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ECL`

ExperimentPCR

ExperimentPCR[Samples]⟹Protocol

creates a Protocol object for running a polymerase chain reaction (PCR) experiment, which uses a thermocycler to amplify target sequences from the Samples.

ExperimentPCR[Samples,PrimerPairs]⟹Protocol

creates a Protocol object for running a polymerase chain reaction (PCR) experiment, which uses a thermocycler to amplify target sequences from the Samples using the PrimerPairs.

    
Polymerase Chain Reaction (PCR) is a method used to amplify a target sequence from a small quantity of template nucleic acid using oligonucleotide primers complementary to the two ends of the target sequence. Typically, the method entails thermocycling reaction mixtures composed of the template, primers, polymerase, nucleotides, and buffer, resulting in an exponential amplification of the target sequence.
    

Experimental Principles

    Figure 1.1: Step 1: Reaction mixtures are prepared in a 96-well PCR plate. Step 2: The polymerase can be heat-activated in hot start PCR. Steps 3-5: The samples undergo the thermocycling procedure, which includes denaturation, annealing, and extension. Step 6: The PCR products can go through a final extension step. Step 7: The products are held at a set temperature.

Instrumentation

    Automated Thermal Cycler

    Figure 2.1: The Automated Thermal Cycler allows programmable 96-well plate-based thermocycling in the temperature range from 4 °C to 105 °C, with a maximum ramp rate of 3.5 °C/sec. Additionally, its automated plate cover can be heated up to 105 °C, which improves thermal contact and minimizes condensation on the plate seal.

Experiment Options

    General

    Instrument

    The instrument for running the polymerase chain reaction (PCR) experiment.
    Default Value: Model[Instrument, Thermocycler, Automated Thermal Cycler]
    Pattern Description: An object of type or subtype Model[Instrument, Thermocycler] or Object[Instrument, Thermocycler]
    Programmatic Pattern: ObjectP[{Model[Instrument, Thermocycler], Object[Instrument, Thermocycler]}]

    LidTemperature

    The temperature of the instrument's plate lid throughout the reaction. The lid is heated to prevent water from condensing on the plate seal.
    Default Value: 99 degrees Celsius
    Pattern Description: Greater than or equal to 30 degrees Celsius and less than or equal to 105 degrees Celsius.
    Programmatic Pattern: RangeP[30*Celsius, 105*Celsius]

    Preparation

    Indicates if this unit operation is carried out primarily robotically or manually. Manual unit operations are executed by a laboratory operator and robotic unit operations are executed by a liquid handling work cell.
    Default Value: Automatic
    Pattern Description: Manual or Robotic.
    Programmatic Pattern: PreparationMethodP | Automatic

    WorkCell

    The automated workstation with a collection of integrated instruments on which this unit operation will be will be performed 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

    Sample Preparation

    SampleVolume

    For each sample, the volume to add to the reaction.
    Default Value: Automatic
    Default Calculation: Automatically set to 2 Microliter if PreparedPlate is not True, and automatically set to 0 Microliter if it is True.
    Pattern Description: Greater than or equal to 0 microliters and less than or equal to 100 microliters.
    Programmatic Pattern: RangeP[0*Microliter, 100*Microliter] | Automatic
    Index Matches to: experiment samples

    ForwardPrimerVolume

    For each sample, the forward primer volume(s) to add to the reaction.
    Default Value: Automatic
    Default Calculation: Automatically set to 1 microliter for each forward primer specified, or Null otherwise.
    Pattern Description: Multiple forward primers or Single forward primer or Null.
    Programmatic Pattern: ((RangeP[0*Microliter, 100*Microliter] | {RangeP[0*Microliter, 100*Microliter]..}) | Automatic) | Null
    Index Matches to: experiment samples

    ReversePrimerVolume

    For each sample, the reverse primer volume(s) to add to the reaction.
    Default Value: Automatic
    Default Calculation: Automatically set to match ForwardPrimerVolume.
    Pattern Description: Multiple forward primers or Single forward primer or Null.
    Programmatic Pattern: ((RangeP[0*Microliter, 100*Microliter] | {RangeP[0*Microliter, 100*Microliter]..}) | Automatic) | Null
    Index Matches to: experiment samples

    BufferVolume

    For each sample, the buffer volume to add to bring each reaction to ReactionVolume.
    Default Value: Automatic
    Default Calculation: Automatically set according to the equation BufferVolume=ReactionVolume-(SampleVolume+MasterMixVolume+ForwardPrimerVolume+ReversePrimerVolume) if Buffer is not set to Null, or Null otherwise.
    Pattern Description: Multiple forward primers or Single forward primer or Null.
    Programmatic Pattern: ((RangeP[0*Microliter, 100*Microliter] | {RangeP[0*Microliter, 100*Microliter]..}) | Automatic) | Null
    Index Matches to: experiment samples

