modified_by_id":202,"protocol_id":3488},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2151,"name":"Genotyping RAD alleles","due_date":null,"description":null,"x":68,"y":0,"my_module_group_id":1167,"created_at":"2018-11-12T08:39:44.243Z","updated_at":"2018-12-17T07:51:25.147Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":433,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":5925,"input_id":2154,"output_id":2151}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3489,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2151,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-12T08:39:44.247Z","updated_at":"2018-12-21T10:26:41.366Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4424,"name":"RAD 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\"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003e The RAD library was prepared as originally described in \u003ca href=\"https://www.ncbi.nlm.nih.gov/pubmed/18852878/\" target=\"_blank\" rel=\"noopener\"\u003earticle\u003c/a\u003e.\u003cbr\u003e\u003cbr\u003eAt least 30 specimens need to be chosen.\u003cbr\u003e\u003cbr\u003eEach sample is digested at 37°C for 40 min with restriction enzyme:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e6 U \u003cem\u003erestriction enzyme\u003c/em\u003e per μg genomic DNA in 1× Reaction Buffer 4 at a final concentration of about 1 μg DNA per 50 μL reaction volume\u003c/li\u003e\n\u003cli\u003eThe samples are heat-inactivated at 65°C for 20 min.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003eIndividual-specific P1 adapters, each with a unique 5 or 7 bp barcode is ligated to the digested DNA at 22°C for 15 min by adding:\u003cbr\u003e\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003e0.6 μL (DNA samples) 100 nmol/L P1 adapter\u003c/li\u003e\n\u003cli\u003e0.15 μL 100 mmol/L rATP \u003c/li\u003e\n\u003cli\u003e0.25 μL 10× Reaction Buffer 2\u003c/li\u003e\n\u003cli\u003e0.125 μL T4 ligase \u003c/li\u003e\n\u003cli\u003ereaction volumes made up to 15 μL with nuclease-free water \u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003eAfter heat-inactivation, the ligation reactions are slowly cooled to room temperature then combined in appropriate multiplex pools.\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-12T14:34:29.463Z","updated_at":"2018-12-21T10:21:18.478Z","last_modified_by_id":202,"protocol_id":3488},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2151,"name":"Genotyping RAD alleles","due_date":null,"description":null,"x":68,"y":0,"my_module_group_id":1167,"created_at":"2018-11-12T08:39:44.243Z","updated_at":"2018-12-17T07:51:25.147Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":433,"state":"uncompleted","completed_on":null},"outputs":[{"id":5925,"input_id":2154,"output_id":2151}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3489,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2151,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-12T08:39:44.247Z","updated_at":"2018-12-21T10:26:41.366Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4424,"name":"RAD markers","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eReads of low quality must be discarded. \u003cbr\u003eRetained reads are sorted into loci and genotypes using software developed for that purpose. It will assigns loci using a likelihood-based algorithm to separate actual SNPs from SNPs likely to have arisen from sequencing error. \u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eParameters:\u003c/strong\u003e\u003cbr\u003e\n\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eDe novo assembly parameters.\u003c/li\u003e\n\u003cli\u003eMinimum stack depth of 5.\u003c/li\u003e\n\u003cli\u003eMaximum of 2 mismatches.\u003c/li\u003e\n\u003cli\u003eNo more than 1 mismatch between alleles.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-12T14:59:18.147Z","updated_at":"2018-12-21T10:25:44.853Z","last_modified_by_id":202,"protocol_id":3489},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5194,"name":"RAD library construction","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eSequencing data from filtered Informative RAD markers is combined into a single alignment of alleles in RAD library construction. Data analysis is carried out using R and an associated R/\u003cem\u003eadegenet\u003c/em\u003e package for Principal Component Analysis (PCA) and Discriminant Analysis of Principal Components (DAPC).\u003cem\u003e\u003cstrong\u003e PCA creates simplified models of the total variation within the dataset.\u003c/strong\u003e \u003cstrong\u003eDAPC identifies clusters of genetically related individuals.\u003c/strong\u003e\u003c/em\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T07:50:46.898Z","updated_at":"2018-12-21T10:26:41.233Z","last_modified_by_id":202,"protocol_id":3489},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2154,"name":"SNP-assay design","due_date":null,"description":null,"x":102,"y":0,"my_module_group_id":1167,"created_at":"2018-11-12T08:39:44.312Z","updated_at":"2018-12-17T07:51:25.150Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":3,"experiment_id":433,"state":"uncompleted","completed_on":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3492,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2154,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-12T08:39:44.325Z","updated_at":"2018-12-24T08:48:47.618Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4428,"name":"Genotype assignment","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eReading the fluorescence emission of the FAM and HEX fluorophores for each sample, in comparison to no-template control reactions, using a Real Time PCR Thermal Cycler and Quansoft endpoint genotyping software.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-12T15:22:18.606Z","updated_at":"2018-11-12T15:22:18.606Z","last_modified_by_id":202,"protocol_id":3492},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4427,"name":"SNP assays","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eSNP of interest at a given locus need to be at least 20 bp from the end of a given sequence, to allow for primer design. SNP assays were designed and manufactured for use with KASP genotyping technology.\u003cbr\u003e\u003cbr\u003eOptimisation assay conditions:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e94°C for 15 min;\u003c/li\u003e\n\u003cli\u003e10 cycles 94°C for 20 s, 61–55°C for 120 s (0.6°C drop per cycle)\u003c/li\u003e\n\u003cli\u003e40 cycles 94°C for 20 s, 55°C for 120 s \u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-12T15:20:06.636Z","updated_at":"2018-12-24T08:48:47.577Z","last_modified_by_id":202,"protocol_id":3492},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[{"id":455,"step_id":4427,"table_id":573}],"tables":[{"id":573,"created_at":"2018-11-12T15:20:07.148Z","updated_at":"2018-12-24T08:48:47.564Z","created_by_id":202,"last_modified_by_id":202,"name":"Reaction mastermix","team_id":1,"contents":"eyJkYXRhIjpbWyJDb21wb25lbnQiLCJWb2x1bWUiXSxbIjLDlyBLQVNQIE1h\nc3RlciBNaXgiLCIyLjUgzrxMIl0sWyJLQVNQIEFzc2F5IE1peCIsIjAuMDcg\nzrxMIl0sWyJUZW1wbGF0ZSBETkEiLCIwLjQgzrxMIl0sWyJVbHRyYXB1cmUg\nd2F0ZXIiLCIyLjEgzrxMIl1dfQ==\n","data_vector":"JzAuMDcnOjE1ICcwLjQnOjIwICcyJzozICcyLjEnOjI1ICcyLjUnOjkgJzIy\nNyc6NSAnMjc0bCc6MTEsMTcsMjIsMjcgJzMwMyc6NCAnMzE2JzoxMCwxNiwy\nMSwyNiAnYXNzYXknOjEzICdjb21wb25lbnQnOjEgJ2RuYSc6MTkgJ2thc3An\nOjYsMTIgJ21hc3Rlcic6NyAnbWl4Jzo4LDE0ICd0ZW1wbGF0ZSc6MTggJ3Vs\ndHJhcHVyZSc6MjMgJ3ZvbHVtZSc6MiAnd2F0ZXInOjI0\n"}]}]}],"results":[]}],"my_module_groups":[{"id":1167,"created_at":"2018-12-17T07:51:25.142Z","updated_at":"2018-12-17T07:51:25.142Z","created_by_id":202,"experiment_id":433}]}
\ No newline at end of file
diff --git a/app/assets/templates/experiment_436/experiment.json b/app/assets/templates/experiment_436/experiment.json
index 0d6605b27..45f3283e5 100644
--- a/app/assets/templates/experiment_436/experiment.json
+++ b/app/assets/templates/experiment_436/experiment.json
@@ -1 +1 @@
-{"experiment":{"id":436,"name":"Transformation of E. coli with electroporation","description":"Electroporation is the use of high-voltage electric shocks to introduce DNA into cells. 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The method has been used principally with plasmid pBR322 and its derivatives in E.coli strains HB101, RRI and SK 15921. \u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-13T09:33:57.218Z","updated_at":"2018-12-21T09:14:37.945Z","last_modified_by_id":202,"protocol_id":3505},"checklists":[{"checklist":{"id":955,"name":"Guidelines:","step_id":5186,"created_at":"2018-12-21T09:14:37.947Z","updated_at":"2018-12-21T09:14:37.947Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3922,"text":"Selected clones are grown in 2.5 ml of L-broth containing 100 ug/ml ampicillin in 6-ml vials.","checked":false,"checklist_id":955,"created_at":"2018-12-21T09:14:37.950Z","updated_at":"2018-12-21T09:14:37.950Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3923,"text":"After 18 h incubation, 0.5 ml of culture is transferred to a 1.5 ml Eppendorf tube for plasmid extraction.","checked":false,"checklist_id":955,"created_at":"2018-12-21T09:14:37.957Z","updated_at":"2018-12-21T09:14:37.957Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3924,"text":"The remainder is stored at -20°C after the addition of glycerol to 40%.","checked":false,"checklist_id":955,"created_at":"2018-12-21T09:14:37.964Z","updated_at":"2018-12-21T09:14:37.964Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4441,"name":"Resuspension and storage","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eThe plasmids were resuspended in 20µl TE (10 mM tris-CI pH 8.0, 1 mM EDTA) and store in aliquots at -20°C.  \u003cbr\u003eDNA concentration is measured in two ways:\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003eMeasuring ABS\u003csub\u003e260\u003c/sub\u003e and calculating the concentration assuming a molar extinction coefficient of 1.3 x 10\u003csup\u003e4\u003c/sup\u003e L mol\u003csup\u003e-1\u003c/sup\u003e cm\u003csup\u003e-1\u003c/sup\u003e (1 ABS\u003csub\u003e260\u003c/sub\u003e unit = 50 µg/mL). \u003c/li\u003e\n\u003cli\u003eLinearizing the plasmid DNA by restriction digestion and comparison of band intensity on an ethidium bromide-stained agarose gel with that of several other linear DNA species of known mass.\u003c/li\u003e\n\u003c/ol\u003e\n\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-13T12:30:26.870Z","updated_at":"2018-12-24T08:31:00.240Z","last_modified_by_id":202,"protocol_id":3505},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5187,"name":"Plasmid DNA isolation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eAll manipulations are carried out at room temperature unless otherwise indicated. \u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\n\u003cbr\u003eLysozyme solution:\u003cbr\u003e\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003ePrepare fresh daily from crystalline lysozyme and stock solutions of the other components.\u003c/li\u003e\n\u003cli\u003eStore at 0°C.\u003c/li\u003e\n\u003cli\u003e2 mg/ml lysozyme.\u003c/li\u003e\n\u003cli\u003e50 mM glucose.\u003c/li\u003e\n\u003cli\u003e10 mM CDTA.\u003c/li\u003e\n\u003cli\u003e25 mM Tris-HC1 (pH 8.0). \u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003e\u003cbr\u003eAlkaline SDS solution:\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003eStore at room temperature\u003c/li\u003e\n\u003cli\u003eStable for about 1 week\u003c/li\u003e\n\u003cli\u003e0.2 N NaOH\u003c/li\u003e\n\u003cli\u003e1% sodium dodecyl sulfate (SDS)\u003c/li\u003e\n\u003c/ul\u003e\n \u003cbr\u003eHigh salt solution:\u003cbr\u003e\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003eStore at room temperature.\u003c/li\u003e\n\u003cli\u003e3 M sodium acetate (pH 4.8).\u003c/li\u003e\n\u003cli\u003eAdjusting to pH 4.8 with glacial acetic acid.\u003c/li\u003e\n\u003cli\u003eAdjusting volume to 1 l.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-13T10:48:53.179Z","updated_at":"2018-12-21T09:22:56.930Z","last_modified_by_id":202,"protocol_id":3505},"checklists":[{"checklist":{"id":956,"name":"Guidelines:","step_id":5187,"created_at":"2018-12-21T09:22:56.932Z","updated_at":"2018-12-21T09:22:56.932Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3925,"text":"The tube is centrifuged for 15 seconds. The supernatant is carefully removed with a fine-tip aspirator and the cell pellet is thoroughly suspended in 100 ul of lysozyme solution.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.934Z","updated_at":"2018-12-21T09:22:56.934Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3926,"text":"After a 30 minute period of incubation at 0°C, 200 ml of alkaline SDS solution is added and the tube is gently vortexed. The suspension should become almost clear and slightly viscous.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.942Z","updated_at":"2018-12-21T09:22:56.942Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3927,"text":"The tube is maintained for 5 min at 0°C and then 150 ul of high-salt solution added. The contents of the tube are gently mixed by inversion for a few seconds during which time a clot of DNA forms.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.949Z","updated_at":"2018-12-21T09:22:56.949Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3928,"text":"The tube is maintained at 0°C for 60 min to allow most of the protein, high molecular weight RNA and chromosomal DNA to precipitate.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.957Z","updated_at":"2018-12-21T09:22:56.957Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3929,"text":"Centrifugation for 5 min yields an almost clear supernatant. Four-tenths of a ml of the supernatant is removed and transferred to a second centrifuge tube. Small amounts of floating material may be carried over at this time.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.964Z","updated_at":"2018-12-21T09:22:56.964Z","created_by_id":null,"last_modified_by_id":null,"position":4},{"id":3930,"text":"One ml of cold ethanol is added and the tube is held at -20°C for 30 min.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.971Z","updated_at":"2018-12-21T09:22:56.971Z","created_by_id":null,"last_modified_by_id":null,"position":5},{"id":3931,"text":"The precipitate is collected by centrifugation for 2 min and the supernatant removed by aspiration.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.977Z","updated_at":"2018-12-21T09:22:56.977Z","created_by_id":null,"last_modified_by_id":null,"position":6},{"id":3932,"text":"The pellet is dissolved in 100 ul of 0.1 M sodium acetate/0.05 M Tris-HCl (pH 8) and reprecipitated with 2 volumes of cold ethanol.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.984Z","updated_at":"2018-12-21T09:22:56.984Z","created_by_id":null,"last_modified_by_id":null,"position":7},{"id":3933,"text":"Redissolve once more in 100 ul of 0.1 M sodium acetate/0.05 M Tris-HCl (pH 8) and reprecipitated with 2 volumes of cold ethanol.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.992Z","updated_at":"2018-12-21T09:22:56.992Z","created_by_id":null,"last_modified_by_id":null,"position":8}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2162,"name":"Storage of 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html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the steps for centrifugation below.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-13T10:55:00.370Z","updated_at":"2018-12-24T08:25:52.273Z","last_modified_by_id":202,"protocol_id":3504},"checklists":[{"checklist":{"id":954,"name":"Guidelines:","step_id":4438,"created_at":"2018-12-21T07:49:43.577Z","updated_at":"2018-12-21T07:49:43.577Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3917,"text":"Centrifuge samples for 10 min at 5000 r.p.m.","checked":false,"checklist_id":954,"created_at":"2018-12-21T07:49:43.580Z","updated_at":"2018-12-21T07:49:43.580Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3918,"text":"Resuspension in a volume of cold 10% sterile glycerol equal to the original culture volume.","checked":false,"checklist_id":954,"created_at":"2018-12-21T07:49:43.588Z","updated_at":"2018-12-21T07:49:43.588Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3919,"text":"Cells are collected by spinning for 10 min at 5000 r.p.m. at 4°C.","checked":false,"checklist_id":954,"created_at":"2018-12-21T07:49:43.595Z","updated_at":"2018-12-21T07:49:43.595Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3920,"text":"After decanting the supernatant, cells are resuspended in the volume of glycerol remaining in the centrifiuge bottles and spun for 10 min at 7000 r.p.m. in a centrifuge.","checked":false,"checklist_id":954,"created_at":"2018-12-21T07:49:43.604Z","updated_at":"2018-12-21T07:49:43.604Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3921,"text":"After decanting the supernatant, cells are resuspended in 10% glycerol, using a volume of between 2 and 2.25 m/L initial culture.","checked":false,"checklist_id":954,"created_at":"2018-12-21T07:49:43.611Z","updated_at":"2018-12-21T07:49:43.611Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4434,"name":"Inoculation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eA fresh overnight culture of \u003cspan class=\"TextRun SCXO206656968\" lang=\"EN-US\" xml:lang=\"EN-US\"\u003e\u003cspan class=\"NormalTextRun SCXO206656968\"\u003e\u003cem\u003eEscherichia coli\u003c/em\u003e \u003c/span\u003e\u003c/span\u003eis diluted 1:1000 for growth in SOB medium. \u003cbr\u003eIncubation until density is 10\u003csup\u003e8 \u003c/sup\u003e- 2x10\u003csup\u003e8 \u003c/sup\u003e.\u003cbr\u003e\u003cbr\u003e\u003cbr\u003eSOB medium:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e2% (w/v) Bacto Tryptone\u003c/li\u003e\n\u003cli\u003e0,5% (w/v) yeast extract\u003c/li\u003e\n\u003cli\u003e10mM NaCl\u003c/li\u003e\n\u003cli\u003e2,5 mM KCl\u003c/li\u003e\n\u003cli\u003e10 mM MgCl2\u003c/li\u003e\n\u003cli\u003e10 mM MgS04\u003c/li\u003e\n\u003cli\u003eAutoclaved\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-13T10:23:13.538Z","updated_at":"2018-12-24T09:43:44.372Z","last_modified_by_id":202,"protocol_id":3504},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4435,"name":"Collection and storage","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eCulture samples are aliquoted to microfuge tubes (100-200 µL/tube) and frozen quickly in a dry ice-ethanol bath. Store at -70°C until use.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-13T10:35:19.862Z","updated_at":"2018-12-20T12:44:38.990Z","last_modified_by_id":202,"protocol_id":3504},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4437,"name":"Incubation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cul\u003e\n\u003cli\u003eGrown at 37°C \u003c/li\u003e\n\u003cli\u003eShaking at 200 r.p.m. to an OD550 of 0.7\u003c/li\u003e\n\u003c/ul\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-13T10:44:55.407Z","updated_at":"2018-12-21T07:48:36.840Z","last_modified_by_id":202,"protocol_id":3504},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2165,"name":"Electroporation","due_date":null,"description":null,"x":33,"y":7,"my_module_group_id":1165,"created_at":"2018-11-13T12:54:50.584Z","updated_at":"2018-12-13T15:38:36.166Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":436,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":5917,"input_id":2166,"output_id":2165}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3507,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2165,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-13T12:54:50.592Z","updated_at":"2018-12-24T09:45:09.458Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4444,"name":"Preparation of material","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eMark the required number of microcentrifuge tubes. 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Do not leave an air bubble in the droplet of cells; the pressure of a bubble may cause arcing and loss of the sample. Place the chamber in a slot and note its position. \u003cbr\u003eRepeat the process if more than one sample is to be pulsed. Handle the cuvettes gently to avoid accidentally displacing the sample. Close the lid and secure it with the draw latch. Set the electroporation settings.\u003cspan style=\"background-color: #f6d5d9;\"\u003e\u003cbr\u003e\u003c/span\u003e\u003cbr\u003eElectroporations are performed in duplicate.\u003cbr\u003e\u003cbr\u003eConditions:\u003c/p\u003e\n\u003cul\u003e\n\u003cli style=\"text-align: justify;\"\u003e100Ω\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003e1.8 kV\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003e25µF\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-13T15:19:26.546Z","updated_at":"2018-12-24T09:45:09.285Z","last_modified_by_id":202,"protocol_id":3507},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2166,"name":"Analysis of transformation","due_date":null,"description":null,"x":67,"y":7,"my_module_group_id":1165,"created_at":"2018-11-13T15:51:41.812Z","updated_at":"2018-12-13T15:38:36.161Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":3,"experiment_id":436,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3508,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2166,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-13T15:51:41.820Z","updated_at":"2018-12-24T09:41:24.379Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5189,"name":"Obtaining single colonies","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eFor each electroporation, 2.5, 25 and 250 pl of cells, each in duplicate, were spread on LB plates containing 12.5 mg/mL chloramphenicol. For transformations of ligations with the vector, plates contained 50 µg/mL X-gal and 25 µg/ml IPTG.\u003cbr\u003e\u003cbr\u003e\u003cbr\u003eGrowth conditions: \u003cbr\u003e\n\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e37°C\u003c/li\u003e\n\u003cli\u003e24 hours\u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003eScoring of colonies.\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-13T15:04:47.190Z","updated_at":"2018-12-21T08:03:52.684Z","last_modified_by_id":202,"protocol_id":3508},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5190,"name":"Analysis","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eThere are many factors that can influence transformation efficiency. Therefore after each transformation, an assessment of efficiency is needed.\u003cbr\u003eFor gene expression common methods used: \u003c/p\u003e\n\u003col\u003e\n\u003cli\u003eFlow Cytometry \u003c/li\u003e\n\u003cli\u003eqPCR\u003c/li\u003e\n\u003c/ol\u003e\nFor protein expression common methods are:\u003cbr\u003e\n\u003col\u003e\n\u003cli\u003eWestern blot analysis (\u003ca href=\"https://www.protocols.io/view/12-sds-page-western-blot-rwrd7d6\" target=\"_blank\" rel=\"noopener\"\u003eClick here\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003eMicroscopy (visualization of cells with your gene of interest)\u003c/li\u003e\n\u003c/ol\u003e\n\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-13T15:24:58.739Z","updated_at":"2018-12-24T09:41:24.341Z","last_modified_by_id":202,"protocol_id":3508},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]}],"my_module_groups":[{"id":1165,"created_at":"2018-12-13T15:38:36.158Z","updated_at":"2018-12-13T15:38:36.158Z","created_by_id":202,"experiment_id":436}]}
\ No newline at end of file
+{"experiment":{"id":436,"name":"Transformation of E. coli with electroporation","description":"Electroporation is the use of high-voltage electric shocks to introduce DNA into cells. It can be used with most cell types, yields a high frequency of both stable transformation and transient gene expression and, because it requires fewer steps, can be easier than alternate techniques.","project_id":223,"created_by_id":202,"last_modified_by_id":202,"archived":false,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-13T09:57:55.843Z","updated_at":"2018-12-13T15:44:35.608Z","workflowimg_file_name":"wimg20181213-1-tptre.png","workflowimg_content_type":"image/png","workflowimg_file_size":3029,"workflowimg_updated_at":"2018-12-13T15:44:35.608Z","uuid":"ac0f3545-85ac-40dc-b971-2e37ee013d55"},"my_modules":[{"my_module":{"id":2163,"name":"Preparation of DNA","due_date":null,"description":null,"x":0,"y":16,"my_module_group_id":1165,"created_at":"2018-11-13T11:54:32.038Z","updated_at":"2018-12-13T15:38:36.168Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":0,"experiment_id":436,"state":"uncompleted","completed_on":null},"outputs":[{"id":5918,"input_id":2165,"output_id":2163}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3505,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2163,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-13T11:54:32.112Z","updated_at":"2018-12-24T08:31:00.304Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5186,"name":"Growth of clones","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003ePlasmid DNA isolation procedure by Birnboim and Doly (1979). The method has been used principally with plasmid pBR322 and its derivatives in E.coli strains HB101, RRI and SK 15921. \u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-13T09:33:57.218Z","updated_at":"2018-12-21T09:14:37.945Z","last_modified_by_id":202,"protocol_id":3505},"checklists":[{"checklist":{"id":955,"name":"Guidelines:","step_id":5186,"created_at":"2018-12-21T09:14:37.947Z","updated_at":"2018-12-21T09:14:37.947Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3922,"text":"Selected clones are grown in 2.5 ml of L-broth containing 100 ug/ml ampicillin in 6-ml vials.","checked":false,"checklist_id":955,"created_at":"2018-12-21T09:14:37.950Z","updated_at":"2018-12-21T09:14:37.950Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3923,"text":"After 18 h incubation, 0.5 ml of culture is transferred to a 1.5 ml Eppendorf tube for plasmid extraction.","checked":false,"checklist_id":955,"created_at":"2018-12-21T09:14:37.957Z","updated_at":"2018-12-21T09:14:37.957Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3924,"text":"The remainder is stored at -20°C after the addition of glycerol to 40%.","checked":false,"checklist_id":955,"created_at":"2018-12-21T09:14:37.964Z","updated_at":"2018-12-21T09:14:37.964Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4441,"name":"Resuspension and storage","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eThe plasmids were resuspended in 20µl TE (10 mM tris-CI pH 8.0, 1 mM EDTA) and store in aliquots at -20°C.  \u003cbr\u003eDNA concentration is measured in two ways:\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003eMeasuring ABS\u003csub\u003e260\u003c/sub\u003e and calculating the concentration assuming a molar extinction coefficient of 1.3 x 10\u003csup\u003e4\u003c/sup\u003e L mol\u003csup\u003e-1\u003c/sup\u003e cm\u003csup\u003e-1\u003c/sup\u003e (1 ABS\u003csub\u003e260\u003c/sub\u003e unit = 50 µg/mL). \u003c/li\u003e\n\u003cli\u003eLinearizing the plasmid DNA by restriction digestion and comparison of band intensity on an ethidium bromide-stained agarose gel with that of several other linear DNA species of known mass.\u003c/li\u003e\n\u003c/ol\u003e\n\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-13T12:30:26.870Z","updated_at":"2018-12-24T08:31:00.240Z","last_modified_by_id":202,"protocol_id":3505},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5187,"name":"Plasmid DNA isolation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eAll manipulations are carried out at room temperature unless otherwise indicated. \u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\n\u003cbr\u003eLysozyme solution:\u003cbr\u003e\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003ePrepare fresh daily from crystalline lysozyme and stock solutions of the other components.\u003c/li\u003e\n\u003cli\u003eStore at 0°C.\u003c/li\u003e\n\u003cli\u003e2 mg/ml lysozyme.\u003c/li\u003e\n\u003cli\u003e50 mM glucose.\u003c/li\u003e\n\u003cli\u003e10 mM CDTA.\u003c/li\u003e\n\u003cli\u003e25 mM Tris-HC1 (pH 8.0). \u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003e\u003cbr\u003eAlkaline SDS solution:\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003eStore at room temperature\u003c/li\u003e\n\u003cli\u003eStable for about 1 week\u003c/li\u003e\n\u003cli\u003e0.2 N NaOH\u003c/li\u003e\n\u003cli\u003e1% sodium dodecyl sulfate (SDS)\u003c/li\u003e\n\u003c/ul\u003e\n \u003cbr\u003eHigh salt solution:\u003cbr\u003e\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003eStore at room temperature.\u003c/li\u003e\n\u003cli\u003e3 M sodium acetate (pH 4.8).\u003c/li\u003e\n\u003cli\u003eAdjusting to pH 4.8 with glacial acetic acid.\u003c/li\u003e\n\u003cli\u003eAdjusting volume to 1 l.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-13T10:48:53.179Z","updated_at":"2018-12-21T09:22:56.930Z","last_modified_by_id":202,"protocol_id":3505},"checklists":[{"checklist":{"id":956,"name":"Guidelines:","step_id":5187,"created_at":"2018-12-21T09:22:56.932Z","updated_at":"2018-12-21T09:22:56.932Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3925,"text":"The tube is centrifuged for 15 seconds. The supernatant is carefully removed with a fine-tip aspirator and the cell pellet is thoroughly suspended in 100 ul of lysozyme solution.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.934Z","updated_at":"2018-12-21T09:22:56.934Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3926,"text":"After a 30 minute period of incubation at 0°C, 200 ml of alkaline SDS solution is added and the tube is gently vortexed. The suspension should become almost clear and slightly viscous.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.942Z","updated_at":"2018-12-21T09:22:56.942Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3927,"text":"The tube is maintained for 5 min at 0°C and then 150 ul of high-salt solution added. The contents of the tube are gently mixed by inversion for a few seconds during which time a clot of DNA forms.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.949Z","updated_at":"2018-12-21T09:22:56.949Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3928,"text":"The tube is maintained at 0°C for 60 min to allow most of the protein, high molecular weight RNA and chromosomal DNA to precipitate.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.957Z","updated_at":"2018-12-21T09:22:56.957Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3929,"text":"Centrifugation for 5 min yields an almost clear supernatant. Four-tenths of a ml of the supernatant is removed and transferred to a second centrifuge tube. Small amounts of floating material may be carried over at this time.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.964Z","updated_at":"2018-12-21T09:22:56.964Z","created_by_id":null,"last_modified_by_id":null,"position":4},{"id":3930,"text":"One ml of cold ethanol is added and the tube is held at -20°C for 30 min.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.971Z","updated_at":"2018-12-21T09:22:56.971Z","created_by_id":null,"last_modified_by_id":null,"position":5},{"id":3931,"text":"The precipitate is collected by centrifugation for 2 min and the supernatant removed by aspiration.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.977Z","updated_at":"2018-12-21T09:22:56.977Z","created_by_id":null,"last_modified_by_id":null,"position":6},{"id":3932,"text":"The pellet is dissolved in 100 ul of 0.1 M sodium acetate/0.05 M Tris-HCl (pH 8) and reprecipitated with 2 volumes of cold ethanol.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.984Z","updated_at":"2018-12-21T09:22:56.984Z","created_by_id":null,"last_modified_by_id":null,"position":7},{"id":3933,"text":"Redissolve once more in 100 ul of 0.1 M sodium acetate/0.05 M Tris-HCl (pH 8) and reprecipitated with 2 volumes of cold ethanol.","checked":false,"checklist_id":956,"created_at":"2018-12-21T09:22:56.992Z","updated_at":"2018-12-21T09:22:56.992Z","created_by_id":null,"last_modified_by_id":null,"position":8}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2162,"name":"Storage of bacteria","due_date":null,"description":null,"x":0,"y":0,"my_module_group_id":1165,"created_at":"2018-11-13T10:11:52.799Z","updated_at":"2018-12-13T15:38:36.163Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":1,"experiment_id":436,"state":"uncompleted","completed_on":null},"outputs":[{"id":5916,"input_id":2165,"output_id":2162}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3504,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2162,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-13T10:11:52.850Z","updated_at":"2018-12-24T09:43:44.417Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4438,"name":"Centrifugation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the steps for centrifugation below.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-13T10:55:00.370Z","updated_at":"2018-12-24T08:25:52.273Z","last_modified_by_id":202,"protocol_id":3504},"checklists":[{"checklist":{"id":954,"name":"Guidelines:","step_id":4438,"created_at":"2018-12-21T07:49:43.577Z","updated_at":"2018-12-21T07:49:43.577Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3917,"text":"Centrifuge samples for 10 min at 5000 r.p.m.","checked":false,"checklist_id":954,"created_at":"2018-12-21T07:49:43.580Z","updated_at":"2018-12-21T07:49:43.580Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3918,"text":"Resuspension in a volume of cold 10% sterile glycerol equal to the original culture volume.","checked":false,"checklist_id":954,"created_at":"2018-12-21T07:49:43.588Z","updated_at":"2018-12-21T07:49:43.588Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3919,"text":"Cells are collected by spinning for 10 min at 5000 r.p.m. at 4°C.","checked":false,"checklist_id":954,"created_at":"2018-12-21T07:49:43.595Z","updated_at":"2018-12-21T07:49:43.595Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3920,"text":"After decanting the supernatant, cells are resuspended in the volume of glycerol remaining in the centrifiuge bottles and spun for 10 min at 7000 r.p.m. in a centrifuge.","checked":false,"checklist_id":954,"created_at":"2018-12-21T07:49:43.604Z","updated_at":"2018-12-21T07:49:43.604Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3921,"text":"After decanting the supernatant, cells are resuspended in 10% glycerol, using a volume of between 2 and 2.25 m/L initial culture.","checked":false,"checklist_id":954,"created_at":"2018-12-21T07:49:43.611Z","updated_at":"2018-12-21T07:49:43.611Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4434,"name":"Inoculation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eA fresh overnight culture of \u003cspan class=\"TextRun SCXO206656968\" lang=\"EN-US\" xml:lang=\"EN-US\"\u003e\u003cspan class=\"NormalTextRun SCXO206656968\"\u003e\u003cem\u003eEscherichia coli\u003c/em\u003e \u003c/span\u003e\u003c/span\u003eis diluted 1:1000 for growth in SOB medium. \u003cbr\u003eIncubation until density is 10\u003csup\u003e8 \u003c/sup\u003e- 2x10\u003csup\u003e8 \u003c/sup\u003e.\u003cbr\u003e\u003cbr\u003e\u003cbr\u003eSOB medium:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e2% (w/v) Bacto Tryptone\u003c/li\u003e\n\u003cli\u003e0,5% (w/v) yeast extract\u003c/li\u003e\n\u003cli\u003e10mM NaCl\u003c/li\u003e\n\u003cli\u003e2,5 mM KCl\u003c/li\u003e\n\u003cli\u003e10 mM MgCl2\u003c/li\u003e\n\u003cli\u003e10 mM MgS04\u003c/li\u003e\n\u003cli\u003eAutoclaved\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-13T10:23:13.538Z","updated_at":"2018-12-24T09:43:44.372Z","last_modified_by_id":202,"protocol_id":3504},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4435,"name":"Collection and storage","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eCulture samples are aliquoted to microfuge tubes (100-200 µL/tube) and frozen quickly in a dry ice-ethanol bath. Store at -70°C until use.