ExperimentSampleManipulation

ExperimentSampleManipulation[Primitives]⟹Protocol

generates a sample manipulation Protocol to accomplish Primitives, which involves one or several steps of transfering, aliquoting, consolidating, or mixing of the samples specified in Primitives.

ExperimentSampleManipulation is the work horse of the lab. It allows for a wide range of sample preparation over a large scale. Liquid samples with volumes 1 µL - 50mL can be transferred on a robotic liquid handler. Liquids and solids can be transferred using standard lab techniques at scales up to 20L or 50 kg. Additionally sample manipulation also allows for filtration, incubation, mixing and centrifugation to be done in-line with volume and mass transfer. All the primitives used to perform your sample preparation can be inserted into SamplePreparation option.

Experimental Principles

Figure 1.1: An example workflow that can be performed on the robotic liquid handler deck via ExperimentSampleManipulation.

Figure 1.2: The available primitives that can be chained together in a Sample Manipulation workflow. For more information, please consult each primitive's help file or view the examples below.

Instrumentation

Hamilton STARlet

Figure 2.1.1: An overview of the robotic workcell. It is capable of processing plate operations including incubation, shaking, and magnetic bead separation on-deck and filtration and absorbance/fluorescence/luminescence measurement off-deck, with a robot arm facilitating the plate movements.

Figure 2.1.2: Overhead view of the liquid handling instrument deck.

Super STAR

Figure 2.2.1: An overview of the robotic workcell. It is capable of processing plate operations including incubation, shaking, and magnetic bead separation on-deck and centrifugation, filtration, and absorbance/fluorescence/luminescence measurement off-deck, with a robot arm facilitating the plate movements.

Figure 2.2.2: Overhead view of the liquid handling instrument deck.

Transfer

transferRules

Indicates whether the destination should be restricted from automatic use is any of your team's experiments that request the sample's models. (Restricted samples can only be used in experiments when specifically provided as input to the experiment functions by a team member.)

Default Value: Automatic

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Index Matches to: Source

DestinationWell

The position in the destination container in which the source sample will be placed.

Default Value: Automatic

Default Calculation: Automatically set to the position of the given Object[Sample]. Otherwise, is set to the first empty well of the container. Otherwise, is set to "A1".

Pattern Description: Any valid container position or any well from A1 to H12.

Programmatic Pattern: (WellPositionP | LocationPositionP) | Automatic

Index Matches to: Source

MultichannelTransfer

Indicates if this transfer will occur simultaneously with the other transfer that occur before/after it, up to the number of channels that are available in the pipette chosen via the Instrument option.

Default Value: Automatic

Default Calculation: Automatically set to True if (1) the samples are in a plate, (2) the samples to be transferred before/after this sample are in the same row or well of the plate, (3) the volume of the samples to be transferred is the same, and (4) the spacing of the wells in the plate are compatible with the spacing between the channels in the pipette (HorizontalPitch/VerticalPitch/ChannelOffset).

Pattern Description: True or False or Null.

Programmatic Pattern: ((Null | BooleanP) | Automatic) | Null

Index Matches to: Source

IntermediateDecant

Indicates if the source will need to be decanted into an intermediate container in order for the precise amount requested to be transferred via pipette. Intermediate decants are necessary if the container geometry prevents the Instrument from reaching the liquid level of the sample in the container (plus the delta of volume that is to be transferred). The container geometry is automatically calculated from the inverse of the volume calibration function when the container is parameterized upon receiving. This option will be set to Null if Preparation->Robotic.

Default Value: Automatic

Default Calculation: Automatically set to True if the source is in a container that in a container that is pipette-inaccessible and the Instrument set to perform the transfer is a pipette.

Pattern Description: True or False or Null.

Programmatic Pattern: ((Null | BooleanP) | Automatic) | Null

Index Matches to: Source

IntermediateContainer

The container that the source will be decanted into in order to make the final transfer via pipette into the final destination.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

MeasureVolume

Indicates if any liquid samples that are modified in the course of the experiment should have their volumes measured and updated after running the experiment. Please note that public samples are volume measured regardless of the value of this option.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

ImageSample

Indicates if any samples that are modified in the course of the experiment should be freshly imaged after running the experiment. Please note that public samples are imaged regardless of the value of this option.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Define

name

The named reference to a sample, container, or model.

Pattern: _String

Method

Sample

The sample or model object or a sample location whose reference name is defined by this Define primitive.

Default Value: Automatic

Default Calculation: Automatically resolves from the Container if specified as a vessel or is Null.

Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample or {Container, Well} or Null.

Programmatic Pattern: (((ObjectP[{Object[Sample], Model[Sample]}] | _String) | {ObjectP[{Object[Container], Model[Container]}] | _String, WellPositionP}) | Automatic) | Null

Container

The container object whose reference name is defined by this Define primitive.

Default Value: Automatic

Default Calculation: Automatically resolves from the Sample if specified as a sample or is Null.

Pattern Description: An object of type or subtype Object[Container] or Model[Container] or a prepared sample or Null.

Programmatic Pattern: ((ObjectP[{Object[Container], Model[Container]}] | _String) | Automatic) | Null

Well

The container well of the sample whose reference name is defined by this Define primitive.

Default Value: Automatic

Default Calculation: Automatically resolves from the Sample if specified as a sample or is Null.

Pattern Description: A string that matches the pattern: WellPositionP or Null.

Programmatic Pattern: (WellPositionP | Automatic) | Null

ContainerName

If a specified sample is named, it's container can be named using this option.

Default Value: Null

Pattern Description: A string or Null.

Programmatic Pattern: _String | Null

Model

If a new sample will be created in the defined position, this option specifies the model of the created sample.

Default Value: Automatic

Default Calculation: Automatically resolves at runtime based on the nature of the new sample's sources.

Pattern Description: An object of type or subtype Model[Sample] or Null.

Programmatic Pattern: (ObjectP[Model[Sample]] | Automatic) | Null

StorageCondition

If a new sample will be created in the defined position, this option specifies the storage condition of the created sample.

Default Value: Automatic

Default Calculation: Automatically resolves from SamplesOutStorageCondition option of the protocol.

Pattern Description: AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, BacteriaIncubation, MammalianIncubation, TissueCultureCellsIncubation, MicrobialCellsIncubation, MicrobialCellsShakingIncubation, YeastCellsIncubation, YeastCellsShakingIncubation, ViralIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, or UVVisLightTesting or an object of type or subtype Model[StorageCondition] or Null.

Programmatic Pattern: ((SampleStorageTypeP | ObjectP[Model[StorageCondition]]) | Automatic) | Null

ExpirationDate

If a new sample will be created in the defined position, this option specifies the expiration date of the created sample.

If a new sample will be created in the defined position, a new model will be created with this unsealed shelf life.

Default Value: Null

Pattern Description: Greater than 0 days or Null.

Programmatic Pattern: GreaterP[0*Day] | Null

DefaultStorageCondition

If a new sample will be created in the defined position, a new model will be created with this storage condition.

Default Value: Automatic

Programmatic Pattern: ((SampleStorageTypeP | ObjectP[Model[StorageCondition]]) | Automatic) | Null

DefaultTransportWarmed

If a new sample will be created in the defined position, a new model will be created with this default transportation temperature.

Default Value: Null

Pattern Description: Greater than 0 kelvins or Null.

Programmatic Pattern: GreaterP[0*Kelvin] | Null

Aliquot

aliquotRules

Pattern Description: Greater than 0 molar or greater than 0 grams per liter or Null.

Programmatic Pattern: ((Null | (GreaterP[0*Molar] | GreaterP[(0*Gram)/Liter])) | Automatic) | Null

Index Matches to: Source

Nested Index Matches to: Source

TargetConcentrationAnalyte

The substance whose final concentration is attained with the TargetConcentration option.

Default Value: Automatic

Default Calculation: Automatically set to the first value in the Analytes field of the input sample, or, if not populated, to the first analyte in the Composition field of the input sample, or if none exist, the first identity model of any kind in the Composition field.

Pattern Description: An object of type or subtype Model[Molecule], Model[Molecule, cDNA], Model[Molecule, Oligomer], Model[Molecule, Transcript], Model[Molecule, Protein], Model[Molecule, Protein, Antibody], Model[Molecule, Carbohydrate], Model[Molecule, Polymer], Model[Resin], Model[Resin, SolidPhaseSupport], Model[Lysate], Model[ProprietaryFormulation], Model[Virus], Model[Cell], Model[Cell, Mammalian], Model[Cell, Bacteria], Model[Cell, Yeast], Model[Tissue], Model[Material], or Model[Species] or Null.

Programmatic Pattern: ((Null | ObjectP[IdentityModelTypes]) | Automatic) | Null

Index Matches to: Source

Nested Index Matches to: Source

AssayVolume

The desired total volume of the aliquoted sample plus dilution buffer.

Default Value: Automatic

Default Calculation: Automatically determined based on Volume, Mass, and TargetConcentration option values.

Pattern Description: Greater than or equal to 1 microliter and less than or equal to 20 liters or Null.

Programmatic Pattern: ((Null | RangeP[1*Microliter, 20*Liter]) | Automatic) | Null

Index Matches to: Source

ContainerOut

The desired type of container that should be used to prepare and house the aliquot samples, with indices indicating grouping of samples in the same plates, if desired.

Default Value: Automatic

Default Calculation: Automatically set as the PreferredContainer for the AssayVolume of the sample. For plates, attempts to fill all wells of a single plate with the same model before aliquoting into the next.

Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or {Index, Container}

Programmatic Pattern: ((ObjectP[{Model[Container], Object[Container]}] | _String) | {GreaterEqualP[1, 1] | Automatic, (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic

Index Matches to: Source

SampleOutLabel

The label of the sample(s) that become the SamplesOut.

Default Value: Automatic

Pattern Description: A string or Null.

Programmatic Pattern: ((Null | _String) | Automatic) | Null

Index Matches to: Source

Pattern Description: Manual or Robotic.

