Commands & Types

This page lists the commands and types available in Roboliq protocols. Note that:

Types begin with an uppercase letter, whereas command and namespaces begin with a lowercase letter.
A namespace group related commands and types, such as the pipetter namespace contains items relevant to pipetting. Normally the namespaces will be nouns by convention.
As a matter of convention, all commands belong to a namespace. Normally commands will start with a verb. For example, pipetter.mix is a command to use the pipetter to mix well contents.
Commands and types that begin with an underscore, such as pipetter._mix, are low-level commands. Normally you will not need to use them and can use the other higher-level commands instead.

Basic types

Duration

Duration specified as a string. Parsing is handled by mathjs. Valid units are: second (s, secs, seconds), minute (mins, minutes), hour (h, hr, hrs, hours), day (days), week (weeks), month (months), year (years), decade (decades), century (centuries), millennium (millennia)

Example:

1s = 1 second
3 minutes = 3 minutes
4 h = 4 hours

SiteOrStay

When a command is performed on a plate, sometimes the plate first needs to be moved to the proper equipment (e.g. you might put a plate onto a shaker in order to shake it). By default, the plate will be moved back to its prior location after the command is finished. Such commands have a destinationAfter property with type SiteOrStay which can be used to override this behavior. Either you can specify different Site where the plate should be moved to after the command, or you can specify "stay" to leave the plate there.

Object types

scale

The scale commands specify actions using weight scale equipment.

Scale

Scale equipment.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Scale	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item

scale.ScaleProgram

Program for scale.

scale.weigh

Weigh an object.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program	scale.ScaleProgram	Program for shaking
object	Plate	Plate identifier	required
site	Site	Site identifier on scale
destinationAfter	SiteOrStay	Site to move the plate to after this command

absorbanceReader

The absorbanceReader commands specify actions using equipment for absorbance readouts.

Reader

Reader equipment.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Reader	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item

absorbanceReader.measurePlate

Measure the absorbance of a plate.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program		Program parameters
shakerProgramBefore		Program for shaker.
excitationWavelength	Length	Excitation wavelength
excitationBandwidth	Length	Excitation bandwidth
excitationWavelengthMin	Length	Minimum excitation wavelength for a scan
excitationWavelengthMax	Length	Maximum excitation wavelength for a scan
excitationWavelengthStep	Length	Size of steps for a scan
wells	Wells	Array of wells to read
wellDesignFactor	string	Name of design column that indicates which wells to measure (deprecated, use `output.joinKey`)
userValues	object	User-specificed values that should be included in the output table (deprecated, use `output.userValues`)
programFileTemplate	string	Program template; well information will be substituted into the template automatically.
programFile	string	Program filename
programData		Program data
outputFile	string	Filename for output (deprecated, use `output.writeTo`)
outputDataset	string	Name of dataset to which the measurements values will be appended. (deprecated, use `output.appendTo`)
output		Output definition for where and how to save the measurements
joinKey	string	The key used to left-join the measurement values with the current DATA
writeTo	string	Filename to write measurements to as JSON
appendTo	string	Filename to append measurements to as newline-delimited JSON
userValues	object	User-specificed values that should be included in the output table
simulated	string	An expression to evaluate with mathjs
units		Map of factor names to unit type; converts the factor values to plain numbers in the given units.
object	Plate	Plate identifier	required
site	Site	Site identifier in reader
destinationAfter	SiteOrStay	Site to move the plate to after measurement

centrifuge

The centrifuge commands specify actions using centrifuge equipment.