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-13T10:35:19.862Z","updated_at":"2018-12-20T12:44:38.990Z","last_modified_by_id":202,"protocol_id":3504},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4437,"name":"Incubation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cul\u003e\n\u003cli\u003eGrown at 37°C \u003c/li\u003e\n\u003cli\u003eShaking at 200 r.p.m. to an OD550 of 0.7\u003c/li\u003e\n\u003c/ul\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-13T10:44:55.407Z","updated_at":"2018-12-21T07:48:36.840Z","last_modified_by_id":202,"protocol_id":3504},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2165,"name":"Electroporation","due_date":null,"description":null,"x":33,"y":7,"my_module_group_id":1165,"created_at":"2018-11-13T12:54:50.584Z","updated_at":"2018-12-13T15:38:36.166Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":436,"state":"uncompleted","completed_on":null},"outputs":[{"id":5917,"input_id":2166,"output_id":2165}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3507,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2165,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-13T12:54:50.592Z","updated_at":"2018-12-24T09:45:09.458Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4444,"name":"Preparation of material","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eMark the required number of microcentrifuge tubes. Place the required number of cuvettes (0.1 cm gap) on ice. Before use remove the bacteria and aliquots of DNA from the freezer, thaw briefly at room temperature, then place on ice before electroporation. A mixture of cells and DNA: 30µL of cells and 2 µL DNA is added to microfuge tubes.\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-13T12:56:40.301Z","updated_at":"2018-12-21T08:01:32.797Z","last_modified_by_id":202,"protocol_id":3507},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4449,"name":"After electroporation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv style=\"text-align: justify;\"\u003eInoculate samples in cuvettes with 0.5 mL SOC is immediately after electroporation. \u003c/div\u003e\n\u003cdiv style=\"text-align: justify;\"\u003eContent is transferred to sterile glass culture tubes.\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cdiv style=\"text-align: justify;\"\u003e45 minutes\u003c/div\u003e\n\u003c/li\u003e\n\u003cli\u003eShaking\u003c/li\u003e\n\u003cli\u003e37°C \u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-13T15:48:41.251Z","updated_at":"2018-12-20T12:46:06.598Z","last_modified_by_id":202,"protocol_id":3507},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4448,"name":"Electroporation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eUsing a micropipette, pipette 20 µL of the cell-DNA mixture in cuvettes. Do not leave an air bubble in the droplet of cells; the pressure of a bubble may cause arcing and loss of the sample. Place the chamber in a slot and note its position. \u003cbr\u003eRepeat the process if more than one sample is to be pulsed. Handle the cuvettes gently to avoid accidentally displacing the sample. Close the lid and secure it with the draw latch. Set the electroporation settings.\u003cspan style=\"background-color: #f6d5d9;\"\u003e\u003cbr\u003e\u003c/span\u003e\u003cbr\u003eElectroporations are performed in duplicate.\u003cbr\u003e\u003cbr\u003eConditions:\u003c/p\u003e\n\u003cul\u003e\n\u003cli style=\"text-align: justify;\"\u003e100Ω\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003e1.8 kV\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003e25µF\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-13T15:19:26.546Z","updated_at":"2018-12-24T09:45:09.285Z","last_modified_by_id":202,"protocol_id":3507},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2166,"name":"Analysis of transformation","due_date":null,"description":null,"x":67,"y":7,"my_module_group_id":1165,"created_at":"2018-11-13T15:51:41.812Z","updated_at":"2018-12-13T15:38:36.161Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":3,"experiment_id":436,"state":"uncompleted","completed_on":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3508,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2166,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-13T15:51:41.820Z","updated_at":"2018-12-24T09:41:24.379Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5189,"name":"Obtaining single colonies","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eFor each electroporation, 2.5, 25 and 250 pl of cells, each in duplicate, were spread on LB plates containing 12.5 mg/mL chloramphenicol. For transformations of ligations with the vector, plates contained 50 µg/mL X-gal and 25 µg/ml IPTG.\u003cbr\u003e\u003cbr\u003e\u003cbr\u003eGrowth conditions: \u003cbr\u003e\n\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e37°C\u003c/li\u003e\n\u003cli\u003e24 hours\u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003eScoring of colonies.\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-13T15:04:47.190Z","updated_at":"2018-12-21T08:03:52.684Z","last_modified_by_id":202,"protocol_id":3508},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5190,"name":"Analysis","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eThere are many factors that can influence transformation efficiency. Therefore after each transformation, an assessment of efficiency is needed.\u003cbr\u003eFor gene expression common methods used: \u003c/p\u003e\n\u003col\u003e\n\u003cli\u003eFlow Cytometry \u003c/li\u003e\n\u003cli\u003eqPCR\u003c/li\u003e\n\u003c/ol\u003e\nFor protein expression common methods are:\u003cbr\u003e\n\u003col\u003e\n\u003cli\u003eWestern blot analysis (\u003ca href=\"https://www.protocols.io/view/12-sds-page-western-blot-rwrd7d6\" target=\"_blank\" rel=\"noopener\"\u003eClick here\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003eMicroscopy (visualization of cells with your gene of interest)\u003c/li\u003e\n\u003c/ol\u003e\n\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-13T15:24:58.739Z","updated_at":"2018-12-24T09:41:24.341Z","last_modified_by_id":202,"protocol_id":3508},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]}],"my_module_groups":[{"id":1165,"created_at":"2018-12-13T15:38:36.158Z","updated_at":"2018-12-13T15:38:36.158Z","created_by_id":202,"experiment_id":436}]}
\ No newline at end of file
diff --git a/app/assets/templates/experiment_440/experiment.json b/app/assets/templates/experiment_440/experiment.json
index 88963a182..a6ebbf525 100644
--- a/app/assets/templates/experiment_440/experiment.json
+++ b/app/assets/templates/experiment_440/experiment.json
@@ -1 +1 @@
-{"experiment":{"id":440,"name":"Microbiological sampling_QA","description":"Quality assurance (QA) is a process, where primarily concerns are controls of errors in the performance of tests and verification of test results. All materials, equipment and procedures must be adequately controlled.  \r\nThe objectives of microbiological sampling are to allow statements of density, types and locations of microorganism which reside on different surfaces.","project_id":223,"created_by_id":202,"last_modified_by_id":202,"archived":false,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-15T09:56:28.245Z","updated_at":"2019-01-31T09:56:15.702Z","workflowimg_file_name":"wimg20190131-1-rg9zf4.png","workflowimg_content_type":"image/png","workflowimg_file_size":5190,"workflowimg_updated_at":"2019-01-31T09:56:15.702Z","uuid":"eef319cd-8f18-4ec8-809b-ca44336c85b5"},"my_modules":[{"my_module":{"id":2548,"name":"Gram Stain Test","due_date":null,"description":null,"x":0,"y":50,"my_module_group_id":null,"created_at":"2019-01-31T09:55:55.557Z","updated_at":"2019-01-31T09:55:55.557Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":-1,"experiment_id":440,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":4193,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2548,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2019-01-31T09:55:55.566Z","updated_at":"2019-02-01T14:19:25.278Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5475,"name":"Reagents","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eReagents bellow can be made or purchased.\u003cbr\u003e\u003cstrong\u003e\u003cbr\u003eCrystal Violet Staining Reagent:\u003cbr\u003e\u003c/strong\u003e\u003cspan style=\"text-decoration: underline;\"\u003e\u003cbr\u003eSolution A for crystal violet staining reagent\u003c/span\u003e\u003cbr\u003e\n\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eCrystal violet (certified 90% dye content), 2g \u003c/li\u003e\n\u003cli\u003eEthanol, 95% (vol/vol), 20 mL\u003c/li\u003e\n\u003c/ul\u003e\n\u003cspan style=\"text-decoration: underline;\"\u003eSolution B for crystal violet staining reagent\u003cbr\u003e\u003c/span\u003e\n\u003cul\u003e\n\u003cli\u003eAmmonium oxalate, 0.8 g\u003c/li\u003e\n\u003cli\u003eDistilled water, 80 mL\u003c/li\u003e\n\u003c/ul\u003e\nMix A and B to obtain crystal violet staining reagent. Store for 24 h and filter through paper prior to use.\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eGram's Iodine:\u003c/strong\u003e\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003eIodine, 1.0 g\u003c/li\u003e\n\u003cli\u003ePotassium iodide, 2.0 g\u003c/li\u003e\n\u003cli\u003eDistilled water, 300 mL\u003c/li\u003e\n\u003c/ul\u003e\nGrind the iodine and potassium iodide in a mortar and add water slowly with continuous grinding until the iodine is dissolved. Store in amber bottles.\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eSafranin:\u003cbr\u003e\u003cbr\u003e\u003c/strong\u003e\u003cspan style=\"text-decoration-line: underline;\"\u003eStock solution:\u003c/span\u003e\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003e2.5g Safranin O\u003c/li\u003e\n\u003cli\u003e100 ml 95% Ethanol\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003e\u003cspan style=\"text-decoration: underline;\"\u003eWorking Solution:\u003c/span\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e10 ml Stock Solution \u003c/li\u003e\n\u003cli\u003e90 ml Distilled water\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-01-31T10:29:45.535Z","updated_at":"2019-01-31T10:29:45.535Z","last_modified_by_id":202,"protocol_id":4193},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5488,"name":"Gram staining","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines below.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T14:18:22.722Z","updated_at":"2019-02-01T14:20:09.992Z","last_modified_by_id":202,"protocol_id":4193},"checklists":[{"checklist":{"id":1010,"name":"Guidelines:","step_id":5488,"created_at":"2019-02-01T14:18:22.724Z","updated_at":"2019-02-01T14:18:22.724Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":4124,"text":"Flood air-dried, heat-fixed smear of cells for 1 minute with crystal violet staining reagent. Please note that the quality of the smear (too heavy or too light cell concentration) will affect the Gram Stain results.","checked":false,"checklist_id":1010,"created_at":"2019-02-01T14:18:22.727Z","updated_at":"2019-02-01T14:18:22.727Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":4125,"text":"Wash slide in a gentle and indirect stream of tap water for 2 seconds.","checked":false,"checklist_id":1010,"created_at":"2019-02-01T14:18:22.742Z","updated_at":"2019-02-01T14:18:22.742Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":4126,"text":"Flood slide with the mordant: Gram's iodine. Wait 1 minute.","checked":false,"checklist_id":1010,"created_at":"2019-02-01T14:18:22.753Z","updated_at":"2019-02-01T14:18:22.753Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":4127,"text":"Wash slide in a gentle and indirect stream of tap water for 2 seconds.","checked":false,"checklist_id":1010,"created_at":"2019-02-01T14:18:22.764Z","updated_at":"2019-02-01T14:18:22.764Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":4128,"text":"Flood slide with decolorizing agent. Wait 15 seconds or add drop by drop to slide until decolorizing agent running from the slide runs clear.","checked":false,"checklist_id":1010,"created_at":"2019-02-01T14:18:22.771Z","updated_at":"2019-02-01T14:18:22.771Z","created_by_id":null,"last_modified_by_id":null,"position":4},{"id":4129,"text":"Flood slide with counterstain, safranin. Wait 30 seconds to 1 minute.","checked":false,"checklist_id":1010,"created_at":"2019-02-01T14:18:22.779Z","updated_at":"2019-02-01T14:18:22.779Z","created_by_id":null,"last_modified_by_id":null,"position":5},{"id":4130,"text":"Wash slide in a gentile and indirect stream of tap water until no color appears in the effluent and then blot dry with absorbent paper.","checked":false,"checklist_id":1010,"created_at":"2019-02-01T14:18:22.786Z","updated_at":"2019-02-01T14:18:22.786Z","created_by_id":null,"last_modified_by_id":null,"position":6},{"id":4131,"text":"Observe the results of the staining procedure under oil immersion using a Brightfield microscope. At the completion of the Gram Stain, gram-negative bacteria will stain pink/red and gram-positive bacteria will stain blue/purple.","checked":false,"checklist_id":1010,"created_at":"2019-02-01T14:18:22.793Z","updated_at":"2019-02-01T14:18:22.793Z","created_by_id":null,"last_modified_by_id":null,"position":7}]}],"step_comments":[],"step_assets":[{"id":2981,"step_id":5488,"asset_id":3633}],"assets":[{"id":3633,"created_at":"2019-02-01T14:19:25.009Z","updated_at":"2019-02-01T14:20:09.983Z","file_file_name":"gram-stain-procedure.png","file_content_type":"image/png","file_file_size":202146,"file_updated_at":"2019-02-01T14:20:09.556Z","created_by_id":202,"last_modified_by_id":null,"estimated_size":222360,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]},{"step":{"id":5476,"name":"Preparation of  smear","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eWipe the slides with spirit or alcohol. After cleaning, dry the slides and place them on laboratory towels until ready for use. Drawing a circle on the underside of the slide using a glassware-marking pen may be helpful to clearly designate the area in which you will prepare the smear.  You may also label the slide with the initials of the name of the organism on the edge of the slide. \u003cbr\u003eWith a sterile cooled loop, place a drop of sterile water or saline solution on the slide. \u003cstrong\u003eSterilize and cool the loop again and pick up a very small sample of a bacterial colony and gently stir into the drop of water/saline on the slide to create an emulsion.\u003c/strong\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-01-31T11:56:43.730Z","updated_at":"2019-02-01T14:10:09.347Z","last_modified_by_id":202,"protocol_id":4193},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5487,"name":"Heat fixing","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eHeat fixing kills the bacteria in the smear, firmly adheres the smear to the slide, and allows the sample to more readily take up stains.\u003cbr\u003eAllow the smear to air dry. After the smear has air-dried, hold the slide at one end and pass the entire slide through the flame of a Bunsen burner \u003cstrong\u003etwo to three times with the smear-side up.\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e \u003c/p\u003e\n\u003cp\u003e \u003c/p\u003e\n\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T14:13:27.107Z","updated_at":"2019-02-01T14:13:27.107Z","last_modified_by_id":202,"protocol_id":4193},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2551,"name":"Catalase 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test","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines: \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-04T13:21:21.550Z","updated_at":"2019-02-04T13:30:56.251Z","last_modified_by_id":202,"protocol_id":4196},"checklists":[{"checklist":{"id":1014,"name":"Guidelines:","step_id":5496,"created_at":"2019-02-04T13:30:56.249Z","updated_at":"2019-02-04T13:30:56.249Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":4149,"text":"Add 4 to 5 drops of 3% H2O2 to in a test tube.","checked":false,"checklist_id":1014,"created_at":"2019-02-04T13:30:56.251Z","updated_at":"2019-02-04T13:30:56.251Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":4150,"text":"Using a wooden applicator stick, collect a small amount of organism from a well-isolated 18- to 24-hour colony and place into the test tube (Note: Be careful not to pick up any agar).","checked":false,"checklist_id":1014,"created_at":"2019-02-04T13:30:56.260Z","updated_at":"2019-02-04T13:30:56.260Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":4151,"text":"Place the tube against a dark background and observe for immediate bubble formation at the end of the wooden applicator stick.","checked":false,"checklist_id":1014,"created_at":"2019-02-04T13:30:56.267Z","updated_at":"2019-02-04T13:30:56.267Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5495,"name":"Slide test","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines bellow. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-04T13:18:55.135Z","updated_at":"2019-02-04T13:18:55.140Z","last_modified_by_id":202,"protocol_id":4196},"checklists":[{"checklist":{"id":1013,"name":"Guidelines:","step_id":5495,"created_at":"2019-02-04T13:18:55.138Z","updated_at":"2019-02-04T13:18:55.138Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":4145,"text":"Transfer a small amount of bacterial colony to a surface of clean, dry glass slide using a loop","checked":false,"checklist_id":1013,"created_at":"2019-02-04T13:18:55.140Z","updated_at":"2019-02-04T13:18:55.140Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":4146,"text":"Place a drop of 3% H2O2 on to the slide and mix.","checked":false,"checklist_id":1013,"created_at":"2019-02-04T13:18:55.155Z","updated_at":"2019-02-04T13:18:55.155Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":4147,"text":"Look for a rapid evolution of oxygen (within 5-10 seconds) as evidenced by bubbling.","checked":false,"checklist_id":1013,"created_at":"2019-02-04T13:18:55.163Z","updated_at":"2019-02-04T13:18:55.163Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":4148,"text":"Dispose of your slide in the biohazard glass disposal container.","checked":false,"checklist_id":1013,"created_at":"2019-02-04T13:21:32.881Z","updated_at":"2019-02-04T13:21:32.881Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5497,"name":"Results interpretation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cem\u003e\u003cstrong\u003eCatalase is an enzyme, which is produced by microorganisms that live in oxygenated environments to neutralize toxic forms of oxygen metabolites.\u003c/strong\u003e\u003c/em\u003e Anaerobes generally lack the catalase enzyme. Catalase enzyme hydrolyzes the hydrogen peroxide and forms bubbles. \u003cstrong\u003e\u003cbr\u003e\u003cbr\u003eImmediate effervescence (bubble formation): \u003c/strong\u003eCatalase positive reactions\u003cstrong\u003e\u003cbr\u003eNo bubble formation: \u003c/strong\u003eCatalase Negative reaction\u003cstrong\u003e\u003cbr\u003e\u003c/strong\u003e\n\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-04T13:38:56.063Z","updated_at":"2019-02-04T13:39:32.375Z","last_modified_by_id":202,"protocol_id":4196},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2550,"name":"Oxidase Test","due_date":null,"description":null,"x":70,"y":50,"my_module_group_id":null,"created_at":"2019-01-31T09:55:55.606Z","updated_at":"2019-01-31T09:55:55.606Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":-1,"experiment_id":440,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":4195,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2550,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2019-01-31T09:55:55.611Z","updated_at":"2019-02-01T14:54:17.326Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5492,"name":"Oxidase test","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines bellow: \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T14:49:04.449Z","updated_at":"2019-02-01T14:49:04.453Z","last_modified_by_id":202,"protocol_id":4195},"checklists":[{"checklist":{"id":1012,"name":"Guidelines:","step_id":5492,"created_at":"2019-02-01T14:49:04.452Z","updated_at":"2019-02-01T14:49:04.452Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":4141,"text":"Take a filter paper soaked with the substrate tetramethyl-p-phenylenediamine dihydrochloride.","checked":false,"checklist_id":1012,"created_at":"2019-02-01T14:49:04.454Z","updated_at":"2019-02-01T14:49:04.454Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":4142,"text":"Moisten the paper with a sterile distilled water.","checked":false,"checklist_id":1012,"created_at":"2019-02-01T14:49:04.462Z","updated_at":"2019-02-01T14:49:04.462Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":4143,"text":"Pick the colony to be tested with wooden or platinum loop and smear in the filter paper.","checked":false,"checklist_id":1012,"created_at":"2019-02-01T14:49:04.469Z","updated_at":"2019-02-01T14:49:04.469Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":4144,"text":"Observe inoculated area of paper for a color change to deep blue or purple within 10-30 seconds.","checked":false,"checklist_id":1012,"created_at":"2019-02-01T14:49:04.475Z","updated_at":"2019-02-01T14:49:04.475Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5493,"name":"Results interpretation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eOxidase test is used for identification of \u003cem\u003ePseudomonas\u003c/em\u003e spp, \u003cem\u003eAeromonas\u003c/em\u003e spp,  \u003cem\u003eNeisserias\u003c/em\u003e spp, \u003cem\u003eVibrio\u003c/em\u003e spp and \u003cem\u003ePasteurella\u003c/em\u003e spp, all of which produces oxidase enzyme. \u003cbr\u003e\u003cbr\u003e\u003cstrong\u003e\u003cspan style=\"color: #333399;\"\u003eBlue-purple colour:\u003c/span\u003e\u003c/strong\u003e Oxidase positive\u003cbr\u003eNo purple colour: Oxidase negative\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T14:54:17.285Z","updated_at":"2019-02-01T14:54:17.285Z","last_modified_by_id":202,"protocol_id":4195},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2549,"name":"Acid-Fast Stain Test","due_date":null,"description":null,"x":35,"y":50,"my_module_group_id":null,"created_at":"2019-01-31T09:55:55.586Z","updated_at":"2019-01-31T09:55:55.586Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":-1,"experiment_id":440,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":4194,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2549,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2019-01-31T09:55:55.591Z","updated_at":"2019-02-01T15:01:31.039Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5489,"name":"Preparation of smear","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eWipe the slides with spirit or alcohol. After cleaning, dry the slides and place them on laboratory towels until ready for use. Drawing a circle on the underside of the slide using a glassware-marking pen may be helpful to clearly designate the area in which you will prepare the smear.  You may also label the slide with the initials of the name of the organism on the edge of the slide. \u003cbr\u003eWith a sterile cooled loop, place a drop of sterile water or saline solution on the slide. \u003cstrong\u003eSterilize and cool the loop again and pick up a very small sample of a bacterial colony and gently stir into the drop of water/saline on the slide to create an emulsion.\u003c/strong\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T14:22:44.942Z","updated_at":"2019-02-01T14:22:44.942Z","last_modified_by_id":202,"protocol_id":4194},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5490,"name":"Heat-fixing","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eHeat fixing kills the bacteria in the smear, firmly adheres the smear to the slide, and allows the sample to more readily take up stains.\u003cbr\u003eAllow the smear to air dry. After the smear has air-dried, hold the slide at one end and pass the entire slide through the flame of a Bunsen burner \u003cstrong\u003etwo to three times with the smear-side up.\u003c/strong\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T14:23:09.650Z","updated_at":"2019-02-01T14:23:09.650Z","last_modified_by_id":202,"protocol_id":4194},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5491,"name":"Acid-Fast Staining","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines below:\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003e\u003cspan style=\"color: #ff0000;\"\u003eImportant: \u003c/span\u003e\u003c/strong\u003e\u003cspan style=\"color: #000000;\"\u003e Great care must be taken when heating the carbol fuchsin especially if staining is carried out over a tray or other container in which highly flammable chemicals have collected from the previous staining. Only a small flame should be applied under the slides using an ignited swab previously dampened with a few drops of acid alcohol or 70% v/v ethanol or methanol. Do not use a large ethanol soaked swab because this is a fire risk.\u003c/span\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T14:33:15.222Z","updated_at":"2019-02-01T14:45:11.703Z","last_modified_by_id":202,"protocol_id":4194},"checklists":[{"checklist":{"id":1011,"name":"Guideline:","step_id":5491,"created_at":"2019-02-01T14:33:15.225Z","updated_at":"2019-02-01T14:33:15.225Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":4132,"text":"Cover the smear with carbol fuchsin stain.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.227Z","updated_at":"2019-02-01T14:33:15.227Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":4133,"text":"Heat the stain until vapour just begins to rise (i.e. about 60°C). Do not overheat. Allow the heated stain to remain on the slide for 5 minutes.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.235Z","updated_at":"2019-02-01T14:33:15.235Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":4134,"text":"Wash off the stain with distilled water.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.244Z","updated_at":"2019-02-01T14:41:45.127Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":4135,"text":"Cover the smear with 3% v/v acid alcohol for 5 minutes or until the smear is sufficiently decolorized, i.e. pale pink.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.252Z","updated_at":"2019-02-01T14:33:15.252Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":4136,"text":"Wash well with distilled water.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.259Z","updated_at":"2019-02-01T14:41:45.136Z","created_by_id":null,"last_modified_by_id":null,"position":4},{"id":4137,"text":"Cover the smear with methylene blue dye for 1–2 minutes.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.266Z","updated_at":"2019-02-01T14:41:45.144Z","created_by_id":null,"last_modified_by_id":null,"position":5},{"id":4138,"text":"Wash off the stain with distilled water.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.273Z","updated_at":"2019-02-01T14:41:45.151Z","created_by_id":null,"last_modified_by_id":null,"position":6},{"id":4139,"text":"Wipe the back of the slide clean, and place it in a draining rack for the smear to air-dry (do not blot dry).","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.280Z","updated_at":"2019-02-01T14:33:15.280Z","created_by_id":null,"last_modified_by_id":null,"position":7},{"id":4140,"text":"Examine the smear microscopically, using the 100 X oil immersion objective.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.286Z","updated_at":"2019-02-01T14:33:15.286Z","created_by_id":null,"last_modified_by_id":null,"position":8}]}],"step_comments":[],"step_assets":[{"id":2984,"step_id":5491,"asset_id":3636}],"assets":[{"id":3636,"created_at":"2019-02-01T14:44:32.274Z","updated_at":"2019-02-01T14:45:11.689Z","file_file_name":"acid-fast_stain.png","file_content_type":"image/png","file_file_size":137068,"file_updated_at":"2019-02-01T14:45:11.001Z","created_by_id":202,"last_modified_by_id":null,"estimated_size":150774,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]},{"step":{"id":5494,"name":"Result interpretation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cstrong\u003eSome\u003c/strong\u003e\u003cem\u003e\u003cstrong\u003e bacteria contain a waxy lipid, mycolic acid, in their cell wall.\u003c/strong\u003e\u003c/em\u003e This lipid makes the cells more durable and is commonly associated with pathogens.\u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003e\u003cspan style=\"color: #ff0000;\"\u003eRED: \u003c/span\u003e\u003c/strong\u003e\u003cspan style=\"color: #000000;\"\u003eAcid fast organisms \u003cbr\u003e\u003cstrong\u003e\u003cspan style=\"color: #0000ff;\"\u003eBLUE:\u003c/span\u003e\u003c/strong\u003e\u003cspan style=\"color: #0000ff;\"\u003e \u003cspan style=\"color: #000000;\"\u003eNon-acid fast organisms\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\n\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T15:01:30.991Z","updated_at":"2019-02-01T15:01:30.991Z","last_modified_by_id":202,"protocol_id":4194},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2192,"name":"Plate preparation","due_date":null,"description":"","x":1,"y":16,"my_module_group_id":1236,"created_at":"2018-11-15T09:56:30.961Z","updated_at":"2019-01-31T09:55:55.903Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":0,"experiment_id":440,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":6218,"input_id":2188,"output_id":2192},{"id":6219,"input_id":2190,"output_id":2192},{"id":6220,"input_id":2194,"output_id":2192}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3548,"name":null,"authors":null,"description":null,"added_by_id":202,"my_module_id":2192,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-15T09:56:31.020Z","updated_at":"2019-01-31T09:33:37.119Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4533,"name":"Examine the plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines bellow. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:31.091Z","updated_at":"2018-12-24T08:23:09.402Z","last_modified_by_id":202,"protocol_id":3548},"checklists":[{"checklist":{"id":924,"name":"Guideline:","step_id":4533,"created_at":"2018-12-12T07:16:14.619Z","updated_at":"2018-12-24T08:23:09.400Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3812,"text":"Monitor refrigerator temperature and record it in Results.","checked":false,"checklist_id":924,"created_at":"2018-12-12T07:16:14.622Z","updated_at":"2018-12-12T07:16:14.622Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3813,"text":"Contact plates and/or Settle plates are taken to the room temperature.  They will be used depending on the surface of the sampling.","checked":false,"checklist_id":924,"created_at":"2018-12-12T07:16:14.634Z","updated_at":"2018-12-12T07:16:14.634Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3814,"text":"Examine the plates for contamination prior to use. If any plates are contaminated they should be discarded according to protocol.","checked":false,"checklist_id":924,"created_at":"2018-12-12T07:16:14.641Z","updated_at":"2018-12-12T07:16:14.641Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4535,"name":"Preincubation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003ePreincubate the empty plates in incubator \u003cstrong\u003e30°C-35°C\u003c/strong\u003e for \u003cstrong\u003e48 hours\u003c/strong\u003e to check for any accidental contamination. Check for contamination again. If there is contamination record it and discard according to appropriate procedures. Take contamination-free plates to room temperature an hour before exposure.\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:31.144Z","updated_at":"2019-01-29T12:33:40.426Z","last_modified_by_id":202,"protocol_id":3548},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2194,"name":"Contact Plate Sampling","due_date":null,"description":"Protocol for direct testing of surfaces. Contact plates are allowing us to detect microorganisms that are on flat surfaces in relatively low numbers.","x":35,"y":0,"my_module_group_id":1236,"created_at":"2018-11-15T09:56:31.528Z","updated_at":"2019-01-31T09:55:55.891Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":1,"experiment_id":440,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":6221,"input_id":2195,"output_id":2194}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3552,"name":null,"authors":null,"description":null,"added_by_id":202,"my_module_id":2194,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-15T09:56:31.582Z","updated_at":"2019-01-31T09:38:26.038Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4549,"name":"Collect all the plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAfter all the samples are taken, collect all sample plates together, remove them from the sampling area and incubate as directed. Complete and enclose the necessary documentation \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#coun\"\u003e[#Counting and recording...~tsk~ZU]\u003c/span\u003e.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:31.742Z","updated_at":"2019-01-25T12:41:23.609Z","last_modified_by_id":202,"protocol_id":3552},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5447,"name":"Labeling of plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eAssemble the plates required and label them. Ensure that correct information about sampling is written on the base of the plate with a permanent ink marker.\u003cbr\u003eThe following sampling details should be recorded on the plate:\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eInitials of a person who is sampling\u003c/li\u003e\n\u003cli\u003eSampling location code\u003c/li\u003e\n\u003cli\u003eDate and time of the day of sampling/plating \u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-01-25T12:10:43.950Z","updated_at":"2019-01-25T12:18:51.523Z","last_modified_by_id":202,"protocol_id":3552},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4551,"name":"Surface sampling with contact plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003eTransfer the contact plates into the area to be tested. Enter the area according to the procedures. Ensure that the testing area is dry. \u003cbr\u003e\u003cbr\u003eWhen sampling surfaces with contact plates, remove the lid and place the agar surface in maximum contact with the sampling site for \u003cstrong\u003e10 seconds\u003c/strong\u003e by applying a constant force spread evenly over the whole contact plate without twisting or sliding and avoiding the creation of bubbles. After contact with the sample surface, remove and replace the lid, avoiding any unnecessary hand movement near or over the agar surface. Clean it with disinfectant to remove any possible traces of agar.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:31.793Z","updated_at":"2019-01-29T12:34:02.242Z","last_modified_by_id":202,"protocol_id":3552},"checklists":[{"checklist":{"id":810,"name":"Sample locations (examples):","step_id":4551,"created_at":"2018-11-15T09:56:31.809Z","updated_at":"2018-12-12T07:32:30.595Z","created_by_id":202,"last_modified_by_id":202},"checklist_items":[{"id":3410,"text":"Filling machine control panel","checked":false,"checklist_id":810,"created_at":"2018-11-15T09:56:31.836Z","updated_at":"2018-12-12T07:29:55.968Z","created_by_id":202,"last_modified_by_id":202,"position":0},{"id":3411,"text":"Surface of Balance Table","checked":false,"checklist_id":810,"created_at":"2018-11-15T09:56:31.847Z","updated_at":"2018-12-12T07:29:55.975Z","created_by_id":202,"last_modified_by_id":202,"position":1},{"id":3412,"text":"Surface of table","checked":false,"checklist_id":810,"created_at":"2018-11-15T09:56:31.860Z","updated_at":"2018-12-12T07:29:55.981Z","created_by_id":202,"last_modified_by_id":202,"position":2},{"id":3413,"text":"Surface of door to pass trough","checked":false,"checklist_id":810,"created_at":"2018-11-15T09:56:31.872Z","updated_at":"2018-12-12T07:29:55.990Z","created_by_id":202,"last_modified_by_id":202,"position":3},{"id":3414,"text":"Surface of door","checked":false,"checklist_id":810,"created_at":"2018-11-15T09:56:31.885Z","updated_at":"2018-12-12T07:29:55.997Z","created_by_id":202,"last_modified_by_id":202,"position":4},{"id":3417,"text":"Surface of the wall","checked":false,"checklist_id":810,"created_at":"2018-11-15T09:56:31.923Z","updated_at":"2018-12-12T07:32:44.480Z","created_by_id":202,"last_modified_by_id":202,"position":5},{"id":3420,"text":"Surface of solid curtain","checked":false,"checklist_id":810,"created_at":"2018-11-15T09:56:31.960Z","updated_at":"2018-12-12T07:32:44.487Z","created_by_id":202,"last_modified_by_id":202,"position":6},{"id":3815,"text":"Stopper bowl","checked":false,"checklist_id":810,"created_at":"2018-12-12T07:32:30.611Z","updated_at":"2018-12-12T07:32:44.494Z","created_by_id":null,"last_modified_by_id":null,"position":7},{"id":3816,"text":"Plexiglass barrier","checked":false,"checklist_id":810,"created_at":"2018-12-12T07:32:30.618Z","updated_at":"2018-12-12T07:32:44.501Z","created_by_id":null,"last_modified_by_id":null,"position":8}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5165,"name":"Sampling guidlines for glove and gowning test","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003e\u003cstrong\u003eTesting conditions:\u003c/strong\u003e Sampling should take place at the end of a work session, but before the person would carry out any cleaning. Before performing the test the person should ensure that gloves are dry and free of any disinfectant. \u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eGlove test:\u003c/strong\u003e The person doing the sampling should lift the lid of the plate, with the opposite hand to that being tested, and keeping hold of the lid in the other hand, touch the agar surface with the tips of all fingers then the thumb (in the gap on the plate behind where fingers were tested) on the hand being tested. A firm and even pressure should be applied for approximately \u003cstrong\u003e5 to 10 seconds\u003c/strong\u003e, taking care not to damage the agar surface. Replace the lid of the plate. Repeat for the other hand. Ensure that the glove surfaces tested are cleaned with a suitable disinfectant to remove any possible traces of agar before performing any other operations.