Programmatic Pattern: PreparationMethodP | Automatic

Post Experiment

SamplesOutStorageCondition

Default Value: Null

Programmatic Pattern: (Null | (Alternatives[SampleStorageTypeP | Disposal])) | Null

Index Matches to: Source

SamplesInStorageCondition

Default Value: Null

Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null

MeasureWeight

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

MeasureVolume

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

ImageSample

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Consolidation

consolidationRules

Programmatic Pattern: (PipettingPositionP | Automatic) | Null

AspirationPositionOffset

The distance from the top or bottom of the container, depending on AspirationPosition, from which liquid should be aspirated.

Default Value: Automatic

Default Calculation: Automatically resolves from DispensePositionOffset if it is specified, or if AspirationPosition is not Null resolves to 2 Millimeter, otherwise resolves to Null and is determined at runtime by inspecting a sample's container type.

Pattern Description: Greater than or equal to 0 millimeters or Null.

Programmatic Pattern: (GreaterEqualP[0*Millimeter] | Automatic) | Null

DispensePositionOffset

The distance from the top or bottom of the container, depending on DispensePosition, from which liquid should be dispensed.

Default Value: Automatic

Default Calculation: Automatically resolves from AspirationPositionOffset if it is specified, or if DispensePosition is not Null resolves to 2 Millimeter, otherwise resolves to Null and is determined at runtime by inspecting a sample's container type.

Pattern Description: Greater than or equal to 0 millimeters or Null.

Programmatic Pattern: (GreaterEqualP[0*Millimeter] | Automatic) | Null

CorrectionCurve

The relationship between a target volume and the corrected volume that needs to be aspirated or dispensed to reach the target volume.

Default Value: Automatic

Default Calculation: Automatically resolves from PipettingMethod if it is specified, or the default correction curve empirically determined for water.

Pattern Description: List of one or more {Target Volume, Actual Volume} entries or Null.

Programmatic Pattern: ({{RangeP[0*Microliter, 1000*Microliter], RangeP[0*Microliter, 1250*Microliter]}..} | Automatic) | Null

DynamicAspiration

Indicates if droplet formation should be prevented during liquid transfer. This should only be used for solvents that have high vapor pressure.

Default Value: Automatic

Default Calculation: Automatically resolves to False if unspecified.

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Acoustic Liquid Handling

InWellSeparation

Indicates how the droplets of different samples are transferred into the same destination well. If True, the droplets are targeted to be spatially separated to avoid mixing with each other until additional volume is added to the well. This option is specific to ExperimentAcousticLiquidHandling.

Default Value: Null

Pattern Description: True or False or Null.

Programmatic Pattern: BooleanP | Null

Mix

Sample

The sample to be mixed.

Pattern: NonSelfContainedSampleP | NonSelfContainedSampleModelP | ObjectP[{Model[Container, Vessel], Model[Container, ReactionVessel], Model[Container, Cuvette], Object[Container, Vessel], Object[Container, ReactionVessel], Object[Container, Cuvette]}] | {ObjectP[{Model[Container, Plate], Object[Container, Plate]}], WellP}

General

Sample

The samples that should be mixed.

Default Value: Null

Pattern Description: Container with Well Position or Sample or Container.

Programmatic Pattern: (ObjectP[{Object[Sample], Object[Container]}] | _String) | {Alternatives @@ Flatten[AllWells[NumberOfWells -> 384]] | LocationPositionP, ObjectP[{Object[Container]}] | _String}

Index Matches to: Sample

SampleLabel

A user defined word or phrase used to identify the samples that are being incubated, for use in downstream unit operations.

Default Value: Automatic

Pattern Description: A string or Null.

Programmatic Pattern: ((Null | _String) | Automatic) | Null

Index Matches to: Sample

During light exposure experiments, a set of samples that are placed in an opaque box to receive identical incubation conditions without exposure to light. This option can only be set if incubating other samples in an environmental stability chamber with light exposure.

Default Value: Null

Pattern Description: List of one or more an object of type or subtype Object[Sample] or Object[Container] or a prepared sample entries or Null.

Programmatic Pattern: {(ObjectP[{Object[Sample], Object[Container]}] | _String)..} | Null

WorkCell

Indicates the work cell that this primitive will be run on if Preparation->Robotic.

Default Value: Automatic

Default Calculation: Automatically set to STAR if Preparation->Robotic.

Pattern Description: STAR, bioSTAR, microbioSTAR, or qPix or Null.

Programmatic Pattern: (WorkCellP | Automatic) | Null

Preparation

The angle that the sample's container will be tilted during the mixing of the sample. The container is pivoted on its left edge when tilting occurs. This option can only be provided if Preparation->Robotic.

Default Value: Null

Pattern Description: Greater than or equal to 0 degrees and less than or equal to 10 degrees in increments of 1 degree or Null.

Programmatic Pattern: (Null | RangeP[0*AngularDegree, 10*AngularDegree, 1*AngularDegree]) | Null

Index Matches to: Sample

CorrectionCurve

The relationship between a target volume and the corrected volume that needs to be aspirated or dispensed to reach the target volume. This option can only be set if Preparation->Robotic.

Default Value: Automatic

Default Calculation: Automatically resolves to correction curve set in the PipettingMethod for the Object[Sample] if MixType->Pipette and Preparation->Robotic.

Pattern Description: List of one or more {Target Volume, Actual Volume} entries or Null.

Programmatic Pattern: ((Null | {{RangeP[0*Microliter, 1000*Microliter], RangeP[0*Microliter, 1250*Microliter]}..}) | Automatic) | Null

Index Matches to: Sample

Tips

The pipette tips used to aspirate and dispense the requested volume..

Default Value: Automatic

Default Calculation: Automatically set based on the incompatible materials of the sample(s) that the tip will come in contact with and the MixVolume, if MixType->Pipette.

Pattern Description: An object of type or subtype Model[Item, Tips] or Object[Item, Tips] or Null.

Programmatic Pattern: ((Null | ObjectP[{Model[Item, Tips], Object[Item, Tips]}]) | Automatic) | Null

Index Matches to: Sample

TipType

The tip type to use to mix liquid in the manipulation..

Default Value: Automatic

Default Calculation: Automatically resolves based on the amount being mixed or TipSize specification, if MixType->Pipette.

Pattern Description: Normal, Barrier, WideBore, GelLoading, or Aspirator or Null.

Programmatic Pattern: ((Null | TipTypeP) | Automatic) | Null

Index Matches to: Sample

Indicates if the incubation and/or mixing should continue after Time/MaxTime has finished while waiting to progress to the next step in the protocol.

Figure 3.2: Set ResidualIncubation to False if you wish the plate to be moved back to its original deck position after the prescribed incubation time has passed.

Default Value: Automatic

Default Calculation: Automatically set to True if Temperature is non-Ambient and the samples being incubated are TransportWarmed or TransportChilled.

Pattern Description: True or False or Null.

Programmatic Pattern: ((Null | BooleanP) | Automatic) | Null

Index Matches to: Sample

The rotational speed or the force that will be applied to the samples by centrifugation prior to starting the experiment.

Default Value: Automatic

Pattern Description: Greater than 0 revolutions per minute or greater than 0 standard accelerations due to gravity on the surface of the earth or Null.

Programmatic Pattern: ((Null | (GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration])) | Automatic) | Null

Index Matches to: Sample

CentrifugeTime

The amount of time for which the SamplesIn should be centrifuged prior to starting the experiment.

Default Value: Automatic

Pattern Description: Greater than 0 minutes or Null.

Programmatic Pattern: ((Null | GreaterP[0*Minute]) | Automatic) | Null

Index Matches to: Sample

The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.

Default Value: Automatic

Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.

Pattern Description: Any well from A1 to H12 or list of one or more any well from A1 to H12 or any well from A1 to H12 entries or Null.

Programmatic Pattern: ((WellPositionP | {((Automatic | Null) | WellPositionP)..}) | Automatic) | Null

AliquotPreparation

Indicates the desired scale at which liquid handling used to generate aliquots will occur.

Default Value: Automatic

Default Calculation: Automatic resolution will occur based on manipulation volumes and container types.

Pattern Description: Manual or Robotic or Null.

Programmatic Pattern: (PreparationMethodP | Automatic) | Null

ConsolidateAliquots

Indicates if identical aliquots should be prepared in the same container/position.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

AliquotContainer

The desired type of container that should be used to prepare and house the aliquot samples, with indices indicating grouping of samples in the same plates, if desired.

Default Value: Automatic

Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or Automatic or Null or {Index, Container} or list of one or more an object of type or subtype Model[Container] or Object[Container] or a prepared sample or Automatic or Null entries or list of one or more Automatic or Null or {Index, Container} entries or Null or Null.

Programmatic Pattern: ((Null | ((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null) | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | {((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null))..} | {({GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | (Automatic | Null))..})) | Automatic) | Null

Post Experiment

SamplesInStorageCondition

Default Value: Null

Programmatic Pattern: (Null | (Alternatives[SampleStorageTypeP | Disposal])) | Null

Index Matches to: Sample

MeasureWeight

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

MeasureVolume

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

ImageSample

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Incubate

Sample

The sample to be incubated.

General

Sample

The samples that should be incubated.

Default Value: Null

Pattern Description: Container with Well Position or Sample or Container.

Programmatic Pattern: (ObjectP[{Object[Sample], Object[Container]}] | _String) | {Alternatives @@ Flatten[AllWells[NumberOfWells -> 384]] | LocationPositionP, ObjectP[{Object[Container]}] | _String}

Index Matches to: Sample

SampleLabel

A user defined word or phrase used to identify the samples that are being incubated, for use in downstream unit operations.

Default Value: Automatic

Pattern Description: A string or Null.

Programmatic Pattern: ((Null | _String) | Automatic) | Null

Index Matches to: Sample

SampleContainerLabel

A user defined word or phrase used to identify the containers of the samples that are being incubated, for use in downstream unit operations.

Default Value: Automatic

Pattern Description: A string or Null.

Programmatic Pattern: ((Null | _String) | Automatic) | Null

Index Matches to: Sample

RelativeHumidity

The amount of water vapor present in air that the samples will be exposed to during incubation, relative to the amount needed for saturation.

Default Value: Automatic

Default Calculation: Automatically set to 70 Percent if using an environmental chamber with relative humidity control.

Pattern Description: Greater than or equal to 0 percent and less than or equal to 100 percent in increments of 1 percent or Null.