Centrifuge

Centrifuge equipment.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Centrifuge	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item
sitesInternal	array		required

Example:

centrifuge:
    type: Centrifuge
    sitesInternal: ["ourlab.mario.site.CENTRIFUGE_1", "ourlab.mario.site.CENTRIFUGE_2", "ourlab.mario.site.CENTRIFUGE_3", "ourlab.mario.site.CENTRIFUGE_4"]

centrifuge.centrifuge2

Centrifuge two plates.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program		Program for centrifuging	required
object1	Plate	Plate identifier 1	required
object2	Plate	Plate identifier 2	required
site1	Site	Location identifier for the centrifugation site of object1
site2	Site	Location identifier for the centrifugation site of object2
destinationAfter1	SiteOrStay	Location identifier for where object1 should be placed after centrifugation
destinationAfter2	SiteOrStay	Location identifier for where object2 should be placed after centrifugation

Example:

This will centrifuge 2 plates at 3000rpm for 2 minutes at 25°C:

{
  "command": "centrifuge.centrifuge2",
  "object1": "plate1",
  "object2": "plate2",
  "program": {
    "rpm": 3000,
    "duration": "2 minutes",
    "temperature": "25 degC"
  }
}

centrifuge.insertPlates2

Insert up to two plates into the centrifuge.

Properties:

Name	Type	Description
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
object1	Plate	Plate identifier 1
object2	Plate	Plate identifier 2
site1	Site	Location identifier for the centrifugation site of object1
site2	Site	Location identifier for the centrifugation site of object2

Example:

This will insert two plates into the centrifuge:

{
  "command": "centrifuge.insertPlates2",
  "object1": "plate1",
  "object2": "plate2",
}

equipment

The equipment commands specify generic actions such as 'run' and 'open' that may apply to various types of equipment.

equipment._run

Run the given equipment.

This is a generic command, and any addition parameters may be passed that are required by the target equipment.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required

equipment.open

Open the given equipment.

This is a generic command that expands to a sub-command named equipment.open|${agent}|${equipment}. That command should be defined in your configuration for your lab.

The handler should return effects indicating that the equipment is open.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required

equipment.openSite

Open an equipment site. This command assumes that only one equipment site can be open at a time.

This is a generic command that expands to a sub-command named equipment.openSite|${agent}|${equipment}. That command should be defined in your configuration for your lab.

The handler should return effects indicating that the equipment is open, the given site is open, and all other equipment sites are closed.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required
site	Site	Site identifier	required

equipment.close

Close the given equipment.

This is a generic command that expands to a sub-command named equipment.close|${agent}|${equipment}. That command should be defined in your lab configuration.

The handler should return effects indicating the the equipment is closed and all of its sites are closed.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required

equipment.start

Start the given equipment.

This is a generic command that expands to a sub-command named equipment.start|${agent}|${equipment}. That command should be defined in your configuration for your lab. Any addition parameters may be passed that are required by the target equipment.

The handler returns effects indicating that the equipment is running.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required

equipment.stop

Stop the given equipment.

This is a generic command that expands to a sub-command named equipment.stop|${agent}|${equipment}. That command should be defined in your configuration for your lab. Any addition parameters may be passed that are required by the target equipment.

The handler returns effects indicating that the equipment is not running.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required

incubator

The incubator commands specify actions using incubator equipment.

Incubator

Incubator equipment.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Incubator	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item
sitesInternal	array		required

Example:

"incubator": {
  "type": "Incubator",
  "sitesInternal": ["ourlab.luigi.site.BOX_1", "ourlab.luigi.site.BOX_2", "ourlab.luigi.site.BOX_3", "ourlab.luigi.site.BOX_4", "ourlab.luigi.site.BOX_5", "ourlab.luigi.site.BOX_6", "ourlab.luigi.site.BOX_7", "ourlab.luigi.site.BOX_8"],
}

incubator.incubatePlates

Incubate the given plates.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program		Program for incubation	required
plates	array	List of plates to incubate	required
sites	array	Internal sites to put the plates on
destinationAfters	array	Location identifier for where the plates should be placed after incubation

Example:

This will incubate 2 plates at 300rpm for 2 minutes at 25°C:

{
  "command": "incubator.incubatePlates",
  "plates": ["plate1", "plate2"],
  "program": {
    "rpm": 300,
    "duration": "2 minutes",
    "temperature": "25 degC"
  }
}

incubator.insertPlates

Insert up to two plates into the incubator.