\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eGowning test:\u003c/strong\u003e The person doing the sampling should lift the lid of the plate and keep hold of the lid, touch the gown in the chest and clavicle area with agar surface. A firm and even pressure should be applied for approximately \u003cstrong\u003e5 to 10 seconds\u003c/strong\u003e, taking care not to damage the agar surface. Replace the lid of the plate. Ensure that the gown surfaces tested are cleaned with a suitable disinfectant to remove any possible traces of agar before performing any other operations.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T07:58:32.639Z","updated_at":"2019-01-29T12:34:24.814Z","last_modified_by_id":202,"protocol_id":3552},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2190,"name":"Sampling of uneven surfaces","due_date":null,"description":"A method using swabs that makes microbiological load visible on uneven surfaces.","x":35,"y":33,"my_module_group_id":1236,"created_at":"2018-11-15T09:56:30.349Z","updated_at":"2019-01-31T09:55:55.897Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":440,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":6217,"input_id":2195,"output_id":2190}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3544,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2190,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-15T09:56:30.402Z","updated_at":"2019-01-29T12:36:12.849Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5448,"name":"Labeling of plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eAssemble the plates required and label them. Ensure that correct information about sampling is written on the base of the plate with a permanent ink marker.\u003cbr\u003eThe following sampling details should be recorded on the plate:\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eInitials of a person who is sampling\u003c/li\u003e\n\u003cli\u003eSampling location code\u003c/li\u003e\n\u003cli\u003eDate and time of the day of sampling/plating \u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-01-25T12:11:53.234Z","updated_at":"2019-01-25T12:18:18.027Z","last_modified_by_id":202,"protocol_id":3544},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4523,"name":"Collect all the swabs","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAfter all the samples are taken, collect all sample swabs together, remove them from the sampling area and plate them as directed in the next step. Complete and enclose all the necessary documentation in \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#countin\"\u003e[#Counting and recording...~tsk~ZU]\u003c/span\u003e.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:30.601Z","updated_at":"2019-01-25T12:40:08.288Z","last_modified_by_id":202,"protocol_id":3544},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4521,"name":"Sampling with a swab","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003e\u003cstrong\u003eSampling:\u003c/strong\u003e Wipe the swab over the sample area in close parallel streaks, using firm even pressure and rotating the swab between fingers to maximise sample pick-up. The swab should be held at a 30° angle to the contact surface. With the same swab, repeat this process at right angles to the first streaks to ensure that the entire sample area is swabbed. Replace swab into transport tube ensuring that swab comes into contact with the transport medium by pushing down hard. Clean the surface tested with disinfectant.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:30.480Z","updated_at":"2019-01-25T12:15:22.003Z","last_modified_by_id":202,"protocol_id":3544},"checklists":[{"checklist":{"id":809,"name":"Sample locations:","step_id":4521,"created_at":"2018-11-15T09:56:30.495Z","updated_at":"2018-11-15T09:56:30.495Z","created_by_id":202,"last_modified_by_id":202},"checklist_items":[{"id":3405,"text":"Filling needle","checked":false,"checklist_id":809,"created_at":"2018-11-15T09:56:30.509Z","updated_at":"2018-11-15T10:08:47.925Z","created_by_id":202,"last_modified_by_id":202,"position":0},{"id":3406,"text":"Interior of the stopper chute","checked":false,"checklist_id":809,"created_at":"2018-11-15T09:56:30.522Z","updated_at":"2018-11-15T10:08:47.935Z","created_by_id":202,"last_modified_by_id":202,"position":1},{"id":3407,"text":"Helix/in-fed worm","checked":false,"checklist_id":809,"created_at":"2018-11-15T09:56:30.534Z","updated_at":"2018-11-15T10:08:47.944Z","created_by_id":202,"last_modified_by_id":202,"position":2},{"id":3408,"text":"In-feed belt","checked":false,"checklist_id":809,"created_at":"2018-11-15T09:56:30.546Z","updated_at":"2018-11-15T10:08:47.954Z","created_by_id":202,"last_modified_by_id":202,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5172,"name":"Plating of swabs","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines below for plating of swabs.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":4,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T11:02:15.588Z","updated_at":"2019-01-25T12:15:21.953Z","last_modified_by_id":202,"protocol_id":3544},"checklists":[{"checklist":{"id":952,"name":"Guidelines:","step_id":5172,"created_at":"2018-12-21T06:58:27.768Z","updated_at":"2018-12-21T06:58:27.768Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3906,"text":"Prepare a safe and sterile workspace: Sterilize all instruments, solutions, and media prior to using them for plating procedures. Clear away all materials cluttering your work area on the laboratory bench. Clean work area with disinfectant to minimize possible contamination.","checked":false,"checklist_id":952,"created_at":"2018-12-21T06:58:27.770Z","updated_at":"2018-12-21T06:58:27.770Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3907,"text":"Set up a Bunsen burner: Work slowly, carefully, and deliberately within the sterile field area created by the updraft of the flame.","checked":false,"checklist_id":952,"created_at":"2018-12-21T06:58:27.777Z","updated_at":"2018-12-21T06:58:27.777Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3908,"text":"Prepare lab equipment and settle plates.","checked":false,"checklist_id":952,"created_at":"2018-12-21T06:58:27.784Z","updated_at":"2018-12-21T06:58:27.784Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3909,"text":"Arrange all the supplies needed for the procedure on the laboratory bench near the sterile field. Make sure all the materials are properly labelled.","checked":false,"checklist_id":952,"created_at":"2018-12-21T06:58:27.791Z","updated_at":"2018-12-21T06:58:27.791Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3910,"text":"Carefully open the lid of the plate. A standard streaking out method should be used when plating out the swab. The method should ensure that the swab is rotated as it is run over the surface of the media to ensure that any microorganisms recovered from the surface sample are deposited onto the surface of the plate.\r\nReplace the lid.","checked":false,"checklist_id":952,"created_at":"2018-12-21T06:58:27.797Z","updated_at":"2018-12-21T06:58:27.797Z","created_by_id":null,"last_modified_by_id":null,"position":4},{"id":3911,"text":"Complete and enclose all the necessary documentation.","checked":false,"checklist_id":952,"created_at":"2018-12-21T06:58:27.804Z","updated_at":"2018-12-21T06:58:27.804Z","created_by_id":null,"last_modified_by_id":null,"position":5}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4519,"name":"Preparation of swabs before sampling","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eMake sure the sampling surface it is dry. Assemble the needle and \u003cstrong\u003e10 mL\u003c/strong\u003e syringe. Open the ampoule of \u003cstrong\u003e0.9%\u003c/strong\u003e NaCl Injection BP and draw up the contents. Push a small amount of liquid (about\u003cstrong\u003e 0.5 mL\u003c/strong\u003e) from the syringe directly onto the swab. Do not allow the needle tip to come into contact with the swab.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:30.420Z","updated_at":"2019-01-29T12:36:12.805Z","last_modified_by_id":202,"protocol_id":3544},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2188,"name":"Settle Plates Sampling","due_date":null,"description":"Settle plates asses the likely number of microorganisms depositing on the surface in a given time.","x":35,"y":16,"my_module_group_id":1236,"created_at":"2018-11-15T09:56:29.638Z","updated_at":"2019-01-31T09:55:55.888Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":3,"experiment_id":440,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":6214,"input_id":2195,"output_id":2188}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3540,"name":null,"authors":null,"description":null,"added_by_id":202,"my_module_id":2188,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-15T09:56:29.693Z","updated_at":"2019-01-31T09:52:51.146Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4511,"name":"Collect all the plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAfter all the samples are taken, collect all sample plates together, remove them from the sampling area and incubate as directed. Complete and enclose the necessary documentation \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#coun\"\u003e[#Counting and recording...~tsk~ZU]\u003c/span\u003e.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:29.770Z","updated_at":"2019-01-25T12:42:42.158Z","last_modified_by_id":202,"protocol_id":3540},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5449,"name":"Labeling of plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eAssemble the plates required and label them. Ensure that correct information about sampling is written on the base of the plate with a permanent ink marker.\u003cbr\u003eThe following sampling details should be recorded on the plate:\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eInitials of a person who is sampling\u003c/li\u003e\n\u003cli\u003eSampling location code\u003c/li\u003e\n\u003cli\u003eDate and time of the day of sampling/plating \u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-01-25T12:12:27.694Z","updated_at":"2019-01-25T12:17:41.431Z","last_modified_by_id":202,"protocol_id":3540},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4515,"name":"Passive Air Sampling with settle plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv style=\"text-align: justify;\"\u003eTransfer the contact plates into the area to be tested. Enter the area according to the procedures. \u003cbr\u003e\u003cstrong\u003eSampling:\u003c/strong\u003e Place the plates to the appropriate location with lids still on. Raise lids to expose the surface of the medium, rest the lid on the very edge of the plate so the entire agar surface is completely exposed. Take care not to put fingers on plates and avoid passing anything over the top of plates being exposed. Leave plates exposed for the full shift and/or \u003cstrong\u003e4 hours\u003c/strong\u003e. The exposure time should be recorded before sending plates for incubation. After exposure, replace the lids of the plates. Clean the surface, where the plates were placed.\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:29.887Z","updated_at":"2019-01-29T12:36:43.079Z","last_modified_by_id":202,"protocol_id":3540},"checklists":[{"checklist":{"id":808,"name":"Sampling locations (examples):","step_id":4515,"created_at":"2018-11-15T09:56:29.965Z","updated_at":"2018-12-12T09:33:45.454Z","created_by_id":202,"last_modified_by_id":202},"checklist_items":[{"id":3399,"text":"Door to pass trough","checked":false,"checklist_id":808,"created_at":"2018-11-15T09:56:29.981Z","updated_at":"2018-11-15T10:21:48.064Z","created_by_id":202,"last_modified_by_id":202,"position":0},{"id":3401,"text":"In front of the door","checked":false,"checklist_id":808,"created_at":"2018-11-15T09:56:30.054Z","updated_at":"2019-01-29T12:36:43.082Z","created_by_id":202,"last_modified_by_id":202,"position":1},{"id":3402,"text":"Inside the curtain","checked":false,"checklist_id":808,"created_at":"2018-11-15T09:56:30.070Z","updated_at":"2019-01-29T12:36:43.092Z","created_by_id":202,"last_modified_by_id":202,"position":2},{"id":3403,"text":"Inside the middle of the pass trough","checked":false,"checklist_id":808,"created_at":"2018-11-15T09:56:30.083Z","updated_at":"2019-01-29T12:36:43.101Z","created_by_id":202,"last_modified_by_id":202,"position":3},{"id":3404,"text":"Behind the fill machine","checked":false,"checklist_id":808,"created_at":"2018-11-15T09:56:30.096Z","updated_at":"2019-01-29T12:36:43.107Z","created_by_id":202,"last_modified_by_id":202,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5167,"name":"Active Air Sampling with settle plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003e\u003cstrong\u003ePreparation of sampling location and air sampler:\u003c/strong\u003e Ensure air sampler is fully charged. Sanitize the external surfaces of the unit with sterile \u003cstrong\u003e70%\u003c/strong\u003e isopropyl alcohol. Press the black colour button on the bottom side to start the air sampler. \u003cbr\u003e\u003cstrong\u003eSampling:\u003c/strong\u003e Select standard mode and press confirm. Select \u003cstrong\u003e10 000L\u003c/strong\u003e of air volume and press enter key to confirm. After pressing the enter key START FOR 10 000 will appear on display. Carefully remove the cover from the sieve. Place the settle plate on the air sampler and screw the sieve head. Start the air sampler by pressing enter. Sampling should last around \u003cstrong\u003e10 minutes\u003c/strong\u003e. \u003cbr\u003e\u003cstrong\u003eAfter air sampling is finished: \u003c/strong\u003eUnscrew the sieve head of the air sampler. Carefully remove the agar plate and cover it with lid. Swab areas where plates have been exposed with a suitable disinfectant to remove any trace of media or condensation from the lids, which may contaminate the room. Swab areas where plates have been exposed with a suitable disinfectant to remove any trace of media or condensation from the lids, which may contaminate the clean room.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T10:05:21.914Z","updated_at":"2019-01-29T12:37:19.979Z","last_modified_by_id":202,"protocol_id":3540},"checklists":[{"checklist":{"id":925,"name":"Sample location (examples):","step_id":5167,"created_at":"2018-12-12T10:08:05.163Z","updated_at":"2018-12-12T10:08:05.163Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3817,"text":"In front of the door","checked":false,"checklist_id":925,"created_at":"2018-12-12T10:08:05.165Z","updated_at":"2018-12-12T10:08:05.165Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3818,"text":"Inside the curtain","checked":false,"checklist_id":925,"created_at":"2018-12-12T10:08:05.173Z","updated_at":"2018-12-12T10:08:05.173Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3819,"text":"Behind the fill machine","checked":false,"checklist_id":925,"created_at":"2018-12-12T10:08:05.179Z","updated_at":"2018-12-12T10:08:05.179Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3820,"text":"In front of pass trough","checked":false,"checklist_id":925,"created_at":"2018-12-12T10:08:05.185Z","updated_at":"2018-12-12T10:08:05.185Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2195,"name":"Incubation","due_date":null,"description":"Incubation instructions for all types of plates","x":70,"y":16,"my_module_group_id":1236,"created_at":"2018-11-15T09:56:32.117Z","updated_at":"2019-01-31T09:55:55.885Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":4,"experiment_id":440,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":6215,"input_id":2196,"output_id":2195},{"id":6216,"input_id":2200,"output_id":2195}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3554,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2195,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-15T09:56:32.169Z","updated_at":"2019-01-29T12:38:17.361Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4553,"name":"Incubation for growing bacteria","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cspan style=\"color: #ff0000;\"\u003e\u003cstrong\u003eImportant!:\u003c/strong\u003e \u003c/span\u003eIf the medium is dropped or touched by a person performing the sampling then this should be reported, the sample should be marked accordingly and treated as usual. Under no circumstances should samples that have been taken be refrigerated.\u003cbr\u003e\u003cbr\u003eFollowing testing, the samples should be incubated as soon as possible and should be held at room temperature with the medium uppermost until incubated or manipulated.\u003cbr\u003e\u003cbr\u003eIncubation of samples:\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003eInverted plates\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003e30 - 35°C\u003c/strong\u003e\u003c/li\u003e\n\u003cli\u003eAt least \u003cstrong\u003e2 days \u003c/strong\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\nIncubation conditions should be monitored to ensure that the appropriate incubation temperature is maintained throughout the incubation phase.\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:32.215Z","updated_at":"2019-01-29T12:37:59.184Z","last_modified_by_id":202,"protocol_id":3554},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4555,"name":"Counting and Recording","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAfter appropriate incubation microbiological contamination should grow into discrete macroscopic colonies that can be enumerated and the number of discrete colonies forming units (CFU) can be counted on each sample. \u003cbr\u003eRecord the number (per unit surface area) on the results tab. Separate colony counts may be tabulated for mould and bacteria.\u003cbr\u003e\u003cbr\u003eColony types may be identified if this is considered appropriate.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:32.267Z","updated_at":"2018-12-12T11:14:01.114Z","last_modified_by_id":202,"protocol_id":3554},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4552,"name":"Incubation for growing fungi","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cspan style=\"color: #ff0000;\"\u003e\u003cstrong\u003eImportant!:\u003c/strong\u003e \u003c/span\u003eIf the medium is dropped or touched by a person performing the sampling then this should be reported, the sample should be marked accordingly and treated as usual. Under no circumstances should samples that have been taken be refrigerated.\u003cbr\u003e\u003cbr\u003eFollowing testing, the samples should be incubated as soon as possible and should be held at room temperature with the medium uppermost until incubated or manipulated.\u003cbr\u003eIncubation of samples:\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003eInverted plates\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003e20 - 25°C\u003c/strong\u003e\u003c/li\u003e\n\u003cli\u003eAt least \u003cstrong\u003e5 days \u003c/strong\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003eIncubation conditions should be monitored to ensure that the appropriate incubation temperature is maintained throughout the incubation phase.\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:32.186Z","updated_at":"2019-01-29T12:38:17.317Z","last_modified_by_id":202,"protocol_id":3554},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2200,"name":"Counting colonies and recording data","due_date":null,"description":null,"x":104,"y":16,"my_module_group_id":1236,"created_at":"2018-11-15T09:56:33.039Z","updated_at":"2019-01-31T09:55:55.900Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":5,"experiment_id":440,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3564,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2200,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-15T09:56:33.091Z","updated_at":"2019-01-28T09:02:38.281Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5174,"name":"Discarding plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAll samples (contaminated or not) should be disposed of according to procedures.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T11:23:59.242Z","updated_at":"2018-12-12T11:24:31.752Z","last_modified_by_id":202,"protocol_id":3564},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5173,"name":"Counting colonies and recording","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAfter appropriate incubation microbiological contamination should grow into discrete macroscopic colonies that can be enumerated and the number of discrete colonies forming units (CFU) can be counted on each sample. \u003cbr\u003eRecord the number (per unit surface area) on the results tab. Separate colony counts may be tabulated for mould and bacteria.\u003cbr\u003e\u003cbr\u003eColony types may be identified if this is considered appropriate.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T11:21:40.888Z","updated_at":"2019-01-25T13:21:04.649Z","last_modified_by_id":202,"protocol_id":3564},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4567,"name":"Action to be taken","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv style=\"text-align: justify;\"\u003eRecording of data provides oversight for microbiological cleanliness. In order for results to provide meaningful data, it is of key importance that alert and action limits are established. \u003cem\u003e\u003cstrong\u003eAlert levels ensure that any excursion of the parameter can be detected early. Action levels deviate more from the standard. If the alert level is exceeded repeatedly, this is considered equivalent to exceeding the action level.\u003c/strong\u003e\u003c/em\u003e In practice, several statistical methods including normal, Poisson, and negative binomial modelling have been routinely used to set these limits. \u003cbr\u003e\u003cbr\u003eExceeding action levels on isolated occasions may not require more action than an examination of control systems. However, the frequency of exceeding the limit should be examined and should be low. \u003cstrong\u003eIf the frequency is high or shows an upward trend then action should be taken which may include an increase in the frequency of testing, observation of operator technique or investigation of cleaning procedures.\u003cbr\u003e\u003cbr\u003e\u003c/strong\u003e\n\u003c/div\u003e\n\u003cdiv style=\"text-align: justify;\"\u003eIdentification of the causative microorganism(s) may aid tracing the \u003cstrong\u003esource of the contamination\u003c/strong\u003e. Successive results greater than the action levels demand that appropriate action is taken to reduce contamination to within limits. Where a problem has been observed the contaminating microorganisms should be identified. Isolated instances require no more action than an examination of control systems. If repeated contamination appears an investigation into the problem should take place and\u003cstrong\u003e corrective action should be carried out which will rectify the problem\u003c/strong\u003e. The corrective action should investigate the root cause of the problem and identify steps, with the timescale, that will be taken to reduce the contamination levels to \"normal\". A record of all action taken should be made in an \"Abnormal Event Log\".\u003c/div\u003e\n\u003cdiv style=\"text-align: justify;\"\u003eThe following areas should be examined where action levels are repeatedly breached:\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eIdentify:\u003c/strong\u003e\n\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003ePossible cause\u003c/li\u003e\n\u003cli\u003eContaminating microorganisms\u003c/li\u003e\n\u003c/ul\u003e\n\u003cstrong\u003eInvestigate:\u003c/strong\u003e\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003eWhether an isolated sample or whole area involved\u003c/li\u003e\n\u003cli\u003ePersonnel - operator status (grade), level of training, health, technique, wash up\u003c/li\u003e\n\u003cli\u003eCleaning procedures\u003c/li\u003e\n\u003cli\u003eChanging procedure\u003c/li\u003e\n\u003cli\u003eHEPA filter integrity of room/clean air device\u003c/li\u003e\n\u003cli\u003eProcesses carried out\u003c/li\u003e\n\u003cli\u003ePrevious test results for trends or other identified problems.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cstrong\u003eLiase with:\u003c/strong\u003e \u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003eAseptic personnel\u003c/li\u003e\n\u003cli\u003eMicrobiology personnel\u003c/li\u003e\n\u003cli\u003eQA/QC personnel\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:33.108Z","updated_at":"2019-01-28T09:02:38.188Z","last_modified_by_id":202,"protocol_id":3564},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2196,"name":"Colony Isolation and identification","due_date":null,"description":null,"x":70,"y":33,"my_module_group_id":1236,"created_at":"2018-11-15T09:56:32.322Z","updated_at":"2019-01-31T09:55:55.894Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":6,"experiment_id":440,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3556,"name":null,"authors":null,"description":null,"added_by_id":202,"my_module_id":2196,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-15T09:56:32.376Z","updated_at":"2019-01-31T09:52:32.680Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5177,"name":"Discarding plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAll samples should be discarded according to procedures. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":4,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T11:42:25.451Z","updated_at":"2018-12-12T11:42:25.451Z","last_modified_by_id":202,"protocol_id":3556},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4558,"name":"Streak plate procedure","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow streaking procedure as displayed on image and guidelines below.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:32.459Z","updated_at":"2019-01-29T12:40:50.937Z","last_modified_by_id":202,"protocol_id":3556},"checklists":[{"checklist":{"id":953,"name":"Guidelines:","step_id":4558,"created_at":"2018-12-21T07:19:34.041Z","updated_at":"2018-12-21T07:19:34.041Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3912,"text":"Label the base of the plate. Open the lids and flame metal loop using a Bunsen burner before obtaining the inoculum for the plate.","checked":false,"checklist_id":953,"created_at":"2018-12-21T07:19:34.043Z","updated_at":"2018-12-21T07:19:34.043Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3913,"text":"The metal should become red hot. Move the wire so the flame approaches the loop. Spread sample over about one-quarter of the surface of the medium using a rapid, smooth, back-and-forth motion.","checked":false,"checklist_id":953,"created_at":"2018-12-21T07:19:34.053Z","updated_at":"2018-12-21T07:19:34.053Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3914,"text":"Lift the bottom half of an inverted plate from the bench. Move the loop back and forth many times across the agar surface from the rim to the centre of the plate. Reflame the metal loop. Turn the Petri dish 90 ° to streak the second quadrant. Using the back-and-forth pattern, cross over the last half of the streaks in the first quadrant then move into the empty second quadrant. Repeat until all 4 quadrants are done.","checked":false,"checklist_id":953,"created_at":"2018-12-21T07:19:34.060Z","updated_at":"2018-12-21T07:19:34.060Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3915,"text":"Cover all the plates with their lids.","checked":false,"checklist_id":953,"created_at":"2018-12-21T07:19:34.067Z","updated_at":"2018-12-21T07:19:34.067Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3916,"text":"Clean the area with disinfectant.","checked":false,"checklist_id":953,"created_at":"2018-12-21T07:19:34.073Z","updated_at":"2018-12-21T07:19:34.073Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[{"id":2980,"step_id":4558,"asset_id":3631}],"assets":[{"id":3631,"created_at":"2019-01-29T12:40:35.070Z","updated_at":"2019-01-29T12:40:50.875Z","file_file_name":"Plate_streaking.png","file_content_type":"image/png","file_file_size":100610,"file_updated_at":"2019-01-29T12:40:38.649Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":110671,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]},{"step":{"id":5175,"name":"Incubation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the protocol for incubation in \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#inc\"\u003e[#Incubation~tsk~ZP]\u003c/span\u003e \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T11:36:16.853Z","updated_at":"2019-01-25T12:47:34.060Z","last_modified_by_id":202,"protocol_id":3556},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4559,"name":"Prepare a safe and sterile workspace","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv class=\"row\" style=\"text-align: justify;\"\u003ePrepare a safe and sterile workspace: Sterilize all instruments, solutions, and media prior to using them for plating procedures. Clear away all materials cluttering your work area on the laboratory bench. Clean work area with disinfectant to minimize possible contamination. Set up a Bunsen burner. Work slowly, carefully, and deliberately within the sterile field area created by the updraft of the flame. Arrange all the supplies needed for the procedure on the laboratory bench near the sterile field. Make sure all the materials are properly labelled. Prepare new settle plates and settle plates from where you are isolating colonies.\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:32.486Z","updated_at":"2018-12-21T07:17:09.419Z","last_modified_by_id":202,"protocol_id":3556},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5176,"name":"Identification","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eUse different tests to identify microorganisms:\u003c/p\u003e\n\u003cul\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe Gram stain test, which is used to determine if the organism is Gram-negative or Gram-positive\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe acid-fast test, which identifies Mycobacterium\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe oxidase test, which identifies organisms that produce the enzyme cytochrome oxidase\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe catalase test, which differentiates Staphylococci (a catalase positive organism) from Streptococci (a catalase negative organism)\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe starch hydrolysis test, which evaluates the organism’s ability to synthesize and secrete enzymes to break down starch into smaller subunits to be used by the organism\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe mannitol and glucose fermentation test, which investigates how an organism metabolizes sugars\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe Voges-Proskauer test, which tests the organism’s ability to produce non-acidic end products from the metabolism of glucose and is helpful in differentiating the Enterobacteriaceae\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe citrate test, which studies the organism’s ability to apply citrate as a carbon source and is also helpful in differentiating the Enterobacteriaceae;\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe nitrate reductase test, which investigates bacteria’s ability or inability to reduce nitrate to nitrite\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe novobiocin sensitivity test, which evaluates an organism’s susceptibility to novobiocin, an antibiotic that obstructs DNA replication and is helpful in differentiating among Gram-positive cocci\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T11:40:09.563Z","updated_at":"2019-01-31T09:44:24.368Z","last_modified_by_id":202,"protocol_id":3556},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]}],"my_module_groups":[{"id":1236,"created_at":"2019-01-31T09:55:55.882Z","updated_at":"2019-01-31T09:55:55.882Z","created_by_id":202,"experiment_id":440}]}
\ No newline at end of file