Programmatic Pattern: ((Null | RangeP[0*Percent, 100*Percent, 1*Percent]) | Automatic) | Null

Index Matches to: Sample

LightExposure

The range of wavelengths of light that the incubated samples will be exposed to. Only available when incubating the samples in an environmental chamber with UVLight and VisibleLight control.

Default Value: Automatic

Pattern Description: UVLight or VisibleLight or Null.

Programmatic Pattern: ((Null | EnvironmentalChamberLightTypeP) | Automatic) | Null

Index Matches to: Sample

LightExposureIntensity

Default Value: Automatic

Default Calculation: Automatically set to 19 Watt/Meter^2 if LightExposure is set to UVLight and Lumen/Meter^2 if LightExposure is set to VisibleLight. Otherwise, set to Null.

Pattern Description: UV Light Intensity or Visible Light Intensity or Null.

Programmatic Pattern: ((Null | (RangeP[(2*Watt)/Meter^2, (36*Watt)/Meter^2] | RangeP[(2*Lumen)/Meter^2, (29000*Lumen)/Meter^2])) | Automatic) | Null

Index Matches to: Sample

TotalLightExposure

Default Value: Automatic

Default Calculation: Automatically calculated from the LightExposureIntensity and Time options.

Pattern Description: UV Light Exposure or Visible Light Exposure or Null.

Programmatic Pattern: ((Null | (GreaterP[(0*Watt*Hour)/Meter^2] | GreaterP[(0*Lumen*Hour)/Meter^2])) | Automatic) | Null

Index Matches to: Sample

LightExposureStandard

Default Value: Null

Pattern Description: List of one or more an object of type or subtype Object[Sample] or Object[Container] or a prepared sample entries or Null.

Programmatic Pattern: {(ObjectP[{Object[Sample], Object[Container]}] | _String)..} | Null

WorkCell

Indicates the work cell that this primitive will be run on if Preparation->Robotic.

Default Value: Automatic

Default Calculation: Automatically set to STAR if Preparation->Robotic.

Pattern Description: STAR, bioSTAR, microbioSTAR, or qPix or Null.

Programmatic Pattern: (WorkCellP | Automatic) | Null

Preparation

Programmatic Pattern: ((Null | MixTypeP) | Automatic) | Null

Index Matches to: Sample

MixUntilDissolved

Indicates if the mix should be continued up to the MaxTime or MaxNumberOfMixes (chosen according to the mix Type), in an attempt dissolve any solute.

Default Value: Automatic

Default Calculation: Automatically resolves to True if MaxTime or MaxNumberOfMixes is set.

Pattern Description: True or False or Null.

Programmatic Pattern: ((Null | BooleanP) | Automatic) | Null

Index Matches to: Sample

Default Value: Automatic

Default Calculation: Automatically resolves to 2 Millimeter if MixType->Pipette and Preparation->Robotic.

Pattern Description: {X Offset, Y Offset, Z Offset} or Z Offset or Null.

Programmatic Pattern: ((Null | (GreaterEqualP[0*Millimeter] | {RangeP[-100*Centimeter, 100*Centimeter], RangeP[-100*Centimeter, 100*Centimeter], GreaterEqualP[0*Millimeter]})) | Automatic) | Null

The material of the pipette tips used to aspirate and dispense the requested volume during the transfer.

Default Value: Automatic

Default Calculation: Automatically set to the material of the resolved Tips that will be used to perform the transfer, if MixType->Pipette.

Programmatic Pattern: ((Null | MaterialP) | Automatic) | Null

Index Matches to: Sample

MultichannelMix

Indicates if multiple device channels should be used when performing pipette mixing.

Default Value: Automatic

Default Calculation: Automatically set to True if there are multiple samples that will be mixed via pipette, if MixType->Pipette.

Pattern Description: True or False or Null.

Programmatic Pattern: ((Null | BooleanP) | Automatic) | Null

Index Matches to: Sample

DeviceChannel

The channel of the work cell that should be used to perform the pipetting mixing. This option can only be set if Preparation->Robotic and MixType->Pipette.

Default Value: Automatic

Pattern Description: MultiProbeHead, SingleProbe1, SingleProbe2, SingleProbe3, SingleProbe4, SingleProbe5, SingleProbe6, SingleProbe7, or SingleProbe8 or Null.

Programmatic Pattern: ((Null | DeviceChannelP) | Automatic) | Null

Index Matches to: Sample

ResidualIncubation

Indicates if the incubation and/or mixing should continue after Time/MaxTime has finished while waiting to progress to the next step in the protocol.

Figure 3.3: Set ResidualIncubation to False if you wish the plate to be moved back to its original deck position after the prescribed incubation time has passed.

Default Value: Automatic

Default Calculation: Automatically set to True if Temperature is non-Ambient and the samples being incubated are TransportWarmed or TransportChilled.

Pattern Description: True or False or Null.

Programmatic Pattern: ((Null | BooleanP) | Automatic) | Null

Index Matches to: Sample

The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.

Default Value: Automatic

Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.

Pattern Description: Any well from A1 to H12 or Null.

Programmatic Pattern: ((Null | WellPositionP) | Automatic) | Null

Index Matches to: Sample

CentrifugeAliquot

The amount of each sample that should be transferred from the SamplesIn into the CentrifugeAliquotContainer when performing an aliquot before centrifugation.

Default Value: Automatic

Filtration

Default Value: Automatic

Default Calculation: Resolves to True if any of the corresponding Filter options are set. Otherwise, resolves to False.

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Index Matches to: Sample

FiltrationType

The type of filtration method that should be used to perform the filtration.

Default Value: Automatic

Default Calculation: Will automatically resolve to a filtration type appropriate for the volume of sample being filtered.

Pattern Description: PeristalticPump, Centrifuge, Vacuum, Syringe, or AirPressure or Null.

Programmatic Pattern: ((Null | FiltrationTypeP) | Automatic) | Null

The pore size of the filter that should be used when removing impurities from the SamplesIn prior to starting the experiment.

Default Value: Automatic

Default Calculation: Resolves to an appropriate filter pore size for the given sample is Filtration is set to True.

Programmatic Pattern: ((Null | FilterSizeP) | Automatic) | Null

Index Matches to: Sample

The desired container filtered samples should be produced in or transferred into by the end of filtration, with indices indicating grouping of samples in the same plates, if desired.

Default Value: Automatic

Default Calculation: Automatically set as the PreferredContainer for the Volume of the sample. For plates, attempts to fill all wells of a single plate with the same model before using another one.

Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or {Index, Container} or Null.

Index Matches to: Sample

FilterAliquotDestinationWell

The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.

Default Value: Automatic

Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.

Pattern Description: Any well from A1 to H12 or Null.

Programmatic Pattern: ((Null | WellPositionP) | Automatic) | Null

Index Matches to: Sample

FilterAliquot

The amount of each sample that should be transferred from the SamplesIn into the FilterAliquotContainer when performing an aliquot before filtration.

Default Value: Automatic

Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.

Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.

Programmatic Pattern: ((Null | (RangeP[1*Microliter, 20*Liter] | All)) | Automatic) | Null

Index Matches to: Sample

FilterSterile

Indicates if the filtration of the samples should be done in a sterile environment.

Default Value: Automatic

Default Value: Automatic

Programmatic Pattern: ((Null | ObjectP[IdentityModelTypes]) | Automatic) | Null

Index Matches to: Sample

AssayVolume

The desired total volume of the aliquoted sample plus dilution buffer.

Default Value: Automatic

Default Calculation: Automatically determined based on Volume and TargetConcentration option values.

Pattern Description: Greater than or equal to 1 microliter and less than or equal to 20 liters or Null.

Programmatic Pattern: ((Null | RangeP[1*Microliter, 20*Liter]) | Automatic) | Null

Index Matches to: Sample

The buffer that should be added to any aliquots requiring dilution, where the volume of this buffer added is the difference between the AliquotAmount and the total AssayVolume.

Default Value: Automatic

Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is not specified; otherwise, resolves to Null.

Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.

Programmatic Pattern: ((Null | (ObjectP[{Model[Sample], Object[Sample]}] | _String)) | Automatic) | Null

Index Matches to: Sample

Indicates if identical aliquots should be prepared in the same container/position.

Sample

Default Calculation: Automatically set to the value of RetentateLabel if Target -> Retentate, or FiltrateLabel if Target -> Filtrate.

Pattern Description: A string or Null.

Programmatic Pattern: ((Null | _String) | Automatic) | Null

Index Matches to: Sample

ContainerOutLabel

A user defined word or phrase used to identify the container of the sample collected at the end of the filtration (either the Filtrate or Retentate), for use in downstream unit operations.

The amount of sample to be transferred into the filter (if it is not already there) prior to its filtration. This option can only be set if Preparation->Robotic.

Default Value: Automatic

Default Calculation: Automatically set to All if the filtering robotically, or Null otherwise.

Pattern Description: All or Volume or Null.

Programmatic Pattern: ((Null | (All | RangeP[0*Milliliter, 10*Milliliter])) | Automatic) | Null

Index Matches to: Sample

OccludingRetentateContainerLabel

A user defined word or phrase used to identify the container of the sample that clogged a filter and was subsequently collected, for use in downstream unit operations.

Default Value: Automatic

Pattern Description: A string or Null.

Programmatic Pattern: ((Null | _String) | Automatic) | Null

Index Matches to: Sample

WashFlowThroughLabel

The label of the sample that is run through the retentate and filter after initial filtration prior to retentate collection. This value can contain one or multiple different labels for flow through samples per input sample.

Default Value: Automatic

Pattern Description: A string or list of one or more a string or Null or Automatic entries or Null.

Programmatic Pattern: ((Null | (_String | {(_String | (Null | Automatic))..})) | Automatic) | Null

Index Matches to: Sample

Indicates the work cell that this primitive will be run on if Preparation->Robotic.

Default Value: Automatic

Default Calculation: Automatically set to STAR if Preparation->Robotic.

Pattern Description: STAR, bioSTAR, microbioSTAR, or qPix or Null.

Programmatic Pattern: (WorkCellP | Automatic) | Null

Preparation

Index Matches to: Sample

FiltrateDestinationWell

The desired position in the corresponding RetentateContainerOut in which the retentate samples will be placed.