    ReactionVolume

    The total volume of the reaction including the template, primers, master mix, and buffer.
    Default Value: 20 microliters
    Pattern Description: Greater than or equal to 10 microliters and less than or equal to 100 microliters.
    Programmatic Pattern: RangeP[10*Microliter, 100*Microliter]

    PreparedPlate

    Indicates if the input sample or container has already been prepared and does not need to be diluted/mixed with master mix or buffer. If set to True, MasterMix and Buffer will be set to Null and the input sample will be used as is.
    Default Value: Automatic
    Default Calculation: Automatically set to True if MasterMix and Buffer are set to Null and no primers were specified. Otherwise set to False.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic

    MasterMix

    The stock solution composed of the polymerase, nucleotides, and buffer for amplifying the target sequences.
    Default Value: Automatic
    Default Calculation: Automatically set to $PCRDefaultMasterMix if PreparedPlate is not 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

    MasterMixVolume

    The volume of master mix to add to the reaction.
    Default Value: Automatic
    Default Calculation: Automatically set to 0.5*ReactionVolume if MasterMix is not set to Null, or Null otherwise.
    Pattern Description: Greater than or equal to 0 microliters and less than or equal to 100 microliters or Null.
    Programmatic Pattern: (RangeP[0*Microliter, 100*Microliter] | Automatic) | Null

    Buffer

    The solution for bringing each reaction to ReactionVolume once all the reaction components (template, primers, and master mix) are added.
    Default Value: Automatic
    Default Calculation: Automatically set to Model[Sample,"Milli-Q water"] if PreparedPlate is not 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

    Post Experiment

    ForwardPrimerStorageCondition

    For each sample, the non-default conditions under which the forward primers of this experiment should be stored after the protocol is completed. If left unset, the forward primers will be stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: Multiple forward primers or Single forward primer or Null.
    Programmatic Pattern: ((SampleStorageTypeP | Disposal) | {(SampleStorageTypeP | Disposal)..}) | Null
    Index Matches to: experiment samples

    ReversePrimerStorageCondition

    For each sample, the non-default conditions under which the reverse primers of this experiment should be stored after the protocol is completed. If left unset, the reverse primers will be stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: Multiple forward primers or Single forward primer or Null.
    Programmatic Pattern: ((SampleStorageTypeP | Disposal) | {(SampleStorageTypeP | Disposal)..}) | Null
    Index Matches to: experiment samples

    MasterMixStorageCondition

    The non-default condition under which MasterMix of this experiment should be stored after the protocol is completed. If left unset, MasterMix will be stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (SampleStorageTypeP | Disposal) | Null

    SamplesInStorageCondition

    The non-default conditions under which the SamplesIn of this experiment should be stored after the protocol is completed. If left unset, SamplesIn will be stored according to their current StorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null
    Index Matches to: experiment samples

    SamplesOutStorageCondition

    The non-default conditions under which any new samples generated by this experiment should be stored after the protocol is completed. If left unset, the new samples will be stored according to their Models' DefaultStorageCondition.
    Default Value: Null
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null
    Index Matches to: experiment samples

    Polymerase Activation

    Activation

    Indicates if hot start activation should be performed. In order to reduce non-specific amplification, enzymes can be made room temperature stable by inhibiting their activity via thermolabile conjugates. Once an experiment is ready to be run, this inhibition is disabled by heating the reaction to ActivationTemperature.
    Default Value: Automatic
    Default Calculation: Automatically set to True if other Activation options are set, or False otherwise.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic

    ActivationTime

    The length of time for which the sample is held at ActivationTemperature to remove the thermolabile conjugates inhibiting polymerase activity.
    Default Value: Automatic
    Default Calculation: Automatically set to 60 seconds if Activation is set to True, or Null otherwise.
    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

    ActivationTemperature

    The temperature to which the sample is heated to remove the thermolabile conjugates inhibiting polymerase activity.
    Default Value: Automatic
    Default Calculation: Automatically set to 95 degrees Celsius if Activation is set to True, or Null otherwise.
    Pattern Description: Greater than or equal to 4 degrees Celsius and less than or equal to 105 degrees Celsius or Null.
    Programmatic Pattern: (RangeP[4*Celsius, 105*Celsius] | Automatic) | Null