Properties:

Name	Type	Description
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
plates	array	List of plates to incubate
sites	array	Internal sites to put the plates on

Example:

This will insert two plates into the incubator:

{
  "command": "incubator.insertPlates",
  "plates": ["plate1", "plate2"]
}

incubator.run

Run the incubator with the given program.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program	object	Program for shaking and incubating	required
rpm	number
duration	Duration
temperature	Temperature
plates	array	List of plates to incubate	required
sites	array	Internal sites to put the plates on
destinationAfters	array	Location identifier for where the plates should be placed after incubation

Example:

This will incubate 2 plates at 300rpm for 2 minutes at 25°C:

{
  "command": "incubator.incubatePlates",
  "plates": ["plate1", "plate2"],
  "program": {
    "rpm": 300,
    "duration": "2 minutes",
    "temperature": "25 degC"
  }
}

pipetter

The pipetter commands specify actions using pipetting equipment.

Pipetter

Pipetting equipment.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Pipetter	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item

Syringe

Pipetting syringe.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Syringe	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item
tipModel	string	Tip model identifier for the tip currently on the syringe
tipModelPermanent	string	Tip model identifier if this syringe has a permanent tip
contaminants	array	List of contaminants the syringe has had contact with
contents	array	Current contents of the syringe
cleaned	string	Last cleaning intensity

pipetter._MixSpec

Parameters for mixing in higher-level commands like pipetter._PipetteItem.

Properties:

Name	Type	Description	Required
count	integer	Number of times to aspirate and re-dispense	required
volume	Volume	Amount to aspirate, either as a fraction or absolute volume	required

pipetter._AspirateItem

Parameters for pipette items.

Properties:

Name	Type	Description	Required
syringe	number,nameOf Syringe	Syringe identifier	required
source	Well	Source specifier	required
volume	Volume	Volume	required

pipetter._DispenseItem

Parameters for pipette items.

Properties:

Name	Type	Description	Required
syringe	number,nameOf Syringe	Syringe identifier	required
destination	Well	Destination specifier	required
volume	Volume	Volume	required

pipetter._MeasureVolumeItem

Parameters for low-level pipetter._measureVolume items.

Properties:

Name	Type	Description	Required
syringe	number,nameOf Syringe	Syringe identifier	required
well	Well	Well specifier	required

pipetter.MeasureVolumeItem

Parameters for pipetter.measureVolume items.

Properties:

Name	Type	Description
syringe	number,nameOf Syringe	Syringe identifier
well	Well	Well specifier
cleanAfter	pipetter.CleaningIntensity	intensity of cleaning required after this item.

pipetter._MixItem

Parameters for mixing with pipetter.

Properties:

Name	Type	Description	Required
syringe	number,nameOf Syringe	Syringe identifier	required
well	Well	Well to mix	required
count	integer	Number of times to aspirate and re-dispense
volume	Volume	Volume
program	string	Program identifier

pipetter.CleaningIntensity

Intensity of cleaning.

The enum lists the intensities in increase order.

pipetter._PipetteItem

Parameters for low-level pipette items.

Properties:

Name	Type	Description	Required
syringe	number,nameOf Syringe	Syringe identifier	required
source	Well	Source specifier
destination	Well	Destination specifier
volume	Volume	Volume	required
sourceMixing	pipetter._MixSpec	Parameters for mixing the source prior to aspiration
destinationMixing	pipetter._MixSpec	Parameters for mixing the destination after dispense
tipModel	string	Tip model identifier, in order to use a specific tip model

pipetter.PipetteItem

Parameters for pipette items.

Properties:

Name	Type	Description
syringe	number,nameOf Syringe	Syringe identifier
source	Source	Source specifier
destination	Well	Destination specifier
volume	Volume	Volume
volumeCalibrated	object	Calculate a calibrated volume
volumeTotal	Volume	Volume that the well should be brought up to.
program	string	Program identifier
layer		A layer identifier for hinting that to items in the same layer should be grouped together, even if they aren't in adjacent in the items list.
cleanAfter	pipetter.CleaningIntensity	intensity of cleaning required after this item.
sourceMixing	boolean,pipetter.MixSpec	Parameters for mixing the source prior to aspiration
destinationMixing	boolean,pipetter.MixSpec	Parameters for mixing the destination after dispense

pipetter._PunctureItem

Parameters for low-level puncture items.