Default Value: Automatic

Default Calculation: Will be automatically set to .45 Micron if a prefilter membrane material is specified.

Programmatic Pattern: ((Null | FilterSizeP) | Automatic) | Null

Index Matches to: Sample

The desired container retentate samples should be transferred into after filtering, with indices indicating grouping of samples in the same plates.

Default Value: Automatic

Default Calculation: Automatically set as the PreferredContainer for the ResuspensionVolume of the sample. For plates, attempts to fill all wells of a single plate with the same model before using another one. If not collecting the retentate, automatically set to Null.

Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or {Index, Container} or Null.

Index Matches to: Sample

Default Value: Automatic

Default Calculation: Automatically set to AspirationMixRate or DispenseRate if either is specified, otherwise set to 100 Microliter/Second.

Pattern Description: Greater than or equal to 0.4 microliters per second and less than or equal to 500 microliters per second or Null.

Programmatic Pattern: ((Null | (Null | RangeP[(0.4*Microliter)/Second, (500*Microliter)/Second])) | Automatic) | Null

Index Matches to: Sample

AspirationPosition

Default Value: Automatic

Default Calculation: Automatically set to the AspirationPosition in the PipettingMethod if it is specified and Preparation->Robotic, otherwise resolves to TouchOff if Preparation->Robotic.

Pattern Description: Top, Bottom, LiquidLevel, or TouchOff or Null.

Programmatic Pattern: ((Null | (Null | PipettingPositionP)) | Automatic) | Null

Index Matches to: Sample

DispensePosition

Default Value: Automatic

Pattern Description: Top, Bottom, LiquidLevel, or TouchOff or Null.

Programmatic Pattern: ((Null | (Null | PipettingPositionP)) | Automatic) | Null

Index Matches to: Sample

AspirationPositionOffset

Default Value: Automatic

Pattern Description: {X,Y,Z} Coordinate Offset or Z Offset or Null.

Programmatic Pattern: ((Null | (Null | (GreaterEqualP[0*Millimeter] | Coordinate[{DistanceP, DistanceP, GreaterEqualP[0*Millimeter]}]))) | Automatic) | Null

Index Matches to: Sample

AspirationAngle

Default Value: Automatic

Default Calculation: Automatically set to 0 AngularDegree if Preparation->Robotic. Otherwise, set to Null.

Pattern Description: Greater than or equal to 0 degrees and less than or equal to 10 degrees in increments of 1 degree or Null.

Programmatic Pattern: ((Null | (Null | RangeP[0*AngularDegree, 10*AngularDegree, 1*AngularDegree])) | Automatic) | Null

Index Matches to: Sample

Indicates if droplet formation will be prevented during liquid transfer. This will only be used for solvents that have high vapor pressure. This option can only be set if Preparation->Robotic.

Default Value: Automatic

Default Calculation: Automatically set to the DynamicAspiration field in the pipetting method, if available.

Pattern Description: True or False or Null.

Programmatic Pattern: ((Null | (Null | BooleanP)) | Automatic) | Null

Index Matches to: Sample

Default Value: Automatic

Default Calculation: Automatically set to 1/2 the volume of the source sample or the maximum volume of the pipette being used, depending on which value is smaller.

Pattern Description: Greater than or equal to 0 microliters and less than or equal to 50 milliliters or Null.

Programmatic Pattern: ((Null | (Null | RangeP[0*Microliter, 50*Milliliter])) | Automatic) | Null

Index Matches to: Sample

NumberOfAspirationMixes

The number of times the source is quickly aspirated and dispensed to mix the source sample immediately before it is transferred into the destination.

Default Value: Automatic

Default Calculation: Automatically set to 5 if any of the other AspirationMix options are set. Otherwise, set to Null.

Pattern Description: Greater than or equal to 0 and less than or equal to 50 in increments of 1 or Null.

Programmatic Pattern: ((Null | (Null | RangeP[0, 50, 1])) | Automatic) | Null

Index Matches to: Sample

MaxNumberOfAspirationMixes

The number of times the source is quickly aspirated and dispensed to mix the source sample immediately before it is transferred into the destination.

Default Value: Automatic

Default Calculation: Automatically set to 5 if any of the other AspirationMix options are set. Otherwise, set to Null.

Pattern Description: Greater than or equal to 0 and less than or equal to 100 in increments of 1 or Null.

Programmatic Pattern: ((Null | (Null | RangeP[0, 100, 1])) | Automatic) | Null

Index Matches to: Sample

Duration for which SamplesIn should be incubated at the IncubationTemperature, prior to starting the experiment.

Default Value: Automatic

Pattern Description: Greater than or equal to 1 minute and less than or equal to 72 hours or Null.

Programmatic Pattern: ((Null | RangeP[1*Minute, $MaxExperimentTime]) | Automatic) | Null

Index Matches to: Sample

Mix

Indicates if this sample should be mixed while incubated, prior to starting the experiment.

Default Value: Automatic

Default Calculation: Automatically resolves to True if any Mix related options are set. Otherwise, resolves to False.

Pattern Description: True or False or Null.

Programmatic Pattern: ((Null | BooleanP) | Automatic) | Null

Index Matches to: Sample

MixType

Indicates the style of motion used to mix the sample, prior to starting the experiment.

Default Value: Automatic

Default Calculation: Automatically resolves based on the container of the sample and the Mix option.

Pattern Description: Roll, Vortex, Sonicate, Pipette, Invert, Stir, Shake, Homogenize, Swirl, Disrupt, or Nutate or Null.

Programmatic Pattern: ((Null | MixTypeP) | Automatic) | Null

Index Matches to: Sample

MixUntilDissolved

Indicates if the mix should be continued up to the MaxIncubationTime or MaxNumberOfMixes (chosen according to the mix Type), in an attempt dissolve any solute. Any mixing/incubation will occur prior to starting the experiment.

Default Value: Automatic

Default Calculation: Automatically resolves to True if MaxIncubationTime or MaxNumberOfMixes is set.

Pattern Description: True or False or Null.

Programmatic Pattern: ((Null | BooleanP) | Automatic) | Null

Index Matches to: Sample

MaxIncubationTime

Maximum duration of time for which the samples will be mixed while incubated in an attempt to dissolve any solute, if the MixUntilDissolved option is chosen. This occurs prior to starting the experiment.

Default Value: Automatic

Default Calculation: Automatically resolves based on MixType, MixUntilDissolved, and the container of the given sample.

Pattern Description: Greater than or equal to 1 minute and less than or equal to 72 hours or Null.

Programmatic Pattern: ((Null | RangeP[1*Minute, $MaxExperimentTime]) | Automatic) | Null

Index Matches to: Sample

IncubationInstrument

The instrument used to perform the Mix and/or Incubation, prior to starting the experiment.

Default Value: Automatic

Default Calculation: Automatically resolves based on the options Mix, Temperature, MixType and container of the sample.

Programmatic Pattern: ((Null | ObjectP[Join[MixInstrumentModels, MixInstrumentObjects]]) | Automatic) | Null

Index Matches to: Sample

AnnealingTime

Minimum duration for which the SamplesIn should remain in the incubator allowing the system to settle to room temperature after the IncubationTime has passed but prior to starting the experiment.

Default Value: Automatic

Pattern Description: Greater than or equal to 0 minutes and less than or equal to 72 hours or Null.

Programmatic Pattern: ((Null | RangeP[0*Minute, $MaxExperimentTime]) | Automatic) | Null

Index Matches to: Sample

The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.

Default Value: Automatic

Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.

Pattern Description: Any well from A1 to H12 or Null.

Programmatic Pattern: ((Null | WellPositionP) | Automatic) | Null

Index Matches to: Sample

CentrifugeAliquot

The amount of each sample that should be transferred from the SamplesIn into the CentrifugeAliquotContainer when performing an aliquot before centrifugation.

Default Value: Automatic

Default Value: Automatic

Programmatic Pattern: ((Null | ObjectP[IdentityModelTypes]) | Automatic) | Null

Index Matches to: Sample

AssayVolume

The desired total volume of the aliquoted sample plus dilution buffer.

Default Value: Automatic

Default Calculation: Automatically determined based on Volume and TargetConcentration option values.

Pattern Description: Greater than or equal to 1 microliter and less than or equal to 20 liters or Null.

Programmatic Pattern: ((Null | RangeP[1*Microliter, 20*Liter]) | Automatic) | Null

Index Matches to: Sample

The buffer that should be added to any aliquots requiring dilution, where the volume of this buffer added is the difference between the AliquotAmount and the total AssayVolume.

Default Value: Automatic

Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is not specified; otherwise, resolves to Null.

Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.

Programmatic Pattern: ((Null | (ObjectP[{Model[Sample], Object[Sample]}] | _String)) | Automatic) | Null

Index Matches to: Sample

AliquotSampleStorageCondition

The non-default conditions under which any aliquot samples generated by this experiment should be stored after the protocol is completed.

Default Value: Automatic

Programmatic Pattern: ((Null | (SampleStorageTypeP | Disposal)) | Automatic) | Null

Index Matches to: Sample

DestinationWell

The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.

Default Value: Automatic

Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.

Pattern Description: Any well from A1 to H12 or list of one or more any well from A1 to H12 or any well from A1 to H12 entries or Null.

Programmatic Pattern: ((WellPositionP | {((Automatic | Null) | WellPositionP)..}) | Automatic) | Null

AliquotContainer

The desired type of container that should be used to prepare and house the aliquot samples, with indices indicating grouping of samples in the same plates, if desired. This option will resolve to be the length of the SamplesIn * NumberOfReplicates.

Default Value: Automatic

Programmatic Pattern: (((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null) | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | {((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null))..} | {({GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | (Automatic | Null))..}) | Automatic) | Null

AliquotPreparation

Indicates the desired scale at which liquid handling used to generate aliquots will occur.

Default Value: Automatic

Default Calculation: Automatic resolution will occur based on manipulation volumes and container types.

Pattern Description: Manual or Robotic or Null.

Programmatic Pattern: (PreparationMethodP | Automatic) | Null

ConsolidateAliquots

Indicates if identical aliquots should be prepared in the same container/position.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Post Experiment

SamplesOutStorageCondition

Default Value: Null

Programmatic Pattern: (Null | (Alternatives[SampleStorageTypeP | Disposal])) | Null

Index Matches to: Sample

MeasureWeight

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

MeasureVolume

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

ImageSample

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

MoveToMagnet

Sample

The sample/container to be magnetized.

