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June 15, 2015 19:08
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Autodesk WetLabAccelerator omniprotocol testing - rs333 sequencing from buccal sample
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| { | |
| "metadata": { | |
| "id": "f9a628d3-8a70-4d0c-b564-ba408224c32a", | |
| "date": "1434393769046", | |
| "type": "protocol", | |
| "author": {}, | |
| "tags": [ | |
| "sequence", | |
| "snp", | |
| "pcr", | |
| "genomic extraction" | |
| ], | |
| "db": {}, | |
| "version": "1.0.0", | |
| "name": "buccal genomic extraction and sanger sequence rs333" | |
| }, | |
| "parameters": [ | |
| { | |
| "id": "eace8a5f-1d5c-450c-a94b-15dfb937bc4a", | |
| "name": "quickextract", | |
| "type": "container", | |
| "value": { | |
| "isNew": true, | |
| "color": "#00FF00", | |
| "type": "micro-2.0", | |
| "storage": "cold_20" | |
| } | |
| }, | |
| { | |
| "id": "85e9e1aa-3352-43f0-b3b3-6c3c5640de5f", | |
| "name": "mastermix", | |
| "type": "container", | |
| "value": { | |
| "isNew": true, | |
| "color": "#FFA6C9", | |
| "type": "micro-2.0", | |
| "storage": "cold_20" | |
| } | |
| }, | |
| { | |
| "id": "321d64ca-e93f-4eb3-928b-28d2314aca58", | |
| "name": "rs333 primers", | |
| "type": "container", | |
| "value": { | |
| "isNew": true, | |
| "color": "#c5535b", | |
| "type": "micro-2.0", | |
| "storage": "cold_20" | |
| } | |
| }, | |
| { | |
| "id": "4520012f-46c6-4b52-b3c5-363902be3c58", | |
| "name": "thermocycle plate", | |
| "type": "container", | |
| "value": { | |
| "isNew": true, | |
| "color": "#EC0704", | |
| "type": "96-pcr", | |
| "storage": "ambient" | |
| } | |
| }, | |
| { | |
| "id": "fdcd29ac-afd2-4a37-8dc0-f001136c9952", | |
| "name": "resource 1", | |
| "type": "resource", | |
| "category": "custom", | |
| "canParameterize": true, | |
| "description": "Resource from the transcriptic catalog" | |
| }, | |
| { | |
| "id": "165123db-6290-4520-bb3d-394be9941100", | |
| "name": "container 5", | |
| "type": "container", | |
| "value": { | |
| "isNew": true, | |
| "color": "#FFA6C9", | |
| "type": "96-pcr" | |
| } | |
| } | |
| ], | |
| "groups": [ | |
| { | |
| "name": "", | |
| "inputs": {}, | |
| "metadata": { | |
| "description": "" | |
| }, | |
| "loop": 1, | |
| "steps": [ | |
| { | |
| "operation": "provision", | |
| "requirements": {}, | |
| "transforms": [ | |
| { | |
| "wells": "wells" | |
| } | |
| ], | |
| "fields": [ | |
| { | |
| "name": "wells", | |
| "type": "aliquot++", | |
| "value": { | |
| "container": "4520012f-46c6-4b52-b3c5-363902be3c58", | |
| "wells": [ | |
| "A1", | |
| "A2" | |
| ] | |
| }, | |
| "transpose": 0 | |
| }, | |
| { | |
| "name": "volume", | |
| "type": "volume", | |
| "default": { | |
| "value": 50, | |
| "unit": "microliter" | |
| } | |
| }, | |
| { | |
| "name": "resource", | |
| "type": "resource" | |
| } | |
| ], | |
| "op_description": "Dispense a Transcriptic catalog resource into specified wells", | |
| "description": "plate" | |
| } | |
| ] | |
| }, | |
| { | |
| "name": "", | |
| "inputs": {}, | |
| "metadata": { | |
| "description": "" | |
| }, | |
| "loop": 1, | |
| "steps": [ | |
| { | |
| "operation": "transfer", | |
| "requirements": {}, | |
| "transforms": [ | |
| { | |
| "wells": "to" | |
| }, | |
| { | |
| "wells": "from" | |
| } | |
| ], | |
| "fields": [ | |
| { | |
| "name": "volume", | |
| "type": "volume", | |
| "value": { | |
| "unit": "microliter", | |
| "value": 50 | |
| } | |
| }, | |
| { | |
| "name": "from", | |
| "type": "aliquot++", | |
| "value": { | |
| "container": "eace8a5f-1d5c-450c-a94b-15dfb937bc4a" | |
| } | |
| }, | |
| { | |
| "name": "to", | |
| "type": "aliquot++", | |
| "value": { | |