+{"experiment":{"id":440,"name":"Microbiological sampling_QA","description":"Quality assurance (QA) is a process, where primarily concerns are controls of errors in the performance of tests and verification of test results. 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Store in amber bottles.\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eSafranin:\u003cbr\u003e\u003cbr\u003e\u003c/strong\u003e\u003cspan style=\"text-decoration-line: underline;\"\u003eStock solution:\u003c/span\u003e\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003e2.5g Safranin O\u003c/li\u003e\n\u003cli\u003e100 ml 95% Ethanol\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003e\u003cspan style=\"text-decoration: underline;\"\u003eWorking Solution:\u003c/span\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e10 ml Stock Solution \u003c/li\u003e\n\u003cli\u003e90 ml Distilled water\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-01-31T10:29:45.535Z","updated_at":"2019-01-31T10:29:45.535Z","last_modified_by_id":202,"protocol_id":4193},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5488,"name":"Gram staining","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines below.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T14:18:22.722Z","updated_at":"2019-02-01T14:20:09.992Z","last_modified_by_id":202,"protocol_id":4193},"checklists":[{"checklist":{"id":1010,"name":"Guidelines:","step_id":5488,"created_at":"2019-02-01T14:18:22.724Z","updated_at":"2019-02-01T14:18:22.724Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":4124,"text":"Flood air-dried, heat-fixed smear of cells for 1 minute with crystal violet staining reagent. Please note that the quality of the smear (too heavy or too light cell concentration) will affect the Gram Stain results.","checked":false,"checklist_id":1010,"created_at":"2019-02-01T14:18:22.727Z","updated_at":"2019-02-01T14:18:22.727Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":4125,"text":"Wash slide in a gentle and indirect stream of tap water for 2 seconds.","checked":false,"checklist_id":1010,"created_at":"2019-02-01T14:18:22.742Z","updated_at":"2019-02-01T14:18:22.742Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":4126,"text":"Flood slide with the mordant: Gram's iodine. Wait 1 minute.","checked":false,"checklist_id":1010,"created_at":"2019-02-01T14:18:22.753Z","updated_at":"2019-02-01T14:18:22.753Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":4127,"text":"Wash slide in a gentle and indirect stream of tap water for 2 seconds.","checked":false,"checklist_id":1010,"created_at":"2019-02-01T14:18:22.764Z","updated_at":"2019-02-01T14:18:22.764Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":4128,"text":"Flood slide with decolorizing agent. Wait 15 seconds or add drop by drop to slide until decolorizing agent running from the slide runs clear.","checked":false,"checklist_id":1010,"created_at":"2019-02-01T14:18:22.771Z","updated_at":"2019-02-01T14:18:22.771Z","created_by_id":null,"last_modified_by_id":null,"position":4},{"id":4129,"text":"Flood slide with counterstain, safranin. Wait 30 seconds to 1 minute.","checked":false,"checklist_id":1010,"created_at":"2019-02-01T14:18:22.779Z","updated_at":"2019-02-01T14:18:22.779Z","created_by_id":null,"last_modified_by_id":null,"position":5},{"id":4130,"text":"Wash slide in a gentile and indirect stream of tap water until no color appears in the effluent and then blot dry with absorbent paper.","checked":false,"checklist_id":1010,"created_at":"2019-02-01T14:18:22.786Z","updated_at":"2019-02-01T14:18:22.786Z","created_by_id":null,"last_modified_by_id":null,"position":6},{"id":4131,"text":"Observe the results of the staining procedure under oil immersion using a Brightfield microscope. 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After cleaning, dry the slides and place them on laboratory towels until ready for use. Drawing a circle on the underside of the slide using a glassware-marking pen may be helpful to clearly designate the area in which you will prepare the smear.  You may also label the slide with the initials of the name of the organism on the edge of the slide. \u003cbr\u003eWith a sterile cooled loop, place a drop of sterile water or saline solution on the slide. \u003cstrong\u003eSterilize and cool the loop again and pick up a very small sample of a bacterial colony and gently stir into the drop of water/saline on the slide to create an emulsion.\u003c/strong\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-01-31T11:56:43.730Z","updated_at":"2019-02-01T14:10:09.347Z","last_modified_by_id":202,"protocol_id":4193},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5487,"name":"Heat fixing","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eHeat fixing kills the bacteria in the smear, firmly adheres the smear to the slide, and allows the sample to more readily take up stains.\u003cbr\u003eAllow the smear to air dry. After the smear has air-dried, hold the slide at one end and pass the entire slide through the flame of a Bunsen burner \u003cstrong\u003etwo to three times with the smear-side up.\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e \u003c/p\u003e\n\u003cp\u003e \u003c/p\u003e\n\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T14:13:27.107Z","updated_at":"2019-02-01T14:13:27.107Z","last_modified_by_id":202,"protocol_id":4193},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2551,"name":"Catalase Test","due_date":null,"description":null,"x":105,"y":50,"my_module_group_id":null,"created_at":"2019-01-31T09:55:55.627Z","updated_at":"2019-01-31T09:55:55.627Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":-1,"experiment_id":440,"state":"uncompleted","completed_on":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":4196,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2551,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2019-01-31T09:55:55.631Z","updated_at":"2019-02-04T13:39:32.426Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5496,"name":"Tube test","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines: \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-04T13:21:21.550Z","updated_at":"2019-02-04T13:30:56.251Z","last_modified_by_id":202,"protocol_id":4196},"checklists":[{"checklist":{"id":1014,"name":"Guidelines:","step_id":5496,"created_at":"2019-02-04T13:30:56.249Z","updated_at":"2019-02-04T13:30:56.249Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":4149,"text":"Add 4 to 5 drops of 3% H2O2 to in a test tube.","checked":false,"checklist_id":1014,"created_at":"2019-02-04T13:30:56.251Z","updated_at":"2019-02-04T13:30:56.251Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":4150,"text":"Using a wooden applicator stick, collect a small amount of organism from a well-isolated 18- to 24-hour colony and place into the test tube (Note: Be careful not to pick up any agar).","checked":false,"checklist_id":1014,"created_at":"2019-02-04T13:30:56.260Z","updated_at":"2019-02-04T13:30:56.260Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":4151,"text":"Place the tube against a dark background and observe for immediate bubble formation at the end of the wooden applicator stick.","checked":false,"checklist_id":1014,"created_at":"2019-02-04T13:30:56.267Z","updated_at":"2019-02-04T13:30:56.267Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5495,"name":"Slide test","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines bellow. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-04T13:18:55.135Z","updated_at":"2019-02-04T13:18:55.140Z","last_modified_by_id":202,"protocol_id":4196},"checklists":[{"checklist":{"id":1013,"name":"Guidelines:","step_id":5495,"created_at":"2019-02-04T13:18:55.138Z","updated_at":"2019-02-04T13:18:55.138Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":4145,"text":"Transfer a small amount of bacterial colony to a surface of clean, dry glass slide using a loop","checked":false,"checklist_id":1013,"created_at":"2019-02-04T13:18:55.140Z","updated_at":"2019-02-04T13:18:55.140Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":4146,"text":"Place a drop of 3% H2O2 on to the slide and mix.","checked":false,"checklist_id":1013,"created_at":"2019-02-04T13:18:55.155Z","updated_at":"2019-02-04T13:18:55.155Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":4147,"text":"Look for a rapid evolution of oxygen (within 5-10 seconds) as evidenced by bubbling.","checked":false,"checklist_id":1013,"created_at":"2019-02-04T13:18:55.163Z","updated_at":"2019-02-04T13:18:55.163Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":4148,"text":"Dispose of your slide in the biohazard glass disposal container.","checked":false,"checklist_id":1013,"created_at":"2019-02-04T13:21:32.881Z","updated_at":"2019-02-04T13:21:32.881Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5497,"name":"Results interpretation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cem\u003e\u003cstrong\u003eCatalase is an enzyme, which is produced by microorganisms that live in oxygenated environments to neutralize toxic forms of oxygen metabolites.\u003c/strong\u003e\u003c/em\u003e Anaerobes generally lack the catalase enzyme. Catalase enzyme hydrolyzes the hydrogen peroxide and forms bubbles. \u003cstrong\u003e\u003cbr\u003e\u003cbr\u003eImmediate effervescence (bubble formation): \u003c/strong\u003eCatalase positive reactions\u003cstrong\u003e\u003cbr\u003eNo bubble formation: \u003c/strong\u003eCatalase Negative reaction\u003cstrong\u003e\u003cbr\u003e\u003c/strong\u003e\n\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-04T13:38:56.063Z","updated_at":"2019-02-04T13:39:32.375Z","last_modified_by_id":202,"protocol_id":4196},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2550,"name":"Oxidase Test","due_date":null,"description":null,"x":70,"y":50,"my_module_group_id":null,"created_at":"2019-01-31T09:55:55.606Z","updated_at":"2019-01-31T09:55:55.606Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":-1,"experiment_id":440,"state":"uncompleted","completed_on":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":4195,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2550,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2019-01-31T09:55:55.611Z","updated_at":"2019-02-01T14:54:17.326Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5492,"name":"Oxidase test","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines bellow: \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T14:49:04.449Z","updated_at":"2019-02-01T14:49:04.453Z","last_modified_by_id":202,"protocol_id":4195},"checklists":[{"checklist":{"id":1012,"name":"Guidelines:","step_id":5492,"created_at":"2019-02-01T14:49:04.452Z","updated_at":"2019-02-01T14:49:04.452Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":4141,"text":"Take a filter paper soaked with the substrate tetramethyl-p-phenylenediamine dihydrochloride.","checked":false,"checklist_id":1012,"created_at":"2019-02-01T14:49:04.454Z","updated_at":"2019-02-01T14:49:04.454Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":4142,"text":"Moisten the paper with a sterile distilled water.","checked":false,"checklist_id":1012,"created_at":"2019-02-01T14:49:04.462Z","updated_at":"2019-02-01T14:49:04.462Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":4143,"text":"Pick the colony to be tested with wooden or platinum loop and smear in the filter paper.","checked":false,"checklist_id":1012,"created_at":"2019-02-01T14:49:04.469Z","updated_at":"2019-02-01T14:49:04.469Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":4144,"text":"Observe inoculated area of paper for a color change to deep blue or purple within 10-30 seconds.","checked":false,"checklist_id":1012,"created_at":"2019-02-01T14:49:04.475Z","updated_at":"2019-02-01T14:49:04.475Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5493,"name":"Results interpretation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eOxidase test is used for identification of \u003cem\u003ePseudomonas\u003c/em\u003e spp, \u003cem\u003eAeromonas\u003c/em\u003e spp,  \u003cem\u003eNeisserias\u003c/em\u003e spp, \u003cem\u003eVibrio\u003c/em\u003e spp and \u003cem\u003ePasteurella\u003c/em\u003e spp, all of which produces oxidase enzyme. \u003cbr\u003e\u003cbr\u003e\u003cstrong\u003e\u003cspan style=\"color: #333399;\"\u003eBlue-purple colour:\u003c/span\u003e\u003c/strong\u003e Oxidase positive\u003cbr\u003eNo purple colour: Oxidase negative\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T14:54:17.285Z","updated_at":"2019-02-01T14:54:17.285Z","last_modified_by_id":202,"protocol_id":4195},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2549,"name":"Acid-Fast Stain 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Drawing a circle on the underside of the slide using a glassware-marking pen may be helpful to clearly designate the area in which you will prepare the smear.  You may also label the slide with the initials of the name of the organism on the edge of the slide. \u003cbr\u003eWith a sterile cooled loop, place a drop of sterile water or saline solution on the slide. \u003cstrong\u003eSterilize and cool the loop again and pick up a very small sample of a bacterial colony and gently stir into the drop of water/saline on the slide to create an emulsion.\u003c/strong\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T14:22:44.942Z","updated_at":"2019-02-01T14:22:44.942Z","last_modified_by_id":202,"protocol_id":4194},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5490,"name":"Heat-fixing","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eHeat fixing kills the bacteria in the smear, firmly adheres the smear to the slide, and allows the sample to more readily take up stains.\u003cbr\u003eAllow the smear to air dry. After the smear has air-dried, hold the slide at one end and pass the entire slide through the flame of a Bunsen burner \u003cstrong\u003etwo to three times with the smear-side up.\u003c/strong\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T14:23:09.650Z","updated_at":"2019-02-01T14:23:09.650Z","last_modified_by_id":202,"protocol_id":4194},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5491,"name":"Acid-Fast Staining","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines below:\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003e\u003cspan style=\"color: #ff0000;\"\u003eImportant: \u003c/span\u003e\u003c/strong\u003e\u003cspan style=\"color: #000000;\"\u003e Great care must be taken when heating the carbol fuchsin especially if staining is carried out over a tray or other container in which highly flammable chemicals have collected from the previous staining. Only a small flame should be applied under the slides using an ignited swab previously dampened with a few drops of acid alcohol or 70% v/v ethanol or methanol. Do not use a large ethanol soaked swab because this is a fire risk.\u003c/span\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T14:33:15.222Z","updated_at":"2019-02-01T14:45:11.703Z","last_modified_by_id":202,"protocol_id":4194},"checklists":[{"checklist":{"id":1011,"name":"Guideline:","step_id":5491,"created_at":"2019-02-01T14:33:15.225Z","updated_at":"2019-02-01T14:33:15.225Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":4132,"text":"Cover the smear with carbol fuchsin stain.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.227Z","updated_at":"2019-02-01T14:33:15.227Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":4133,"text":"Heat the stain until vapour just begins to rise (i.e. about 60°C). Do not overheat. Allow the heated stain to remain on the slide for 5 minutes.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.235Z","updated_at":"2019-02-01T14:33:15.235Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":4134,"text":"Wash off the stain with distilled water.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.244Z","updated_at":"2019-02-01T14:41:45.127Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":4135,"text":"Cover the smear with 3% v/v acid alcohol for 5 minutes or until the smear is sufficiently decolorized, i.e. pale pink.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.252Z","updated_at":"2019-02-01T14:33:15.252Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":4136,"text":"Wash well with distilled water.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.259Z","updated_at":"2019-02-01T14:41:45.136Z","created_by_id":null,"last_modified_by_id":null,"position":4},{"id":4137,"text":"Cover the smear with methylene blue dye for 1–2 minutes.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.266Z","updated_at":"2019-02-01T14:41:45.144Z","created_by_id":null,"last_modified_by_id":null,"position":5},{"id":4138,"text":"Wash off the stain with distilled water.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.273Z","updated_at":"2019-02-01T14:41:45.151Z","created_by_id":null,"last_modified_by_id":null,"position":6},{"id":4139,"text":"Wipe the back of the slide clean, and place it in a draining rack for the smear to air-dry (do not blot dry).","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.280Z","updated_at":"2019-02-01T14:33:15.280Z","created_by_id":null,"last_modified_by_id":null,"position":7},{"id":4140,"text":"Examine the smear microscopically, using the 100 X oil immersion objective.","checked":false,"checklist_id":1011,"created_at":"2019-02-01T14:33:15.286Z","updated_at":"2019-02-01T14:33:15.286Z","created_by_id":null,"last_modified_by_id":null,"position":8}]}],"step_comments":[],"step_assets":[{"id":2984,"step_id":5491,"asset_id":3636}],"assets":[{"id":3636,"created_at":"2019-02-01T14:44:32.274Z","updated_at":"2019-02-01T14:45:11.689Z","file_file_name":"acid-fast_stain.png","file_content_type":"image/png","file_file_size":137068,"file_updated_at":"2019-02-01T14:45:11.001Z","created_by_id":202,"last_modified_by_id":null,"estimated_size":150774,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]},{"step":{"id":5494,"name":"Result interpretation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cstrong\u003eSome\u003c/strong\u003e\u003cem\u003e\u003cstrong\u003e bacteria contain a waxy lipid, mycolic acid, in their cell wall.\u003c/strong\u003e\u003c/em\u003e This lipid makes the cells more durable and is commonly associated with pathogens.\u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003e\u003cspan style=\"color: #ff0000;\"\u003eRED: \u003c/span\u003e\u003c/strong\u003e\u003cspan style=\"color: #000000;\"\u003eAcid fast organisms \u003cbr\u003e\u003cstrong\u003e\u003cspan style=\"color: #0000ff;\"\u003eBLUE:\u003c/span\u003e\u003c/strong\u003e\u003cspan style=\"color: #0000ff;\"\u003e \u003cspan style=\"color: #000000;\"\u003eNon-acid fast organisms\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\n\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-02-01T15:01:30.991Z","updated_at":"2019-02-01T15:01:30.991Z","last_modified_by_id":202,"protocol_id":4194},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2192,"name":"Plate preparation","due_date":null,"description":"","x":1,"y":16,"my_module_group_id":1236,"created_at":"2018-11-15T09:56:30.961Z","updated_at":"2019-01-31T09:55:55.903Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":0,"experiment_id":440,"state":"uncompleted","completed_on":null},"outputs":[{"id":6218,"input_id":2188,"output_id":2192},{"id":6219,"input_id":2190,"output_id":2192},{"id":6220,"input_id":2194,"output_id":2192}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3548,"name":null,"authors":null,"description":null,"added_by_id":202,"my_module_id":2192,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-15T09:56:31.020Z","updated_at":"2019-01-31T09:33:37.119Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4533,"name":"Examine the plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines bellow. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:31.091Z","updated_at":"2018-12-24T08:23:09.402Z","last_modified_by_id":202,"protocol_id":3548},"checklists":[{"checklist":{"id":924,"name":"Guideline:","step_id":4533,"created_at":"2018-12-12T07:16:14.619Z","updated_at":"2018-12-24T08:23:09.400Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3812,"text":"Monitor refrigerator temperature and record it in Results.","checked":false,"checklist_id":924,"created_at":"2018-12-12T07:16:14.622Z","updated_at":"2018-12-12T07:16:14.622Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3813,"text":"Contact plates and/or Settle plates are taken to the room temperature.  They will be used depending on the surface of the sampling.","checked":false,"checklist_id":924,"created_at":"2018-12-12T07:16:14.634Z","updated_at":"2018-12-12T07:16:14.634Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3814,"text":"Examine the plates for contamination prior to use. If any plates are contaminated they should be discarded according to protocol.","checked":false,"checklist_id":924,"created_at":"2018-12-12T07:16:14.641Z","updated_at":"2018-12-12T07:16:14.641Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4535,"name":"Preincubation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003ePreincubate the empty plates in incubator \u003cstrong\u003e30°C-35°C\u003c/strong\u003e for \u003cstrong\u003e48 hours\u003c/strong\u003e to check for any accidental contamination. Check for contamination again. If there is contamination record it and discard according to appropriate procedures. Take contamination-free plates to room temperature an hour before exposure.\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:31.144Z","updated_at":"2019-01-29T12:33:40.426Z","last_modified_by_id":202,"protocol_id":3548},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2194,"name":"Contact Plate Sampling","due_date":null,"description":"Protocol for direct testing of surfaces. Contact plates are allowing us to detect microorganisms that are on flat surfaces in relatively low numbers.","x":35,"y":0,"my_module_group_id":1236,"created_at":"2018-11-15T09:56:31.528Z","updated_at":"2019-01-31T09:55:55.891Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":1,"experiment_id":440,"state":"uncompleted","completed_on":null},"outputs":[{"id":6221,"input_id":2195,"output_id":2194}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3552,"name":null,"authors":null,"description":null,"added_by_id":202,"my_module_id":2194,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-15T09:56:31.582Z","updated_at":"2019-01-31T09:38:26.038Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4549,"name":"Collect all the plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAfter all the samples are taken, collect all sample plates together, remove them from the sampling area and incubate as directed. Complete and enclose the necessary documentation \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#coun\"\u003e[#Counting and recording...~tsk~ZU]\u003c/span\u003e.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:31.742Z","updated_at":"2019-01-25T12:41:23.609Z","last_modified_by_id":202,"protocol_id":3552},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5447,"name":"Labeling of plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eAssemble the plates required and label them. Ensure that correct information about sampling is written on the base of the plate with a permanent ink marker.\u003cbr\u003eThe following sampling details should be recorded on the plate:\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eInitials of a person who is sampling\u003c/li\u003e\n\u003cli\u003eSampling location code\u003c/li\u003e\n\u003cli\u003eDate and time of the day of sampling/plating \u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-01-25T12:10:43.950Z","updated_at":"2019-01-25T12:18:51.523Z","last_modified_by_id":202,"protocol_id":3552},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4551,"name":"Surface sampling with contact plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003eTransfer the contact plates into the area to be tested. Enter the area according to the procedures. Ensure that the testing area is dry. \u003cbr\u003e\u003cbr\u003eWhen sampling surfaces with contact plates, remove the lid and place the agar surface in maximum contact with the sampling site for \u003cstrong\u003e10 seconds\u003c/strong\u003e by applying a constant force spread evenly over the whole contact plate without twisting or sliding and avoiding the creation of bubbles. After contact with the sample surface, remove and replace the lid, avoiding any unnecessary hand movement near or over the agar surface. Clean it with disinfectant to remove any possible traces of agar.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:31.793Z","updated_at":"2019-01-29T12:34:02.242Z","last_modified_by_id":202,"protocol_id":3552},"checklists":[{"checklist":{"id":810,"name":"Sample locations (examples):","step_id":4551,"created_at":"2018-11-15T09:56:31.809Z","updated_at":"2018-12-12T07:32:30.595Z","created_by_id":202,"last_modified_by_id":202},"checklist_items":[{"id":3410,"text":"Filling machine control panel","checked":false,"checklist_id":810,"created_at":"2018-11-15T09:56:31.836Z","updated_at":"2018-12-12T07:29:55.968Z","created_by_id":202,"last_modified_by_id":202,"position":0},{"id":3411,"text":"Surface of Balance Table","checked":false,"checklist_id":810,"created_at":"2018-11-15T09:56:31.847Z","updated_at":"2018-12-12T07:29:55.975Z","created_by_id":202,"last_modified_by_id":202,"position":1},{"id":3412,"text":"Surface of table","checked":false,"checklist_id":810,"created_at":"2018-11-15T09:56:31.860Z","updated_at":"2018-12-12T07:29:55.981Z","created_by_id":202,"last_modified_by_id":202,"position":2},{"id":3413,"text":"Surface of door to pass trough","checked":false,"checklist_id":810,"created_at":"2018-11-15T09:56:31.872Z","updated_at":"2018-12-12T07:29:55.990Z","created_by_id":202,"last_modified_by_id":202,"position":3},{"id":3414,"text":"Surface of door","checked":false,"checklist_id":810,"created_at":"2018-11-15T09:56:31.885Z","updated_at":"2018-12-12T07:29:55.997Z","created_by_id":202,"last_modified_by_id":202,"position":4},{"id":3417,"text":"Surface of the wall","checked":false,"checklist_id":810,"created_at":"2018-11-15T09:56:31.923Z","updated_at":"2018-12-12T07:32:44.480Z","created_by_id":202,"last_modified_by_id":202,"position":5},{"id":3420,"text":"Surface of solid curtain","checked":false,"checklist_id":810,"created_at":"2018-11-15T09:56:31.960Z","updated_at":"2018-12-12T07:32:44.487Z","created_by_id":202,"last_modified_by_id":202,"position":6},{"id":3815,"text":"Stopper bowl","checked":false,"checklist_id":810,"created_at":"2018-12-12T07:32:30.611Z","updated_at":"2018-12-12T07:32:44.494Z","created_by_id":null,"last_modified_by_id":null,"position":7},{"id":3816,"text":"Plexiglass barrier","checked":false,"checklist_id":810,"created_at":"2018-12-12T07:32:30.618Z","updated_at":"2018-12-12T07:32:44.501Z","created_by_id":null,"last_modified_by_id":null,"position":8}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5165,"name":"Sampling guidlines for glove and gowning test","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003e\u003cstrong\u003eTesting conditions:\u003c/strong\u003e Sampling should take place at the end of a work session, but before the person would carry out any cleaning. Before performing the test the person should ensure that gloves are dry and free of any disinfectant. \u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eGlove test:\u003c/strong\u003e The person doing the sampling should lift the lid of the plate, with the opposite hand to that being tested, and keeping hold of the lid in the other hand, touch the agar surface with the tips of all fingers then the thumb (in the gap on the plate behind where fingers were tested) on the hand being tested. A firm and even pressure should be applied for approximately \u003cstrong\u003e5 to 10 seconds\u003c/strong\u003e, taking care not to damage the agar surface. Replace the lid of the plate. Repeat for the other hand. Ensure that the glove surfaces tested are cleaned with a suitable disinfectant to remove any possible traces of agar before performing any other operations.\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eGowning test:\u003c/strong\u003e The person doing the sampling should lift the lid of the plate and keep hold of the lid, touch the gown in the chest and clavicle area with agar surface. A firm and even pressure should be applied for approximately \u003cstrong\u003e5 to 10 seconds\u003c/strong\u003e, taking care not to damage the agar surface. Replace the lid of the plate. Ensure that the gown surfaces tested are cleaned with a suitable disinfectant to remove any possible traces of agar before performing any other operations.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T07:58:32.639Z","updated_at":"2019-01-29T12:34:24.814Z","last_modified_by_id":202,"protocol_id":3552},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2190,"name":"Sampling of uneven surfaces","due_date":null,"description":"A method using swabs that makes microbiological load visible on uneven surfaces.","x":35,"y":33,"my_module_group_id":1236,"created_at":"2018-11-15T09:56:30.349Z","updated_at":"2019-01-31T09:55:55.897Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":440,"state":"uncompleted","completed_on":null},"outputs":[{"id":6217,"input_id":2195,"output_id":2190}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3544,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2190,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-15T09:56:30.402Z","updated_at":"2019-01-29T12:36:12.849Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5448,"name":"Labeling of plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eAssemble the plates required and label them. Ensure that correct information about sampling is written on the base of the plate with a permanent ink marker.\u003cbr\u003eThe following sampling details should be recorded on the plate:\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eInitials of a person who is sampling\u003c/li\u003e\n\u003cli\u003eSampling location code\u003c/li\u003e\n\u003cli\u003eDate and time of the day of sampling/plating \u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-01-25T12:11:53.234Z","updated_at":"2019-01-25T12:18:18.027Z","last_modified_by_id":202,"protocol_id":3544},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4523,"name":"Collect all the swabs","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAfter all the samples are taken, collect all sample swabs together, remove them from the sampling area and plate them as directed in the next step. Complete and enclose all the necessary documentation in \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#countin\"\u003e[#Counting and recording...~tsk~ZU]\u003c/span\u003e.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:30.601Z","updated_at":"2019-01-25T12:40:08.288Z","last_modified_by_id":202,"protocol_id":3544},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4521,"name":"Sampling with a swab","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003e\u003cstrong\u003eSampling:\u003c/strong\u003e Wipe the swab over the sample area in close parallel streaks, using firm even pressure and rotating the swab between fingers to maximise sample pick-up. The swab should be held at a 30° angle to the contact surface. With the same swab, repeat this process at right angles to the first streaks to ensure that the entire sample area is swabbed. Replace swab into transport tube ensuring that swab comes into contact with the transport medium by pushing down hard. Clean the surface tested with disinfectant.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:30.480Z","updated_at":"2019-01-25T12:15:22.003Z","last_modified_by_id":202,"protocol_id":3544},"checklists":[{"checklist":{"id":809,"name":"Sample locations:","step_id":4521,"created_at":"2018-11-15T09:56:30.495Z","updated_at":"2018-11-15T09:56:30.495Z","created_by_id":202,"last_modified_by_id":202},"checklist_items":[{"id":3405,"text":"Filling needle","checked":false,"checklist_id":809,"created_at":"2018-11-15T09:56:30.509Z","updated_at":"2018-11-15T10:08:47.925Z","created_by_id":202,"last_modified_by_id":202,"position":0},{"id":3406,"text":"Interior of the stopper chute","checked":false,"checklist_id":809,"created_at":"2018-11-15T09:56:30.522Z","updated_at":"2018-11-15T10:08:47.935Z","created_by_id":202,"last_modified_by_id":202,"position":1},{"id":3407,"text":"Helix/in-fed worm","checked":false,"checklist_id":809,"created_at":"2018-11-15T09:56:30.534Z","updated_at":"2018-11-15T10:08:47.944Z","created_by_id":202,"last_modified_by_id":202,"position":2},{"id":3408,"text":"In-feed belt","checked":false,"checklist_id":809,"created_at":"2018-11-15T09:56:30.546Z","updated_at":"2018-11-15T10:08:47.954Z","created_by_id":202,"last_modified_by_id":202,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5172,"name":"Plating of swabs","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines below for plating of swabs.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":4,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T11:02:15.588Z","updated_at":"2019-01-25T12:15:21.953Z","last_modified_by_id":202,"protocol_id":3544},"checklists":[{"checklist":{"id":952,"name":"Guidelines:","step_id":5172,"created_at":"2018-12-21T06:58:27.768Z","updated_at":"2018-12-21T06:58:27.768Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3906,"text":"Prepare a safe and sterile workspace: Sterilize all instruments, solutions, and media prior to using them for plating procedures. Clear away all materials cluttering your work area on the laboratory bench. Clean work area with disinfectant to minimize possible contamination.","checked":false,"checklist_id":952,"created_at":"2018-12-21T06:58:27.770Z","updated_at":"2018-12-21T06:58:27.770Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3907,"text":"Set up a Bunsen burner: Work slowly, carefully, and deliberately within the sterile field area created by the updraft of the flame.","checked":false,"checklist_id":952,"created_at":"2018-12-21T06:58:27.777Z","updated_at":"2018-12-21T06:58:27.777Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3908,"text":"Prepare lab equipment and settle plates.","checked":false,"checklist_id":952,"created_at":"2018-12-21T06:58:27.784Z","updated_at":"2018-12-21T06:58:27.784Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3909,"text":"Arrange all the supplies needed for the procedure on the laboratory bench near the sterile field. Make sure all the materials are properly labelled.","checked":false,"checklist_id":952,"created_at":"2018-12-21T06:58:27.791Z","updated_at":"2018-12-21T06:58:27.791Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3910,"text":"Carefully open the lid of the plate. A standard streaking out method should be used when plating out the swab. The method should ensure that the swab is rotated as it is run over the surface of the media to ensure that any microorganisms recovered from the surface sample are deposited onto the surface of the plate.\r\nReplace the lid.","checked":false,"checklist_id":952,"created_at":"2018-12-21T06:58:27.797Z","updated_at":"2018-12-21T06:58:27.797Z","created_by_id":null,"last_modified_by_id":null,"position":4},{"id":3911,"text":"Complete and enclose all the necessary documentation.","checked":false,"checklist_id":952,"created_at":"2018-12-21T06:58:27.804Z","updated_at":"2018-12-21T06:58:27.804Z","created_by_id":null,"last_modified_by_id":null,"position":5}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4519,"name":"Preparation of swabs before sampling","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eMake sure the sampling surface it is dry. Assemble the needle and \u003cstrong\u003e10 mL\u003c/strong\u003e syringe. Open the ampoule of \u003cstrong\u003e0.9%\u003c/strong\u003e NaCl Injection BP and draw up the contents. Push a small amount of liquid (about\u003cstrong\u003e 0.5 mL\u003c/strong\u003e) from the syringe directly onto the swab. Do not allow the needle tip to come into contact with the swab.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:30.420Z","updated_at":"2019-01-29T12:36:12.805Z","last_modified_by_id":202,"protocol_id":3544},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2188,"name":"Settle Plates Sampling","due_date":null,"description":"Settle plates asses the likely number of microorganisms depositing on the surface in a given time.","x":35,"y":16,"my_module_group_id":1236,"created_at":"2018-11-15T09:56:29.638Z","updated_at":"2019-01-31T09:55:55.888Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":3,"experiment_id":440,"state":"uncompleted","completed_on":null},"outputs":[{"id":6214,"input_id":2195,"output_id":2188}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3540,"name":null,"authors":null,"description":null,"added_by_id":202,"my_module_id":2188,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-15T09:56:29.693Z","updated_at":"2019-01-31T09:52:51.146Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4511,"name":"Collect all the plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAfter all the samples are taken, collect all sample plates together, remove them from the sampling area and incubate as directed. Complete and enclose the necessary documentation \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#coun\"\u003e[#Counting and recording...~tsk~ZU]\u003c/span\u003e.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:29.770Z","updated_at":"2019-01-25T12:42:42.158Z","last_modified_by_id":202,"protocol_id":3540},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5449,"name":"Labeling of plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eAssemble the plates required and label them. Ensure that correct information about sampling is written on the base of the plate with a permanent ink marker.\u003cbr\u003eThe following sampling details should be recorded on the plate:\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eInitials of a person who is sampling\u003c/li\u003e\n\u003cli\u003eSampling location code\u003c/li\u003e\n\u003cli\u003eDate and time of the day of sampling/plating \u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2019-01-25T12:12:27.694Z","updated_at":"2019-01-25T12:17:41.431Z","last_modified_by_id":202,"protocol_id":3540},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4515,"name":"Passive Air Sampling with settle plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv style=\"text-align: justify;\"\u003eTransfer the contact plates into the area to be tested. Enter the area according to the procedures. \u003cbr\u003e\u003cstrong\u003eSampling:\u003c/strong\u003e Place the plates to the appropriate location with lids still on. Raise lids to expose the surface of the medium, rest the lid on the very edge of the plate so the entire agar surface is completely exposed. Take care not to put fingers on plates and avoid passing anything over the top of plates being exposed. Leave plates exposed for the full shift and/or \u003cstrong\u003e4 hours\u003c/strong\u003e. The exposure time should be recorded before sending plates for incubation. After exposure, replace the lids of the plates. Clean the surface, where the plates were placed.