RemoveFromMagnet

Sample

The sample/container to be removed from magnetization.

Centrifuge

centrifugeRules

The list of key/value pairs that specify the samples and their centrifugation parameters.

Pattern: {Sample -> ListableP[NonSelfContainedSampleP | NonSelfContainedSampleModelP | ObjectP[{Model[Container, Vessel], Model[Container, ReactionVessel], Model[Container, Cuvette], Object[Container, Vessel], Object[Container, ReactionVessel], Object[Container, Cuvette]}] | {ObjectP[{Model[Container, Plate], Object[Container, Plate]}], WellP}], Time -> ListableP[GreaterEqualP[0*Minute]], Intensity -> Automatic | Null | GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration], Temperature -> ListableP[Ambient | TemperatureP], Instrument -> ListableP[ObjectP[{Model[Instrument, Centrifuge], Model[Instrument, Centrifuge]}] | Null]}

General

Sample

The samples that should be centrifuged.

Default Value: Null

Pattern Description: Container with Well Position or Sample or Container.

Programmatic Pattern: (ObjectP[{Object[Sample], Object[Container]}] | _String) | {Alternatives @@ Flatten[AllWells[NumberOfWells -> 384]] | LocationPositionP, ObjectP[{Object[Container]}] | _String}

Index Matches to: Sample

SampleLabel

A user defined word or phrase used to identify the samples that are being centrifuged, for use in downstream unit operations.

Default Value: Automatic

Pattern Description: A string or Null.

Programmatic Pattern: ((Null | _String) | Automatic) | Null

Index Matches to: Sample

The amount of time for which the samples will be centrifuged.

Default Value: 5 minutes

Pattern Description: Greater than 0 minutes.

Programmatic Pattern: GreaterP[0*Minute]

Index Matches to: Sample

Temperature

The temperature at which the centrifuge chamber will be held while the samples are being centrifuged.

Default Value: Automatic

Default Calculation: Automatically resolves to Ambient. If ChilledRotor is specified to True, automatically resolves to 4 Celsius.

Pattern Description: Ambient or greater than or equal to -10 degrees Celsius and less than or equal to 40 degrees Celsius.

Programmatic Pattern: (Ambient | RangeP[-10*Celsius, 40*Celsius]) | Automatic

Index Matches to: Sample

CollectionContainer

The container that should be stacked on the bottom of the sample's container to collect the filtrate passing through the filter container.

Default Value: Automatic

Default Calculation: Automatically set to Model[Container, Plate, "96-well 2mL Deep Well Plate"] if the sample is in a filter plate.

Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or {Index, Container} or Null.

Programmatic Pattern: ((Null | ((ObjectP[{Model[Container], Object[Container]}] | _String) | {Alternatives[GreaterEqualP[1, 1]], (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic})) | Automatic) | Null

Index Matches to: Sample

Preparation

Default Value: Automatic

Pattern Description: Manual or Robotic.

Programmatic Pattern: PreparationMethodP | Automatic

WorkCell

Indicates the work cell that this primitive will be run on if Preparation->Robotic.

Default Value: Automatic

Default Calculation: Automatically set to STAR if Preparation->Robotic.

Pattern Description: STAR, bioSTAR, or microbioSTAR or Null.

Programmatic Pattern: ((STAR | bioSTAR | microbioSTAR) | Automatic) | Null

Index Matches to: Sample

MixType

Indicates the style of motion used to mix the sample, prior to starting the experiment.

The instrument that should be used to perform the filtration.

Default Value: Automatic

Default Calculation: Will automatically resolved to an instrument appropriate for the filtration type.

Index Matches to: Sample

Filter

The filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.

Default Value: Automatic

Default Calculation: Will automatically resolve to a filter appropriate for the filtration type and instrument.

Pattern Description: An object of type or subtype Model[Container, Plate, Filter], Model[Container, Vessel, Filter], or Model[Item, Filter] or Null.

Programmatic Pattern: ((Null | ObjectP[{Model[Container, Plate, Filter], Model[Container, Vessel, Filter], Model[Item, Filter]}]) | Automatic) | Null

Index Matches to: Sample

FilterMaterial

The membrane material of the filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.

Default Value: Automatic

Default Calculation: Resolves to an appropriate filter material for the given sample is Filtration is set to True.

Pattern Description: Cellulose, Cotton, Polyethylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, Silica, or HLB or Null.

Programmatic Pattern: ((Null | FilterMembraneMaterialP) | Automatic) | Null

Index Matches to: Sample

PrefilterMaterial

The material from which the prefilter filtration membrane should be made of to remove impurities from the SamplesIn prior to starting the experiment.

Default Value: Automatic

Default Calculation: By default, no prefiltration is performed on samples, even when Filter->True.

Pattern Description: Cellulose, Cotton, Polyethylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, Silica, or HLB or Null.

Programmatic Pattern: ((Null | FilterMembraneMaterialP) | Automatic) | Null

Index Matches to: Sample

FilterPoreSize

The pore size of the filter that should be used when removing impurities from the SamplesIn prior to starting the experiment.

Default Value: Automatic

Default Calculation: Resolves to an appropriate filter pore size for the given sample is Filtration is set to True.

Programmatic Pattern: ((Null | FilterSizeP) | Automatic) | Null

Index Matches to: Sample

The desired container filtered samples should be produced in or transferred into by the end of filtration, with indices indicating grouping of samples in the same plates, if desired.

Default Value: Automatic

Default Calculation: Automatically set as the PreferredContainer for the Volume of the sample. For plates, attempts to fill all wells of a single plate with the same model before using another one.

Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or {Index, Container} or Null.

Index Matches to: Sample

FilterAliquotDestinationWell

The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.

Default Value: Automatic

Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.

Pattern Description: Any well from A1 to H12 or Null.

Programmatic Pattern: ((Null | WellPositionP) | Automatic) | Null

Index Matches to: Sample

Default Value: Automatic

Pattern Description: All or Count or Count or Mass or Volume or Null.

Index Matches to: Sample

TargetConcentration

Default Value: Automatic

Default Calculation: Automatically calculated based on aliquot and buffer volumes.

Pattern Description: Greater than 0 molar or greater than 0 grams per liter or Null.

Programmatic Pattern: ((Null | (GreaterP[0*Molar] | GreaterP[(0*Gram)/Liter])) | Automatic) | Null

Index Matches to: Sample

TargetConcentrationAnalyte

The substance whose final concentration is attained with the TargetConcentration option.

Default Value: Automatic

Programmatic Pattern: ((Null | ObjectP[IdentityModelTypes]) | Automatic) | Null

Index Matches to: Sample

AssayVolume

The desired total volume of the aliquoted sample plus dilution buffer.

Default Value: Automatic

Default Calculation: Automatically determined based on Volume and TargetConcentration option values.

Pattern Description: Greater than or equal to 1 microliter and less than or equal to 20 liters or Null.

Programmatic Pattern: ((Null | RangeP[1*Microliter, 20*Liter]) | Automatic) | Null

Index Matches to: Sample

The buffer that should be added to any aliquots requiring dilution, where the volume of this buffer added is the difference between the AliquotAmount and the total AssayVolume.

Default Value: Automatic

Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is not specified; otherwise, resolves to Null.

Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.

Programmatic Pattern: ((Null | (ObjectP[{Model[Sample], Object[Sample]}] | _String)) | Automatic) | Null

Index Matches to: Sample

AliquotSampleStorageCondition

The non-default conditions under which any aliquot samples generated by this experiment should be stored after the protocol is completed.

Default Value: Automatic

Programmatic Pattern: ((Null | (SampleStorageTypeP | Disposal)) | Automatic) | Null

Index Matches to: Sample

DestinationWell

The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.

Default Value: Automatic

Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.

Pattern Description: Any well from A1 to H12 or list of one or more any well from A1 to H12 or any well from A1 to H12 entries or Null.

Programmatic Pattern: ((WellPositionP | {((Automatic | Null) | WellPositionP)..}) | Automatic) | Null

AliquotContainer

Default Value: Automatic

AliquotPreparation

Indicates the desired scale at which liquid handling used to generate aliquots will occur.

Default Value: Automatic

Default Calculation: Automatic resolution will occur based on manipulation volumes and container types.

Pattern Description: Manual or Robotic or Null.

Programmatic Pattern: (PreparationMethodP | Automatic) | Null

ConsolidateAliquots

Indicates if identical aliquots should be prepared in the same container/position.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Post Experiment

SamplesInStorageCondition

Default Value: Null

Programmatic Pattern: (Null | (Alternatives[SampleStorageTypeP | Disposal])) | Null

Index Matches to: Sample

MeasureWeight

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

MeasureVolume

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

ImageSample

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Protocol

NumberOfReplicates

Number of times each of the input samples should be centrifuged using identical experimental parameters.

Default Value: Null

Pattern Description: Greater than or equal to 1 in increments of 1 or Null.

Programmatic Pattern: GreaterEqualP[1, 1] | Null

ReadPlate

Sample

The sample whose absorbance/fluorescence/luminescence should be read.

General

Type

The style of plate reading to perform

Default Value: Automatic

Default Calculation: Automatically set based by considering provided options specific to given types, for instance if PrimaryInjectionTime is set it's assumed that a kinetics experiment is being done.

Pattern Description: AbsorbanceIntensity, AbsorbanceSpectroscopy, AbsorbanceKinetics, AlphaScreen, FluorescenceIntensity, FluorescenceSpectroscopy, FluorescenceKinetics, LuminescenceIntensity, LuminescenceSpectroscopy, or LuminescenceKinetics.

Programmatic Pattern: ReadPlateTypeP | Automatic

ReadLocation

Indicates if fluorescence should be measured using an optic above the plate or one below the plate.

Default Value: Automatic

Default Calculation: Defaults to Bottom if RetainCover is set to True, otherwise defaults to Top.

Pattern Description: Top or Bottom.

Programmatic Pattern: ReadLocationP | Automatic

Temperature

The temperature at which the experiment will be performed, if using a plate reader with temperature incubation controls.