    ActivationRampRate

    The rate at which the sample is heated to reach ActivationTemperature.
    Default Value: Automatic
    Default Calculation: Automatically set to 3.5 degrees Celsius per second if Activation is set to True, or Null otherwise.
    Pattern Description: Greater than or equal to 0.2 degrees Celsius per second and less than or equal to 3.5 degrees Celsius per second or Null.
    Programmatic Pattern: (RangeP[0.2*(Celsius/Second), 3.5*(Celsius/Second)] | Automatic) | Null

    Denaturation

    DenaturationTime

    The length of time for which the sample is held at DenaturationTemperature to allow the dissociation of the double stranded template into single strands.
    Default Value: 30 seconds
    Pattern Description: Greater than or equal to 1 second and less than or equal to 1 hour.
    Programmatic Pattern: RangeP[1*Second, 1*Hour]

    DenaturationTemperature

    The temperature to which the sample is heated to allow the dissociation of the double stranded template into single strands.
    Default Value: 95 degrees Celsius
    Pattern Description: Greater than or equal to 4 degrees Celsius and less than or equal to 105 degrees Celsius.
    Programmatic Pattern: RangeP[4*Celsius, 105*Celsius]

    DenaturationRampRate

    The rate at which the sample is heated to reach DenaturationTemperature.
    Default Value: 3.5 degrees Celsius per second
    Pattern Description: Greater than or equal to 0.2 degrees Celsius per second and less than or equal to 3.5 degrees Celsius per second.
    Programmatic Pattern: RangeP[0.2*(Celsius/Second), 3.5*(Celsius/Second)]

    Primer Annealing

    PrimerAnnealing

    Indicates if annealing should be performed as a separate step instead of as part of extension. Lowering the temperature during annealing allows primers to bind to the template and serve as anchor points for the polymerase in the subsequent extension.
    Default Value: Automatic
    Default Calculation: Automatically set to True if other PrimerAnnealing options are set, or False otherwise.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic

    PrimerAnnealingTime

    The length of time for which the sample is held at PrimerAnnealingTemperature to allow primers to bind to the template.
    Default Value: Automatic
    Default Calculation: Automatically set to 30 seconds if PrimerAnnealing is set to True, or Null otherwise.
    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

    PrimerAnnealingTemperature

    The temperature to which the sample is cooled to allow primers to bind to the template.
    Default Value: Automatic
    Default Calculation: Automatically set to 60 degrees Celsius if PrimerAnnealing is set to True, or Null otherwise.
    Pattern Description: Greater than or equal to 4 degrees Celsius and less than or equal to 105 degrees Celsius or Null.
    Programmatic Pattern: (RangeP[4*Celsius, 105*Celsius] | Automatic) | Null

    PrimerAnnealingRampRate

    The rate at which the sample is cooled to reach PrimerAnnealingTemperature.
    Default Value: Automatic
    Default Calculation: Automatically set to 3.5 degrees Celsius per second if PrimerAnnealing is set to True, or Null otherwise.
    Pattern Description: Greater than or equal to 0.2 degrees Celsius per second and less than or equal to 3.5 degrees Celsius per second or Null.
    Programmatic Pattern: (RangeP[0.2*(Celsius/Second), 3.5*(Celsius/Second)] | Automatic) | Null

    Strand Extension

    ExtensionTime

    The length of time for which sample is held at ExtensionTemperature to allow the polymerase to synthesize a new strand using the template and primers.
    Default Value: 60 seconds
    Pattern Description: Greater than or equal to 1 second and less than or equal to 1 hour.
    Programmatic Pattern: RangeP[1*Second, 1*Hour]

    ExtensionTemperature

    The temperature to which the sample is heated/cooled to allow the polymerase to synthesize a new strand using the template and primers.
    Default Value: 72 degrees Celsius
    Pattern Description: Greater than or equal to 4 degrees Celsius and less than or equal to 105 degrees Celsius.
    Programmatic Pattern: RangeP[4*Celsius, 105*Celsius]

    ExtensionRampRate

    The rate at which the sample is heated/cooled to reach ExtensionTemperature.
    Default Value: 3.5 degrees Celsius per second
    Pattern Description: Greater than or equal to 0.2 degrees Celsius per second and less than or equal to 3.5 degrees Celsius per second.
    Programmatic Pattern: RangeP[0.2*(Celsius/Second), 3.5*(Celsius/Second)]

    Cycling

    NumberOfCycles

    The number of times the sample will undergo repeated cycles of denaturation, primer annealing (optional), and strand extension.
    Default Value: 40
    Pattern Description: Greater than or equal to 1 and less than or equal to 60 in increments of 1.
    Programmatic Pattern: RangeP[1, 60, 1]