Properties:

Name	Type	Description	Required
syringe	number,nameOf Syringe	Syringe identifier	required
well	Well	Well specifier	required
distance	Length	Distance for puncturing	required

pipetter.PunctureItem

Parameters for puncture items.

Properties:

Name	Type	Description
syringe	number,nameOf Syringe	Syringe identifier
well	Well	Well specifier
distance	Length	Distance for puncturing
cleanAfter	pipetter.CleaningIntensity	intensity of cleaning required after this item.

pipetter.DilutionItem

Parameters for a dilution series.

Properties:

Name	Type	Description	Required
syringe	number,Syringe	Syringe identifier
source	Source	Source specifier
destinations	Wells	Destination wells	required
volume	Volume	Volume

pipetter.MixItem

Parameters for mixing with pipetter.

Properties:

Name	Type	Description
syringe	number,nameOf Syringe	Syringe identifier
well	Well	Well to mix
count	integer	Number of times to aspirate and re-dispense
amount	Volume,number	Amount to aspirate, either as a fraction or absolute volume
program	string	Program identifier

pipetter.MixSpec

Parameters for mixing (used in higher-level commands like pipetter.pipette and pipetter.pipetteDilutionSeries).

Properties:

Name	Type	Description
count	integer	Number of times to aspirate and re-dispense
amount	Volume,number	Amount to aspirate, either as a fraction or absolute volume
program	string	Program identifier

pipetter._aspirate

Aspirate liquids from sources into syringes.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required
program	string	Program identifier	required
items	array	Data about what should be aspirated from where

pipetter._dispense

Dispense liquids from sryinges into destinations.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required
program	string	Program identifier	required
items	array	Data about what should be dispensed where

pipetter._measureVolume

Measure well volume using pipetter tips.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required
program	string	Program identifier
items	array	List of parameters for individual wells	required
output		Output definition for where and how to save the measurements
joinKey	string	The key used to left-join the measurement values with the current DATA
writeTo	string	Filename to write measured to as JSON
appendTo	string	Filename to append measured to as newline-delimited JSON

pipetter._mix

Mix liquids by aspirating and re-dispensing.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required
program	string	Program identifier	required
itemDefaults		Default values for items
count	integer	Number of times to aspirate and re-dispense
volume	Volume	Volume
items	array	Data about mixing

pipetter._pipette

Pipette liquids from sources to destinations.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required
program	string	Program identifier	required
sourceProgram	string	Program identifier for aspirating from source, if it should differ from 'program'
items	array	Data about what should be pipetted where
sourceMixing	pipetter._MixSpec	Parameters for mixing the source prior to aspiration
destinationMixing	pipetter._MixSpec	Parameters for mixing the destination after dispense

pipetter._punctureSeal

Puncture the seal on a plate using pipetter tips.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required
items	array	List of parameters for individual punctures	required

pipetter._washTips

Clean the pipetter tips by washing.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required
program	name,object	Program identifier	required
syringes	array	List of syringe identifiers	required
intensity	pipetter.CleaningIntensity	Intensity of the cleaning	required

pipetter.cleanTips

Clean the pipetter tips.

Properties:

Name	Type	Description
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program	string	Program identifier
items	array	List of which syringes to clean at which intensity
syringes	array	Optional list of syringes to serve as default for missing syringes in items list
intensity	pipetter.CleaningIntensity	Optional intensity to serve as default intensity for missing intensities in items list

pipetter.measureVolume

Measure well volume using pipetter tips.

Properties:

Name	Type	Description
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program	string	Program identifier
items	array	List of parameters for individual wells to measure
wellLabware	Plate	Labware for wells
wells	Wells	Specifier for well(s) to measure, if missing from items
syringes	array	Specifier for syringe(s) to use, if missing from items
clean	string	Default value for cleaning intensity (see cleanBegin, cleanBetween, cleanEnd)
cleanBegin	string	intensity of cleaning before the first puncture.
cleanBetween	string	Intensity of cleaning between wells.
cleanEnd	string	Intensity of cleaning after the last puncture.
tipModel	string	Tip model identifier, in order to use a specific tip model
output		Output definition for where and how to save the measurements
joinKey	string	The key used to left-join the measurement values with the current DATA
appendTo	string	Filename to append measured to as newline-delimited JSON
userValues		Map of user-defined key-values to include in the output

pipetter.mix

Mix well contents by aspirating and re-dispensing.