Default Value: Ambient

Pattern Description: Ambient or greater than or equal to 25 degrees Celsius and less than or equal to 45 degrees Celsius.

Programmatic Pattern: RangeP[$AmbientTemperature, 45*Celsius] | Ambient

EquilibrationTime

The length of time for which the assay plates should equilibrate at the assay temperature in the plate reader before being read.

Default Value: Automatic

Default Calculation: Defaults to 0 Second if Temperature is set to Ambient. Otherwise defaults to 5 Minute.

Pattern Description: Greater than or equal to 0 minutes and less than or equal to 1 hour.

Programmatic Pattern: RangeP[0*Minute, 1*Hour] | Automatic

NumberOfReadings

Number of redundant readings which should be taken by the detector to determine a single averaged fluorescence intensity reading.

Default Value: 100

Pattern Description: Greater than or equal to 1 and less than or equal to 200.

Programmatic Pattern: RangeP[1, 200]

FocalHeight

The distance from the bottom of the plate carrier to the focal point. If set to Automatic, the focal height will be adjusted based on the Gain adjustment, which will occur only if the gain values are set to percentages.

Default Value: Automatic

Pattern Description: Auto or greater than or equal to 0 millimeters and less than or equal to 25 millimeters or Null.

Programmatic Pattern: ((RangeP[0*Millimeter, 25*Millimeter] | Auto) | Automatic) | Null

WorkCell

Indicates the work cell that this primitive will be run on if Preparation->Robotic.

Default Value: Automatic

Default Calculation: Automatically set to STAR if Preparation->Robotic.

Pattern Description: STAR, bioSTAR, microbioSTAR, or qPix or Null.

Programmatic Pattern: (WorkCellP | Automatic) | Null

The gain which should be applied to the signal reaching the primary detector. This may be specified either as a direct voltage, or as a percentage (which indicates that the gain should be set such that the AdjustmentSample fluoresces at that percentage of the instrument's dynamic range).

Default Value: Automatic

Default Calculation: If unspecified defaults to 90% if an adjustment sample is provided or if the instrument can scan the entire plate to determine gain. Otherwise defaults to 2500 Microvolt

Pattern Description: Greater than or equal to 1 microvolt and less than or equal to 4095 microvolts or greater than or equal to 1 percent and less than or equal to 95 percent.

Programmatic Pattern: (RangeP[1*Percent, 95*Percent] | RangeP[1*Microvolt, 4095*Microvolt]) | Automatic

Index Matches to: ExcitationWavelength

DualEmissionGain

The gain to apply to the signal reaching the secondary detector. This may be specified either as a direct voltage, or as a percentage relative to the AdjustmentSample option.

Indicates if samples should be mixed inside the plate reader chamber.

Default Value: Automatic

Default Calculation: Automatically set to True if any other plate reader mix options are specified.

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

PlateReaderMixTime

The amount of time samples should be mixed inside the plate reader chamber.

Default Value: Automatic

Default Calculation: Automatically set to 30 second if any other plate reader mix options are specified.

Pattern Description: Greater than or equal to 1 second and less than or equal to 1 hour or Null.

Programmatic Pattern: (RangeP[1*Second, 1*Hour] | Automatic) | Null

PlateReaderMixRate

The rate at which the plate should be agitated inside the plate reader chamber.

Default Value: Automatic

Default Calculation: Automatically set to 700 RPM if any other plate reader mix options are specified.

Pattern Description: Greater than or equal to 100 revolutions per minute and less than or equal to 700 revolutions per minute or Null.

Programmatic Pattern: (RangeP[100*RPM, 700*RPM] | Automatic) | Null

PlateReaderMixMode

The pattern of motion which should be employed to shake the plate.

Default Value: Automatic

Default Calculation: Automatically set to DoubleOrbital if any other plate reader mix options are specified.

Pattern Description: Orbital, DoubleOrbital, or Linear or Null.

Programmatic Pattern: (MechanicalShakingP | Automatic) | Null

ReadDirection

Indicates the order in which wells should be read by specifying the plate path the instrument should follow when measuring fluorescence.

Default Value: Row

Pattern Description: Row, Column, SerpentineRow, or SerpentineColumn.

Programmatic Pattern: ReadDirectionP

InjectionSampleStorageCondition

The non-default conditions under which any injection samples used by this experiment should be stored after the protocol is completed.

Default Value: Null

Programmatic Pattern: (SampleStorageTypeP | Disposal) | Null

Sampling

SamplingPattern

Indicates where in the well measurements are taken.

Default Value: Automatic

Pattern Description: Matrix, Spiral, Ring, or Center.

Programmatic Pattern: PlateReaderSamplingP | Automatic

SamplingDistance

Indicates the length of the region over which sampling measurements are taken.

Default Value: Automatic

Default Calculation: Automatically resolves to Null if SamplingPattern is set to Center otherwise resolves to 80% of the diameter of the well.

Pattern Description: Greater than or equal to 1 millimeter and less than or equal to 6 millimeters or Null.

Programmatic Pattern: (RangeP[1*Millimeter, 6*Millimeter] | Automatic) | Null

SamplingDimension

Specifies the size of the grid used for Matrix sampling. For example SamplingDimension->5 will scan a 5 x 5 grid.

Default Value: Automatic

Default Calculation: If the SamplingPattern is set to Matrix, SamplingDimension will be set to 3.

Pattern Description: Greater than or equal to 2 and less than or equal to 30 or Null.

Programmatic Pattern: (RangeP[2, 30] | Automatic) | Null

Post Experiment

SamplesInStorageCondition

Default Value: Null

Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null

Index Matches to: experiment samples

Optics

ExcitationWavelength

The wavelength(s) which should be used to excite fluorescence in the samples.

Default Value: Automatic

Pattern Description: Greater than or equal to 320 nanometers and less than or equal to 740 nanometers.

Programmatic Pattern: RangeP[320*Nanometer, 740*Nanometer] | Automatic

Index Matches to: ExcitationWavelength

EmissionWavelength

The wavelength(s) at which fluorescence emitted from the sample should be measured.

Default Value: Automatic

Pattern Description: Greater than or equal to 320 nanometers and less than or equal to 740 nanometers.

Programmatic Pattern: RangeP[320*Nanometer, 740*Nanometer] | Automatic

Index Matches to: ExcitationWavelength

DualEmissionWavelength

The time between the movement of the plate and the beginning of the measurement. It reduces potential vibration of the samples in plate due to the stop and go motion of the plate carrier.

Default Value: 0 milliseconds

Pattern Description: Greater than or equal to 0 seconds and less than or equal to 1 second.

Programmatic Pattern: RangeP[0*Second, 1*Second]

ExcitationTime

The time that the samples will be excited by the light source and the singlet Oxygen is generated.

Default Value: 80 milliseconds

Pattern Description: Greater than or equal to 0.01 seconds and less than or equal to 1 second.

Programmatic Pattern: RangeP[0.01*Second, 1*Second]

Data Processing

BlankAbsorbance

Indicates if blank samples are prepared to account for the background signal when reading absorbance of the assay samples.

Default Value: True

Pattern Description: True or False.

Programmatic Pattern: BooleanP

Blank

The source used to generate a blank sample whose absorbance is subtracted as background from the absorbance readings of the input sample.

Default Value: Automatic

Default Calculation: Automatically set to Null if BlankAbsorbance is False, and Model[Sample, "Milli-Q water"] if BlankAbsorbance is True.

Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.

Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null

Spectral Scanning

AdjustmentEmissionWavelength

The wavelength at which fluorescence should be read in order to perform automatic adjustments of gain and focal height values at run time.

Default Value: Automatic

Default Calculation: If unspecified uses the wavelength in the middle of the requested emission wavelength range if the gain is not being set directly.

Pattern Description: Greater than or equal to 320 nanometers and less than or equal to 740 nanometers or Null.

Programmatic Pattern: (RangeP[320*Nanometer, 740*Nanometer] | Automatic) | Null

AdjustmentExcitationWavelength

The wavelength at which the sample should be excited in order to perform automatic adjustments of gain and focal height values at run time.

Default Value: Automatic

Default Calculation: If unspecified uses the wavelength in the middle of the requested excitation wavelength range if the gain is not being set directly.

Pattern Description: Greater than or equal to 320 nanometers and less than or equal to 740 nanometers or Null.

Programmatic Pattern: (RangeP[320*Nanometer, 740*Nanometer] | Automatic) | Null

FillToVolume

fillToVolumeRules

Pattern Description: Ultrasonic or Volumetric.

Programmatic Pattern: FillToVolumeMethodP | Automatic

Index Matches to: Sample

SolventLabel

A user defined word or phrase used to identify the solvent that is used for the fill to volume, for use in downstream unit operations.

Default Value: Automatic

Pattern Description: A string or Null.

Programmatic Pattern: ((Null | _String) | Automatic) | Null

Index Matches to: Sample

SolventContainer

The container that the source sample will be located in during the transfer. This option can only be Null when using a WaterPurifier (which directly dispenses into a graduated cylinder).

Default Value: Automatic

Default Calculation: Automatically set to the Object[Container, Vessel] if an Object[Sample] is specified in the Solvent option. Otherwise, automatically set to a Model[Container, Vessel] on any existing samples that can be used to fulfill the Model[Sample] request or based on the container that the default product for the Model[Sample] comes in.

Pattern Description: Existing Container or New Container or Null.

Index Matches to: Sample

Instrument

Default Value: Automatic

Index Matches to: Sample

TransferEnvironment

Default Value: Automatic

Default Calculation: Automatically set to an instrument that can handle the any safety requirements of the samples being transferred.

Index Matches to: Sample

Tips

The pipette tips used to aspirate and dispense the requested volume.

Default Value: Automatic

Pattern Description: An object of type or subtype Model[Item, Tips] or Object[Item, Tips] or Null.

Programmatic Pattern: ((Null | ObjectP[{Model[Item, Tips], Object[Item, Tips]}]) | Automatic) | Null

Index Matches to: Sample

TipType

The type of pipette tips used to aspirate and dispense the requested volume during the transfer.

The funnel that is used to guide the source sample into the intermediate container when pouring.