    Final Extension

    FinalExtension

    Indicates if final extension should be performed to fill in any incomplete products and/or obtain a poly-adenosine overhang on the 3' end of the product.
    Default Value: Automatic
    Default Calculation: Automatically set to True if other FinalExtension options are set, or False otherwise.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic

    FinalExtensionTime

    The length of time for which the sample is held at FinalExtensionTemperature to fill in any incomplete products and/or obtain a poly-adenosine overhang on the 3' end of the product.
    Default Value: Automatic
    Default Calculation: Automatically set to 10 minutes if FinalExtension is set to True, or Null otherwise
    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

    FinalExtensionTemperature

    The temperature to which the sample is heated/cooled to to fill in any incomplete products and/or obtain a poly-adenosine overhang on the 3' end of the product.
    Default Value: Automatic
    Default Calculation: Automatically set to ExtensionTemperature if FinalExtension is set to True, or Null otherwise.
    Pattern Description: Greater than or equal to 4 degrees Celsius and less than or equal to 105 degrees Celsius or Null.
    Programmatic Pattern: (RangeP[4*Celsius, 105*Celsius] | Automatic) | Null

    FinalExtensionRampRate

    The rate at which the sample is heated/cooled to reach ActivationTemperature.
    Default Value: Automatic
    Default Calculation: Automatically set to 3.5 degrees Celsius per second if FinalExtension is set to True, or Null otherwise.
    Pattern Description: Greater than or equal to 0.2 degrees Celsius per second and less than or equal to 3.5 degrees Celsius per second or Null.
    Programmatic Pattern: (RangeP[0.2*(Celsius/Second), 3.5*(Celsius/Second)] | Automatic) | Null

    Infinite Hold

    HoldTemperature

    The temperature to which the sample is cooled and held after the thermocycling procedure.
    Default Value: 10 degrees Celsius
    Pattern Description: Greater than or equal to 4 degrees Celsius and less than or equal to 105 degrees Celsius.
    Programmatic Pattern: RangeP[4*Celsius, 105*Celsius]

    Model Input

    PreparedModelContainer

    Indicates the container in which a Model[Sample] specified as input to the experiment function will be prepared.
    Default Value: Automatic
    Default Calculation: If PreparedModelAmount is set to All and when the input model has a product associated with both Amount and DefaultContainerModel populated, automatically set to the DefaultContainerModel value in the product. Otherwise set to Model[Container, Vessel, "2mL Tube"].
    Pattern Description: An object of type or subtype Model[Container] or Null.
    Programmatic Pattern: (ObjectP[Model[Container]] | Automatic) | Null
    Index Matches to: experiment samples

    PreparedModelAmount

    Indicates the amount of a Model[Sample] specified as input to the experiment function that will be prepared in the PreparedModelContainer. When set to All and the input model sample is not preparable, the entire amount of the input model sample that comes from one of the Products is prepared. The selected product must have both Amount and DefaultContainerModel populated, and it must not be a KitProduct. When set to All and the input model is preparable such as water, 1 Milliliter of the input model sample is prepared.
    Default Value: Automatic
    Default Calculation: Automatically set to 1 Milliliter.
    Pattern Description: All or Count or Count or Mass or Volume or Null.
    Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | RangeP[1*Milligram, 20*Kilogram] | GreaterP[0*Unit, 1*Unit] | GreaterP[0., 1.] | All) | Automatic) | Null
    Index Matches to: experiment samples

Sample Prep Options

    Sample Preparation

    PreparatoryUnitOperations

    Specifies a sequence of transferring, aliquoting, consolidating, or mixing of new or existing samples before the main experiment. These prepared samples can be used in the main experiment by referencing their defined name. For more information, please reference the documentation for ExperimentSamplePreparation.
    Default Value: Null
    Pattern Description: List of one or more unit Operation ManualSamplePreparation or RoboticSamplePreparation or unit Operation must match SamplePreparationP entries or Null.
    Programmatic Pattern: {((ManualSamplePreparationMethodP | RoboticSamplePreparationMethodP) | SamplePreparationP)..} | Null

    Preparatory Incubation

    Incubate

    Indicates if the SamplesIn should be incubated at a fixed temperature prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).
    Default Value: Automatic
    Default Calculation: Resolves to True if any of the corresponding Incubation options are set. Otherwise, resolves to False.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    IncubationTemperature

    Temperature at which the SamplesIn should be incubated for the duration of the IncubationTime prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: Ambient or greater than or equal to -20 degrees Celsius and less than or equal to 500 degrees Celsius or Null.
    Programmatic Pattern: ((Ambient | RangeP[$MinIncubationTemperature, $MaxIncubationTemperature]) | Automatic) | Null
    Index Matches to: experiment samples

