protocolRandomDispensing1.yaml

# Run with:
#  npm run processor -- --progress -P 'C:\ProgramData\Tecan\EVOware\database\scripts\CR' --evoware testdata/bsse-mario/Carrier.cfg,testdata/bsse-mario/NewLayout_Feb2015.ewt,ourlab.mario.evoware config/bsse-mario.js protocolRandomDispensi ng1.yaml
roboliq: v1
description: |
  Random dispensing to check the volume model.

parameters:
  excitationWavelength:
    description: excitation wavelength to red absorbance
    value: 480nm

objects:
  plate1:
    type: Plate
    description: dye plate
    model: ourlab.model.plateModel_96_round_transparent_nunc
    location: ourlab.mario.site.P3
  dyeLightLabware:
    type: Plate
    description: trough for dye
    model: ourlab.model.troughModel_100ml
    location: ourlab.mario.site.R5
    contents: [Infinity l, dyeLight]
  dyeLight:
    type: Liquid
    description: dye with a low concentration
    wells: dyeLightLabware(C01 down F01)
  dyeDarkLabware:
    type: Plate
    description: trough for dye
    model: ourlab.model.troughModel_100ml
    location: ourlab.mario.site.R4
    contents: [Infinity l, dyeDark]
  dyeDark:
    type: Liquid
    description: dye with a high concentration
    wells: dyeDarkLabware(C01 down F01)
  waterLabware:
    type: Plate
    description: trough for water
    model: ourlab.model.troughModel_100ml
    location: ourlab.mario.site.R6
    contents: [Infinity l, water]
  water:
    type: Liquid
    description: liquid water
    wells: waterLabware(C01 down F01)

  design1:
    type: Design
    description: Random dispensing of volumes in a plate
    conditions:
      plate: plate1
      .case1*:
        - {wl: 0, wu: 0}
        # - {wl: 1, wu: 3}
        - {wl: 3, wu: 10}
        - {wl: 10, wu: 50}
        - {wl: 50, wu: 100}
      waterVolume=calculate:
        expression: 'bignumber(random(number(wl), number(wu)))'
        decimals: 1
        units: ul
      .case2*:
        - {dl: 0, du: 0}
        # - {dl: 1, du: 3}
        - {dl: 3, du: 10}
        - {dl: 10, du: 50}
        - {dl: 50, du: 100}
      dyeVolume=calculate:
        expression: 'bignumber(random(number(dl), number(du)))'
        decimals: 1
        units: ul
      dyeSource=calculate: '(dyeVolume < 20 ul) ? "dyeDark" : "dyeLight"'
      replicate*: 6
      well=allocateWells:
        rows: 8
        columns: 12
        order: shuffle
      .liquidClasses=:
        values:
          - firstLiquidClass: Roboliq_Water_Air_1000
            secondLiquidClass: Roboliq_Water_Air_1000
          - firstLiquidClass: Roboliq_Water_Air_1000
            secondLiquidClass: Roboliq_Water_Dry_1000
          - firstLiquidClass: Roboliq_Water_Dry_1000
            secondLiquidClass: Roboliq_Water_Air_1000
          - firstLiquidClass: Roboliq_Water_Dry_1000
            secondLiquidClass: Roboliq_Water_Wet_1000
        order: reshuffle
      firstPipetting=:
        values:
          - firstPipetting: waterFirst
          - firstPipetting: dyeFirst
        order: reshuffle
      syringe=:
        values: [1,2,3,4]
        order: repeat
      id=range: {}

steps:
  data: {source: design1}
  1:
    description: Read absorbance of empty wells
    command: absorbanceReader.measurePlate
    object: $plate
    program:
      excitationWavelength: $#excitationWavelength
    output:
      joinKey: well
      appendTo: measurements
      userValues:
        stage: empty
      units:
        totalVolume: ul
        dyeVolume: ul
        waterVolume: ul

  2:
    data: {where: 'firstPipetting=="waterFirst" and waterVolume > (0 ul)'}
    description: Pre-distribute water to wells that don't require dry-contact
    description: "`a: {{$firstPipetting}}`"
    command: pipetter.pipette
    program: $$firstLiquidClass
    sources: water
    destinationLabware: $plate
    destinations: $$well
    volumes: $$waterVolume
    syringes: $$syringe
    clean: light
    cleanBetween: none
  3:
    data: {where: 'firstPipetting=="waterFirst"'}
    description: Pre-distribute water to wells that don't require dry-contact
    command: pipetter.pipette
    program: $$secondLiquidClass
    sources: $$dyeSource
    destinationLabware: $plate
    destinations: $$well
    volumes: $$dyeVolume
    syringes: $$syringe
    clean: light
    cleanBetween: flush
  4:
    data: {where: 'firstPipetting=="dyeFirst"'}
    description: Pre-distribute water to wells that don't require dry-contact
    command: pipetter.pipette
    program: $$firstLiquidClass
    sources: $$dyeSource
    destinationLabware: $plate
    destinations: $$well
    volumes: $$dyeVolume
    syringes: $$syringe
    clean: light
    cleanBetween: flush
    cleanAfter: thorough
  5:
    data: {where: 'firstPipetting=="dyeFirst"'}
    description: Pre-distribute water to wells that don't require dry-contact
    command: pipetter.pipette
    program: $$secondLiquidClass
    sources: water
    destinationLabware: $plate
    destinations: $$well
    volumes: $$waterVolume
    syringes: $$syringe
    clean: light
    cleanBetween: none

  6:
    description: Read absorbance of wells after adding water and dye
    command: absorbanceReader.measurePlate
    object: $plate
    program:
      excitationWavelength: $#excitationWavelength
    output:
      joinKey: well
      appendTo: measurements
      units:
        totalVolume: ul
        dyeVolume: ul
        waterVolume: ul