Properties:

Name	Type	Description
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program	string	Program identifier
items	array	Data about which wells to mix and how to mix them
wellLabware	Plate	Labware for wells
wells	Wells	Specifier for well(s) to mix, if missing from items
counts	integer	Number of times to aspirate, if missing from items
amounts	Volume,number	Amount to aspirate, either as a fraction or absolute volume, if missing from items
syringes	array	Specifier for syringe(s) to use, if missing from items
clean	string	Default value for cleaning intensity (see cleanBegin, cleanBetween, cleanBetweenSameSource, cleanEnd)
cleanBegin	string	intensity of first cleaning at beginning of pipetting, before first aspiration.
cleanBetween	string	Intensity of cleaning between different liquids.
cleanBetweenSameSource	string	Intensity of cleaning between transfers of the same liquid.
cleanEnd	string	Intensity of cleaning after the last dispense.

pipetter.pipette

Pipette liquids from sources to destinations.

Properties:

Name	Type	Description
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program	array,string	Program identifier
sourceProgram	string	Program identifier for aspirating from source, if it should differ from 'program'
items	array	Data about what should be pipetted where
sourceLabware	Plate	Labware for source wells
destinationLabware	Plate	Labware for source wells
sources	Sources	Specifier for source(s) to aspirate from, if missing from items
destinations	Wells	Specifier for destination(s) to despense to, if missing from items
volumes	Volumes	Volume(s) to pipette, if missing from items
syringes	array	Specifier for syringe(s) to use, if missing from items
clean	string	Default value for cleaning intensity (see cleanBegin, cleanBetween, cleanBetweenSameSource, cleanEnd)
cleanBegin	string	intensity of first cleaning at beginning of pipetting, before first aspiration.
cleanBetween	string	Intensity of cleaning between different liquids.
cleanBetweenSameSource	string	Intensity of cleaning between transfers of the same liquid.
cleanEnd	string	Intensity of cleaning after the last dispense.
sourceMixing	boolean,pipetter.MixSpec	Parameters for mixing the source wells with pipetter before aspirating
destinationMixing	boolean,pipetter.MixSpec	Parameters for mixing the destination after dispense
tipModel	string	Tip model identifier, in order to use a specific tip model
calibrators	object	A map from calibrator names to calibrator data (DOCUMENTAITON REQUIRED)

pipetter.pipetteDilutionSeries

Pipette a dilution series.

First the diluent is distributed to the destination wells (if diluent is specified). Then the source is transfered to the first destination well of each item (if source is specified -- otherwise the first destination well is assumed to be already prepared). Then aliquots are serially transfered from the first destination well to the next, and so on for each item. In general, mixing should be performed after each dilution dispense, and perhaps also before the first aspriation -- this can be specified how ???

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program	string	Program identifier
dilutionFactor	number	Dilution factor by which each subsequent well is diluted
dilutionMethod	string	How to dilute -- `begin`: distribute diluent to destination wells first (default); `before`: add diluent right before transfering aliquot; `after`: add diluent right after transfering aliquot; `source`: dilute the well that the aliquot will be extracted from. One of: begin,before,after,source
lastWellHandling	string	How to handle the last well in a series One of: none,diluteOnly,diluteAndExtract
items	array	Array of dilution items	required
diluent	Source	Diluent to be used in dilution
sourceLabware	Plate	Labware for source wells
destinationLabware	Plate	Labware for source wells
volume	Volume	Final volume of dilution wells (with the possible exception of the last well, see parameter `lastWellHandling`)
cleanBegin	string	Intensity of first cleaning at beginning of pipetting, before first aspiration.
cleanEnd	string	Intensity of cleaning after the last dispense.
sourceParams		Extra parameters for pipetting the source
diluentParams		Extra parameters for pipetting the diluent
dilutionParams		Extra parameters for pipetting the diluted aliquots