    IncubationTime

    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: (RangeP[1*Minute, $MaxExperimentTime] | Automatic) | Null
    Index Matches to: experiment samples

    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: (BooleanP | Automatic) | Null
    Index Matches to: experiment samples

    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: (MixTypeP | Automatic) | Null
    Index Matches to: experiment samples

    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: (BooleanP | Automatic) | Null
    Index Matches to: experiment samples

    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: (RangeP[1*Minute, $MaxExperimentTime] | Automatic) | Null
    Index Matches to: experiment samples

    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.
    Pattern Description: An object of type or subtype Model[Instrument, Roller], Model[Instrument, OverheadStirrer], Model[Instrument, Vortex], Model[Instrument, Shaker], Model[Instrument, BottleRoller], Model[Instrument, Roller], Model[Instrument, Sonicator], Model[Instrument, HeatBlock], Model[Instrument, Homogenizer], Model[Instrument, Disruptor], Model[Instrument, Nutator], Model[Instrument, Thermocycler], Model[Instrument, EnvironmentalChamber], Model[Instrument, Pipette], Object[Instrument, Roller], Object[Instrument, OverheadStirrer], Object[Instrument, Vortex], Object[Instrument, Shaker], Object[Instrument, BottleRoller], Object[Instrument, Roller], Object[Instrument, Sonicator], Object[Instrument, HeatBlock], Object[Instrument, Homogenizer], Object[Instrument, Disruptor], Object[Instrument, Nutator], Object[Instrument, Thermocycler], Object[Instrument, EnvironmentalChamber], or Object[Instrument, Pipette] or Null.
    Programmatic Pattern: (ObjectP[Join[MixInstrumentModels, MixInstrumentObjects]] | Automatic) | Null
    Index Matches to: experiment samples

    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: (RangeP[0*Minute, $MaxExperimentTime] | Automatic) | Null
    Index Matches to: experiment samples

    IncubateAliquotContainer

    The desired type of container that should be used to prepare and house the incubation samples which should be used in lieu of the SamplesIn for the experiment.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.
    Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
    Index Matches to: experiment samples

    IncubateAliquotDestinationWell

    The desired position in the corresponding IncubateAliquotContainer 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: (WellPositionP | Automatic) | Null
    Index Matches to: experiment samples

    IncubateAliquot

    The amount of each sample that should be transferred from the SamplesIn into the IncubateAliquotContainer when performing an aliquot before incubation.
    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: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null
    Index Matches to: experiment samples

    Preparatory Centrifugation

    Centrifuge

    Indicates if the SamplesIn should be centrifuged prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).
    Default Value: Automatic
    Default Calculation: Resolves to True if any of the corresponding Centrifuge options are set. Otherwise, resolves to False.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    CentrifugeInstrument

    The centrifuge that will be used to spin the provided samples prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Instrument, Centrifuge] or Object[Instrument, Centrifuge] or Null.
    Programmatic Pattern: (ObjectP[{Model[Instrument, Centrifuge], Object[Instrument, Centrifuge]}] | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeIntensity

    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: ((GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration]) | Automatic) | Null
    Index Matches to: experiment samples

    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: (GreaterP[0*Minute] | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeTemperature

    The temperature at which the centrifuge chamber should be held while the samples are being centrifuged prior to starting the experiment.
    Default Value: Automatic
    Pattern Description: Ambient or greater than or equal to -10 degrees Celsius and less than or equal to 40 degrees Celsius or Null.
    Programmatic Pattern: ((Ambient | RangeP[-10*Celsius, 40*Celsius]) | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeAliquotContainer

    The desired type of container that should be used to prepare and house the centrifuge samples which should be used in lieu of the SamplesIn for the experiment.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.
    Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
    Index Matches to: experiment samples

    CentrifugeAliquotDestinationWell

    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: (WellPositionP | Automatic) | Null
    Index Matches to: experiment samples

    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 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: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null
    Index Matches to: experiment samples

    Preparatory Filtering

    Filtration

    Indicates if the SamplesIn should be filter prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).
    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: experiment samples

    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: (FiltrationTypeP | Automatic) | Null
    Index Matches to: experiment samples