Default Value: Automatic

Default Calculation: Automatically set to a funnel that can fit inside the IntermediateContainer, if an IntermediateDecant is required.

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

MeasureVolume

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

ImageSample

Programmatic Pattern: ((Null | RangeP[0*Microliter, 50*Milliliter]) | Automatic) | Null

Index Matches to: Sample

NumberOfAspirationMixes

The number of times the source is quickly aspirated and dispensed to mix the source sample immediately before it is transferred into the destination.

Default Value: Automatic

Default Calculation: Automatically set to 5 if any of the other AspirationMix options are set. Otherwise, set to Null.

Pattern Description: Greater than or equal to 0 and less than or equal to 50 in increments of 1 or Null.

Programmatic Pattern: ((Null | RangeP[0, 50, 1]) | Automatic) | Null

Index Matches to: Sample

MaxNumberOfAspirationMixes

The number of times the source is quickly aspirated and dispensed to mix the source sample immediately before it is transferred into the destination.

Default Value: Automatic

Default Calculation: Automatically set to 5 if any of the other AspirationMix options are set. Otherwise, set to Null.

Pattern Description: Greater than or equal to 0 and less than or equal to 100 in increments of 1 or Null.

Programmatic Pattern: ((Null | RangeP[0, 100, 1]) | Automatic) | Null

Index Matches to: Sample

DispenseMixVolume

Default Value: Automatic

Default Calculation: Automatically set to 1/2 the volume of the destination sample or the maximum volume of the pipette being used, depending on which value is smaller.

Pattern Description: Greater than or equal to 0 microliters and less than or equal to 50 milliliters or Null.

Programmatic Pattern: ((Null | RangeP[0*Microliter, 50*Milliliter]) | Automatic) | Null

Index Matches to: Sample

NumberOfDispenseMixes

The number of times the destination is quickly aspirated and dispensed to mix the destination sample immediately after the source is dispensed.

Default Value: Automatic

Default Calculation: Automatically set to 5 if any of the other DispenseMix options are set. Otherwise, set to Null.

Pattern Description: Greater than or equal to 0 and less than or equal to 50 in increments of 1 or Null.

Programmatic Pattern: ((Null | RangeP[0, 50, 1]) | Automatic) | Null

Index Matches to: Sample

Pattern Description: Greater than or equal to 0 minutes and less than or equal to 72 hours or Null.

Programmatic Pattern: ((Null | RangeP[0*Minute, $MaxExperimentTime]) | Automatic) | Null

Index Matches to: Sample

SourceEquilibrationCheck

Default Value: Automatic

Default Calculation: Automatically set to Null.

Pattern Description: ImmersionThermometer or IRThermometer or Null.

Programmatic Pattern: ((Null | EquilibrationCheckP) | Automatic) | Null

Index Matches to: Sample

DestinationTemperature

Default Value: Automatic

Default Calculation: Automatically set to the TransferTemperature or TransportTemperature (whichever is first filled out) of the destination sample. Otherwise, is transferred at Ambient temperature.

Pattern Description: Ambient or greater than or equal to -20 degrees Celsius and less than or equal to 90 degrees Celsius or Null.

Programmatic Pattern: ((Null | (RangeP[$MinIncubationTemperature, 90*Celsius] | Ambient)) | Automatic) | Null

Index Matches to: Sample

DestinationEquilibrationTime

The duration of time for which the samples will be heated/cooled to the target DestinationTemperature.

Default Value: Automatic

Default Calculation: Automatically set to 5 Minute if DestinationTemperature is not set to Ambient.

Pattern Description: Greater than or equal to 0 minutes and less than or equal to 72 hours or Null.

Programmatic Pattern: ((Null | RangeP[0*Minute, $MaxExperimentTime]) | Automatic) | Null

Index Matches to: Sample

MaxDestinationEquilibrationTime

Default Value: Automatic

Default Calculation: Automatically set to 30 Minute if DestinationEquilibrationCheck is set.

Pattern Description: Greater than or equal to 0 minutes and less than or equal to 72 hours or Null.

Programmatic Pattern: ((Null | RangeP[0*Minute, $MaxExperimentTime]) | Automatic) | Null

Index Matches to: Sample

DestinationEquilibrationCheck

Default Value: Automatic

Default Calculation: Automatically set to Null.

Pattern Description: ImmersionThermometer or IRThermometer or Null.

Programmatic Pattern: ((Null | EquilibrationCheckP) | Automatic) | Null

Index Matches to: Sample

Wait

duration

The amount of time to pause during execution of primitives.

Pattern: GreaterP[0*Second]

General

Duration

The amount of time to pause before continuing the execution of future unit operations.

Default Value: Null

Pattern Description: Greater than 0 seconds.

Programmatic Pattern: GreaterP[0*Second]

Experiment Options

Protocol

LiquidHandlingScale

Indicates the desired scale at which liquid handling will occur.

Default Value: Automatic

Default Calculation: Automatic resolution will occur based on manipulation volumes and container types.

Pattern Description: MacroLiquidHandling or MicroLiquidHandling.

Programmatic Pattern: LiquidHandlingScaleP | Automatic

OptimizePrimitives

Indicates that input liquid-handling primitives can be modified and merged to be most efficient for the instrument executing the liquid transfers. Optimization will not modify the order of primitives or their source(s), destination(s), and amount(s).

Figure 3.1: Any liquid handling operations (Transfer, Aliquot, and Consolidation) will be "optimized" such that the transfers are grouped and executed using the most efficient pipetting channels. Multiple Transfer, Aliquot, and Consolidation primitives may be merged into the same Transfer primitive to be executed simultaneously. Therefore, it is not necessarily important to use the "listable" syntax when creating primitives. Full plate-to-plate transfers will automatically use the MultiProbeHead to perform all transfers simultaneously. The single-probe channels are optimized by performing transfers in column-wise format. For instance, simultaneous aspiration can occur from wells A1, B1, C1, D1, E1, F1, G1, and H1 but not A1 through A8 of a plate. Because of this, the order of sources and destinations may be modified during optimization. However, order-dependence will be conserved where - for example - any destination locations that then become source locations in downstream primitives will not be re-ordered.

Default Value: True

Pattern Description: True or False.

Programmatic Pattern: BooleanP

LiquidHandler

Indicates the liquid handler which should be used to perform the provided manipulations.

Default Value: Automatic

Default Calculation: Automatically resolves based on the containers required by the manipulations.

Pattern Description: An object of type or subtype Model[Instrument, LiquidHandler] or Object[Instrument, LiquidHandler] or Null.

Programmatic Pattern: (ObjectP[{Model[Instrument, LiquidHandler], Object[Instrument, LiquidHandler]}] | Automatic) | Null

TareWeighContainers

Indicates if empty containers should be tare weighed prior to running the experiment. Tare weighing of each container improves accuracy of any subsequent weighing or gravimetric volume measurement performed in the container.

Default Value: Automatic

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

PostProcessing

PreferredSampleImageOrientation

Indicates the preferred orientation in which the SamplesOut manipulated in the course of the experiment should be imaged after running the experiment.

Default Value: Automatic

Pattern Description: Side or Top or Null.

Programmatic Pattern: (ImagingDirectionP | Automatic) | Null

Post Experiment

SamplesInStorageCondition

Default Value: Null

Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null

SamplesOutStorageCondition

Default Value: Null

Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null

General

PlaceLids

Indicates if lids are placed on all plates after the manipulations have completed. This should decrease evaporation.

Default Value: Automatic

Default Calculation: If automatic, resolves to True if no Cover or Uncover primitives are specified.

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Protocol Options

Organizational Information

Name

A object name which should be used to refer to the output object in lieu of an automatically generated ID number.

Default Value: Null

Pattern Description: A string or Null.

Programmatic Pattern: _String | Null

Post Experiment

MeasureWeight

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

MeasureVolume

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

ImageSample

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Example Calls

Basic Examples:

Transfer a specified volume of a sample to an empty container:

Transfer a sample into another existing sample by directly specifying the source and destination samples:

Transfer enough of the sample into the container until a desired final volume is reached:

Transfer a chemical to an empty container without specifying a particular sample:

Transfer a chemical to any empty container of a given type:

Preferred Input Containers

SBS Format Plates

2mL and 50mL Tubes

Data Processing

Plot the TADM pressure traces

Warnings and Errors

Messages (98)

AllManipulationsRemoved (1)

If ALL provided manipulations are automatically removed due to containing zero amounts, a hard error will be returned and no protocol generated:

ConflictingCoolingShaking (1)

Cooling and Shaking cannot be performed on the same sample at MicroLiquidHandling scale:

ConflictingFilterPrimitiveKeys (1)

A Filter primitive's keys must be specific for either micro or macro liquid handling, but not both:

ConflictingIncubation (1)

Incubate primitives cannot specify different parameters for the same container or samples in the same container:

DeprecatedModels (1)

Models marked as deprecated may not be involved in manipulations; inclusion of such models will result in an error:

DiscardedSamples (1)

Discarded samples may not be involved in manipulations; inclusion of any such samples or containers will result in an error:

DrainedWell (2)

A warning will be thrown if, based on current sample volume information, a manipulation is expected to draw more from a given sample than will exist at that time:

The DrainedWell check will take into account previous manipulations that supplement existing sample volumes, and not throw an error in this case:

DuplicateModelName (1)

Error if a ModelName is used multiple times:

DuplicateName (1)

If a sample manipulation protocol already exists with the specified name, returns and error and does not create a protocol:

DuplicateSamplesDefined (1)

Error if the same sample was Defined multiple times:

EmptySourceContainer (1)

An error will be thrown if the source container is empty for a Transfer primitive:

EmptyWells (1)

A ReadPlate primitive's has to specify a sample in a plate and not an empty well:

Error::FilterManipConflictsWithResolvedScale (1)

If a primitive requires macro liquid handling scale (here the Incubate primitive), the Filter primitive's keys cannot be requiring micro liquid handling:

Error::InvalidCollectionContainer (1)

On micro liquid handling scale, a Filter primitive's CollectionContainer must be a plate, and that plate currently must be of the type 'Model[Container, Plate, "96-well 2mL Deep Well Plate"]':

FillToVolumeConflictsWithScale (1)