pipetter.pipetteMixtures

Pipette the given mixtures into the given destinations.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program	string	Program identifier
mixtures	array	Array of arrays, where each sub-array is a list of components to be mixed into a destination well	required
sourceLabware	Plate	Labware for source wells
destinationLabware	Plate	Labware for source wells
destinations	Wells	Destination specifier
order	array	Order in which to pipette the mixtures. Defaults to the order given in the mixtures array.
clean	string	Default value for cleaning intensity (see cleanBegin, cleanBetween, cleanBetweenSameSource, cleanEnd)
cleanBegin	string	intensity of first cleaning at beginning of pipetting, before first aspiration.
cleanBetween	string	Intensity of cleaning between different liquids.
cleanBetweenSameSource	string	Intensity of cleaning between transfers of the same liquid.
cleanEnd	string	Intensity of cleaning after the last dispense.

pipetter.punctureSeal

Puncture the seal on a plate using pipetter tips.

Properties:

Name	Type	Description
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
items	array	List of parameters for individual punctures
wellLabware	Plate	Labware for wells
wells	Wells	Specifier for well(s) to puncture, if missing from items
syringes	array	Specifier for syringe(s) to use, if missing from items
distances	Length,array	Distance for puncturing
clean	string	Default value for cleaning intensity (see cleanBegin, cleanBetween, cleanEnd)
cleanBegin	string	intensity of cleaning before the first puncture.
cleanBetween	string	Intensity of cleaning between wells.
cleanEnd	string	Intensity of cleaning after the last puncture.
tipModel	string	Tip model identifier, in order to use a specific tip model

fluorescenceReader

The fluorescenceReader commands specify actions using equipment for fluorescence readouts.

Reader

Reader equipment.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Reader	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item

fluorescenceReader.measurePlate

Measure the fluorescence of wells on a plate.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program		Program parameters
shakerProgram		Program for shaker.
excitationWavelength	Length	Excitation wavelength
emissionWavelength	Length	Emission wavelength
wells	Wells	Array of wells to read
programFileTemplate	string	Program template; well information will be substituted into the template automatically.
programFile	string	Program filename
programData		Program data
output		Output definition for where and how to save the measurements
joinKey	string	The key used to left-join the measurement values with the current DATA
writeTo	string	Filename to write measurements to as JSON
appendTo	string	Filename to append measurements to as newline-delimited JSON
userValues	object	User-specificed values that should be included in the output table
simulated	string	An expression to evaluate with mathjs
units		Map of factor names to unit type; converts the factor values to plain numbers in the given units.
object	Plate	Plate identifier	required
site	Site	Site identifier in reader
destinationAfter	SiteOrStay	Site to move the plate to after measurement

data

The data module contains two commands for working with data tables:

data.forEachRow executes sub-steps for each row in the active data table.
data.forEachGroup executes sub-steps for each group of rows in active data table. The grouping criterion is specified by groupBy parameter.

data.forEachGroup

Perform sub-steps for every grouping of rows in the active data table.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
groupBy	array,string	The factor(s) to group by	required
distinctBy	array,string	The factor(s) to distinguish row by
orderBy	array,string	The factor(s) to order by
durationTotal	Duration	The total duration of this step. The execution of all groups should complete within the allotted time. If execution completes earlier, the protocol will sleep for the remainder of the duration.
durationGroup	Duration	The duration of each row. The execution of each group should complete within the allotted time. If execution completes earlier, the protocol will sleep for the remainder of the duration.
interleave	Duration	The time offset for interleaving each group
timers	array	Timers that should be used
startTimerAfterStep	integer	The duration timer will be started after this step rather than from the beginning, if specified
steps	object	The sequence of commands to perform for each set of factor values.

data.forEachRow

Perform sub-steps for every row in the active data table. The row's values are placed in SCOPE for the sub-steps.