    FilterInstrument

    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.
    Pattern Description: An object of type or subtype Model[Instrument, FilterBlock], Object[Instrument, FilterBlock], Model[Instrument, PeristalticPump], Object[Instrument, PeristalticPump], Model[Instrument, VacuumPump], Object[Instrument, VacuumPump], Model[Instrument, Centrifuge], Object[Instrument, Centrifuge], Model[Instrument, SyringePump], or Object[Instrument, SyringePump] or Null.
    Programmatic Pattern: (ObjectP[{Model[Instrument, FilterBlock], Object[Instrument, FilterBlock], Model[Instrument, PeristalticPump], Object[Instrument, PeristalticPump], Model[Instrument, VacuumPump], Object[Instrument, VacuumPump], Model[Instrument, Centrifuge], Object[Instrument, Centrifuge], Model[Instrument, SyringePump], Object[Instrument, SyringePump]}] | Automatic) | Null
    Index Matches to: experiment samples

    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: (ObjectP[{Model[Container, Plate, Filter], Model[Container, Vessel, Filter], Model[Item, Filter]}] | Automatic) | Null
    Index Matches to: experiment samples

    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, Polypropylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, AgaroseResin, CobaltResin, Silica, HLB, or AnoporeAlumina or Null.
    Programmatic Pattern: (FilterMembraneMaterialP | Automatic) | Null
    Index Matches to: experiment samples

    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, Polypropylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, AgaroseResin, CobaltResin, Silica, HLB, or AnoporeAlumina or Null.
    Programmatic Pattern: (FilterMembraneMaterialP | Automatic) | Null
    Index Matches to: experiment samples

    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.
    Pattern Description: 0.008 micrometers, 0.02 micrometers, 0.1 micrometers, 0.2 micrometers, 0.22 micrometers, 0.45 micrometers, 1. micrometer, 1.1 micrometers, 2.5 micrometers, 6. micrometers, 20. micrometers, 30. micrometers, or 100. micrometers or Null.
    Programmatic Pattern: (FilterSizeP | Automatic) | Null
    Index Matches to: experiment samples

    PrefilterPoreSize

    The pore size of the filter; all particles larger than this should be removed during the filtration.
    Default Value: Automatic
    Default Calculation: By default, no prefiltration is performed on samples, even when Filter->True.
    Pattern Description: 0.008 micrometers, 0.02 micrometers, 0.1 micrometers, 0.2 micrometers, 0.22 micrometers, 0.45 micrometers, 1. micrometer, 1.1 micrometers, 2.5 micrometers, 6. micrometers, 20. micrometers, 30. micrometers, or 100. micrometers or Null.
    Programmatic Pattern: (FilterSizeP | Automatic) | Null
    Index Matches to: experiment samples

    FilterSyringe

    The syringe used to force that sample through a filter.
    Default Value: Automatic
    Default Calculation: Resolves to an syringe appropriate to the volume of sample being filtered, if Filtration is set to True.
    Pattern Description: An object of type or subtype Model[Container, Syringe] or Object[Container, Syringe] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Container, Syringe], Object[Container, Syringe]}] | _String) | Automatic) | Null
    Index Matches to: experiment samples

    FilterHousing

    The filter housing that should be used to hold the filter membrane when filtration is performed using a standalone filter membrane.
    Default Value: Automatic
    Default Calculation: Resolve to an housing capable of holding the size of the membrane being used, if filter with Membrane FilterType is being used and Filtration is set to True.
    Pattern Description: An object of type or subtype Model[Instrument, FilterHousing], Object[Instrument, FilterHousing], Model[Instrument, FilterBlock], or Object[Instrument, FilterBlock] or Null.
    Programmatic Pattern: (ObjectP[{Model[Instrument, FilterHousing], Object[Instrument, FilterHousing], Model[Instrument, FilterBlock], Object[Instrument, FilterBlock]}] | Automatic) | Null
    Index Matches to: experiment samples

    FilterIntensity

    The rotational speed or force at which the samples will be centrifuged during filtration.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 2000 GravitationalAcceleration if FiltrationType is Centrifuge and Filtration is True.
    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: ((GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration]) | Automatic) | Null
    Index Matches to: experiment samples

    FilterTime

    The amount of time for which the samples will be centrifuged during filtration.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 5 Minute if FiltrationType is Centrifuge and Filtration is True.
    Pattern Description: Greater than 0 minutes or Null.
    Programmatic Pattern: (GreaterP[0*Minute] | Automatic) | Null
    Index Matches to: experiment samples

    FilterTemperature

    The temperature at which the centrifuge chamber will be held while the samples are being centrifuged during filtration.
    Default Value: Automatic
    Default Calculation: Will automatically resolve to 22 Celsius if FiltrationType is Centrifuge and Filtration is True.
    Pattern Description: Greater than or equal to 4 degrees Celsius or Null.
    Programmatic Pattern: ((Alternatives[GreaterEqualP[4*Celsius]]) | Automatic) | Null
    Index Matches to: experiment samples