| "container": "4520012f-46c6-4b52-b3c5-363902be3c58" | |
| } | |
| }, | |
| { | |
| "name": "dispense_speed", | |
| "type": "speed", | |
| "optional": true, | |
| "default": { | |
| "value": 100, | |
| "unit": "microliter/second" | |
| } | |
| }, | |
| { | |
| "name": "aspirate_speed", | |
| "type": "speed", | |
| "optional": true, | |
| "default": { | |
| "value": 100, | |
| "unit": "microliter/second" | |
| } | |
| }, | |
| { | |
| "name": "mix_before", | |
| "type": "mixwrap", | |
| "optional": true, | |
| "default": { | |
| "volume": { | |
| "value": 10, | |
| "unit": "microliter" | |
| }, | |
| "repetitions": 5, | |
| "speed": { | |
| "value": 100, | |
| "unit": "microliter/second" | |
| } | |
| } | |
| }, | |
| { | |
| "name": "mix_after", | |
| "type": "mixwrap", | |
| "optional": true, | |
| "default": { | |
| "volume": { | |
| "value": 10, | |
| "unit": "microliter" | |
| }, | |
| "repetitions": 5, | |
| "speed": { | |
| "value": 100, | |
| "unit": "microliter/second" | |
| } | |
| } | |
| }, | |
| { | |
| "name": "one_tip", | |
| "type": "boolean", | |
| "optional": true, | |
| "default": false, | |
| "value": true | |
| } | |
| ], | |
| "op_description": "Transfer contents from one container to another, either 1-to-n or n-to-n", | |
| "description": "quickextract to plate" | |
| } | |
| ] | |
| }, | |
| { | |
| "name": "", | |
| "inputs": {}, | |
| "metadata": { | |
| "description": "" | |
| }, | |
| "loop": 1, | |
| "steps": [ | |
| { | |
| "operation": "thermocycle", | |
| "requirements": {}, | |
| "transforms": [ | |
| { | |
| "container": "object" | |
| } | |
| ], | |
| "fields": [ | |
| { | |
| "name": "dataref", | |
| "type": "string", | |
| "optional": true, | |
| "default": "thermocycle_${unfolded}" | |
| }, | |
| { | |
| "name": "object", | |
| "type": "container", | |
| "value": { | |
| "container": "4520012f-46c6-4b52-b3c5-363902be3c58" | |
| } | |
| }, | |
| { | |
| "name": "volume", | |
| "type": "volume", | |
| "default": { | |
| "value": 10, | |
| "unit": "microliter" | |
| } | |
| }, | |
| { | |
| "name": "groups", | |
| "type": "thermocycleGroups", | |
| "value": [ | |
| { | |
| "type": "thermocycleGroup", | |
| "value": { | |
| "cycles": 1, | |
| "steps": [ | |
| { | |
| "temperature": { | |
| "unit": "celsius", | |
| "value": 35 | |
| }, | |
| "duration": { | |
| "unit": "minute", | |
| "value": 3 | |
| } | |
| }, | |
| { | |
| "temperature": { | |
| "unit": "celsius", | |
| "value": 65 | |
| }, | |
| "duration": { | |
| "unit": "minute", | |
| "value": 3 | |
| } | |
| } | |
| ] | |
| } | |
| } | |
| ] | |
| }, | |
| { | |
| "name": "dyes", | |
| "type": "thermocycleDyes", | |
| "optional": true, | |
| "value": [ | |
| { | |
| "color": "#dd22dd" | |
| }, | |
| { | |
| "color": "#2222dd" | |
| }, | |
| { | |
| "color": "#22dd22" | |
| }, | |
| { | |
| "color": "#dddd22" | |
| }, | |
| { | |
| "color": "#dd2222" | |
| } | |
| ] | |
| }, | |
| { | |
| "name": "melting", | |
| "type": "thermocycleMelting", | |
| "optional": true | |
| } | |
| ], | |
| "op_description": "Thermocycle a container, putting through several temperature cycles, e.g. to run a PCR", | |
| "description": "extract buccal cell genome" | |
| } | |
| ] | |
| }, | |
| { | |
| "name": "", | |
| "inputs": {}, | |
| "metadata": { | |
| "description": "" | |
| }, | |
| "loop": 1, | |
| "steps": [ | |
| { | |
| "operation": "transfer", | |
| "requirements": {}, | |
| "transforms": [ | |
| { | |
| "wells": "to" | |
| }, | |
| { | |
| "wells": "from" | |
| } | |
| ], | |
| "fields": [ | |
| { | |
| "name": "volume", | |
| "type": "volume", | |
| "value": { | |
| "unit": "microliter", | |
| "value": 10 | |
| } | |
| }, | |
| { | |
| "name": "from", | |
| "type": "aliquot++", | |
| "value": { | |