Properties:

Name	Type	Description
agent	Agent	Agent identifier
distinctBy	array,string	The factor(s) to distinguish row by
orderBy	array,string	The factor(s) to order by
durationTotal	Duration	The total duration of this step. The execution of all rows should complete within the allotted time. If execution completes earlier, the protocol will sleep for the remainder of the duration.
durationRow	Duration	The duration of each row. The execution of each row should complete within the allotted time. If execution completes earlier, the protocol will sleep for the remainder of the duration.
interleave	Duration	The time offset for interleaving each group
timers	array	Timers that should be used
steps	object	The sequence of commands to perform for each set of factor values.

sealer

The sealer commands specify actions using sealing equipment.

Sealer

Sealing equipment.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Sealer	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item

sealer.sealPlate

Seal a plate.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program	string	Program identifier for sealing
object	Plate	Plate identifier	required
site	Site	Site identifier of sealer
count	number	Number of times to seal (defaults to 1)
destinationAfter	SiteOrStay	Site to move the plate to after this command

Agent

An agent that can execute commands.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Agent	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item

Data

Specification of an experimental design.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Data	required
description	markdown	Optional user description of this item
design	object
actions	array

Lid

Lid labware

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Lid	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item
model	string		required
location	string

LidModel

Model for lid labware

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: LidModel	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item

Liquid

Liquid substance.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Liquid	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item
wells	array

Plate

Plate labware.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Plate	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item
model	PlateModel		required
location	Site
contents	object,array
sealed	boolean	Indicated whether the plate is sealed

PlateModel

Model for plate labware.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: PlateModel	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item
rows	integer		required
columns	integer		required

Site

Represents a bench site where labware can placed.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Site	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item

Template

A template object, used by the system.call command.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Template	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item
template

Variable

User-defined variable.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Variable	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item
value

system

The system commands specify several general, high-level actions that are not specific to any particular type of equipment.

system._description

Include the value as a description in the generated script.

Properties:

Name	Type	Description	Required
text	string	Description text

system._echo

Include the value in the generated script for trouble-shooting.

Properties:

Name	Type	Description	Required
name	string	Name of echoed thing
value		Thing to echo

system.call

Call a template function.

The template function should be an object of type Template with a property template holding either a Handlebars template string or an object whose properties may be Handlebars template strings. The template will be expanded using the values passed in the params property.

Properties:

Name	Type	Description	Required
name	Object	Name of the template function.	required
lazyParams	object	Parameters to pass to the template function.

system.description

Include the value as a description in the generated script.

Properties:

Name	Type	Description	Required
value		Value to use as description

system.echo

Include the value in the generated script for trouble-shooting.

Properties:

Name	Type	Description	Required
value		Value to echo

system.if

Conditionally execute steps depending on a conditional test.

Properties:

Name	Type	Description	Required
test	boolean	A boolean value; if true, the `then` steps are executed.	required
then	object	The sequence of steps to perform if the test is true.
else	object	The sequence of steps to perform if the test is false.

system.repeat

Repeat sub-steps a given number of times.

Properties:

Name	Type	Description	Required
count	integer	The number of times to repeat.	required
steps	object	The sequence of commands to repeat.
variableName	string	If provided, a variable will this name will be added to the scope containing the loop index (starting from 1).

system.runtimeExitLoop

Test at run-time whether to exit the current loop.

Properties:

Name	Type	Description	Required
testType	string	The type of code to execute to determine whether to break; a JSON truthy value should be returned. One of: nodejs,R	required
test	string	The code to execute at runtime that will test whether to exit.	required

system.runtimeLoadVariables

Load the runtime values into variables.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
varset	string	Name of the variable set to load	required
variables	array	Array of variables to load from 'varset'	required

system.runtimeSteps

Handle steps that require runtime variables.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
varset	string	Name of the variable set to load	required
variables	array	Array of variables to load from 'varset'	required
steps	array,object	Steps to compile at runtime	required

timer

The timer commands specify actions using timer equipment.

Timer

Timer equipment.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Timer	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item

timer._sleep

Sleep for a given duration using a specific timer.

Handler should return effects that the timer is not running.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required
duration	Duration	Duration to sleep	required
stop	boolean	Whether to stop the timer after waiting, or let it continue

timer._start

Start the given timer.

Handler should return effects that the timer is running.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required

timer._stop

Stop the given timer.

Handler should return effects that the timer is not running.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required

timer._wait

Wait until the given timer has reacher the given elapsed time.