    FilterContainerOut

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

    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: (WellPositionP | Automatic) | Null
    Index Matches to: experiment samples

    FilterAliquotContainer

    The desired type of container that should be used to prepare and house the filter samples which should be used in lieu of the SamplesIn for the experiment.
    Default Value: Automatic
    Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.
    Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
    Index Matches to: experiment samples

    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: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null
    Index Matches to: experiment samples

    FilterSterile

    Indicates if the filtration of the samples should be done in a sterile environment.
    Default Value: Automatic
    Default Calculation: Resolve to False if Filtration is indicated. If sterile filtration is desired, this option must manually be set to True.
    Pattern Description: True or False or Null.
    Programmatic Pattern: (BooleanP | Automatic) | Null
    Index Matches to: experiment samples

    Aliquoting

    Aliquot

    Indicates if aliquots should be taken from the SamplesIn and transferred into new AliquotSamples used in lieu of the SamplesIn for the experiment. Note that if NumberOfReplicates is specified this indicates that the input samples will also be aliquoted that number of times. Note that Aliquoting (if specified) occurs after any Sample Preparation (if specified).
    Default Value: Automatic
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    AliquotAmount

    The amount of a sample that should be transferred from the input samples into aliquots.
    Default Value: Automatic
    Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container if a liquid, or the current Mass or Count if a solid or counted item, respectively.
    Pattern Description: All or Count or Count or Mass or Volume or Null.
    Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | RangeP[1*Milligram, 20*Kilogram] | GreaterP[0*Unit, 1*Unit] | GreaterP[0., 1.] | All) | Automatic) | Null
    Index Matches to: experiment samples

    TargetConcentration

    The desired final concentration of analyte in the AliquotSamples after dilution of aliquots of SamplesIn with the ConcentratedBuffer and BufferDiluent which should be used in lieu of the SamplesIn for the experiment.
    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: ((GreaterP[0*Molar] | GreaterP[0*(Gram/Liter)]) | Automatic) | Null
    Index Matches to: experiment samples

    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: (ObjectP[IdentityModelTypes] | Automatic) | Null
    Index Matches to: experiment samples

    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: (RangeP[1*Microliter, 20*Liter] | Automatic) | Null
    Index Matches to: experiment samples

    ConcentratedBuffer

    The concentrated buffer which should be diluted by the BufferDilutionFactor in the final solution (i.e., the combination of the sample, ConcentratedBuffer, and BufferDiluent). The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.
    Default Value: Automatic
    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
    Index Matches to: experiment samples

    BufferDilutionFactor

    The dilution factor by which the concentrated buffer should be diluted in the final solution (i.e., the combination of the sample, ConcentratedBuffer, and BufferDiluent). The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.
    Default Value: Automatic
    Default Calculation: If ConcentratedBuffer is specified, automatically set to the ConcentratedBufferDilutionFactor of that sample; otherwise, set to Null.
    Pattern Description: Greater than or equal to 1 or Null.
    Programmatic Pattern: (GreaterEqualP[1] | Automatic) | Null
    Index Matches to: experiment samples

    BufferDiluent

    The buffer used to dilute the aliquot sample such that ConcentratedBuffer is diluted by BufferDilutionFactor in the final solution. The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers 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 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: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null
    Index Matches to: experiment samples

    AssayBuffer

    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: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null
    Index Matches to: experiment samples

    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
    Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: ((SampleStorageTypeP | Disposal) | Automatic) | Null
    Index Matches to: experiment samples

    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
    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 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.
    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

Protocol Options

    Organizational Information

    Template

    A template protocol whose methodology should be reproduced in running this experiment. Option values will be inherited from the template protocol, but can be individually overridden by directly specifying values for those options to this Experiment function.
    Default Value: Null
    Pattern Description: An object of type or subtype Object[Protocol] or an object of type or subtype of Object[Protocol] with UnresolvedOptions, ResolvedOptions specified or Null.
    Programmatic Pattern: (ObjectP[Object[Protocol]] | FieldReferenceP[Object[Protocol], {UnresolvedOptions, ResolvedOptions}]) | Null

    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

    Indicates if any solid samples that are modified in the course of the experiment should have their weights measured and updated after running the experiment. Please note that public samples are weighed regardless of the value of this option.
    Default Value: False
    Pattern Description: True or False or Null.
    Programmatic Pattern: (Null | BooleanP) | 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: False
    Pattern Description: True or False or Null.
    Programmatic Pattern: (Null | BooleanP) | 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: False
    Pattern Description: True or False or Null.
    Programmatic Pattern: (Null | BooleanP) | Null