\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:29.887Z","updated_at":"2019-01-29T12:36:43.079Z","last_modified_by_id":202,"protocol_id":3540},"checklists":[{"checklist":{"id":808,"name":"Sampling locations (examples):","step_id":4515,"created_at":"2018-11-15T09:56:29.965Z","updated_at":"2018-12-12T09:33:45.454Z","created_by_id":202,"last_modified_by_id":202},"checklist_items":[{"id":3399,"text":"Door to pass trough","checked":false,"checklist_id":808,"created_at":"2018-11-15T09:56:29.981Z","updated_at":"2018-11-15T10:21:48.064Z","created_by_id":202,"last_modified_by_id":202,"position":0},{"id":3401,"text":"In front of the door","checked":false,"checklist_id":808,"created_at":"2018-11-15T09:56:30.054Z","updated_at":"2019-01-29T12:36:43.082Z","created_by_id":202,"last_modified_by_id":202,"position":1},{"id":3402,"text":"Inside the curtain","checked":false,"checklist_id":808,"created_at":"2018-11-15T09:56:30.070Z","updated_at":"2019-01-29T12:36:43.092Z","created_by_id":202,"last_modified_by_id":202,"position":2},{"id":3403,"text":"Inside the middle of the pass trough","checked":false,"checklist_id":808,"created_at":"2018-11-15T09:56:30.083Z","updated_at":"2019-01-29T12:36:43.101Z","created_by_id":202,"last_modified_by_id":202,"position":3},{"id":3404,"text":"Behind the fill machine","checked":false,"checklist_id":808,"created_at":"2018-11-15T09:56:30.096Z","updated_at":"2019-01-29T12:36:43.107Z","created_by_id":202,"last_modified_by_id":202,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5167,"name":"Active Air Sampling with settle plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003e\u003cstrong\u003ePreparation of sampling location and air sampler:\u003c/strong\u003e Ensure air sampler is fully charged. Sanitize the external surfaces of the unit with sterile \u003cstrong\u003e70%\u003c/strong\u003e isopropyl alcohol. Press the black colour button on the bottom side to start the air sampler. \u003cbr\u003e\u003cstrong\u003eSampling:\u003c/strong\u003e Select standard mode and press confirm. Select \u003cstrong\u003e10 000L\u003c/strong\u003e of air volume and press enter key to confirm. After pressing the enter key START FOR 10 000 will appear on display. Carefully remove the cover from the sieve. Place the settle plate on the air sampler and screw the sieve head. Start the air sampler by pressing enter. Sampling should last around \u003cstrong\u003e10 minutes\u003c/strong\u003e. \u003cbr\u003e\u003cstrong\u003eAfter air sampling is finished: \u003c/strong\u003eUnscrew the sieve head of the air sampler. Carefully remove the agar plate and cover it with lid. Swab areas where plates have been exposed with a suitable disinfectant to remove any trace of media or condensation from the lids, which may contaminate the room. Swab areas where plates have been exposed with a suitable disinfectant to remove any trace of media or condensation from the lids, which may contaminate the clean room.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T10:05:21.914Z","updated_at":"2019-01-29T12:37:19.979Z","last_modified_by_id":202,"protocol_id":3540},"checklists":[{"checklist":{"id":925,"name":"Sample location (examples):","step_id":5167,"created_at":"2018-12-12T10:08:05.163Z","updated_at":"2018-12-12T10:08:05.163Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3817,"text":"In front of the door","checked":false,"checklist_id":925,"created_at":"2018-12-12T10:08:05.165Z","updated_at":"2018-12-12T10:08:05.165Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3818,"text":"Inside the curtain","checked":false,"checklist_id":925,"created_at":"2018-12-12T10:08:05.173Z","updated_at":"2018-12-12T10:08:05.173Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3819,"text":"Behind the fill machine","checked":false,"checklist_id":925,"created_at":"2018-12-12T10:08:05.179Z","updated_at":"2018-12-12T10:08:05.179Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3820,"text":"In front of pass trough","checked":false,"checklist_id":925,"created_at":"2018-12-12T10:08:05.185Z","updated_at":"2018-12-12T10:08:05.185Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2195,"name":"Incubation","due_date":null,"description":"Incubation instructions for all types of plates","x":70,"y":16,"my_module_group_id":1236,"created_at":"2018-11-15T09:56:32.117Z","updated_at":"2019-01-31T09:55:55.885Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":4,"experiment_id":440,"state":"uncompleted","completed_on":null},"outputs":[{"id":6215,"input_id":2196,"output_id":2195},{"id":6216,"input_id":2200,"output_id":2195}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3554,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2195,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-15T09:56:32.169Z","updated_at":"2019-01-29T12:38:17.361Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4553,"name":"Incubation for growing bacteria","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cspan style=\"color: #ff0000;\"\u003e\u003cstrong\u003eImportant!:\u003c/strong\u003e \u003c/span\u003eIf the medium is dropped or touched by a person performing the sampling then this should be reported, the sample should be marked accordingly and treated as usual. Under no circumstances should samples that have been taken be refrigerated.\u003cbr\u003e\u003cbr\u003eFollowing testing, the samples should be incubated as soon as possible and should be held at room temperature with the medium uppermost until incubated or manipulated.\u003cbr\u003e\u003cbr\u003eIncubation of samples:\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003eInverted plates\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003e30 - 35°C\u003c/strong\u003e\u003c/li\u003e\n\u003cli\u003eAt least \u003cstrong\u003e2 days \u003c/strong\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\nIncubation conditions should be monitored to ensure that the appropriate incubation temperature is maintained throughout the incubation phase.\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:32.215Z","updated_at":"2019-01-29T12:37:59.184Z","last_modified_by_id":202,"protocol_id":3554},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4555,"name":"Counting and Recording","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAfter appropriate incubation microbiological contamination should grow into discrete macroscopic colonies that can be enumerated and the number of discrete colonies forming units (CFU) can be counted on each sample. \u003cbr\u003eRecord the number (per unit surface area) on the results tab. Separate colony counts may be tabulated for mould and bacteria.\u003cbr\u003e\u003cbr\u003eColony types may be identified if this is considered appropriate.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:32.267Z","updated_at":"2018-12-12T11:14:01.114Z","last_modified_by_id":202,"protocol_id":3554},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4552,"name":"Incubation for growing fungi","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cspan style=\"color: #ff0000;\"\u003e\u003cstrong\u003eImportant!:\u003c/strong\u003e \u003c/span\u003eIf the medium is dropped or touched by a person performing the sampling then this should be reported, the sample should be marked accordingly and treated as usual. Under no circumstances should samples that have been taken be refrigerated.\u003cbr\u003e\u003cbr\u003eFollowing testing, the samples should be incubated as soon as possible and should be held at room temperature with the medium uppermost until incubated or manipulated.\u003cbr\u003eIncubation of samples:\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003eInverted plates\u003c/li\u003e\n\u003cli\u003e\u003cstrong\u003e20 - 25°C\u003c/strong\u003e\u003c/li\u003e\n\u003cli\u003eAt least \u003cstrong\u003e5 days \u003c/strong\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003eIncubation conditions should be monitored to ensure that the appropriate incubation temperature is maintained throughout the incubation phase.\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:32.186Z","updated_at":"2019-01-29T12:38:17.317Z","last_modified_by_id":202,"protocol_id":3554},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2200,"name":"Counting colonies and recording data","due_date":null,"description":null,"x":104,"y":16,"my_module_group_id":1236,"created_at":"2018-11-15T09:56:33.039Z","updated_at":"2019-01-31T09:55:55.900Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":5,"experiment_id":440,"state":"uncompleted","completed_on":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3564,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2200,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-15T09:56:33.091Z","updated_at":"2019-01-28T09:02:38.281Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5174,"name":"Discarding plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAll samples (contaminated or not) should be disposed of according to procedures.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T11:23:59.242Z","updated_at":"2018-12-12T11:24:31.752Z","last_modified_by_id":202,"protocol_id":3564},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5173,"name":"Counting colonies and recording","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAfter appropriate incubation microbiological contamination should grow into discrete macroscopic colonies that can be enumerated and the number of discrete colonies forming units (CFU) can be counted on each sample. \u003cbr\u003eRecord the number (per unit surface area) on the results tab. Separate colony counts may be tabulated for mould and bacteria.\u003cbr\u003e\u003cbr\u003eColony types may be identified if this is considered appropriate.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T11:21:40.888Z","updated_at":"2019-01-25T13:21:04.649Z","last_modified_by_id":202,"protocol_id":3564},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4567,"name":"Action to be taken","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv style=\"text-align: justify;\"\u003eRecording of data provides oversight for microbiological cleanliness. In order for results to provide meaningful data, it is of key importance that alert and action limits are established. \u003cem\u003e\u003cstrong\u003eAlert levels ensure that any excursion of the parameter can be detected early. Action levels deviate more from the standard. If the alert level is exceeded repeatedly, this is considered equivalent to exceeding the action level.\u003c/strong\u003e\u003c/em\u003e In practice, several statistical methods including normal, Poisson, and negative binomial modelling have been routinely used to set these limits. \u003cbr\u003e\u003cbr\u003eExceeding action levels on isolated occasions may not require more action than an examination of control systems. However, the frequency of exceeding the limit should be examined and should be low. \u003cstrong\u003eIf the frequency is high or shows an upward trend then action should be taken which may include an increase in the frequency of testing, observation of operator technique or investigation of cleaning procedures.\u003cbr\u003e\u003cbr\u003e\u003c/strong\u003e\n\u003c/div\u003e\n\u003cdiv style=\"text-align: justify;\"\u003eIdentification of the causative microorganism(s) may aid tracing the \u003cstrong\u003esource of the contamination\u003c/strong\u003e. Successive results greater than the action levels demand that appropriate action is taken to reduce contamination to within limits. Where a problem has been observed the contaminating microorganisms should be identified. Isolated instances require no more action than an examination of control systems. If repeated contamination appears an investigation into the problem should take place and\u003cstrong\u003e corrective action should be carried out which will rectify the problem\u003c/strong\u003e. The corrective action should investigate the root cause of the problem and identify steps, with the timescale, that will be taken to reduce the contamination levels to \"normal\". A record of all action taken should be made in an \"Abnormal Event Log\".\u003c/div\u003e\n\u003cdiv style=\"text-align: justify;\"\u003eThe following areas should be examined where action levels are repeatedly breached:\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eIdentify:\u003c/strong\u003e\n\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003ePossible cause\u003c/li\u003e\n\u003cli\u003eContaminating microorganisms\u003c/li\u003e\n\u003c/ul\u003e\n\u003cstrong\u003eInvestigate:\u003c/strong\u003e\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003eWhether an isolated sample or whole area involved\u003c/li\u003e\n\u003cli\u003ePersonnel - operator status (grade), level of training, health, technique, wash up\u003c/li\u003e\n\u003cli\u003eCleaning procedures\u003c/li\u003e\n\u003cli\u003eChanging procedure\u003c/li\u003e\n\u003cli\u003eHEPA filter integrity of room/clean air device\u003c/li\u003e\n\u003cli\u003eProcesses carried out\u003c/li\u003e\n\u003cli\u003ePrevious test results for trends or other identified problems.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cstrong\u003eLiase with:\u003c/strong\u003e \u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003eAseptic personnel\u003c/li\u003e\n\u003cli\u003eMicrobiology personnel\u003c/li\u003e\n\u003cli\u003eQA/QC personnel\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:33.108Z","updated_at":"2019-01-28T09:02:38.188Z","last_modified_by_id":202,"protocol_id":3564},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2196,"name":"Colony Isolation and identification","due_date":null,"description":null,"x":70,"y":33,"my_module_group_id":1236,"created_at":"2018-11-15T09:56:32.322Z","updated_at":"2019-01-31T09:55:55.894Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":null,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":6,"experiment_id":440,"state":"uncompleted","completed_on":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3556,"name":null,"authors":null,"description":null,"added_by_id":202,"my_module_id":2196,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-15T09:56:32.376Z","updated_at":"2019-01-31T09:52:32.680Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5177,"name":"Discarding plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAll samples should be discarded according to procedures. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":4,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T11:42:25.451Z","updated_at":"2018-12-12T11:42:25.451Z","last_modified_by_id":202,"protocol_id":3556},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4558,"name":"Streak plate procedure","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow streaking procedure as displayed on image and guidelines below.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:32.459Z","updated_at":"2019-01-29T12:40:50.937Z","last_modified_by_id":202,"protocol_id":3556},"checklists":[{"checklist":{"id":953,"name":"Guidelines:","step_id":4558,"created_at":"2018-12-21T07:19:34.041Z","updated_at":"2018-12-21T07:19:34.041Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3912,"text":"Label the base of the plate. Open the lids and flame metal loop using a Bunsen burner before obtaining the inoculum for the plate.","checked":false,"checklist_id":953,"created_at":"2018-12-21T07:19:34.043Z","updated_at":"2018-12-21T07:19:34.043Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3913,"text":"The metal should become red hot. Move the wire so the flame approaches the loop. Spread sample over about one-quarter of the surface of the medium using a rapid, smooth, back-and-forth motion.","checked":false,"checklist_id":953,"created_at":"2018-12-21T07:19:34.053Z","updated_at":"2018-12-21T07:19:34.053Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3914,"text":"Lift the bottom half of an inverted plate from the bench. Move the loop back and forth many times across the agar surface from the rim to the centre of the plate. Reflame the metal loop. Turn the Petri dish 90 ° to streak the second quadrant. Using the back-and-forth pattern, cross over the last half of the streaks in the first quadrant then move into the empty second quadrant. Repeat until all 4 quadrants are done.","checked":false,"checklist_id":953,"created_at":"2018-12-21T07:19:34.060Z","updated_at":"2018-12-21T07:19:34.060Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3915,"text":"Cover all the plates with their lids.","checked":false,"checklist_id":953,"created_at":"2018-12-21T07:19:34.067Z","updated_at":"2018-12-21T07:19:34.067Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3916,"text":"Clean the area with disinfectant.","checked":false,"checklist_id":953,"created_at":"2018-12-21T07:19:34.073Z","updated_at":"2018-12-21T07:19:34.073Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[{"id":2980,"step_id":4558,"asset_id":3631}],"assets":[{"id":3631,"created_at":"2019-01-29T12:40:35.070Z","updated_at":"2019-01-29T12:40:50.875Z","file_file_name":"Plate_streaking.png","file_content_type":"image/png","file_file_size":100610,"file_updated_at":"2019-01-29T12:40:38.649Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":110671,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]},{"step":{"id":5175,"name":"Incubation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the protocol for incubation in \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#inc\"\u003e[#Incubation~tsk~ZP]\u003c/span\u003e \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T11:36:16.853Z","updated_at":"2019-01-25T12:47:34.060Z","last_modified_by_id":202,"protocol_id":3556},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4559,"name":"Prepare a safe and sterile workspace","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv class=\"row\" style=\"text-align: justify;\"\u003ePrepare a safe and sterile workspace: Sterilize all instruments, solutions, and media prior to using them for plating procedures. Clear away all materials cluttering your work area on the laboratory bench. Clean work area with disinfectant to minimize possible contamination. Set up a Bunsen burner. Work slowly, carefully, and deliberately within the sterile field area created by the updraft of the flame. Arrange all the supplies needed for the procedure on the laboratory bench near the sterile field. Make sure all the materials are properly labelled. Prepare new settle plates and settle plates from where you are isolating colonies.\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-15T09:56:32.486Z","updated_at":"2018-12-21T07:17:09.419Z","last_modified_by_id":202,"protocol_id":3556},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5176,"name":"Identification","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eUse different tests to identify microorganisms:\u003c/p\u003e\n\u003cul\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe Gram stain test, which is used to determine if the organism is Gram-negative or Gram-positive\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe acid-fast test, which identifies Mycobacterium\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe oxidase test, which identifies organisms that produce the enzyme cytochrome oxidase\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe catalase test, which differentiates Staphylococci (a catalase positive organism) from Streptococci (a catalase negative organism)\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe starch hydrolysis test, which evaluates the organism’s ability to synthesize and secrete enzymes to break down starch into smaller subunits to be used by the organism\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe mannitol and glucose fermentation test, which investigates how an organism metabolizes sugars\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe Voges-Proskauer test, which tests the organism’s ability to produce non-acidic end products from the metabolism of glucose and is helpful in differentiating the Enterobacteriaceae\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe citrate test, which studies the organism’s ability to apply citrate as a carbon source and is also helpful in differentiating the Enterobacteriaceae;\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe nitrate reductase test, which investigates bacteria’s ability or inability to reduce nitrate to nitrite\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eThe novobiocin sensitivity test, which evaluates an organism’s susceptibility to novobiocin, an antibiotic that obstructs DNA replication and is helpful in differentiating among Gram-positive cocci\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-12T11:40:09.563Z","updated_at":"2019-01-31T09:44:24.368Z","last_modified_by_id":202,"protocol_id":3556},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]}],"my_module_groups":[{"id":1236,"created_at":"2019-01-31T09:55:55.882Z","updated_at":"2019-01-31T09:55:55.882Z","created_by_id":202,"experiment_id":440}]}
\ No newline at end of file
diff --git a/app/assets/templates/experiment_454/experiment.json b/app/assets/templates/experiment_454/experiment.json
index 472347148..53153717f 100644
--- a/app/assets/templates/experiment_454/experiment.json
+++ b/app/assets/templates/experiment_454/experiment.json
@@ -1 +1 @@
-{"experiment":{"id":454,"name":"Bottom-up Proteomics","description":"This template will help you prepare protein samples, followed by the cleanup and mass spectrometry analysis.  \r\nIn bottom-up proteomics, the protein is first broken up into peptides, either by chemical or enzymatic digestion. In the first step, sample preparation is required after gel electrophoresis, liquid chromatography or affinity capture. Samples can (optionally) be enriched at the peptide level. With mass spectrometry, in the end, you can identify and characterize biological molecules.","project_id":223,"created_by_id":202,"last_modified_by_id":202,"archived":false,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-26T08:55:55.988Z","updated_at":"2019-01-29T09:46:44.060Z","workflowimg_file_name":"wimg20181219-1-nlf5rk.png","workflowimg_content_type":"image/png","workflowimg_file_size":4681,"workflowimg_updated_at":"2019-01-29T09:46:44.060Z","uuid":"03e6efa3-209f-498f-9c04-1000c7e2f3e5"},"my_modules":[{"my_module":{"id":2274,"name":"Protein preparation: Affinity Capture","due_date":null,"description":null,"x":0,"y":32,"my_module_group_id":1179,"created_at":"2018-11-27T17:13:44.860Z","updated_at":"2018-12-19T09:02:54.892Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":0,"experiment_id":454,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":5981,"input_id":2345,"output_id":2274}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3704,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2274,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-27T17:13:44.867Z","updated_at":"2019-01-31T08:29:28.974Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4872,"name":"Elute protein from the matrix","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv\u003eDown below are the guidelines for elution of proteins.  \u003cbr\u003e\u003cbr\u003e\n\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-27T17:40:37.750Z","updated_at":"2018-12-24T07:26:44.813Z","last_modified_by_id":202,"protocol_id":3704},"checklists":[{"checklist":{"id":858,"name":"Guidelines:","step_id":4872,"created_at":"2018-11-27T17:40:37.753Z","updated_at":"2018-12-20T14:36:53.748Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3564,"text":"Use a 5× volume of 0.1 M glycine, pH 2.5.","checked":false,"checklist_id":858,"created_at":"2018-11-27T17:40:37.755Z","updated_at":"2018-11-27T17:40:37.755Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3565,"text":"Apply the elution buffer and allow the buffer to thoroughly wet the matrix for 5 to 10 min.","checked":false,"checklist_id":858,"created_at":"2018-11-27T17:40:37.764Z","updated_at":"2018-11-27T17:40:37.764Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3566,"text":"Collect the eluate.","checked":false,"checklist_id":858,"created_at":"2018-11-27T17:40:37.772Z","updated_at":"2018-11-27T17:40:37.772Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3567,"text":"To enhance recovery, wash the matrix with an additional 5× volume of 0.1 M glycine, pH 2.5.","checked":false,"checklist_id":858,"created_at":"2018-11-27T17:40:37.780Z","updated_at":"2018-11-27T17:40:37.780Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3568,"text":"Adjust eluate to neutral pH by addition of an equal volume of 200 mM NH4HCO3.","checked":false,"checklist_id":858,"created_at":"2018-11-27T17:40:37.788Z","updated_at":"2018-11-27T17:40:37.788Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4873,"name":"Reduction of disulfide bonds","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cem\u003e\u003cstrong\u003eDisulfide (sulfur-sulfur) linkages between two cysteine residues are an integral component of the three-dimensional structure of many proteins.\u003c/strong\u003e \u003c/em\u003eDisulfide reducing agents are routinely used in biochemical reactions for peptides and proteins prior to MS analysis. \u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-27T17:42:41.887Z","updated_at":"2018-12-24T07:32:38.099Z","last_modified_by_id":202,"protocol_id":3704},"checklists":[{"checklist":{"id":859,"name":"To do:","step_id":4873,"created_at":"2018-11-27T17:42:41.891Z","updated_at":"2018-11-27T17:42:41.891Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3569,"text":"Add DTT to a final concentration of 10 mM or TCEP to a final concentration of 5 mM.","checked":false,"checklist_id":859,"created_at":"2018-11-27T17:42:41.894Z","updated_at":"2018-11-27T17:42:41.894Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3570,"text":"Incubate sample at room temperature with vortexing  for 10 min with TCEP or 30 min with DTT.","checked":false,"checklist_id":859,"created_at":"2018-11-27T17:42:41.915Z","updated_at":"2018-11-27T17:42:41.915Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3571,"text":"Next, to alkylate free cysteines, add iodoacetamide to a final concentration of 10 mM","checked":false,"checklist_id":859,"created_at":"2018-11-27T17:42:41.923Z","updated_at":"2018-11-27T17:42:41.923Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3572,"text":"Place at room temperature in the dark for 30 min.","checked":false,"checklist_id":859,"created_at":"2018-11-27T17:42:41.934Z","updated_at":"2018-11-27T17:42:41.934Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4874,"name":"Digestion of the protein sample","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv style=\"text-align: justify;\"\u003eThe protein is cut enzymatically into a limited number of shorter fragments during digestion and these fragments are called peptides and allow for the identification of the protein with their characteristic mass and pattern.\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-27T17:43:58.146Z","updated_at":"2018-12-24T07:33:39.499Z","last_modified_by_id":202,"protocol_id":3704},"checklists":[{"checklist":{"id":947,"name":"Guidelines:","step_id":4874,"created_at":"2018-12-20T14:41:18.229Z","updated_at":"2018-12-20T14:41:18.229Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3886,"text":"Use an appropriate enzyme or chemical. If using trypsin, add sufficient enzyme for final trypsin: protein ratio of 1:20 to 1:100 (w/w).","checked":false,"checklist_id":947,"created_at":"2018-12-20T14:41:18.231Z","updated_at":"2018-12-20T14:41:18.231Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3887,"text":"Vortex briefly.","checked":false,"checklist_id":947,"created_at":"2018-12-20T14:41:18.238Z","updated_at":"2018-12-20T14:41:18.238Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3888,"text":"Seal the tube with Paraffin.","checked":false,"checklist_id":947,"created_at":"2018-12-20T14:41:18.244Z","updated_at":"2018-12-20T14:41:18.244Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3889,"text":"Incubate with end-over-end rotation at 37°C for 4 to 18 hours.","checked":false,"checklist_id":947,"created_at":"2018-12-20T14:41:18.250Z","updated_at":"2018-12-20T14:41:18.250Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3890,"text":"Stop reaction by adding 5 μL of 1.0% trifluoroacetic (TFA) acid.","checked":false,"checklist_id":947,"created_at":"2018-12-20T14:41:18.257Z","updated_at":"2018-12-20T14:41:18.257Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4871,"name":"Wash affinity matrix","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv style=\"text-align: justify;\"\u003e\n\u003cem\u003e\u003cstrong\u003eWash affinity matrix containing the adsorbed protein sample with the wash buffer such as PBS to elute the unbound or nonspecifically bound proteins from the matrix. \u003c/strong\u003e\u003c/em\u003eBeads may be washed by resuspending them in the wash buffer with gentle vortexing, then microcentrifuging at low speed (e.g., \u003cstrong\u003e800 rpm\u003c/strong\u003e in a standard microcentrifuge) at room temperature to pellet the beads, and removing the supernatant by pipetting.\u003cbr\u003e\u003cstrong\u003eIf detergent is present in the starting material, it may be necessary to increase the number of washes to remove residual detergent\u003c/strong\u003e. Often this can be difficult and may require up to ten additional\u003cstrong\u003e 20×\u003c/strong\u003e volume washes (i.e., \u003cstrong\u003e20 times\u003c/strong\u003e the packed volume of the matrix). For most immunocapture methods, PBS is an effective wash buffer, but other neutral-pH saline buffers such as HEPES or Tris·Cl can be used. If greater stringency is required, for example, a high-salt wash or inclusion of a chaotropic agent, perform more stringent washes first followed by additional PBS washes. It is often necessary to optimize wash conditions for individual affinity-capture methods.\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-27T17:15:38.260Z","updated_at":"2019-01-31T08:29:28.933Z","last_modified_by_id":202,"protocol_id":3704},"checklists":[],"step_comments":[],"step_assets":[{"id":2977,"step_id":4871,"asset_id":3628}],"assets":[{"id":3628,"created_at":"2019-01-29T12:29:49.186Z","updated_at":"2019-01-31T08:29:28.856Z","file_file_name":"Bottom_up_proteomics.PNG","file_content_type":"image/png","file_file_size":40808,"file_updated_at":"2019-01-29T12:30:37.347Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":44888,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2262,"name":"Protein preparation: Liquid Chromatography Fraction","due_date":null,"description":null,"x":0,"y":16,"my_module_group_id":1179,"created_at":"2018-11-26T13:45:56.851Z","updated_at":"2018-12-19T09:02:54.890Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":1,"experiment_id":454,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":5980,"input_id":2345,"output_id":2262}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3682,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2262,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-26T13:45:56.859Z","updated_at":"2019-01-31T08:32:20.750Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4840,"name":"Neutralization of samples","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv style=\"text-align: justify;\"\u003eThe pH of the sample may be neutralized either prior to or after drying via vacuum centrifugation to remove acetonitrile and trifluoroacetic acid. \u003cspan style=\"text-align: left;\"\u003eRP-HPLC samples will likely contain aqueous trifluoroacetic acid and acetonitrile since these are the most commonly used mobile phases. \u003c/span\u003e\u003cspan style=\"text-align: left;\"\u003eThe NH\u003c/span\u003e\u003csub style=\"text-align: left;\"\u003e4\u003c/sub\u003e\u003cspan style=\"text-align: left;\"\u003eHCO\u003c/span\u003e\u003csub style=\"text-align: left;\"\u003e3\u003c/sub\u003e\u003cspan style=\"text-align: left;\"\u003e solution should be prepared fresh, as the pH of the solution will increase with age at room temperature. It is possible to store for several days at \u003cstrong\u003e4°C\u003c/strong\u003e, but the pH should be checked prior to use.\u003c/span\u003e\n\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-26T13:50:47.141Z","updated_at":"2019-01-31T08:29:48.858Z","last_modified_by_id":202,"protocol_id":3682},"checklists":[{"checklist":{"id":944,"name":"To neutralize prior to drying:","step_id":4840,"created_at":"2018-12-20T14:20:33.276Z","updated_at":"2018-12-20T14:20:33.276Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3878,"text":"Add sufficient 1 M NH4HCO3, pH8.5.","checked":false,"checklist_id":944,"created_at":"2018-12-20T14:20:33.278Z","updated_at":"2018-12-20T14:20:33.278Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3879,"text":"Adjust final pH to ~8.0.","checked":false,"checklist_id":944,"created_at":"2018-12-20T14:20:33.285Z","updated_at":"2018-12-20T14:20:33.285Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3880,"text":"Then dry via vacuum centrifugation.","checked":false,"checklist_id":944,"created_at":"2018-12-20T14:20:33.292Z","updated_at":"2018-12-20T14:20:33.292Z","created_by_id":null,"last_modified_by_id":null,"position":2}]},{"checklist":{"id":945,"name":"To neutralize after drying:","step_id":4840,"created_at":"2018-12-20T14:21:35.471Z","updated_at":"2018-12-20T14:21:35.471Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3881,"text":"Resuspend dried protein in 100 mM NH4HCO3, pH 8.5.","checked":false,"checklist_id":945,"created_at":"2018-12-20T14:21:35.474Z","updated_at":"2018-12-20T14:21:35.474Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3882,"text":"Spot an aliquot of the neutralized solution on narrow-range pH paper to validate that neutralization (to pH 8.0) has occurred.","checked":false,"checklist_id":945,"created_at":"2018-12-20T14:21:35.481Z","updated_at":"2018-12-20T14:21:35.481Z","created_by_id":null,"last_modified_by_id":null,"position":1}]}],"step_comments":[],"step_assets":[{"id":2978,"step_id":4840,"asset_id":3629}],"assets":[{"id":3629,"created_at":"2019-01-29T12:30:12.184Z","updated_at":"2019-01-31T08:29:48.793Z","file_file_name":"Bottom_up_proteomics.PNG","file_content_type":"image/png","file_file_size":40808,"file_updated_at":"2019-01-29T12:30:37.768Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":44888,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]},{"step":{"id":5148,"name":"Reduction of disulfide bonds and alkyle free cysteine residues","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003e\u003cem\u003e\u003cstrong\u003eReduction of disulfide bonds can be achieved with either dithiothreitol (DTT) or tris (2-carboxyethyl)phosphine hydrochloride (TCEP). \u003c/strong\u003e\u003c/em\u003eDTT works optimally at \u003cstrong\u003epH 7 to 9\u003c/strong\u003e, TCEP is typically more efficient, works at a wider pH range (\u003cstrong\u003epH 2 to 11\u003c/strong\u003e), and has no offensive odour. The concentrations and incubation times for DTT, TCEP, and IAA may vary depending on the amount of protein to be treated. Typical concentrations range from \u003cstrong\u003e5 to 10 mM\u003c/strong\u003e for DTT and TCEP, and \u003cstrong\u003e10 to 50 mM\u003c/strong\u003e for iodoacetamide. Incubation times may range from \u003cstrong\u003e5 min to 1 hr for the reduction step\u003c/strong\u003e and \u003cstrong\u003e10 min to 1 hr for the alkylation step\u003c/strong\u003e. Similarly, the reduction can be performed at room temperature, \u003cstrong\u003e37°C or 56°C\u003c/strong\u003e. Each parameter can be optimized depending on the nature of the protein sample.\u003c/p\u003e\n\u003cdiv\u003e\u003cem\u003eOptional: Following alkylation, adjust the sample to \u003cstrong\u003e40 mM\u003c/strong\u003e DTT.