Handler should:

expect that the timer (identified by the equipment parameter) is running
return effects that the timer is not running

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required
till	Duration	Number of seconds to wait till from the time the timer was started	required
stop	boolean	Whether to stop the timer after waiting, or let it continue	required

timer.doAndWait

Start a timer, perform sub-steps, then wait till duration has elapsed.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
duration	Duration	Duration that this command should last	required
steps	object,array	Sub-steps to perform	required

timer.sleep

Sleep for a given duration.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
duration	Duration	Duration to sleep	required

timer.start

Start a timer.

If no parameters are supplied, a timer will be automatically chosen.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier

timer.stop

Stop a running a timer.

If only one timer is running, this command can be called without any parameters. Otherwise, the equipment identifier must be supplied.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier

timer.wait

Wait until the given timer has reacher the given elapsed time.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
till	Duration	Time that the timer should reach before continuing with the next step	required
stop	boolean	Whether to stop the timer after waiting, or let it continue	required

shaker

The shaker commands specify actions using shaker equipment.

Shaker

Shaker equipment.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Shaker	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item

shaker.ShakerProgram

Program for shaker.

Properties:

Name	Type	Description	Required
amplitude	string	Amplitude One of: min,low,high,max
duration	Duration	Duration of shaking	required
rpm	number	Rotations per minute (RPM)

shaker.shakePlate

Shake a plate. If necessary, the plate will be transfered to the shaker first. By default, the plate will also be automatically moved back to its prior location after shaking.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program	shaker.ShakerProgram	Program for shaking	required
object	Plate	Plate identifier	required
site	Site	Site identifier on shaker
destinationAfter	SiteOrStay	Site to move the plate to after this command

Example:

This will shake plate1 for 1 minute:

command: shaker.shakePlate
program:
  duration: 1 minute
object: plate1

shaker.run

Run the shaker. This will simply run the given shaker program, regardless of what plate is on the shaker or whether the shaker is empty.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program	shaker.ShakerProgram	Program for shaking	required

transporter

The transporter commands specify actions using equipment to transport labware from one location to another.

Transporter

Labware transporter equipment.

Properties:

Name	Type	Description	Required
type	string	Type of this object One of: Transporter	required
description	markdown	Optional user description of this item
label	markdown	Optional user label for this item

transporter._moveLidFromContainerToSite

Transport a lid from a container to a destination site.

Developer notes: Handler should return effects with the lid's new location.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required
program	name	Program identifier for transport	required
object	Labware	Lid identifier	required
container	Plate	Container identifier	required
destination	Site	Site to move the lid to	required

transporter._moveLidFromSiteToContainer

Transport a lid from an origin site to a labware container.

Developer notes: Handler should return effects with the lid's new location.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required
program	name	Program identifier for transport	required
object	Labware	Lid identifier	required
origin	Site	Site to move the lid from	required
container	Plate	Container to place the lid on	required

transporter._movePlate

Transport a plate to a destination.

Handler should return effects with the plate's new location.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier	required
equipment	Equipment	Equipment identifier	required
program	name	Program identifier for transport	required
object	Plate	Plate identifier	required
destination	Site	Site to move the plate to	required

transporter.doThenRestoreLocation

Perform steps, then return the given labwares to their prior locations.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
objects	array	Plate identifier	required
equipment	Equipment	Equipment identifier
program	name	Program identifier for transport
steps	object,array	Sub-steps to perform

transporter.moveLidFromContainerToSite

Transport a lid from a container to a destination site.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program	name	Program identifier for transport
object	Labware	Lid identifier	required
destination	Site	Site to move the lid to	required

transporter.moveLidFromSiteToContainer

Transport a lid from an origin site to a labware container.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program	name	Program identifier for transport
object	Labware	Lid identifier	required
container	Labware	Container to move the lid to	required

transporter.movePlate

Transport a plate to a destination.

Properties:

Name	Type	Description	Required
agent	Agent	Agent identifier
equipment	Equipment	Equipment identifier
program	name	Program identifier for transport
object	Plate	Plate identifier	required
destination	Site	Site to move the plate to	required