Example Calls

    Basics

    To perform a PCR experiment on samples containing both templates and primer pairs, simply run:
    Primer pairs may be specified to indicate that they should be added to the reaction mixtures:

    Multiplexing

    Both singleplex and multiplex reactions can be performed:

    Master Mix

    A stock solution composed of polymerase, co-factor, nucleotides, and buffer used to amplify target sequence(s) may be added to the samples:

    Activation

    An activation step to remove the thermolabile conjugates inhibiting polymerase activity may be added to the beginning of the thermocycling profile:

    Primer Annealing

    An annealing step may be performed prior to the extension step:

    Final Extension

    A final extension step to fill in any incomplete products and/or obtain a poly-adenosine overhang on the 3' end of the product may be added to the end of the thermocycling profile:

    Prepared plate

    A PCR friendly plate with samples inside is given as input and no master mix or buffer is needed:

    Robotic PCR

    The PCR may be performed robotically:

    Robotic PCR with prepared plate

    A PCR friendly plate with samples inside is given as input and no master mix or buffer is needed may be performed robotically:

Preferred Input Containers

    The Automated Thermal Cycler accepts MicroAmp EnduraPlate optical 96-well full-skirted plates for manual operation.
    The Automated Thermal Cycler accepts MicroAmp EnduraPlate optical 96-well semi-skirted plates for manual operation.
    The Automated Thermal Cycler accepts low-profile skirted 96-well plates for manual operation.
    The Automated Thermal Cycler accepts low-profile skirted 96-well plates for robotic operation.

Warnings and Errors

    Messages  (30)

    ActivationMismatch  (1)

    Activation options cannot have conflicts:

    BufferVolumeMismatch  (1)

    BufferVolume cannot have conflicts with Buffer:

    DeprecatedModels  (2)

    The primers cannot have a Model that is Deprecated:

    The sample cannot have a Model that is Deprecated:

    DiscardedSamples  (2)

    The primers cannot have a Status of Discarded:

    The sample cannot have a Status of Discarded:

    DuplicateName  (1)

    The specified Name cannot already exist for another PCR protocol:

    FinalExtensionMismatch  (1)

    FinalExtension options cannot have conflicts:

    ForwardPrimerStorageConditionMismatch  (1)

    ForwardPrimerStorageCondition cannot have conflicts with the specified forward primers:

    ForwardPrimerVolumeMismatch  (1)

    ForwardPrimerVolume cannot have conflicts with the specified forward primers:

    InvalidPreparedPlate  (1)

    When trying to use a prepared plate, all the samples must be in a 96-well Full-Skirted PCR Plate:

    MasterMixStorageConditionMismatch  (1)

    MasterMixStorageCondition cannot have conflicts with MasterMix:

    MasterMixVolumeMismatch  (1)

    MasterMixVolume cannot have conflicts with MasterMix:

    ObjectDoesNotExist  (12)

    Do NOT throw a message if we have a simulated container but a simulation is specified that indicates that it is simulated:

    Do NOT throw a message if we have a simulated primer pair container but a simulation is specified that indicates that it is simulated:

    Do NOT throw a message if we have a simulated primer pair sample but a simulation is specified that indicates that it is simulated:

    Do NOT throw a message if we have a simulated sample but a simulation is specified that indicates that it is simulated:

    Throw a message if we have a container that does not exist (ID form):

    Throw a message if we have a container that does not exist (name form):

    Throw a message if we have a primer pair container that does not exist (ID form):

    Throw a message if we have a primer pair container that does not exist (name form):

    Throw a message if we have a primer pair sample that does not exist (ID form):

    Throw a message if we have a primer pair sample that does not exist (name form):

    Throw a message if we have a sample that does not exist (ID form):

    Throw a message if we have a sample that does not exist (name form):

    PCRTooManySamples  (1)

    The total number of samples cannot exceed 96:

    PrimerAnnealingMismatch  (1)

    PrimerAnnealing options cannot have conflicts:

    ReversePrimerStorageConditionMismatch  (1)

    ReversePrimerStorageCondition cannot have conflicts with the specified reverse primers:

    ReversePrimerVolumeMismatch  (1)

    ReversePrimerVolume cannot have conflicts with the specified reverse primers:

    TotalVolumeOverReactionVolume  (1)

    The total volume cannot exceed ReactionVolume:

Possible Issues

    Missing Primers

    If primer pairs flanking the target sequences are absent from input samples and not provided as a secondary input, no target amplification is likely to occur.
Last modified on Fri 3 Oct 2025 18:38:50

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