\u003c/em\u003e\u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T12:46:55.270Z","updated_at":"2019-01-31T08:30:26.220Z","last_modified_by_id":202,"protocol_id":3682},"checklists":[{"checklist":{"id":946,"name":"Guidelines:","step_id":5148,"created_at":"2018-12-20T14:24:01.663Z","updated_at":"2018-12-20T14:24:01.663Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3883,"text":"Add DTT to a final concentration of 10 mM or TCEP to a final concentration of 5 mM.","checked":false,"checklist_id":946,"created_at":"2018-12-20T14:24:01.666Z","updated_at":"2018-12-20T14:24:01.666Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3884,"text":"Incubate sample at room temperature with agitation (e.g. vortexing, or shaking), for 30 min with DTT or 10 min with TCEP.","checked":false,"checklist_id":946,"created_at":"2018-12-20T14:24:01.680Z","updated_at":"2018-12-20T14:24:01.680Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3885,"text":"Add iodoacetamide (IAA) to a concentration of 10 mM final and place at room temperature in the dark for 30 min.","checked":false,"checklist_id":946,"created_at":"2018-12-20T14:24:01.690Z","updated_at":"2018-12-20T14:24:01.690Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5149,"name":"Digestion of protein samples","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv style=\"text-align: justify;\"\u003eDigest the protein sample into peptides using an \u003cstrong\u003eappropriate enzyme\u003c/strong\u003e (e.g., chymotrypsin, trypsin, LysC, or AspN) or\u003cstrong\u003e chemical\u003c/strong\u003e (CNBr/70% formic acid). If using trypsin, add sufficient enzyme for final trypsin: protein ratio of \u003cstrong\u003e1:20 to 1:100\u003c/strong\u003e (w/w). Vortex briefly, seal the tube with Parafilm and incubate with end-over-end rotation at \u003cstrong\u003e37°C\u003c/strong\u003e for \u003cstrong\u003e4 to 18 hours\u003c/strong\u003e.\u003c/div\u003e\n\u003cdiv style=\"text-align: justify;\"\u003e\n\u003cbr\u003eThe amount of trypsin needed will vary depending on the amount of protein sample present and the desired speed of digestion. To minimize trypsin autolysis, which will add extra peaks to the MS spectra, use the minimum amount of trypsin.\u003cstrong\u003e Typically, a ratio of 1:20 (w/w) is sufficient for complete digestion of 10 μg protein within 4 hr\u003c/strong\u003e. If protein concentration is especially high or the accessibility of trypsin to the cleavage sites is hampered (e.g., due to insolubility), it may be helpful to add another aliquot of trypsin or perform short digestion (\u003cstrong\u003e4 hours\u003c/strong\u003e) with LysC prior to the addition of trypsin. Finally, the activity of trypsin is enhanced in the presence of acetonitrile (\u003cstrong\u003e10% to 50% v/v\u003c/strong\u003e), and, thus, acetonitrile may be added to aid in the solubilization of the protein during tryptic digestion.\u003c/div\u003e\n\u003cdiv style=\"text-align: justify;\"\u003e\n\u003cbr\u003e\u003cstrong\u003eTrypsin activity is greatest at pH 8.0\u003c/strong\u003e. Thus, it is recommended that the pH of the solution be checked prior to the addition of the enzyme. In cases where sample volume is small, a \u003cstrong\u003e1- to 2-μL \u003c/strong\u003esample may be tested using pH paper. Stop reaction by adding \u003cstrong\u003e5 μL\u003c/strong\u003e of\u003cstrong\u003e 1.0%\u003c/strong\u003e trifluoroacetic (TFA) acid (pH after TFA addition should be \u003cstrong\u003e~2 to 3\u003c/strong\u003e).\u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T12:52:36.364Z","updated_at":"2019-01-31T08:32:20.691Z","last_modified_by_id":202,"protocol_id":3682},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2258,"name":"Protein preparation: Polyacrylamide gel","due_date":null,"description":null,"x":0,"y":0,"my_module_group_id":1179,"created_at":"2018-11-26T12:04:02.091Z","updated_at":"2018-12-19T09:02:54.887Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":454,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":5978,"input_id":2345,"output_id":2258}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3678,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2258,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-26T12:04:02.098Z","updated_at":"2019-01-31T08:32:58.479Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5146,"name":"Perform enzymatic digestion","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv style=\"text-align: justify;\"\u003eThe protein is cut enzymatically into a limited number of shorter fragments during digestion and these fragments are called peptides and allow for the identification of the protein with their characteristic mass and pattern.\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":5,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T11:40:40.624Z","updated_at":"2018-12-24T06:40:41.505Z","last_modified_by_id":202,"protocol_id":3678},"checklists":[{"checklist":{"id":942,"name":"Guidelines:","step_id":5146,"created_at":"2018-12-20T14:15:25.669Z","updated_at":"2018-12-20T14:15:25.669Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3869,"text":"Dilute the gel enzyme stock solution ~1:1000 with 25 mM ammonium bicarbonate to obtain a 10 to 20 μg/mL working solution.","checked":false,"checklist_id":942,"created_at":"2018-12-20T14:15:25.671Z","updated_at":"2018-12-20T14:15:25.671Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3870,"text":"Add a sufficient amount of the gel enzyme working solution to cover gel pieces and incubate on ice for 1 hr. For a typical gel band/spot, this is ~10 to 20 μL.","checked":false,"checklist_id":942,"created_at":"2018-12-20T14:15:25.679Z","updated_at":"2018-12-20T14:15:25.679Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3871,"text":"Remove excess gel enzyme solution, then add sufficient 25 mM NH4HCO3 to cover the gel pieces. This increases the pH and thereby inhibits the enzymatic digestion for those enzymes which have low pH optima.","checked":false,"checklist_id":942,"created_at":"2018-12-20T14:15:25.686Z","updated_at":"2018-12-20T14:15:25.686Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3872,"text":"Incubate at 37°C overnight.","checked":false,"checklist_id":942,"created_at":"2018-12-20T14:15:25.693Z","updated_at":"2018-12-20T14:15:25.693Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5145,"name":"Reduce disulfide bonds and alkylate free cysteines","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cem\u003e\u003cstrong\u003eDithiothreitol (DTT) is a reducing agent that converts cystine’s disulfide bond into cysteine’s free sulfhydryl groups.\u003c/strong\u003e\u003c/em\u003e\u003cbr\u003e\u003cem\u003e\u003cstrong\u003eIodoacetamide (IAA) is an alkylating agent that reacts with free sulfhydryl groups of cysteine residues to form S-\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e\u003cem\u003ecarboxyamidomethyl-cysteine, which cannot be reoxidized to form disulfide bonds. This is important for allowing trypsin maximum access to cleavage sites within the protein.\u003c/em\u003e\u003c/strong\u003e\n\u003c/body\u003e\u003c/html\u003e","position":4,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T11:01:14.616Z","updated_at":"2018-12-20T14:13:35.200Z","last_modified_by_id":202,"protocol_id":3678},"checklists":[{"checklist":{"id":941,"name":"Guidelines:","step_id":5145,"created_at":"2018-12-20T14:12:18.059Z","updated_at":"2018-12-20T14:12:18.059Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3865,"text":"Add 100 μL of 10 mM dithiothreitol to the gel piece, then incubate 45 min at 55°C.","checked":false,"checklist_id":941,"created_at":"2018-12-20T14:12:18.062Z","updated_at":"2018-12-20T14:12:18.062Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3866,"text":"Remove solution, add 100 μl 55 mM iodoacetamide, and incubate 30 min at room temperature in the dark.","checked":false,"checklist_id":941,"created_at":"2018-12-20T14:12:18.070Z","updated_at":"2018-12-20T14:12:18.070Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3867,"text":"Remove IAA solution and add 400 μL gel wash solution, incubate at room temperature, and shake for 15 min. Repeat this step twice.","checked":false,"checklist_id":941,"created_at":"2018-12-20T14:12:18.077Z","updated_at":"2018-12-20T14:12:18.077Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3868,"text":"Dehydrate gel pieces with 400 μL of 100% acetonitrile for 10 min, then remove supernatant and dry gel pieces using a vacuum centrifuge.","checked":false,"checklist_id":941,"created_at":"2018-12-20T14:12:18.083Z","updated_at":"2018-12-20T14:12:18.083Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5147,"name":"Extract peptides","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eHere is the guideline how to extract peptides. This step can take up to several hours depending upon the volume used.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":6,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T11:52:09.928Z","updated_at":"2018-12-24T06:42:22.727Z","last_modified_by_id":202,"protocol_id":3678},"checklists":[{"checklist":{"id":943,"name":"Guidelines:","step_id":5147,"created_at":"2018-12-20T14:17:36.750Z","updated_at":"2018-12-20T14:17:36.750Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3873,"text":"Remove supernatant, which now contains peptides, to a new clean microcentrifuge tube.","checked":false,"checklist_id":943,"created_at":"2018-12-20T14:17:36.754Z","updated_at":"2018-12-20T14:17:36.754Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3874,"text":"Add 100 μL gel extraction solution to the gel pieces and incubate while shaking for 20 min at room temperature.","checked":false,"checklist_id":943,"created_at":"2018-12-20T14:17:36.761Z","updated_at":"2018-12-20T14:17:36.761Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3875,"text":"Remove solution and combine with the solution obtained in step 1.","checked":false,"checklist_id":943,"created_at":"2018-12-20T14:17:36.777Z","updated_at":"2018-12-20T14:17:36.777Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3876,"text":"Repeat steps second and third step.","checked":false,"checklist_id":943,"created_at":"2018-12-20T14:17:36.784Z","updated_at":"2018-12-20T14:17:36.784Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3877,"text":"Dry combined supernatants using a vacuum centrifuge.","checked":false,"checklist_id":943,"created_at":"2018-12-20T14:17:36.791Z","updated_at":"2018-12-20T14:17:36.791Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4826,"name":"Coomassie stained gels","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cem\u003e\u003cstrong\u003eCoomassie dyes (also known as Coomassie Brilliant Dyes) are a family of dyes commonly used to stain proteins in sodium dodecyl sulfate and blue native polyacrylamide gel electrophoresis (SDS-PAGE and BN-PAGE, respectively) gels.\u003c/strong\u003e\u003c/em\u003e The gels are soaked in dye and an excess stain is then eluted with a solvent. This treatment allows the visualization of protein bands.\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-26T13:15:06.518Z","updated_at":"2018-12-24T06:34:58.049Z","last_modified_by_id":202,"protocol_id":3678},"checklists":[{"checklist":{"id":917,"name":"Washing:","step_id":4826,"created_at":"2018-12-07T10:52:29.542Z","updated_at":"2018-12-07T11:39:18.108Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3780,"text":"Remove destain solution","checked":false,"checklist_id":917,"created_at":"2018-12-07T10:52:29.545Z","updated_at":"2018-12-07T10:52:29.545Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3781,"text":"Add 400 μl water.","checked":false,"checklist_id":917,"created_at":"2018-12-07T10:52:29.554Z","updated_at":"2018-12-07T10:52:29.554Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3782,"text":"If the gel pieces are still blue, remove the water and repeat until the gel pieces are colourless.","checked":false,"checklist_id":917,"created_at":"2018-12-07T10:52:29.562Z","updated_at":"2018-12-07T10:52:29.562Z","created_by_id":null,"last_modified_by_id":null,"position":2}]},{"checklist":{"id":919,"name":"Dehydration:","step_id":4826,"created_at":"2018-12-07T11:39:18.116Z","updated_at":"2018-12-07T11:39:18.116Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3786,"text":"Dehydrate gel pieces with 400 μl of 100% acetonitrile for 10 min","checked":false,"checklist_id":919,"created_at":"2018-12-07T11:39:18.118Z","updated_at":"2018-12-07T11:39:18.118Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3787,"text":"Remove supernatant","checked":false,"checklist_id":919,"created_at":"2018-12-07T11:39:18.126Z","updated_at":"2018-12-07T11:39:18.126Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3788,"text":"Dry gel pieces in a vacuum centrifuge","checked":false,"checklist_id":919,"created_at":"2018-12-07T11:39:18.133Z","updated_at":"2018-12-07T11:39:18.133Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4824,"name":"Destain gel bands","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eDestain in the microcentrifuge tube for \u003cstrong\u003e30 min\u003c/strong\u003e with \u003cstrong\u003e100 μL\u003c/strong\u003e of the appropriate gel destain solution with vigorous vortexing. The choice of destaining protocol depends on the stain used, and there is a specific destain recipe for each type of gel stain. The choice of protein stain depends on the protein concentration and the dynamic range of the sample. Silver and colloidal Coomassie staining (CCS) stains offer a low limit of detection (\u003cstrong\u003e1 to 10 ng\u003c/strong\u003e) compared to traditional Coomassie staining (\u003cstrong\u003e0.3 to 1 μg)\u003c/strong\u003e.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-26T13:08:09.568Z","updated_at":"2019-01-31T08:32:58.429Z","last_modified_by_id":202,"protocol_id":3678},"checklists":[{"checklist":{"id":940,"name":"Follow:","step_id":4824,"created_at":"2018-12-20T14:03:52.360Z","updated_at":"2018-12-20T14:03:52.360Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3863,"text":"Step 3: Glutaraldehyde-free silver stained gels","checked":false,"checklist_id":940,"created_at":"2018-12-20T14:03:52.362Z","updated_at":"2018-12-20T14:04:56.749Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3864,"text":"Step 4: Coomassie-stained gels","checked":false,"checklist_id":940,"created_at":"2018-12-20T14:03:52.369Z","updated_at":"2018-12-20T14:04:56.761Z","created_by_id":null,"last_modified_by_id":null,"position":1}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4825,"name":"Silver stained gels","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cem\u003e\u003cstrong\u003eSilver staining is used to detect proteins after electrophoretic separation on polyacrylamide gels.\u003c/strong\u003e\u003c/em\u003e It combines excellent sensitivity, whilst using very simple and cheap equipment and chemicals.\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-26T13:14:10.347Z","updated_at":"2018-12-24T06:30:40.360Z","last_modified_by_id":202,"protocol_id":3678},"checklists":[{"checklist":{"id":916,"name":"Washing:","step_id":4825,"created_at":"2018-12-07T10:50:00.146Z","updated_at":"2018-12-07T11:37:14.463Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3776,"text":"Remove destain solution","checked":false,"checklist_id":916,"created_at":"2018-12-07T10:50:00.148Z","updated_at":"2018-12-07T10:50:00.148Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3777,"text":"Wash gel piece with 400 μL water","checked":false,"checklist_id":916,"created_at":"2018-12-07T10:50:00.157Z","updated_at":"2018-12-20T12:00:27.604Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3778,"text":"Shake for 15 min at room temperature","checked":false,"checklist_id":916,"created_at":"2018-12-07T10:50:00.166Z","updated_at":"2018-12-07T10:50:00.166Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3779,"text":"Repeat wash at least twice or until gel pieces are colourless.","checked":false,"checklist_id":916,"created_at":"2018-12-07T10:50:00.175Z","updated_at":"2018-12-07T10:50:00.175Z","created_by_id":null,"last_modified_by_id":null,"position":3}]},{"checklist":{"id":918,"name":"Dehydration:","step_id":4825,"created_at":"2018-12-07T11:36:41.173Z","updated_at":"2018-12-07T11:37:28.556Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3783,"text":"Dehydrate gel pieces with 400 μL of 100% acetonitrile for 10 min","checked":false,"checklist_id":918,"created_at":"2018-12-07T11:36:41.177Z","updated_at":"2018-12-20T12:00:27.594Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3784,"text":"Remove supernatant","checked":false,"checklist_id":918,"created_at":"2018-12-07T11:36:41.204Z","updated_at":"2018-12-07T11:36:41.204Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3785,"text":"Dry gel pieces in a vacuum centrifuge","checked":false,"checklist_id":918,"created_at":"2018-12-07T11:36:41.211Z","updated_at":"2018-12-07T11:36:41.211Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4823,"name":"Excise gel bands","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003eOnce you have run your gel, move it to an\u003cstrong\u003e open UV box\u003c/strong\u003e (be sure to wear proper UV protection - especially for your eyes!), remove it from any gel tray as plastic will block much of the UV and with a clean, sterile razor blade, slice the desired DNA fragment from the gel. Try to get as little excess gel around the band as possible. To do so, it is often important to take the excised band, lay it down on the UV box and trim the top, bottom and sides with the razor blade. This is especially important during the DNA purification step, as many kits cannot handle more than a certain total volume of gel per reaction.\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-26T13:01:32.320Z","updated_at":"2019-01-29T12:30:38.522Z","last_modified_by_id":202,"protocol_id":3678},"checklists":[],"step_comments":[],"step_assets":[{"id":2979,"step_id":4823,"asset_id":3630}],"assets":[{"id":3630,"created_at":"2019-01-29T12:30:25.880Z","updated_at":"2019-01-29T12:30:38.511Z","file_file_name":"Bottom_up_proteomics.PNG","file_content_type":"image/png","file_file_size":40808,"file_updated_at":"2019-01-29T12:30:38.172Z","created_by_id":202,"last_modified_by_id":null,"estimated_size":44888,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2345,"name":"IMAC Phosphopeptide Enrichment (optional*)","due_date":null,"description":null,"x":38,"y":15,"my_module_group_id":1179,"created_at":"2018-12-07T13:34:00.077Z","updated_at":"2018-12-19T09:02:54.880Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":3,"experiment_id":454,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":5979,"input_id":2346,"output_id":2345}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3836,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2345,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-12-07T13:34:00.086Z","updated_at":"2019-01-25T12:07:01.449Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5152,"name":"Elution and collection","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv\u003eDry each eluate containing the multiply phosphorylated peptides, monophosphopeptides, and the IMAC flow through separately using vacuum centrifugation.\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T13:58:12.351Z","updated_at":"2018-12-20T14:48:45.965Z","last_modified_by_id":202,"protocol_id":3836},"checklists":[{"checklist":{"id":950,"name":"Guidelines:","step_id":5152,"created_at":"2018-12-20T14:48:32.247Z","updated_at":"2018-12-20T14:48:32.247Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3897,"text":"Collect the column flow through in microcentrifuge tubes.","checked":false,"checklist_id":950,"created_at":"2018-12-20T14:48:32.249Z","updated_at":"2018-12-20T14:48:32.249Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3898,"text":"Wash the IMAC column with 50 μL IMAC wash solution and pool the eluate with the fraction from the previous step. This need to be done slowly using a Combi-Syringe to apply pressure.","checked":false,"checklist_id":950,"created_at":"2018-12-20T14:48:32.256Z","updated_at":"2018-12-20T14:48:32.256Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3899,"text":"Elute and collect the monophosphopeptides using 50 μl low-pH elution solution. This needs to be done quickly using a Combi-Syringe to apply pressure.","checked":false,"checklist_id":950,"created_at":"2018-12-20T14:48:32.263Z","updated_at":"2018-12-20T14:48:32.263Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3900,"text":"Elute and collect the multiply phosphorylated peptides using 70 μL high-pH elution solution. This step should be performed slowly using a Combi-Syringe to apply pressure.","checked":false,"checklist_id":950,"created_at":"2018-12-20T14:48:32.269Z","updated_at":"2018-12-20T14:48:32.269Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5151,"name":"Add protein sample to IMAC beads","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eSqueeze the tip of the narrow-bore pipet tip nearly shut, as this will prevent bead loss. The Combi-Syringe is only to be used for the generation of pressure in the column, not for measuring and loading the aliquots. The Combi-Syringe is reusable and should therefore not come into contact with any solution.\u003c/p\u003e\n\u003cdiv\u003e \u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T13:50:12.807Z","updated_at":"2019-01-25T12:07:01.391Z","last_modified_by_id":202,"protocol_id":3836},"checklists":[{"checklist":{"id":949,"name":"Guideline:","step_id":5151,"created_at":"2018-12-20T14:47:07.628Z","updated_at":"2018-12-20T14:47:07.628Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3894,"text":"Add protein sample to the IMAC beads in a volume of IMAC wash solution that is 10 times the volume of the packed beads.","checked":false,"checklist_id":949,"created_at":"2018-12-20T14:47:07.630Z","updated_at":"2018-12-20T14:47:07.630Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3895,"text":"Incubate with constant, gentle agitation, at room temperature for 30 to 60 min.","checked":false,"checklist_id":949,"created_at":"2018-12-20T14:47:07.638Z","updated_at":"2018-12-20T14:47:07.638Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3896,"text":"Using a Combi-Syringe and gentle pressure, pack the IMAC beads in a narrow bore tip by gradually adding the bead slurry in 20 μL aliquots.","checked":false,"checklist_id":949,"created_at":"2018-12-20T14:47:07.654Z","updated_at":"2018-12-20T14:47:07.654Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5150,"name":"Wash IMAC beads","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eTo\u003cspan\u003eo many IMAC beads may result in \u003cstrong\u003enonspecific binding of peptides\u003c/strong\u003e because of reduced washing efficiency. A small amount of wash solution should be left in the tube with the beads, to avoid aspirating the beads.\u003c/span\u003e\n\u003c/p\u003e\n\u003cdiv\u003e \u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T13:34:50.552Z","updated_at":"2018-12-20T14:44:55.371Z","last_modified_by_id":202,"protocol_id":3836},"checklists":[{"checklist":{"id":948,"name":"Guideline:","step_id":5150,"created_at":"2018-12-20T14:44:55.374Z","updated_at":"2018-12-20T14:44:55.374Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3891,"text":"Wash IMAC (immobilized metal affinity chromatography) beads. You will need 5 to 7 μL for simple mixtures and 30 to 50 μL for complex mixtures containing ≥120 μg protein.","checked":false,"checklist_id":948,"created_at":"2018-12-20T14:44:55.376Z","updated_at":"2018-12-20T14:44:55.376Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3892,"text":"Applying 50 μL IMAC wash solution, vortex and centrifuge at low speed (e.g., 800 rpm in a benchtop microcentrifuge) at room temperature to pellet the beads.","checked":false,"checklist_id":948,"created_at":"2018-12-20T14:44:55.383Z","updated_at":"2018-12-20T14:44:55.383Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3893,"text":"Remove the supernatant by pipetting.","checked":false,"checklist_id":948,"created_at":"2018-12-20T14:44:55.390Z","updated_at":"2018-12-20T14:44:55.390Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2346,"name":"TiO2 Enrichment (optional*)","due_date":null,"description":null,"x":73,"y":15,"my_module_group_id":1179,"created_at":"2018-12-07T14:01:45.181Z","updated_at":"2018-12-19T09:02:54.895Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":4,"experiment_id":454,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":5983,"input_id":2275,"output_id":2346}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3837,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2346,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-12-07T14:01:45.189Z","updated_at":"2019-01-31T08:39:24.163Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5154,"name":"Elution and collection of samples","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow elution and collection guidelines bellow.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T14:20:38.293Z","updated_at":"2018-12-24T08:06:13.141Z","last_modified_by_id":202,"protocol_id":3837},"checklists":[{"checklist":{"id":951,"name":"Guidelines:","step_id":5154,"created_at":"2018-12-20T14:51:18.465Z","updated_at":"2018-12-20T14:51:18.465Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3901,"text":"If samples have been dried, then resuspended in 3 μL 1 of % SDS. Dilute IMAC–1% TFA and IMAC-FT samples each in 5 volumes of TiO2 loading solution.","checked":false,"checklist_id":951,"created_at":"2018-12-20T14:51:18.467Z","updated_at":"2018-12-20T14:51:18.467Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3902,"text":"Load each of the samples onto one TiO2 column (for simple samples) or three to four TiO2 columns (for complex mixtures containing ≥120 μg protein).","checked":false,"checklist_id":951,"created_at":"2018-12-20T14:51:18.476Z","updated_at":"2018-12-20T14:51:18.476Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3903,"text":"Collect TiO2 flow through in microcentrifuge tubes. Do this step slowly using Combi-Syringe to apply the pressure.","checked":false,"checklist_id":951,"created_at":"2018-12-20T14:51:18.483Z","updated_at":"2018-12-20T14:51:18.483Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3904,"text":"Wash the TiO2 columns using 5 μL TiO2 loading solution and pool the eluates with the TIO2FT fraction from the previous step. Do this step slowly using Combi-Syringe to apply the pressure.","checked":false,"checklist_id":951,"created_at":"2018-12-20T14:51:18.491Z","updated_at":"2018-12-20T14:51:18.491Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3905,"text":"Elute the phosphopeptides using 30 μL high-pH elution solution. Use 30 μL per column and pool the eluates from the same sample. This step should be performed slowly using a Combi-Syringe to apply pressure.\r\nAcidify the eluates using 100% TFA to a pH of ~2 to 3.","checked":false,"checklist_id":951,"created_at":"2018-12-20T14:51:18.499Z","updated_at":"2018-12-20T14:51:18.499Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5156,"name":"Preparation of samples for MS","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eDifferent preparations of samples for different types of mass spectrometry. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T14:34:54.225Z","updated_at":"2018-12-24T08:07:19.825Z","last_modified_by_id":202,"protocol_id":3837},"checklists":[{"checklist":{"id":920,"name":"For MALDI-TOF-MS/MS:","step_id":5156,"created_at":"2018-12-07T14:34:54.228Z","updated_at":"2018-12-07T14:34:54.228Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3789,"text":"Elute the peptides from Oligo R3 column using 5 μL phosphopeptide RP elution buffer","checked":false,"checklist_id":920,"created_at":"2018-12-07T14:34:54.230Z","updated_at":"2018-12-20T12:16:38.311Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3790,"text":"Spot directly onto MALDI sample plate, using a pipet.","checked":false,"checklist_id":920,"created_at":"2018-12-07T14:34:54.239Z","updated_at":"2018-12-07T14:34:54.239Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3791,"text":"As spot is drying, if matrix crystals are not forming well, spot an additional 0.5 μL phosphopeptide RP elution buffer.","checked":false,"checklist_id":920,"created_at":"2018-12-07T14:34:54.248Z","updated_at":"2018-12-20T12:16:38.318Z","created_by_id":null,"last_modified_by_id":null,"position":2}]},{"checklist":{"id":921,"name":"For LC-ESI-MS/MS:","step_id":5156,"created_at":"2018-12-07T14:34:54.261Z","updated_at":"2018-12-07T14:34:54.261Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3792,"text":"Elute the peptides from the Oligo R3 column using 30 μl phosphopeptide RP elution buffer.","checked":false,"checklist_id":921,"created_at":"2018-12-07T14:34:54.263Z","updated_at":"2018-12-07T14:34:54.263Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3793,"text":"Dry pooled eluates by vacuum centrifugation.","checked":false,"checklist_id":921,"created_at":"2018-12-07T14:34:54.271Z","updated_at":"2018-12-07T14:34:54.271Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3794,"text":"Resuspend the monophosphopeptides in 0.5 μL 100% formic acid and add 10 μl of 0.1% formic acid immediately.","checked":false,"checklist_id":921,"created_at":"2018-12-07T14:34:54.278Z","updated_at":"2018-12-20T12:16:38.303Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5155,"name":"Preparation of a slurry of Oligo R3 reversed-phase resin","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv style=\"text-align: justify;\"\u003ePrepare a slurry of Oligo R3 reversed-phase resin in \u003cstrong\u003e50%\u003c/strong\u003e acetonitrile. Pack the Oligo R3 into a P20 narrow-bore pipet tip. Squeeze the tip of the narrow-bore P20 pipet tip to prevent the beads from leaking out. Sufficient Oligo R3 slurry should be added to make the columns \u003cstrong\u003e~5 mm\u003c/strong\u003e long. It is important to have a good seal on these columns, as column breakthrough will block on-line liquid chromatography systems.\u003c/div\u003e\n\u003cdiv style=\"text-align: justify;\"\u003eLoad each of the phosphopeptide-containing eluates that have been enriched with the TiO\u003csub\u003e2 \u003c/sub\u003estrategy onto one (for simple samples) or two to three (for complex mixtures) Oligo R3 columns depending on the amount of material.\u003cbr\u003eWash the Oligo R3 columns using \u003cstrong\u003e30 μL 0.1%\u003c/strong\u003e TFA.\u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T14:31:41.630Z","updated_at":"2019-01-31T08:39:07.689Z","last_modified_by_id":202,"protocol_id":3837},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5153,"name":"Preparation of TiO2 bead slurry","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv style=\"text-align: justify;\"\u003ePrepare a TiO\u003csub\u003e2\u003c/sub\u003e bead slurry in \u003cstrong\u003e100%\u003c/strong\u003e acetonitrile. Pack the TiO\u003csub\u003e2\u003c/sub\u003e in StageTips that have been pre-packed with C\u003csub\u003e8\u003c/sub\u003e disks. The resulting TiO\u003csub\u003e2\u003c/sub\u003e columns should be \u003cstrong\u003e~4 to 5 mm\u003c/strong\u003e long.\u003c/div\u003e\n\u003cdiv style=\"text-align: justify;\"\u003e\u003cem\u003e\u003cstrong\u003eTiO\u003csub\u003e2\u003c/sub\u003e is light sensitive, so keep the powder in an amber or dark glass container or in a microcentrifuge tube covered with aluminium foil. When not in use, TiO\u003csub\u003e2\u003c/sub\u003e should be in a container stored in a dark place (e.g., a drawer). It should not be exposed to light for longer than necessary.\u003c/strong\u003e\u003c/em\u003e\u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T14:15:28.126Z","updated_at":"2019-01-29T10:23:10.142Z","last_modified_by_id":202,"protocol_id":3837},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2275,"name":"Peptide Sample Cleanup","due_date":null,"description":null,"x":73,"y":32,"my_module_group_id":1179,"created_at":"2018-11-27T17:52:31.026Z","updated_at":"2018-12-19T09:02:54.882Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":5,"experiment_id":454,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":5982,"input_id":2276,"output_id":2275}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3705,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2275,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-27T17:52:31.033Z","updated_at":"2019-01-31T08:40:47.434Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4876,"name":"Prepare the column","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv\u003e The processing of samples can be performed using a pipet or centrifuge, or with the aid of a vacuum manifold.\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-27T17:54:41.488Z","updated_at":"2018-11-27T17:57:19.111Z","last_modified_by_id":202,"protocol_id":3705},"checklists":[{"checklist":{"id":860,"name":"To do:","step_id":4876,"created_at":"2018-11-27T17:57:03.419Z","updated_at":"2018-11-27T17:57:03.419Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3573,"text":"Wash the column three times with 200 μl 100% acetonitrile.","checked":false,"checklist_id":860,"created_at":"2018-11-27T17:57:03.421Z","updated_at":"2018-11-27T17:57:03.421Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3574,"text":"Discard flow through.","checked":false,"checklist_id":860,"created_at":"2018-11-27T17:57:03.430Z","updated_at":"2018-11-27T17:57:03.430Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3575,"text":"Rinse the column three times with 200 μL 0.1% TFA.","checked":false,"checklist_id":860,"created_at":"2018-11-27T17:57:03.437Z","updated_at":"2018-12-20T12:17:19.310Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3576,"text":"Discard flow through.","checked":false,"checklist_id":860,"created_at":"2018-11-27T17:57:03.445Z","updated_at":"2018-11-27T17:57:03.445Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4879,"name":"Elute peptides from the column","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eUse \u003cstrong\u003e30 μL\u003c/strong\u003e of RP LC-ESI-MS/MS elution solution for samples that will be analyzed. Collect the eluate in a clean tube. The samples are now ready for MS analysis.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-27T18:01:53.039Z","updated_at":"2019-01-31T08:40:47.389Z","last_modified_by_id":202,"protocol_id":3705},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4878,"name":"Rinse column","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv\u003e\n\u003cstrong\u003eThree to ten times with 200 μL 0.1% TFA\u003c/strong\u003e. The volume required for sufficient rinsing depends on the concentration of salts and other reagents in the sample. If electrospray/nanospray is to be performed, it is advisable to subsequently rinse the column three times with \u003cstrong\u003e200 μL\u003c/strong\u003e water to remove the TFA, which may interfere with ionization in electrospray/nanospray.\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-27T18:00:46.914Z","updated_at":"2019-01-29T10:24:17.412Z","last_modified_by_id":202,"protocol_id":3705},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4877,"name":"Application of samples","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow guidelines for sample preparation. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-27T17:59:44.389Z","updated_at":"2018-12-24T08:07:53.994Z","last_modified_by_id":202,"protocol_id":3705},"checklists":[{"checklist":{"id":861,"name":"Preparation of samples:","step_id":4877,"created_at":"2018-11-27T17:59:44.392Z","updated_at":"2018-11-27T17:59:44.392Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3577,"text":"Add 10% TFA to bring the final concentration to 0.1% TFA to the peptide sample.","checked":false,"checklist_id":861,"created_at":"2018-11-27T17:59:44.394Z","updated_at":"2018-11-27T17:59:44.394Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3578,"text":"Apply the sample to the column","checked":false,"checklist_id":861,"created_at":"2018-11-27T17:59:44.403Z","updated_at":"2018-11-27T17:59:44.403Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3579,"text":"Use a pipette to push sample through slowly","checked":false,"checklist_id":861,"created_at":"2018-11-27T17:59:44.410Z","updated_at":"2018-11-27T17:59:44.410Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2276,"name":"Mass 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\ No newline at end of file