| "container": "85e9e1aa-3352-43f0-b3b3-6c3c5640de5f" | |
| } | |
| }, | |
| { | |
| "name": "to", | |
| "type": "aliquot++", | |
| "value": { | |
| "container": "4520012f-46c6-4b52-b3c5-363902be3c58" | |
| } | |
| }, | |
| { | |
| "name": "dispense_speed", | |
| "type": "speed", | |
| "optional": true, | |
| "default": { | |
| "value": 100, | |
| "unit": "microliter/second" | |
| } | |
| }, | |
| { | |
| "name": "aspirate_speed", | |
| "type": "speed", | |
| "optional": true, | |
| "default": { | |
| "value": 100, | |
| "unit": "microliter/second" | |
| } | |
| }, | |
| { | |
| "name": "mix_before", | |
| "type": "mixwrap", | |
| "optional": true, | |
| "default": { | |
| "volume": { | |
| "value": 10, | |
| "unit": "microliter" | |
| }, | |
| "repetitions": 5, | |
| "speed": { | |
| "value": 100, | |
| "unit": "microliter/second" | |
| } | |
| } | |
| }, | |
| { | |
| "name": "mix_after", | |
| "type": "mixwrap", | |
| "optional": true, | |
| "default": { | |
| "volume": { | |
| "value": 10, | |
| "unit": "microliter" | |
| }, | |
| "repetitions": 5, | |
| "speed": { | |
| "value": 100, | |
| "unit": "microliter/second" | |
| } | |
| } | |
| }, | |
| { | |
| "name": "one_tip", | |
| "type": "boolean", | |
| "optional": true, | |
| "default": false | |
| } | |
| ], | |
| "op_description": "Transfer contents from one container to another, either 1-to-n or n-to-n", | |
| "description": "mastermix to plate" | |
| } | |
| ] | |
| }, | |
| { | |
| "name": "", | |
| "inputs": {}, | |
| "metadata": { | |
| "description": "" | |
| }, | |
| "loop": 1, | |
| "steps": [ | |
| { | |
| "operation": "transfer", | |
| "requirements": {}, | |
| "transforms": [ | |
| { | |
| "wells": "to" | |
| }, | |
| { | |
| "wells": "from" | |
| } | |
| ], | |
| "fields": [ | |
| { | |
| "name": "volume", | |
| "type": "volume", | |
| "value": { | |
| "unit": "microliter", | |
| "value": 1 | |
| } | |
| }, | |
| { | |
| "name": "from", | |
| "type": "aliquot++", | |
| "value": { | |
| "container": "321d64ca-e93f-4eb3-928b-28d2314aca58" | |
| } | |
| }, | |
| { | |
| "name": "to", | |
| "type": "aliquot++", | |
| "value": { | |
| "container": "4520012f-46c6-4b52-b3c5-363902be3c58" | |
| } | |
| }, | |
| { | |
| "name": "dispense_speed", | |
| "type": "speed", | |
| "optional": true, | |
| "default": { | |
| "value": 100, | |
| "unit": "microliter/second" | |
| } | |
| }, | |
| { | |
| "name": "aspirate_speed", | |
| "type": "speed", | |
| "optional": true, | |
| "default": { | |
| "value": 100, | |
| "unit": "microliter/second" | |
| } | |
| }, | |
| { | |
| "name": "mix_before", | |
| "type": "mixwrap", | |
| "optional": true, | |
| "default": { | |
| "volume": { | |
| "value": 10, | |
| "unit": "microliter" | |
| }, | |
| "repetitions": 5, | |
| "speed": { | |
| "value": 100, | |
| "unit": "microliter/second" | |
| } | |
| } | |
| }, | |
| { | |
| "name": "mix_after", | |
| "type": "mixwrap", | |
| "optional": true, | |
| "default": { | |
| "volume": { | |
| "value": 10, | |
| "unit": "microliter" | |
| }, | |
| "repetitions": 5, | |
| "speed": { | |
| "value": 100, | |
| "unit": "microliter/second" | |
| } | |
| }, | |
| "value": { | |
| "volume": { | |
| "unit": "microliter", | |
| "value": 5 | |
| }, | |
| "speed": { | |
| "unit": "microliter/second", | |
| "value": 20 | |
| }, | |
| "repetitions": 4 | |
| } | |
| }, | |
| { | |
| "name": "one_tip", | |
| "type": "boolean", | |
| "optional": true, | |
| "default": false | |
| } | |
| ], | |
| "op_description": "Transfer contents from one container to another, either 1-to-n or n-to-n", | |
| "description": "primers to mastermix" | |
| } | |
| ] | |
| } | |
| ] | |
| } |
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