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ExperimentAbsorbanceKinetics

ExperimentAbsorbanceKinetics[Samples]⟹Protocol

generates a Protocol for measuring absorbance of the provided Samples over a period of time.

    
Absorbance kinetics studies how samples absorb ultraviolet and visible light radiation over time. Samples are exposed to light at a range of wavelengths, and the absorbance is measured by determining how much light at is transmitted through the sample across all these wavelengths. Because samples can be injected into the read plate at a specified time, the change of this absorbance over time can be used to monitor reactions and observe the kinetics of the interactions (say binding or dissociation) between substances.
    

Experimental Principles

    Figure 1.1: Step 1: Samples are prepared in a reader-compatible shallow well plate. Step 2: Injection lines are cleaned and primed. Step 3: The assay plate is optionally held at a specified temperature. Step 4: Injection samples are dispensed into the assay plate. Step 5: The assay plate is shaken. Step 6: Absorbance is read over a period of time. Step 7: Optionally, data may be assessed with AnalyzeKinetics to fit rate constants to the reactions.

Instrumentation

    FLUOstar Omega

    Figure 2.1.1: In the Omega, a Xenon Flash Lamp sends photons through each well of the plate. The light that is not absorbed is then directed through a prism which splits the beam into wavelengths from 220 nm to 1000 nm that are measured by the detector. The plate chamber can be heated up to 45°C and it can mix the plate at up to 700 RPM before the run. The reader has two 300μL syringe pump injectors which can be used for 0.5 - 300 μL injections of two unique samples prior to the run.

    CLARIOstar

    Figure 2.2.1: In the CLARIOstar, a Xenon Flash Lamp sends photons through each well of the plate. The light that is not absorbed is then directed through a prism which splits the beam into wavelengths from 220 nm to 1000 nm that are measured by the detector. The plate chamber can be heated up to 45°C and it can mix the plate at up to 700 RPM before the run. The reader has two 300μL syringe pump injectors which can be used for 0.5 - 300 μL injections of two unique samples prior to the run.

    PHERAstar FS

    Figure 2.3.1: In the PHERAstar, a Xenon Flash Lamp sends photons through each well of the plate. The light that is not absorbed is then directed through a prism which splits the beam into wavelengths from 220 nm to 1000 nm that are measured by the detector. The plate chamber can be heated up to 45°C and it can mix the plate at up to 700 RPM before the run. The reader has two 300μL syringe pump injectors which can be used for 0.5 - 300 μL injections of two unique samples prior to the run.

Experiment Options

    General

    Instrument

    The plate reader used to measure absorbance.
    Default Value: Automatic
    Default Calculation: Resolves to the instrument capable of performing the requested sampling. If any instrument can be used, resolves to use the model with the most available instruments in the lab.
    Pattern Description: An object of type or subtype Model[Instrument, PlateReader] or Object[Instrument, PlateReader]
    Programmatic Pattern: ObjectP[{Model[Instrument, PlateReader], Object[Instrument, PlateReader]}] | Automatic

    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

    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

    NumberOfReplicates

    The number of times to repeat absorbance reading on each provided sample. If Aliquot -> True, this also indicates the number of times each provided sample will be aliquoted. Note that when using the Lunatic, this indicates the number of independent times a 2 uL aliquot will be put into the Lunatic chips and read, and when using the BMG plate readers, this indicates the number of aliquots of the same sample that will be read.
    Default Value: Automatic
    Default Calculation: When using the BMG plate readers, automatically set to 3 if QuantifyConcentration is True for any experiment sample. When using the Lunatic, automatically set to 3 or 2 depending on the total number of the experiment samples and the blank samples if QuantifyConcentration is True. The total number of samples allowed in one Lunatic run is 94. Otherwise automatically set to Null.
    Pattern Description: Greater than or equal to 2 in increments of 1 or Null.
    Programmatic Pattern: (GreaterEqualP[2, 1] | Automatic) | Null