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With mass spectrometry, in the end, you can identify and characterize biological molecules.","project_id":223,"created_by_id":202,"last_modified_by_id":202,"archived":false,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-26T08:55:55.988Z","updated_at":"2019-01-29T09:46:44.060Z","workflowimg_file_name":"wimg20181219-1-nlf5rk.png","workflowimg_content_type":"image/png","workflowimg_file_size":4681,"workflowimg_updated_at":"2019-01-29T09:46:44.060Z","uuid":"8c69cf68-9330-4c6c-9b8b-86043383a825"},"my_modules":[{"my_module":{"id":2274,"name":"Protein preparation: Affinity Capture","due_date":null,"description":null,"x":0,"y":32,"my_module_group_id":1179,"created_at":"2018-11-27T17:13:44.860Z","updated_at":"2018-12-19T09:02:54.892Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":0,"experiment_id":454,"state":"uncompleted","completed_on":null},"outputs":[{"id":5981,"input_id":2345,"output_id":2274}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3704,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2274,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-27T17:13:44.867Z","updated_at":"2019-01-31T08:29:28.974Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4872,"name":"Elute protein from the matrix","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv\u003eDown below are the guidelines for elution of proteins.  \u003cbr\u003e\u003cbr\u003e\n\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-27T17:40:37.750Z","updated_at":"2018-12-24T07:26:44.813Z","last_modified_by_id":202,"protocol_id":3704},"checklists":[{"checklist":{"id":858,"name":"Guidelines:","step_id":4872,"created_at":"2018-11-27T17:40:37.753Z","updated_at":"2018-12-20T14:36:53.748Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3564,"text":"Use a 5× volume of 0.1 M glycine, pH 2.5.","checked":false,"checklist_id":858,"created_at":"2018-11-27T17:40:37.755Z","updated_at":"2018-11-27T17:40:37.755Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3565,"text":"Apply the elution buffer and allow the buffer to thoroughly wet the matrix for 5 to 10 min.","checked":false,"checklist_id":858,"created_at":"2018-11-27T17:40:37.764Z","updated_at":"2018-11-27T17:40:37.764Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3566,"text":"Collect the eluate.","checked":false,"checklist_id":858,"created_at":"2018-11-27T17:40:37.772Z","updated_at":"2018-11-27T17:40:37.772Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3567,"text":"To enhance recovery, wash the matrix with an additional 5× volume of 0.1 M glycine, pH 2.5.","checked":false,"checklist_id":858,"created_at":"2018-11-27T17:40:37.780Z","updated_at":"2018-11-27T17:40:37.780Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3568,"text":"Adjust eluate to neutral pH by addition of an equal volume of 200 mM NH4HCO3.","checked":false,"checklist_id":858,"created_at":"2018-11-27T17:40:37.788Z","updated_at":"2018-11-27T17:40:37.788Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4873,"name":"Reduction of disulfide bonds","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cem\u003e\u003cstrong\u003eDisulfide (sulfur-sulfur) linkages between two cysteine residues are an integral component of the three-dimensional structure of many proteins.\u003c/strong\u003e \u003c/em\u003eDisulfide reducing agents are routinely used in biochemical reactions for peptides and proteins prior to MS analysis. \u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-27T17:42:41.887Z","updated_at":"2018-12-24T07:32:38.099Z","last_modified_by_id":202,"protocol_id":3704},"checklists":[{"checklist":{"id":859,"name":"To do:","step_id":4873,"created_at":"2018-11-27T17:42:41.891Z","updated_at":"2018-11-27T17:42:41.891Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3569,"text":"Add DTT to a final concentration of 10 mM or TCEP to a final concentration of 5 mM.","checked":false,"checklist_id":859,"created_at":"2018-11-27T17:42:41.894Z","updated_at":"2018-11-27T17:42:41.894Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3570,"text":"Incubate sample at room temperature with vortexing  for 10 min with TCEP or 30 min with DTT.","checked":false,"checklist_id":859,"created_at":"2018-11-27T17:42:41.915Z","updated_at":"2018-11-27T17:42:41.915Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3571,"text":"Next, to alkylate free cysteines, add iodoacetamide to a final concentration of 10 mM","checked":false,"checklist_id":859,"created_at":"2018-11-27T17:42:41.923Z","updated_at":"2018-11-27T17:42:41.923Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3572,"text":"Place at room temperature in the dark for 30 min.","checked":false,"checklist_id":859,"created_at":"2018-11-27T17:42:41.934Z","updated_at":"2018-11-27T17:42:41.934Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4874,"name":"Digestion of the protein sample","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv style=\"text-align: justify;\"\u003eThe protein is cut enzymatically into a limited number of shorter fragments during digestion and these fragments are called peptides and allow for the identification of the protein with their characteristic mass and pattern.\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-27T17:43:58.146Z","updated_at":"2018-12-24T07:33:39.499Z","last_modified_by_id":202,"protocol_id":3704},"checklists":[{"checklist":{"id":947,"name":"Guidelines:","step_id":4874,"created_at":"2018-12-20T14:41:18.229Z","updated_at":"2018-12-20T14:41:18.229Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3886,"text":"Use an appropriate enzyme or chemical. If using trypsin, add sufficient enzyme for final trypsin: protein ratio of 1:20 to 1:100 (w/w).","checked":false,"checklist_id":947,"created_at":"2018-12-20T14:41:18.231Z","updated_at":"2018-12-20T14:41:18.231Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3887,"text":"Vortex briefly.","checked":false,"checklist_id":947,"created_at":"2018-12-20T14:41:18.238Z","updated_at":"2018-12-20T14:41:18.238Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3888,"text":"Seal the tube with Paraffin.","checked":false,"checklist_id":947,"created_at":"2018-12-20T14:41:18.244Z","updated_at":"2018-12-20T14:41:18.244Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3889,"text":"Incubate with end-over-end rotation at 37°C for 4 to 18 hours.","checked":false,"checklist_id":947,"created_at":"2018-12-20T14:41:18.250Z","updated_at":"2018-12-20T14:41:18.250Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3890,"text":"Stop reaction by adding 5 μL of 1.0% trifluoroacetic (TFA) acid.","checked":false,"checklist_id":947,"created_at":"2018-12-20T14:41:18.257Z","updated_at":"2018-12-20T14:41:18.257Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4871,"name":"Wash affinity matrix","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv style=\"text-align: justify;\"\u003e\n\u003cem\u003e\u003cstrong\u003eWash affinity matrix containing the adsorbed protein sample with the wash buffer such as PBS to elute the unbound or nonspecifically bound proteins from the matrix. \u003c/strong\u003e\u003c/em\u003eBeads may be washed by resuspending them in the wash buffer with gentle vortexing, then microcentrifuging at low speed (e.g., \u003cstrong\u003e800 rpm\u003c/strong\u003e in a standard microcentrifuge) at room temperature to pellet the beads, and removing the supernatant by pipetting.\u003cbr\u003e\u003cstrong\u003eIf detergent is present in the starting material, it may be necessary to increase the number of washes to remove residual detergent\u003c/strong\u003e. Often this can be difficult and may require up to ten additional\u003cstrong\u003e 20×\u003c/strong\u003e volume washes (i.e., \u003cstrong\u003e20 times\u003c/strong\u003e the packed volume of the matrix). For most immunocapture methods, PBS is an effective wash buffer, but other neutral-pH saline buffers such as HEPES or Tris·Cl can be used. If greater stringency is required, for example, a high-salt wash or inclusion of a chaotropic agent, perform more stringent washes first followed by additional PBS washes. It is often necessary to optimize wash conditions for individual affinity-capture methods.\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-27T17:15:38.260Z","updated_at":"2019-01-31T08:29:28.933Z","last_modified_by_id":202,"protocol_id":3704},"checklists":[],"step_comments":[],"step_assets":[{"id":2977,"step_id":4871,"asset_id":3628}],"assets":[{"id":3628,"created_at":"2019-01-29T12:29:49.186Z","updated_at":"2019-01-31T08:29:28.856Z","file_file_name":"Bottom_up_proteomics.PNG","file_content_type":"image/png","file_file_size":40808,"file_updated_at":"2019-01-29T12:30:37.347Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":44888,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2262,"name":"Protein preparation: Liquid Chromatography Fraction","due_date":null,"description":null,"x":0,"y":16,"my_module_group_id":1179,"created_at":"2018-11-26T13:45:56.851Z","updated_at":"2018-12-19T09:02:54.890Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":1,"experiment_id":454,"state":"uncompleted","completed_on":null},"outputs":[{"id":5980,"input_id":2345,"output_id":2262}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3682,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2262,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-26T13:45:56.859Z","updated_at":"2019-01-31T08:32:20.750Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4840,"name":"Neutralization of samples","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv style=\"text-align: justify;\"\u003eThe pH of the sample may be neutralized either prior to or after drying via vacuum centrifugation to remove acetonitrile and trifluoroacetic acid. \u003cspan style=\"text-align: left;\"\u003eRP-HPLC samples will likely contain aqueous trifluoroacetic acid and acetonitrile since these are the most commonly used mobile phases. \u003c/span\u003e\u003cspan style=\"text-align: left;\"\u003eThe NH\u003c/span\u003e\u003csub style=\"text-align: left;\"\u003e4\u003c/sub\u003e\u003cspan style=\"text-align: left;\"\u003eHCO\u003c/span\u003e\u003csub style=\"text-align: left;\"\u003e3\u003c/sub\u003e\u003cspan style=\"text-align: left;\"\u003e solution should be prepared fresh, as the pH of the solution will increase with age at room temperature. It is possible to store for several days at \u003cstrong\u003e4°C\u003c/strong\u003e, but the pH should be checked prior to use.\u003c/span\u003e\n\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-26T13:50:47.141Z","updated_at":"2019-01-31T08:29:48.858Z","last_modified_by_id":202,"protocol_id":3682},"checklists":[{"checklist":{"id":944,"name":"To neutralize prior to drying:","step_id":4840,"created_at":"2018-12-20T14:20:33.276Z","updated_at":"2018-12-20T14:20:33.276Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3878,"text":"Add sufficient 1 M NH4HCO3, pH8.5.","checked":false,"checklist_id":944,"created_at":"2018-12-20T14:20:33.278Z","updated_at":"2018-12-20T14:20:33.278Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3879,"text":"Adjust final pH to ~8.0.","checked":false,"checklist_id":944,"created_at":"2018-12-20T14:20:33.285Z","updated_at":"2018-12-20T14:20:33.285Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3880,"text":"Then dry via vacuum centrifugation.","checked":false,"checklist_id":944,"created_at":"2018-12-20T14:20:33.292Z","updated_at":"2018-12-20T14:20:33.292Z","created_by_id":null,"last_modified_by_id":null,"position":2}]},{"checklist":{"id":945,"name":"To neutralize after drying:","step_id":4840,"created_at":"2018-12-20T14:21:35.471Z","updated_at":"2018-12-20T14:21:35.471Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3881,"text":"Resuspend dried protein in 100 mM NH4HCO3, pH 8.5.","checked":false,"checklist_id":945,"created_at":"2018-12-20T14:21:35.474Z","updated_at":"2018-12-20T14:21:35.474Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3882,"text":"Spot an aliquot of the neutralized solution on narrow-range pH paper to validate that neutralization (to pH 8.0) has occurred.","checked":false,"checklist_id":945,"created_at":"2018-12-20T14:21:35.481Z","updated_at":"2018-12-20T14:21:35.481Z","created_by_id":null,"last_modified_by_id":null,"position":1}]}],"step_comments":[],"step_assets":[{"id":2978,"step_id":4840,"asset_id":3629}],"assets":[{"id":3629,"created_at":"2019-01-29T12:30:12.184Z","updated_at":"2019-01-31T08:29:48.793Z","file_file_name":"Bottom_up_proteomics.PNG","file_content_type":"image/png","file_file_size":40808,"file_updated_at":"2019-01-29T12:30:37.768Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":44888,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]},{"step":{"id":5148,"name":"Reduction of disulfide bonds and alkyle free cysteine residues","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003e\u003cem\u003e\u003cstrong\u003eReduction of disulfide bonds can be achieved with either dithiothreitol (DTT) or tris (2-carboxyethyl)phosphine hydrochloride (TCEP). \u003c/strong\u003e\u003c/em\u003eDTT works optimally at \u003cstrong\u003epH 7 to 9\u003c/strong\u003e, TCEP is typically more efficient, works at a wider pH range (\u003cstrong\u003epH 2 to 11\u003c/strong\u003e), and has no offensive odour. The concentrations and incubation times for DTT, TCEP, and IAA may vary depending on the amount of protein to be treated. Typical concentrations range from \u003cstrong\u003e5 to 10 mM\u003c/strong\u003e for DTT and TCEP, and \u003cstrong\u003e10 to 50 mM\u003c/strong\u003e for iodoacetamide. Incubation times may range from \u003cstrong\u003e5 min to 1 hr for the reduction step\u003c/strong\u003e and \u003cstrong\u003e10 min to 1 hr for the alkylation step\u003c/strong\u003e. Similarly, the reduction can be performed at room temperature, \u003cstrong\u003e37°C or 56°C\u003c/strong\u003e. Each parameter can be optimized depending on the nature of the protein sample.\u003c/p\u003e\n\u003cdiv\u003e\u003cem\u003eOptional: Following alkylation, adjust the sample to \u003cstrong\u003e40 mM\u003c/strong\u003e DTT.\u003c/em\u003e\u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T12:46:55.270Z","updated_at":"2019-01-31T08:30:26.220Z","last_modified_by_id":202,"protocol_id":3682},"checklists":[{"checklist":{"id":946,"name":"Guidelines:","step_id":5148,"created_at":"2018-12-20T14:24:01.663Z","updated_at":"2018-12-20T14:24:01.663Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3883,"text":"Add DTT to a final concentration of 10 mM or TCEP to a final concentration of 5 mM.","checked":false,"checklist_id":946,"created_at":"2018-12-20T14:24:01.666Z","updated_at":"2018-12-20T14:24:01.666Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3884,"text":"Incubate sample at room temperature with agitation (e.g. vortexing, or shaking), for 30 min with DTT or 10 min with TCEP.","checked":false,"checklist_id":946,"created_at":"2018-12-20T14:24:01.680Z","updated_at":"2018-12-20T14:24:01.680Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3885,"text":"Add iodoacetamide (IAA) to a concentration of 10 mM final and place at room temperature in the dark for 30 min.","checked":false,"checklist_id":946,"created_at":"2018-12-20T14:24:01.690Z","updated_at":"2018-12-20T14:24:01.690Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5149,"name":"Digestion of protein samples","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv style=\"text-align: justify;\"\u003eDigest the protein sample into peptides using an \u003cstrong\u003eappropriate enzyme\u003c/strong\u003e (e.g., chymotrypsin, trypsin, LysC, or AspN) or\u003cstrong\u003e chemical\u003c/strong\u003e (CNBr/70% formic acid). If using trypsin, add sufficient enzyme for final trypsin: protein ratio of \u003cstrong\u003e1:20 to 1:100\u003c/strong\u003e (w/w). Vortex briefly, seal the tube with Parafilm and incubate with end-over-end rotation at \u003cstrong\u003e37°C\u003c/strong\u003e for \u003cstrong\u003e4 to 18 hours\u003c/strong\u003e.\u003c/div\u003e\n\u003cdiv style=\"text-align: justify;\"\u003e\n\u003cbr\u003eThe amount of trypsin needed will vary depending on the amount of protein sample present and the desired speed of digestion. To minimize trypsin autolysis, which will add extra peaks to the MS spectra, use the minimum amount of trypsin.\u003cstrong\u003e Typically, a ratio of 1:20 (w/w) is sufficient for complete digestion of 10 μg protein within 4 hr\u003c/strong\u003e. If protein concentration is especially high or the accessibility of trypsin to the cleavage sites is hampered (e.g., due to insolubility), it may be helpful to add another aliquot of trypsin or perform short digestion (\u003cstrong\u003e4 hours\u003c/strong\u003e) with LysC prior to the addition of trypsin. Finally, the activity of trypsin is enhanced in the presence of acetonitrile (\u003cstrong\u003e10% to 50% v/v\u003c/strong\u003e), and, thus, acetonitrile may be added to aid in the solubilization of the protein during tryptic digestion.\u003c/div\u003e\n\u003cdiv style=\"text-align: justify;\"\u003e\n\u003cbr\u003e\u003cstrong\u003eTrypsin activity is greatest at pH 8.0\u003c/strong\u003e. Thus, it is recommended that the pH of the solution be checked prior to the addition of the enzyme. In cases where sample volume is small, a \u003cstrong\u003e1- to 2-μL \u003c/strong\u003esample may be tested using pH paper. Stop reaction by adding \u003cstrong\u003e5 μL\u003c/strong\u003e of\u003cstrong\u003e 1.0%\u003c/strong\u003e trifluoroacetic (TFA) acid (pH after TFA addition should be \u003cstrong\u003e~2 to 3\u003c/strong\u003e).\u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T12:52:36.364Z","updated_at":"2019-01-31T08:32:20.691Z","last_modified_by_id":202,"protocol_id":3682},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2258,"name":"Protein preparation: Polyacrylamide gel","due_date":null,"description":null,"x":0,"y":0,"my_module_group_id":1179,"created_at":"2018-11-26T12:04:02.091Z","updated_at":"2018-12-19T09:02:54.887Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":454,"state":"uncompleted","completed_on":null},"outputs":[{"id":5978,"input_id":2345,"output_id":2258}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3678,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2258,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-26T12:04:02.098Z","updated_at":"2019-01-31T08:32:58.479Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5146,"name":"Perform enzymatic digestion","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv style=\"text-align: justify;\"\u003eThe protein is cut enzymatically into a limited number of shorter fragments during digestion and these fragments are called peptides and allow for the identification of the protein with their characteristic mass and pattern.\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":5,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T11:40:40.624Z","updated_at":"2018-12-24T06:40:41.505Z","last_modified_by_id":202,"protocol_id":3678},"checklists":[{"checklist":{"id":942,"name":"Guidelines:","step_id":5146,"created_at":"2018-12-20T14:15:25.669Z","updated_at":"2018-12-20T14:15:25.669Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3869,"text":"Dilute the gel enzyme stock solution ~1:1000 with 25 mM ammonium bicarbonate to obtain a 10 to 20 μg/mL working solution.","checked":false,"checklist_id":942,"created_at":"2018-12-20T14:15:25.671Z","updated_at":"2018-12-20T14:15:25.671Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3870,"text":"Add a sufficient amount of the gel enzyme working solution to cover gel pieces and incubate on ice for 1 hr. For a typical gel band/spot, this is ~10 to 20 μL.","checked":false,"checklist_id":942,"created_at":"2018-12-20T14:15:25.679Z","updated_at":"2018-12-20T14:15:25.679Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3871,"text":"Remove excess gel enzyme solution, then add sufficient 25 mM NH4HCO3 to cover the gel pieces. This increases the pH and thereby inhibits the enzymatic digestion for those enzymes which have low pH optima.","checked":false,"checklist_id":942,"created_at":"2018-12-20T14:15:25.686Z","updated_at":"2018-12-20T14:15:25.686Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3872,"text":"Incubate at 37°C overnight.","checked":false,"checklist_id":942,"created_at":"2018-12-20T14:15:25.693Z","updated_at":"2018-12-20T14:15:25.693Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5145,"name":"Reduce disulfide bonds and alkylate free cysteines","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cem\u003e\u003cstrong\u003eDithiothreitol (DTT) is a reducing agent that converts cystine’s disulfide bond into cysteine’s free sulfhydryl groups.\u003c/strong\u003e\u003c/em\u003e\u003cbr\u003e\u003cem\u003e\u003cstrong\u003eIodoacetamide (IAA) is an alkylating agent that reacts with free sulfhydryl groups of cysteine residues to form S-\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e\u003cem\u003ecarboxyamidomethyl-cysteine, which cannot be reoxidized to form disulfide bonds. This is important for allowing trypsin maximum access to cleavage sites within the protein.\u003c/em\u003e\u003c/strong\u003e\n\u003c/body\u003e\u003c/html\u003e","position":4,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T11:01:14.616Z","updated_at":"2018-12-20T14:13:35.200Z","last_modified_by_id":202,"protocol_id":3678},"checklists":[{"checklist":{"id":941,"name":"Guidelines:","step_id":5145,"created_at":"2018-12-20T14:12:18.059Z","updated_at":"2018-12-20T14:12:18.059Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3865,"text":"Add 100 μL of 10 mM dithiothreitol to the gel piece, then incubate 45 min at 55°C.","checked":false,"checklist_id":941,"created_at":"2018-12-20T14:12:18.062Z","updated_at":"2018-12-20T14:12:18.062Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3866,"text":"Remove solution, add 100 μl 55 mM iodoacetamide, and incubate 30 min at room temperature in the dark.","checked":false,"checklist_id":941,"created_at":"2018-12-20T14:12:18.070Z","updated_at":"2018-12-20T14:12:18.070Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3867,"text":"Remove IAA solution and add 400 μL gel wash solution, incubate at room temperature, and shake for 15 min. Repeat this step twice.","checked":false,"checklist_id":941,"created_at":"2018-12-20T14:12:18.077Z","updated_at":"2018-12-20T14:12:18.077Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3868,"text":"Dehydrate gel pieces with 400 μL of 100% acetonitrile for 10 min, then remove supernatant and dry gel pieces using a vacuum centrifuge.","checked":false,"checklist_id":941,"created_at":"2018-12-20T14:12:18.083Z","updated_at":"2018-12-20T14:12:18.083Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5147,"name":"Extract peptides","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eHere is the guideline how to extract peptides. This step can take up to several hours depending upon the volume used.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":6,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T11:52:09.928Z","updated_at":"2018-12-24T06:42:22.727Z","last_modified_by_id":202,"protocol_id":3678},"checklists":[{"checklist":{"id":943,"name":"Guidelines:","step_id":5147,"created_at":"2018-12-20T14:17:36.750Z","updated_at":"2018-12-20T14:17:36.750Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3873,"text":"Remove supernatant, which now contains peptides, to a new clean microcentrifuge tube.","checked":false,"checklist_id":943,"created_at":"2018-12-20T14:17:36.754Z","updated_at":"2018-12-20T14:17:36.754Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3874,"text":"Add 100 μL gel extraction solution to the gel pieces and incubate while shaking for 20 min at room temperature.","checked":false,"checklist_id":943,"created_at":"2018-12-20T14:17:36.761Z","updated_at":"2018-12-20T14:17:36.761Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3875,"text":"Remove solution and combine with the solution obtained in step 1.","checked":false,"checklist_id":943,"created_at":"2018-12-20T14:17:36.777Z","updated_at":"2018-12-20T14:17:36.777Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3876,"text":"Repeat steps second and third step.","checked":false,"checklist_id":943,"created_at":"2018-12-20T14:17:36.784Z","updated_at":"2018-12-20T14:17:36.784Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3877,"text":"Dry combined supernatants using a vacuum centrifuge.","checked":false,"checklist_id":943,"created_at":"2018-12-20T14:17:36.791Z","updated_at":"2018-12-20T14:17:36.791Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4826,"name":"Coomassie stained gels","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cem\u003e\u003cstrong\u003eCoomassie dyes (also known as Coomassie Brilliant Dyes) are a family of dyes commonly used to stain proteins in sodium dodecyl sulfate and blue native polyacrylamide gel electrophoresis (SDS-PAGE and BN-PAGE, respectively) gels.\u003c/strong\u003e\u003c/em\u003e The gels are soaked in dye and an excess stain is then eluted with a solvent. This treatment allows the visualization of protein bands.\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-26T13:15:06.518Z","updated_at":"2018-12-24T06:34:58.049Z","last_modified_by_id":202,"protocol_id":3678},"checklists":[{"checklist":{"id":917,"name":"Washing:","step_id":4826,"created_at":"2018-12-07T10:52:29.542Z","updated_at":"2018-12-07T11:39:18.108Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3780,"text":"Remove destain solution","checked":false,"checklist_id":917,"created_at":"2018-12-07T10:52:29.545Z","updated_at":"2018-12-07T10:52:29.545Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3781,"text":"Add 400 μl water.","checked":false,"checklist_id":917,"created_at":"2018-12-07T10:52:29.554Z","updated_at":"2018-12-07T10:52:29.554Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3782,"text":"If the gel pieces are still blue, remove the water and repeat until the gel pieces are colourless.","checked":false,"checklist_id":917,"created_at":"2018-12-07T10:52:29.562Z","updated_at":"2018-12-07T10:52:29.562Z","created_by_id":null,"last_modified_by_id":null,"position":2}]},{"checklist":{"id":919,"name":"Dehydration:","step_id":4826,"created_at":"2018-12-07T11:39:18.116Z","updated_at":"2018-12-07T11:39:18.116Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3786,"text":"Dehydrate gel pieces with 400 μl of 100% acetonitrile for 10 min","checked":false,"checklist_id":919,"created_at":"2018-12-07T11:39:18.118Z","updated_at":"2018-12-07T11:39:18.118Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3787,"text":"Remove supernatant","checked":false,"checklist_id":919,"created_at":"2018-12-07T11:39:18.126Z","updated_at":"2018-12-07T11:39:18.126Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3788,"text":"Dry gel pieces in a vacuum centrifuge","checked":false,"checklist_id":919,"created_at":"2018-12-07T11:39:18.133Z","updated_at":"2018-12-07T11:39:18.133Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4824,"name":"Destain gel bands","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eDestain in the microcentrifuge tube for \u003cstrong\u003e30 min\u003c/strong\u003e with \u003cstrong\u003e100 μL\u003c/strong\u003e of the appropriate gel destain solution with vigorous vortexing. The choice of destaining protocol depends on the stain used, and there is a specific destain recipe for each type of gel stain. The choice of protein stain depends on the protein concentration and the dynamic range of the sample. Silver and colloidal Coomassie staining (CCS) stains offer a low limit of detection (\u003cstrong\u003e1 to 10 ng\u003c/strong\u003e) compared to traditional Coomassie staining (\u003cstrong\u003e0.3 to 1 μg)\u003c/strong\u003e.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-26T13:08:09.568Z","updated_at":"2019-01-31T08:32:58.429Z","last_modified_by_id":202,"protocol_id":3678},"checklists":[{"checklist":{"id":940,"name":"Follow:","step_id":4824,"created_at":"2018-12-20T14:03:52.360Z","updated_at":"2018-12-20T14:03:52.360Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3863,"text":"Step 3: Glutaraldehyde-free silver stained gels","checked":false,"checklist_id":940,"created_at":"2018-12-20T14:03:52.362Z","updated_at":"2018-12-20T14:04:56.749Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3864,"text":"Step 4: Coomassie-stained gels","checked":false,"checklist_id":940,"created_at":"2018-12-20T14:03:52.369Z","updated_at":"2018-12-20T14:04:56.761Z","created_by_id":null,"last_modified_by_id":null,"position":1}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4825,"name":"Silver stained gels","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cem\u003e\u003cstrong\u003eSilver staining is used to detect proteins after electrophoretic separation on polyacrylamide gels.\u003c/strong\u003e\u003c/em\u003e It combines excellent sensitivity, whilst using very simple and cheap equipment and chemicals.\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-26T13:14:10.347Z","updated_at":"2018-12-24T06:30:40.360Z","last_modified_by_id":202,"protocol_id":3678},"checklists":[{"checklist":{"id":916,"name":"Washing:","step_id":4825,"created_at":"2018-12-07T10:50:00.146Z","updated_at":"2018-12-07T11:37:14.463Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3776,"text":"Remove destain solution","checked":false,"checklist_id":916,"created_at":"2018-12-07T10:50:00.148Z","updated_at":"2018-12-07T10:50:00.148Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3777,"text":"Wash gel piece with 400 μL water","checked":false,"checklist_id":916,"created_at":"2018-12-07T10:50:00.157Z","updated_at":"2018-12-20T12:00:27.604Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3778,"text":"Shake for 15 min at room temperature","checked":false,"checklist_id":916,"created_at":"2018-12-07T10:50:00.166Z","updated_at":"2018-12-07T10:50:00.166Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3779,"text":"Repeat wash at least twice or until gel pieces are colourless.","checked":false,"checklist_id":916,"created_at":"2018-12-07T10:50:00.175Z","updated_at":"2018-12-07T10:50:00.175Z","created_by_id":null,"last_modified_by_id":null,"position":3}]},{"checklist":{"id":918,"name":"Dehydration:","step_id":4825,"created_at":"2018-12-07T11:36:41.173Z","updated_at":"2018-12-07T11:37:28.556Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3783,"text":"Dehydrate gel pieces with 400 μL of 100% acetonitrile for 10 min","checked":false,"checklist_id":918,"created_at":"2018-12-07T11:36:41.177Z","updated_at":"2018-12-20T12:00:27.594Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3784,"text":"Remove supernatant","checked":false,"checklist_id":918,"created_at":"2018-12-07T11:36:41.204Z","updated_at":"2018-12-07T11:36:41.204Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3785,"text":"Dry gel pieces in a vacuum centrifuge","checked":false,"checklist_id":918,"created_at":"2018-12-07T11:36:41.211Z","updated_at":"2018-12-07T11:36:41.211Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4823,"name":"Excise gel bands","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003eOnce you have run your gel, move it to an\u003cstrong\u003e open UV box\u003c/strong\u003e (be sure to wear proper UV protection - especially for your eyes!), remove it from any gel tray as plastic will block much of the UV and with a clean, sterile razor blade, slice the desired DNA fragment from the gel. Try to get as little excess gel around the band as possible. To do so, it is often important to take the excised band, lay it down on the UV box and trim the top, bottom and sides with the razor blade. This is especially important during the DNA purification step, as many kits cannot handle more than a certain total volume of gel per reaction.\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-26T13:01:32.320Z","updated_at":"2019-01-29T12:30:38.522Z","last_modified_by_id":202,"protocol_id":3678},"checklists":[],"step_comments":[],"step_assets":[{"id":2979,"step_id":4823,"asset_id":3630}],"assets":[{"id":3630,"created_at":"2019-01-29T12:30:25.880Z","updated_at":"2019-01-29T12:30:38.511Z","file_file_name":"Bottom_up_proteomics.PNG","file_content_type":"image/png","file_file_size":40808,"file_updated_at":"2019-01-29T12:30:38.172Z","created_by_id":202,"last_modified_by_id":null,"estimated_size":44888,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2345,"name":"IMAC Phosphopeptide Enrichment (optional*)","due_date":null,"description":null,"x":38,"y":15,"my_module_group_id":1179,"created_at":"2018-12-07T13:34:00.077Z","updated_at":"2018-12-19T09:02:54.880Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":3,"experiment_id":454,"state":"uncompleted","completed_on":null},"outputs":[{"id":5979,"input_id":2346,"output_id":2345}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3836,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2345,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-12-07T13:34:00.086Z","updated_at":"2019-01-25T12:07:01.449Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5152,"name":"Elution and collection","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv\u003eDry each eluate containing the multiply phosphorylated peptides, monophosphopeptides, and the IMAC flow through separately using vacuum centrifugation.\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T13:58:12.351Z","updated_at":"2018-12-20T14:48:45.965Z","last_modified_by_id":202,"protocol_id":3836},"checklists":[{"checklist":{"id":950,"name":"Guidelines:","step_id":5152,"created_at":"2018-12-20T14:48:32.247Z","updated_at":"2018-12-20T14:48:32.247Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3897,"text":"Collect the column flow through in microcentrifuge tubes.","checked":false,"checklist_id":950,"created_at":"2018-12-20T14:48:32.249Z","updated_at":"2018-12-20T14:48:32.249Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3898,"text":"Wash the IMAC column with 50 μL IMAC wash solution and pool the eluate with the fraction from the previous step. This need to be done slowly using a Combi-Syringe to apply pressure.","checked":false,"checklist_id":950,"created_at":"2018-12-20T14:48:32.256Z","updated_at":"2018-12-20T14:48:32.256Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3899,"text":"Elute and collect the monophosphopeptides using 50 μl low-pH elution solution. This needs to be done quickly using a Combi-Syringe to apply pressure.","checked":false,"checklist_id":950,"created_at":"2018-12-20T14:48:32.263Z","updated_at":"2018-12-20T14:48:32.263Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3900,"text":"Elute and collect the multiply phosphorylated peptides using 70 μL high-pH elution solution. This step should be performed slowly using a Combi-Syringe to apply pressure.","checked":false,"checklist_id":950,"created_at":"2018-12-20T14:48:32.269Z","updated_at":"2018-12-20T14:48:32.269Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5151,"name":"Add protein sample to IMAC beads","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eSqueeze the tip of the narrow-bore pipet tip nearly shut, as this will prevent bead loss. The Combi-Syringe is only to be used for the generation of pressure in the column, not for measuring and loading the aliquots. The Combi-Syringe is reusable and should therefore not come into contact with any solution.\u003c/p\u003e\n\u003cdiv\u003e \u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T13:50:12.807Z","updated_at":"2019-01-25T12:07:01.391Z","last_modified_by_id":202,"protocol_id":3836},"checklists":[{"checklist":{"id":949,"name":"Guideline:","step_id":5151,"created_at":"2018-12-20T14:47:07.628Z","updated_at":"2018-12-20T14:47:07.628Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3894,"text":"Add protein sample to the IMAC beads in a volume of IMAC wash solution that is 10 times the volume of the packed beads.","checked":false,"checklist_id":949,"created_at":"2018-12-20T14:47:07.630Z","updated_at":"2018-12-20T14:47:07.630Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3895,"text":"Incubate with constant, gentle agitation, at room temperature for 30 to 60 min.","checked":false,"checklist_id":949,"created_at":"2018-12-20T14:47:07.638Z","updated_at":"2018-12-20T14:47:07.638Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3896,"text":"Using a Combi-Syringe and gentle pressure, pack the IMAC beads in a narrow bore tip by gradually adding the bead slurry in 20 μL aliquots.","checked":false,"checklist_id":949,"created_at":"2018-12-20T14:47:07.654Z","updated_at":"2018-12-20T14:47:07.654Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5150,"name":"Wash IMAC beads","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eTo\u003cspan\u003eo many IMAC beads may result in \u003cstrong\u003enonspecific binding of peptides\u003c/strong\u003e because of reduced washing efficiency. A small amount of wash solution should be left in the tube with the beads, to avoid aspirating the beads.