An error will be thrown if the specified LiquidHandlingScale is MicroLiquidHandling, while the manipulations contain a FillToVolume primitive:

FillToVolumeDestinationsNotUnique (1)

An error will be thrown if multiple FillToVolume primitives use the same destination container:

FilterMagnetPrimitives (1)

The Filter and MoveToMagnet/RemoveFromMagnet primitives can't both be specified:

FilterManipConflictsWithScale (1)

A Filter primitive's keys must match the liquid handling scale specified:

IncompatibleChemicals (1)

An error will be thrown if micro liquid handling is requested, but any of the input samples or models have been marked as automated liquid handler-incompatible:

IncompatibleCollectionContainer (1)

A Filter primitive must have a compatible CollectionContainer specified:

IncompatibleFilterContainer (1)

A Filter primitive must use a compatible filter container specified:

IncompatibleIncubationFootprints (1)

Incubate primitives do not support containers with footprints that are not Plate:

IncompatibleLiquidHandler (1)

An error will be thrown if the specified LiquidHandler cannot accommodate Incubate primitives:

IncompatibleMagnetContainer (1)

The sample in the MoveToMagnet/RemoveFromMagnets primitive(s) must be in a 96-well plate:

IncompatiblePipettingParametersScale (1)

Error if MacroLiquidHandling is required but a TipType is specified:

IncompatibleReadPlatePlateModels (1)

Multiple ReadPlate primitives may not use both 96-well and 384-well plates in a single sample manipulation:

IncompatibleTipForMixVolume (1)

Error if a specified tip has a maximum aspiration volume less than the volume being mixed in a Mix primitive:

IncompatibleTipSize (1)

Error if a TipSize is specified that is not compatible with any liquid handlers:

IncubateManipConflictsWithResolvedScale (1)

An error will be thrown if Incubate primitives have keys specific to MicroLiquidHandling, however another primitive requires the scale MacroLiquidHandling:

IncubateManipConflictsWithScale (3)

An error will be thrown if the Incubate primitive lists keys that are specific for MacroLiquidHandling while LiquidHandlingScale is set to MicroLiquidHandling:

An error will be thrown if the Incubate primitive lists keys that are specific for MicroLiquidHandling while LiquidHandlingScale is set to MacroLiquidHandling:

An error will be thrown if the Resuspend primitive lists keys that are specific for MacroLiquidHandling while LiquidHandlingScale is set to MicroLiquidHandling:

InvalidCentrifugePrimitives (1)

Returns $Failed if samples cannot be centrifuged:

InvalidCollectionContainerAccess (1)

Collection plates are not allowed to be transferred into/out of when they are stacked under the filter plate (when the corresponding filter plate is being loaded in preparation for filteration):

InvalidContainerName (1)

Container must be specified or Sample must specify a location if ContainerName is specified:

InvalidFilterContainerAccess (2)

Only one filter plate is allowed to be transferred into at a time (between filterations, so that the filtered material does not drip onto the liquid handling deck):

InvalidFilterSampleLocation (3)

A Filter primitive's Sample must be in a filter plate:

A Filter primitive's Sample referenced container must be a filter plate:

A Filter primitive's Sample referenced name must be in a filter plate:

InvalidFilterSampleSpecification (1)

A Filter primitive must specify a sample in its Sample key:

InvalidFilterSourcePrimitive (1)

Micro filter primitives can only have samples from the same container, since the MPE2 can only filter one filter plate/collection plate stack at a time:

InvalidIncubatePrimitive (1)

An error will be thrown if the Incubate primitive lists keys that are specific for both MicroLiquidHandling and MacroLiquidHandling scales:

InvalidLiquidHandler (1)

An error will be thrown if a provided LiquidHandler option cannot accommodate the manipulations:

InvalidModelParameters (1)

ModelType and ModelName must be specified if any model parameters (TransportWarmed, State, Expires, ShelfLife, UnsealedShelfLife, or DefaultStorageCondition) are specified:

InvalidModelSpecification (1)

Model cannot be specified as well as ModelType or ModelName:

InvalidModelTypeName (1)

ModelName and ModelType must be specified together in Define primitives:

InvalidName (1)

The Name or ContainerName in a Define primitive cannot be a well position:

InvalidNameReference (1)

Names referred to by any primitives must have an associated Define primitive :

InvalidPrimitiveValue (1)

An error will be thrown if any manipulation keys do not match expected patterns:

InvalidReadPlateSample (1)

A ReadPlate primitive's Sample key specifies a sample, model, or container and well position:

InvalidResidualIncubation (1)

ResidualIncubation cannot be False when ResidualTemperature is specified (macro liquid handling):

InvalidResidualMix (1)

ResidualMix cannot be False when ResidualMixRate is specified (macro liquid handling):

InvalidResidualMixRate (1)

On MacroLiquidHandling scale, ResidualMixRate has to be identical to MixRate:

InvalidResidualTemperature (1)

On MacroLiquidHandling scale, ResidualTemperature has to be identical to Temperature:

InvalidSampleContainer (1)

Sample must be a location or Container must be specified if ModelType/ModelName are specified:

InvalidSampleParameters (1)

StorageCondition or ExpirationDate can only be specified for samples that do not already exist:

InvalidTransferFilterPlatePrimitive (1)

Transfers into multiple filter plates within a single primitive are now allowed (since only one filter plate can be stacked on the collection plate at a time, to prevent dripping onto the deck):

InWellSeparationKeyNotAllowed (1)

An error will be thrown if any manipulation contains InWellSeparation Key as it is not supported by ExperimentSampleManipulation:

LiquidHandlerNotCompatibleWithTipType (1)

Error if a set of manipulations requires tips that cannot fit on a specified liquid handler's deck:

MicroPrimitiveMissingKeys (3)

An error will be thrown if Incubate primitives are missing keys that are required for MicroLiquidHandling, when the scale was resolved to MicroLiquidHandling (for instance because no other primitive required macro liquid handling):

An error will be thrown if Incubate primitives are missing keys that are required for MicroLiquidHandling, when the scale was user-specified to MicroLiquidHandling:

An error will be thrown if Resuspend primitives are missing keys that are required for MicroLiquidHandling but mixing is still desired, when the scale was user-specified to MicroLiquidHandling:

MicroScaleNotPossible (2)

An error will be thrown if an explicitly-provided liquid handling scale is not compatible with the requested manipulations; in this case, a solid transfer cannot be performed at micro scale:

An error will be thrown if the specified LiquidHandlingScale is MicroLiquidHandling, while the manipulations require MacroLiquidHandling:

MissingDefineKeys (1)

The Name or ContainerName and Sample or Container keys must be specified in a Define primitive:

MissingMicroFilterKeys (1)

For micro liquid handling scale, the Filter primitive's keys 'Pressure' and 'Time' are required:

MissingMixKeys (1)

Error if a Mix primitive does not include the required keys:

MissingTareWeight (1)

If TareWeighContainers->False and any empty containers' models lack TareWeight, returns an error and does not create a protocol:

ModelNameExists (1)

Error if a ModelName is specified that is already used:

MultiProbeHeadInvalidTransfer (1)

Error if a MultiProbeHead transfer is not specified with exactly 96 wells:

NotCalibratedFillToVolumeDestination (1)

An error will be thrown if FilLToVolume primitives have destination container models without a calibration populated:

OverfilledWell (2)

An error will be thrown if at any point, a destination will have more volume added to it than it can contain:

Transfers into the same destination will be considered cumulatively when determining whether a destination location is overfilled:

PrimitiveAmountsInputInvalid (1)

An error will be thrown if the lengths of the Amounts key and Sources/Destinations key for Aliquot or Consolidation primitives don't match:

PrimitiveInputLengthsInvalid (1)

An error will be thrown if the lengths of the Source and Destination key for Transfer primitives don't match:

ResidualIncubationNeeded (1)

ResidualIncubation cannot be False when ResidualMix is set to True:

ResidualMixNeeded (1)

An error will be thrown if ResidualIncubation is specified or resolved to True, and ResidualMix set to False, even though we're shaking (MacroLiquidHandling):

SampleManipulationAmountOutOfRange (1)

An error will be thrown if any manipulations fall outside currently-measurable ranges:

TipSizeIncompatibleWithContainers (1)

Error if a specified TipType is incompatible with a container:

TipTypeDoesNotExistForSize (1)

Error if a specified TipSize does not exist for a specified TipType:

TipTypeSizeDoesNotExist (1)

Error if a specified TipSize does not match the MaxVolume of the TipType specified:

TooManyContainers (1)

If the desired scale is micro liquid handling, but more containers are provided than will fit on any current micro liquid handling robot deck, an error will be thrown:

TooManyIncubationContainers (1)

Incubate primitives cannot use more than four incubators (only four or fewer containers can be residually incubated or mixed):

TooManyInjectionSamples (1)

A maximum of two unique injection samples can be used across all ReadPlate primitives:

TooManyMacroFilterCollectionPlates (1)

Filtering on macro liquid handling scale does not support samples that would require multiple collection containers if one of them is a plate:

TooManyMacroFilterContainers (1)

Filtering on macro liquid handling scale does not support multiple plates as input into one filter primitive:

TooManyReadPlateContainers (1)

A single ReadPlate primitive must have samples and blanks in the same container:

TooManyTipsRequired (1)

Error if a set of manipulations will require more tips than can fit on the deck:

TransferStateAmountMismatch (1)

Prints a message and returns $Failed if a request to transfer a liquid gives the transfer amount as a mass:

TransferTypeDefaulted (1)

TransferType will be defaulted if the provided value is inconsistent with the requested amount:

UnusedLiquidHandler (1)

A warning will be thrown if a liquid handler instrument is provided but will not be used due to the liquid handling scale:

VentilatedOpenContainer (1)

Throws errors if substances requiring a fume hood are set to be transferred into open containers:

ZeroAmountManipulationRemoved (2)

If an entire manipulation has only zero amounts, it will be automatically removed from the manipulations list:

If an entire manipulation has only zero amounts, it will be automatically removed from the manipulations list. However, warnings will only be displayed if not in Engine:

ZeroAmountRemoved (2)

If an amount of 0 is specified in a manipulation, it will be automatically removed, along with the corresponding source/destination:

Last modified on Tue 28 Feb 2023 20:57:59