\u003c/span\u003e\n\u003c/p\u003e\n\u003cdiv\u003e \u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T13:34:50.552Z","updated_at":"2018-12-20T14:44:55.371Z","last_modified_by_id":202,"protocol_id":3836},"checklists":[{"checklist":{"id":948,"name":"Guideline:","step_id":5150,"created_at":"2018-12-20T14:44:55.374Z","updated_at":"2018-12-20T14:44:55.374Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3891,"text":"Wash IMAC (immobilized metal affinity chromatography) beads. You will need 5 to 7 μL for simple mixtures and 30 to 50 μL for complex mixtures containing ≥120 μg protein.","checked":false,"checklist_id":948,"created_at":"2018-12-20T14:44:55.376Z","updated_at":"2018-12-20T14:44:55.376Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3892,"text":"Applying 50 μL IMAC wash solution, vortex and centrifuge at low speed (e.g., 800 rpm in a benchtop microcentrifuge) at room temperature to pellet the beads.","checked":false,"checklist_id":948,"created_at":"2018-12-20T14:44:55.383Z","updated_at":"2018-12-20T14:44:55.383Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3893,"text":"Remove the supernatant by pipetting.","checked":false,"checklist_id":948,"created_at":"2018-12-20T14:44:55.390Z","updated_at":"2018-12-20T14:44:55.390Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2346,"name":"TiO2 Enrichment (optional*)","due_date":null,"description":null,"x":73,"y":15,"my_module_group_id":1179,"created_at":"2018-12-07T14:01:45.181Z","updated_at":"2018-12-19T09:02:54.895Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":4,"experiment_id":454,"state":"uncompleted","completed_on":null},"outputs":[{"id":5983,"input_id":2275,"output_id":2346}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3837,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2346,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-12-07T14:01:45.189Z","updated_at":"2019-01-31T08:39:24.163Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5154,"name":"Elution and collection of samples","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow elution and collection guidelines bellow.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T14:20:38.293Z","updated_at":"2018-12-24T08:06:13.141Z","last_modified_by_id":202,"protocol_id":3837},"checklists":[{"checklist":{"id":951,"name":"Guidelines:","step_id":5154,"created_at":"2018-12-20T14:51:18.465Z","updated_at":"2018-12-20T14:51:18.465Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3901,"text":"If samples have been dried, then resuspended in 3 μL 1 of % SDS. Dilute IMAC–1% TFA and IMAC-FT samples each in 5 volumes of TiO2 loading solution.","checked":false,"checklist_id":951,"created_at":"2018-12-20T14:51:18.467Z","updated_at":"2018-12-20T14:51:18.467Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3902,"text":"Load each of the samples onto one TiO2 column (for simple samples) or three to four TiO2 columns (for complex mixtures containing ≥120 μg protein).","checked":false,"checklist_id":951,"created_at":"2018-12-20T14:51:18.476Z","updated_at":"2018-12-20T14:51:18.476Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3903,"text":"Collect TiO2 flow through in microcentrifuge tubes. Do this step slowly using Combi-Syringe to apply the pressure.","checked":false,"checklist_id":951,"created_at":"2018-12-20T14:51:18.483Z","updated_at":"2018-12-20T14:51:18.483Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3904,"text":"Wash the TiO2 columns using 5 μL TiO2 loading solution and pool the eluates with the TIO2FT fraction from the previous step. Do this step slowly using Combi-Syringe to apply the pressure.","checked":false,"checklist_id":951,"created_at":"2018-12-20T14:51:18.491Z","updated_at":"2018-12-20T14:51:18.491Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3905,"text":"Elute the phosphopeptides using 30 μL high-pH elution solution. Use 30 μL per column and pool the eluates from the same sample. This step should be performed slowly using a Combi-Syringe to apply pressure.\r\nAcidify the eluates using 100% TFA to a pH of ~2 to 3.","checked":false,"checklist_id":951,"created_at":"2018-12-20T14:51:18.499Z","updated_at":"2018-12-20T14:51:18.499Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5156,"name":"Preparation of samples for MS","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eDifferent preparations of samples for different types of mass spectrometry. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T14:34:54.225Z","updated_at":"2018-12-24T08:07:19.825Z","last_modified_by_id":202,"protocol_id":3837},"checklists":[{"checklist":{"id":920,"name":"For MALDI-TOF-MS/MS:","step_id":5156,"created_at":"2018-12-07T14:34:54.228Z","updated_at":"2018-12-07T14:34:54.228Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3789,"text":"Elute the peptides from Oligo R3 column using 5 μL phosphopeptide RP elution buffer","checked":false,"checklist_id":920,"created_at":"2018-12-07T14:34:54.230Z","updated_at":"2018-12-20T12:16:38.311Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3790,"text":"Spot directly onto MALDI sample plate, using a pipet.","checked":false,"checklist_id":920,"created_at":"2018-12-07T14:34:54.239Z","updated_at":"2018-12-07T14:34:54.239Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3791,"text":"As spot is drying, if matrix crystals are not forming well, spot an additional 0.5 μL phosphopeptide RP elution buffer.","checked":false,"checklist_id":920,"created_at":"2018-12-07T14:34:54.248Z","updated_at":"2018-12-20T12:16:38.318Z","created_by_id":null,"last_modified_by_id":null,"position":2}]},{"checklist":{"id":921,"name":"For LC-ESI-MS/MS:","step_id":5156,"created_at":"2018-12-07T14:34:54.261Z","updated_at":"2018-12-07T14:34:54.261Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3792,"text":"Elute the peptides from the Oligo R3 column using 30 μl phosphopeptide RP elution buffer.","checked":false,"checklist_id":921,"created_at":"2018-12-07T14:34:54.263Z","updated_at":"2018-12-07T14:34:54.263Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3793,"text":"Dry pooled eluates by vacuum centrifugation.","checked":false,"checklist_id":921,"created_at":"2018-12-07T14:34:54.271Z","updated_at":"2018-12-07T14:34:54.271Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3794,"text":"Resuspend the monophosphopeptides in 0.5 μL 100% formic acid and add 10 μl of 0.1% formic acid immediately.","checked":false,"checklist_id":921,"created_at":"2018-12-07T14:34:54.278Z","updated_at":"2018-12-20T12:16:38.303Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5155,"name":"Preparation of a slurry of Oligo R3 reversed-phase resin","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv style=\"text-align: justify;\"\u003ePrepare a slurry of Oligo R3 reversed-phase resin in \u003cstrong\u003e50%\u003c/strong\u003e acetonitrile. Pack the Oligo R3 into a P20 narrow-bore pipet tip. Squeeze the tip of the narrow-bore P20 pipet tip to prevent the beads from leaking out. Sufficient Oligo R3 slurry should be added to make the columns \u003cstrong\u003e~5 mm\u003c/strong\u003e long. It is important to have a good seal on these columns, as column breakthrough will block on-line liquid chromatography systems.\u003c/div\u003e\n\u003cdiv style=\"text-align: justify;\"\u003eLoad each of the phosphopeptide-containing eluates that have been enriched with the TiO\u003csub\u003e2 \u003c/sub\u003estrategy onto one (for simple samples) or two to three (for complex mixtures) Oligo R3 columns depending on the amount of material.\u003cbr\u003eWash the Oligo R3 columns using \u003cstrong\u003e30 μL 0.1%\u003c/strong\u003e TFA.\u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T14:31:41.630Z","updated_at":"2019-01-31T08:39:07.689Z","last_modified_by_id":202,"protocol_id":3837},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5153,"name":"Preparation of TiO2 bead slurry","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv style=\"text-align: justify;\"\u003ePrepare a TiO\u003csub\u003e2\u003c/sub\u003e bead slurry in \u003cstrong\u003e100%\u003c/strong\u003e acetonitrile. Pack the TiO\u003csub\u003e2\u003c/sub\u003e in StageTips that have been pre-packed with C\u003csub\u003e8\u003c/sub\u003e disks. The resulting TiO\u003csub\u003e2\u003c/sub\u003e columns should be \u003cstrong\u003e~4 to 5 mm\u003c/strong\u003e long.\u003c/div\u003e\n\u003cdiv style=\"text-align: justify;\"\u003e\u003cem\u003e\u003cstrong\u003eTiO\u003csub\u003e2\u003c/sub\u003e is light sensitive, so keep the powder in an amber or dark glass container or in a microcentrifuge tube covered with aluminium foil. When not in use, TiO\u003csub\u003e2\u003c/sub\u003e should be in a container stored in a dark place (e.g., a drawer). It should not be exposed to light for longer than necessary.\u003c/strong\u003e\u003c/em\u003e\u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-07T14:15:28.126Z","updated_at":"2019-01-29T10:23:10.142Z","last_modified_by_id":202,"protocol_id":3837},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2275,"name":"Peptide Sample Cleanup","due_date":null,"description":null,"x":73,"y":32,"my_module_group_id":1179,"created_at":"2018-11-27T17:52:31.026Z","updated_at":"2018-12-19T09:02:54.882Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":5,"experiment_id":454,"state":"uncompleted","completed_on":null},"outputs":[{"id":5982,"input_id":2276,"output_id":2275}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3705,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2275,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-27T17:52:31.033Z","updated_at":"2019-01-31T08:40:47.434Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4876,"name":"Prepare the column","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv\u003e The processing of samples can be performed using a pipet or centrifuge, or with the aid of a vacuum manifold.\u003c/div\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-27T17:54:41.488Z","updated_at":"2018-11-27T17:57:19.111Z","last_modified_by_id":202,"protocol_id":3705},"checklists":[{"checklist":{"id":860,"name":"To do:","step_id":4876,"created_at":"2018-11-27T17:57:03.419Z","updated_at":"2018-11-27T17:57:03.419Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3573,"text":"Wash the column three times with 200 μl 100% acetonitrile.","checked":false,"checklist_id":860,"created_at":"2018-11-27T17:57:03.421Z","updated_at":"2018-11-27T17:57:03.421Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3574,"text":"Discard flow through.","checked":false,"checklist_id":860,"created_at":"2018-11-27T17:57:03.430Z","updated_at":"2018-11-27T17:57:03.430Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3575,"text":"Rinse the column three times with 200 μL 0.1% TFA.","checked":false,"checklist_id":860,"created_at":"2018-11-27T17:57:03.437Z","updated_at":"2018-12-20T12:17:19.310Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3576,"text":"Discard flow through.","checked":false,"checklist_id":860,"created_at":"2018-11-27T17:57:03.445Z","updated_at":"2018-11-27T17:57:03.445Z","created_by_id":null,"last_modified_by_id":null,"position":3}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4879,"name":"Elute peptides from the column","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eUse \u003cstrong\u003e30 μL\u003c/strong\u003e of RP LC-ESI-MS/MS elution solution for samples that will be analyzed. Collect the eluate in a clean tube. The samples are now ready for MS analysis.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-27T18:01:53.039Z","updated_at":"2019-01-31T08:40:47.389Z","last_modified_by_id":202,"protocol_id":3705},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4878,"name":"Rinse column","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cdiv\u003e\n\u003cstrong\u003eThree to ten times with 200 μL 0.1% TFA\u003c/strong\u003e. The volume required for sufficient rinsing depends on the concentration of salts and other reagents in the sample. 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\ No newline at end of file
diff --git a/app/assets/templates/experiment_497/experiment.json b/app/assets/templates/experiment_497/experiment.json
index 2863ac892..8bcfba1b0 100644
--- a/app/assets/templates/experiment_497/experiment.json
+++ b/app/assets/templates/experiment_497/experiment.json
@@ -1 +1 @@
-{"experiment":{"id":497,"name":"SDS-PAGE for Protein Characterization","description":"This experiment template will help you separate proteins based on their molecular weight. \r\nProteins are separated by electrophoresis through a gel matrix. Smaller proteins migrate faster due to less resistance from the gel matrix. Other influences on the rate of migration through the gel matrix include the structure and charge of the proteins. In SDS-PAGE, the use of sodium dodecyl sulfate (SDS, also known as sodium lauryl sulfate) and polyacrylamide gel largely eliminates the influence of the structure and charge, and proteins are separated solely based on polypeptide chain length.\r\nStaining with Coomassie blue dyes is commonly used to stain proteins and visualize them. 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Wait for 20-30min to let it gelate.","checked":false,"checklist_id":973,"created_at":"2018-12-24T11:30:55.065Z","updated_at":"2018-12-24T11:30:55.065Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":4010,"text":"Make sure a complete gelation of the stacking gel and take out the comb.","checked":false,"checklist_id":973,"created_at":"2018-12-24T11:30:55.071Z","updated_at":"2018-12-24T11:30:55.071Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":4011,"text":"Take the glass plates out of the casting frame and set them in the cell buffer dam.","checked":false,"checklist_id":973,"created_at":"2018-12-24T11:30:55.076Z","updated_at":"2018-12-24T11:30:55.076Z","created_by_id":null,"last_modified_by_id":null,"position":4},{"id":4012,"text":"Pour the running buffer (electrophoresis buffer) into the inner chamber and keep pouring after overflow untill the buffer surface reaches the required level in the outer chamber.","checked":false,"checklist_id":973,"created_at":"2018-12-24T11:30:55.081Z","updated_at":"2018-12-24T11:30:55.081Z","created_by_id":null,"last_modified_by_id":null,"position":5}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5248,"name":"Preparation of the equipment","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cdiv style=\"text-align: justify;\"\u003eGather combs, glass plates, spacer (silicone tubing), and binder clips. \u003cem\u003e\u003cstrong\u003eA comb is used to make wells (lanes) to load samples.\u003c/strong\u003e\u003c/em\u003e Use an appropriate comb depending on the sample size. Thoroughly clean the glass plates with ethanol, and assemble the gel casting mold, taking care to not leave any space.\u003c/div\u003e\n\u003cdiv style=\"text-align: justify;\"\u003e\n\u003cbr\u003e\u003cstrong\u003eExample:\u003c/strong\u003e Use an \u003cstrong\u003e8-lane\u003c/strong\u003e comb for \u003cstrong\u003e7 samples\u003c/strong\u003e and molecular weight markers.\u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T11:04:34.946Z","updated_at":"2019-01-29T10:02:37.258Z","last_modified_by_id":202,"protocol_id":3902},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5249,"name":"Make the separating gel","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eThe acrylamide percentage in SDS PAGE gel depends on the size of the target protein in the sample. Using a higher acrylamide concentration produces a gel with a smaller mesh size suitable for the separation of small proteins. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T11:12:28.609Z","updated_at":"2019-01-29T10:02:55.233Z","last_modified_by_id":202,"protocol_id":3902},"checklists":[{"checklist":{"id":972,"name":"Guideline:","step_id":5249,"created_at":"2018-12-24T11:23:58.433Z","updated_at":"2018-12-24T11:23:58.433Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":4002,"text":"Prepare the gel solution in a small beaker. AP and TEMED must be added right before each use.","checked":false,"checklist_id":972,"created_at":"2018-12-24T11:23:58.434Z","updated_at":"2018-12-24T11:23:58.434Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":4003,"text":"Swirl the solution gently but thoroughly.","checked":false,"checklist_id":972,"created_at":"2018-12-24T11:23:58.442Z","updated_at":"2018-12-24T11:23:58.442Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":4004,"text":"Pipette appropriate amount of separating gel solution (listed above) into the gap between the glass plates.","checked":false,"checklist_id":972,"created_at":"2018-12-24T11:23:58.448Z","updated_at":"2018-12-24T11:23:58.448Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":4005,"text":"To make the top of the separating gel be horizontal, fill in water (either isopropanol) into the gap until a overflow. Water also prevents contact with oxygen, which inhibits polymerization.","checked":false,"checklist_id":972,"created_at":"2018-12-24T11:23:58.453Z","updated_at":"2018-12-24T11:26:09.996Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":4006,"text":"Wait for 20-30min to let it gelate.","checked":false,"checklist_id":972,"created_at":"2018-12-24T11:23:58.459Z","updated_at":"2018-12-24T11:23:58.459Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[{"id":548,"step_id":5249,"table_id":685}],"tables":[{"id":685,"created_at":"2018-12-24T11:20:43.674Z","updated_at":"2019-01-29T10:02:55.216Z","created_by_id":202,"last_modified_by_id":202,"name":"For 10 mL separating gel:","team_id":1,"contents":"eyJkYXRhIjpbWyJBY3lsYW1pZGUgcGVyY2VudGFnZSIsIjYlIiwiOCUiLCIx\nMCUiLCIxMiUiLCIxNSUiXSxbIkgyTyAobUwpIiwiNS4yIiwiNC42IiwiMy44\nIiwiMy4yIiwiMi4yIl0sWyJBY3J5bGFtaWRlL0Jpcy1hY3J5bGFtaWRlICAo\nbUwpIiwiMiIsIjIuNiIsIjMuNCIsIjQiLCI1Il0sWyIxLjVNIFRyaXM7IHBI\nPTguOCAobUwpIiwiMi42IiwiMi42IiwiMi42IiwiMi42IiwiMi42Il0sWyIx\nMCUgKHcvdilTRFMgKG1MKSIsIjAuMSIsIjAuMSIsIjAuMSIsIjAuMSIsIjAu\nMSJdLFsiMTAlICh3L3YpIGFtbW9uaXVtIHBlcnN1bGZhdGUgKEFQKSAozrxs\nKSIsIjEwMCIsIjEwMCIsIjEwMCIsIjEwMCIsIjEwMCJdLFsiVEVNRUQgKM68\nbCkiLCIxMCIsIjEwIiwiMTAiLCIxMCIsIjEwIl1dfQ==\n","data_vector":"JzAuMSc6MzcsMzgsMzksNDAsNDEgJzEuNSc6MjIgJzEwJzo1LDMzLDQyLDU3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\nJ3cvdic6MzQsNDM=\n"}]}]}],"results":[]},{"my_module":{"id":2384,"name":"Sample preparation","due_date":null,"description":null,"x":33,"y":7,"my_module_group_id":1195,"created_at":"2018-12-24T10:57:17.160Z","updated_at":"2018-12-24T13:43:31.290Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":1,"experiment_id":497,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":6047,"input_id":2386,"output_id":2384}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3901,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2384,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-12-24T10:57:17.170Z","updated_at":"2019-01-29T10:05:04.164Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5251,"name":"Mix samples with buffer","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eMake sure your target protein is \u003cstrong\u003edissolved in the liquid phase\u003c/strong\u003e, and \u003cstrong\u003eno inappropriate ingredients are present\u003c/strong\u003e (e.g. guanidine hydrochloride can interact with SDS and cause precipitation). Generally, to treat your unprepared sample, you can use sonicator, lysis buffer or both to sufficiently make your target protein released, and centrifuge to make supernatant and pellet separated.\u003cbr\u003e\u003cbr\u003e\u003cbr\u003eMix samples with loading buffer. Mix by flicking the tube.\u003cstrong\u003e\u003cbr\u003e\u003cbr\u003e5X Sample buffer (Loading buffer):\u003c/strong\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003e10%\u003c/strong\u003e w/v SDS\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003e10 mM\u003c/strong\u003e Dithiothreitol, or beta-mercapto-ethanol\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003e20 %\u003c/strong\u003e v/v Glycerol\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003e0.2 M\u003c/strong\u003e Tris-HCl; \u003cstrong\u003epH 6.8\u003c/strong\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003e0.05%\u003c/strong\u003e w/v Bromophenolblue\u003c/li\u003e\n\u003c/ul\u003e\n\u003cstrong\u003e\u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003c/strong\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T11:44:32.382Z","updated_at":"2019-01-29T10:04:52.137Z","last_modified_by_id":202,"protocol_id":3901},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5253,"name":"Centrifugation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cstrong\u003eCentrifuge:\u003c/strong\u003e\u003cbr\u003e\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003e15,000 rpm\u003c/li\u003e\n\u003cli\u003e1 minute\u003c/li\u003e\n\u003cli\u003e4°C\u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003eUse \u003cstrong\u003ethe supernatant\u003c/strong\u003e for SDS-PAGE.\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T11:48:19.756Z","updated_at":"2018-12-24T11:48:19.756Z","last_modified_by_id":202,"protocol_id":3901},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5252,"name":"Heat the samples","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eHeat the samples at \u003cstrong\u003e100°C\u003c/strong\u003e for \u003cstrong\u003e3 minutes\u003c/strong\u003e in a heat block.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T11:47:05.158Z","updated_at":"2019-01-29T10:05:04.115Z","last_modified_by_id":202,"protocol_id":3901},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2386,"name":"Electrophoresis","due_date":null,"description":null,"x":66,"y":7,"my_module_group_id":1195,"created_at":"2018-12-24T12:27:59.858Z","updated_at":"2018-12-24T13:43:31.284Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":497,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":6048,"input_id":2387,"output_id":2386},{"id":6049,"input_id":2388,"output_id":2386}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3903,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2386,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-12-24T12:27:59.867Z","updated_at":"2019-01-29T10:05:49.860Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5254,"name":"Sample loading","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eRemove air bubbles and small pieces of gel from the wells and under the gel using a syringe.\u003cbr\u003eLoad prepared samples into wells and make sure not to overflow. Don't forget loading \u003cstrong\u003eprotein marker into the first lane\u003c/strong\u003e. Then cover the top and connect the anodes.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T12:31:41.933Z","updated_at":"2019-01-28T15:33:39.705Z","last_modified_by_id":202,"protocol_id":3903},"checklists":[],"step_comments":[],"step_assets":[{"id":2973,"step_id":5254,"asset_id":3624}],"assets":[{"id":3624,"created_at":"2019-01-28T15:33:28.689Z","updated_at":"2019-01-28T15:33:39.696Z","file_file_name":"SDS_page_electrophoresis.PNG","file_content_type":"image/png","file_file_size":64782,"file_updated_at":"2019-01-28T15:33:38.768Z","created_by_id":202,"last_modified_by_id":null,"estimated_size":71260,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]},{"step":{"id":5256,"name":"Remove the gel","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eRemove the gel assembly from the electrophoresis apparatus. Remove the gel from the glass plates using a spatula, and prepare for subsequent analysis.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T12:39:15.168Z","updated_at":"2018-12-24T12:39:15.168Z","last_modified_by_id":202,"protocol_id":3903},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5255,"name":"Electrophoresis","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eSet an appropriate voltage and run the electrophoresis when everything's done.\u003cbr\u003e\u003cbr\u003eAs for the \u003cstrong\u003etotal running time\u003c/strong\u003e, stop SDS-PAGE running when the downmost sign of the protein marker (if no visible sign, inquire the manufacturer) almost reaches the foot line of the glass plate. 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Place the membrane on a piece of plastic wrap, and add the reagent to the membrane. Allow it to stand for \u003cstrong\u003e1 minute\u003c/strong\u003e, and remove the reagent using a pipette. \u003cbr\u003eWrap the membrane in a piece of plastic wrap, remove any air bubbles, and place it under a chemiluminescence detection apparatus (e.g., CCD camera) for viewing.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T13:34:41.460Z","updated_at":"2019-01-29T10:07:43.690Z","last_modified_by_id":202,"protocol_id":3905},"checklists":[],"step_comments":[],"step_assets":[{"id":2976,"step_id":5265,"asset_id":3627}],"assets":[{"id":3627,"created_at":"2019-01-28T15:50:42.310Z","updated_at":"2019-01-29T10:07:43.634Z","file_file_name":"Detection.PNG","file_content_type":"image/png","file_file_size":10299,"file_updated_at":"2019-01-28T15:50:43.265Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":11328,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2387,"name":"Standard Coomassie Stain","due_date":null,"description":null,"x":99,"y":14,"my_module_group_id":1195,"created_at":"2018-12-24T12:42:30.757Z","updated_at":"2018-12-24T13:43:31.281Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":4,"experiment_id":497,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3904,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2387,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-12-24T12:42:30.765Z","updated_at":"2019-01-29T10:21:07.111Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5260,"name":"Destain","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cstrong\u003eDestain solution\u003c/strong\u003e: Add \u003cstrong\u003e500mL\u003c/strong\u003e of HPLC- grade methanol to \u003cstrong\u003e300 mL\u003c/strong\u003e of HPLC grade water. Add \u003cstrong\u003e100 mL\u003c/strong\u003e of reagent grade acetic acid and, after mixing, adjust the total volume to \u003cstrong\u003e1000mL\u003c/strong\u003e with water. The final concentrations are \u003cstrong\u003e50%\u003c/strong\u003e (v/v) methanol in water with \u003cstrong\u003e10%\u003c/strong\u003e (v/v) acetic acid. \u003cbr\u003e\u003cbr\u003eCover the gel with\u003cstrong\u003e ~250mL\u003c/strong\u003e of the destain solution and allow the gel to destain with gentle agitation. The destain solution should be changed several times, removing it at each change by aspiration. 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Add \u003cstrong\u003e100mL\u003c/strong\u003e of reagent grade acetic acid and adjust the total volume to \u003cstrong\u003e1000 mL\u003c/strong\u003e with HPLC grade water. The final concentrations are \u003cstrong\u003e50%\u003c/strong\u003e (v/v) methanol in water with \u003cstrong\u003e10%\u003c/strong\u003e (v/v) acetic acid. \u003cbr\u003e\u003cbr\u003eContinue to fix the proteins in the gel by incubating overnight at room temperature with gentle agitation. The gel should be covered during this process to avoid contamination and to prevent the evaporation of the solution. At the end of this time, remove the solution by aspiration.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T12:47:54.498Z","updated_at":"2019-01-29T10:09:33.373Z","last_modified_by_id":202,"protocol_id":3904},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5259,"name":"Comassie staining","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003e\u003cstrong\u003eComassie Stain:\u003c/strong\u003e Dissolve \u003cstrong\u003e0.4g\u003c/strong\u003e of Coomassie blue R350 in \u003cstrong\u003e200 mL\u003c/strong\u003e of \u003cstrong\u003e40%\u003c/strong\u003e (v/v) HPLC grade methanol in water with stirring as needed. Filter the solution to remove any insoluble material. Add \u003cstrong\u003e200mL\u003c/strong\u003e of \u003cstrong\u003e20%\u003c/strong\u003e (v/v) acetic acid in water. The final concentration is \u003cstrong\u003e0.1%\u003c/strong\u003e (w/v) Coomassie blue R350, \u003cstrong\u003e20%\u003c/strong\u003e (v/v) methanol, and \u003cstrong\u003e10%\u003c/strong\u003e (v/v) acetic acid.\u003cbr\u003e\u003cbr\u003eCover the gel with \u003cstrong\u003e400mL\u003c/strong\u003e of the Coomassie stain. Stain the gel at room temperature for \u003cstrong\u003e3 to 4 hours\u003c/strong\u003e with gentle agitation. The Coomassie stain is removed by aspiration after staining.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T12:49:39.311Z","updated_at":"2019-01-29T10:19:56.594Z","last_modified_by_id":202,"protocol_id":3904},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5261,"name":"Storage of gels","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cstrong\u003eStorage solution:\u003c/strong\u003e Add \u003cstrong\u003e25mL\u003c/strong\u003e of reagent grade acetic acid to \u003cstrong\u003e400mL\u003c/strong\u003e of HPLC grade water. After mixing, adjust the final volume to \u003cstrong\u003e500mL\u003c/strong\u003e with water. The final concentration of acetic acid is \u003cstrong\u003e5%\u003c/strong\u003e (v/v).\u003cbr\u003e\u003cbr\u003eEquilibrate the gel in the \u003cstrong\u003e500mL\u003c/strong\u003e of the storage solution for at least \u003cstrong\u003e1 hour\u003c/strong\u003e. The gel should return to its original dimensions during this process. Store the gel in the storage solution as needed. It might be convenient to carefully transfer the gel to a heat-sealable bag for longer-term storage.\u003c/body\u003e\u003c/html\u003e","position":4,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T12:52:54.562Z","updated_at":"2019-01-29T10:21:07.061Z","last_modified_by_id":202,"protocol_id":3904},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5257,"name":"Gel fixation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cstrong\u003eGel-fixing solution:\u003c/strong\u003e Add \u003cstrong\u003e500mL\u003c/strong\u003e of USP-grade \u003cstrong\u003e95% (v/v)\u003c/strong\u003e ethanol to \u003cstrong\u003e300 mL\u003c/strong\u003e of HPLC grade water. Add \u003cstrong\u003e100 mL\u003c/strong\u003e of reagent grade acetic acid and adjust the total volume to \u003cstrong\u003e1000 mL\u003c/strong\u003e with water. The final concentrations are \u003cstrong\u003e50%\u003c/strong\u003e (v/v) ethanol in water with \u003cstrong\u003e10%\u003c/strong\u003e (v/v) acetic acid.\u003cbr\u003e\u003cbr\u003eAfter electrophoresis, the gel is washed off the glass plates with 500 mL of the gel-fixing solution and soaked in that solution for \u003cstrong\u003e1 hour.\u003c/strong\u003e\u003cbr\u003e\u003cbr\u003eThe purpose of this step is to gently remove the gel from the plate and begin washing the SDS-containing gel buffers out of the gel. At the end of this time, remove the solution by aspiration.\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T12:45:54.303Z","updated_at":"2019-01-29T10:08:50.637Z","last_modified_by_id":202,"protocol_id":3904},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]}],"my_module_groups":[{"id":1195,"created_at":"2018-12-24T13:43:31.272Z","updated_at":"2018-12-24T13:43:31.272Z","created_by_id":202,"experiment_id":497}]}
\ No newline at end of file
+{"experiment":{"id":497,"name":"SDS-PAGE for Protein Characterization","description":"This experiment template will help you separate proteins based on their molecular weight. \r\nProteins are separated by electrophoresis through a gel matrix. Smaller proteins migrate faster due to less resistance from the gel matrix. Other influences on the rate of migration through the gel matrix include the structure and charge of the proteins. In SDS-PAGE, the use of sodium dodecyl sulfate (SDS, also known as sodium lauryl sulfate) and polyacrylamide gel largely eliminates the influence of the structure and charge, and proteins are separated solely based on polypeptide chain length.\r\nStaining with Coomassie blue dyes is commonly used to stain proteins and visualize them. 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Generally, to treat your unprepared sample, you can use sonicator, lysis buffer or both to sufficiently make your target protein released, and centrifuge to make supernatant and pellet separated.\u003cbr\u003e\u003cbr\u003e\u003cbr\u003eMix samples with loading buffer. Mix by flicking the tube.\u003cstrong\u003e\u003cbr\u003e\u003cbr\u003e5X Sample buffer (Loading buffer):\u003c/strong\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003e10%\u003c/strong\u003e w/v SDS\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003e10 mM\u003c/strong\u003e Dithiothreitol, or beta-mercapto-ethanol\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003e20 %\u003c/strong\u003e v/v Glycerol\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003e0.2 M\u003c/strong\u003e Tris-HCl; \u003cstrong\u003epH 6.8\u003c/strong\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003e0.05%\u003c/strong\u003e w/v Bromophenolblue\u003c/li\u003e\n\u003c/ul\u003e\n\u003cstrong\u003e\u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003c/strong\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T11:44:32.382Z","updated_at":"2019-01-29T10:04:52.137Z","last_modified_by_id":202,"protocol_id":3901},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5253,"name":"Centrifugation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cstrong\u003eCentrifuge:\u003c/strong\u003e\u003cbr\u003e\u003cbr\u003e\n\u003cul\u003e\n\u003cli\u003e15,000 rpm\u003c/li\u003e\n\u003cli\u003e1 minute\u003c/li\u003e\n\u003cli\u003e4°C\u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003eUse \u003cstrong\u003ethe supernatant\u003c/strong\u003e for SDS-PAGE.\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T11:48:19.756Z","updated_at":"2018-12-24T11:48:19.756Z","last_modified_by_id":202,"protocol_id":3901},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5252,"name":"Heat the samples","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eHeat the samples at \u003cstrong\u003e100°C\u003c/strong\u003e for \u003cstrong\u003e3 minutes\u003c/strong\u003e in a heat block.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T11:47:05.158Z","updated_at":"2019-01-29T10:05:04.115Z","last_modified_by_id":202,"protocol_id":3901},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2386,"name":"Electrophoresis","due_date":null,"description":null,"x":66,"y":7,"my_module_group_id":1195,"created_at":"2018-12-24T12:27:59.858Z","updated_at":"2018-12-24T13:43:31.284Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":497,"state":"uncompleted","completed_on":null},"outputs":[{"id":6048,"input_id":2387,"output_id":2386},{"id":6049,"input_id":2388,"output_id":2386}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3903,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2386,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-12-24T12:27:59.867Z","updated_at":"2019-01-29T10:05:49.860Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5254,"name":"Sample loading","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eRemove air bubbles and small pieces of gel from the wells and under the gel using a syringe.\u003cbr\u003eLoad prepared samples into wells and make sure not to overflow. Don't forget loading \u003cstrong\u003eprotein marker into the first lane\u003c/strong\u003e. Then cover the top and connect the anodes.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-24T12:31:41.933Z","updated_at":"2019-01-28T15:33:39.705Z","last_modified_by_id":202,"protocol_id":3903},"checklists":[],"step_comments":[],"step_assets":[{"id":2973,"step_id":5254,"asset_id":3624}],"assets":[{"id":3624,"created_at":"2019-01-28T15:33:28.689Z","updated_at":"2019-01-28T15:33:39.696Z","file_file_name":"SDS_page_electrophoresis.PNG","file_content_type":"image/png","file_file_size":64782,"file_updated_at":"2019-01-28T15:33:38.768Z","created_by_id":202,"last_modified_by_id":null,"estimated_size":71260,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]},{"step":{"id":5256,"name":"Remove the gel","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eRemove the gel assembly from the electrophoresis apparatus. 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\ No newline at end of file