    Sample Handling

    PlateReaderMixSchedule

    Indicates the points at which mixing should occur in the plate reader, for instance after every set of injections.
    Default Value: Automatic
    Default Calculation: Automatically set to AfterInjections when other mix options are set and injections are specified or to BetweenReadings when mixing is specified but there are no injections.
    Pattern Description: BeforeReadings, BetweenReadings, or AfterInjections or Null.
    Programmatic Pattern: (MixingScheduleP | Automatic) | Null

    Temperature

    Indicates the temperature the samples will held at prior to measuring absorbance and during data acquisition within the instrument.
    Default Value: Automatic
    Default Calculation: Sets to Ambient if an instrument is capable of manipulating the temperature of the samples.
    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) | Automatic

    EquilibrationTime

    The length of time for which the samples equilibrate at the requested temperature before being read.
    Default Value: Automatic
    Default Calculation: If an instrument is capable setting the temperature of the samples, sets to 0 second when Temperature is set to Ambient. Otherwise, it is set to 5 minutes.
    Pattern Description: Greater than or equal to 0 seconds and less than or equal to 24 hours or Null.
    Programmatic Pattern: (RangeP[0*Second, 24*Hour] | Automatic) | Null

    PlateReaderMix

    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

    MoatSize

    Indicates the number of concentric perimeters of wells to fill with MoatBuffer in order to slow evaporation of inner assay samples.
    Figure 3.1: Use the moat options, MoatBuffer, MoatVolume and MoatSize to create an outer ring of wells filled with buffer. This has been shown to decrease evaporation during long reads.
    Default Value: Automatic
    Default Calculation: Automatically set to 1 if any other moat options are specified.
    Pattern Description: Greater than 0 in increments of 1 or Null.
    Programmatic Pattern: (GreaterP[0, 1] | Automatic) | Null

    MoatVolume

    Indicates the volume to add to to each moat well.
    Default Value: Automatic
    Default Calculation: Automatically set to the RecommendedFillVolume of the assay plate if informed, or 75% of the MaxVolume of the assay plate if not, if any other moat options are specified.
    Pattern Description: Greater than or equal to 1 microliter and less than or equal to 300 microliters or Null.
    Programmatic Pattern: (RangeP[1*Microliter, 300*Microliter] | Automatic) | Null

    MoatBuffer

    Indicates the sample to use to fill each moat well.
    Default Value: Automatic
    Default Calculation: Automatically set to Milli-Q water if any other moat options are specified.
    Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Object[Sample], Model[Sample]}] | _String) | Automatic) | Null

    RetainCover

    Indicates if the plate seal or lid on the assay container should not be taken off during measurement to decrease evaporation. When this option is set to True, injections cannot be performed as it's not possible to inject samples through the cover. When using the Cuvette Method, automatically set to True.
    Default Value: False
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP

    TertiaryInjectionFlowRate

    The speed at which to transfer injection samples into the assay plate in the third round of injections.
    Default Value: Automatic
    Default Calculation: Defaults to 300 Microliter/Second if tertiary injections are specified.
    Pattern Description: 430 microliters per second, 400 microliters per second, 350 microliters per second, 300 microliters per second, 260 microliters per second, 220 microliters per second, 190 microliters per second, 170 microliters per second, 150 microliters per second, 135 microliters per second, 115 microliters per second, 100 microliters per second, 85 microliters per second, 65 microliters per second, or 50 microliters per second or Null.
    Programmatic Pattern: (BMGFlowRateP | Automatic) | Null

    QuaternaryInjectionFlowRate

    The speed at which to transfer injection samples into the assay plate in the fourth round of injections.
    Default Value: Automatic
    Default Calculation: Defaults to 300 Microliter/Second if quaternary injections are specified.
    Pattern Description: 430 microliters per second, 400 microliters per second, 350 microliters per second, 300 microliters per second, 260 microliters per second, 220 microliters per second, 190 microliters per second, 170 microliters per second, 150 microliters per second, 135 microliters per second, 115 microliters per second, 100 microliters per second, 85 microliters per second, 65 microliters per second, or 50 microliters per second or Null.
    Programmatic Pattern: (BMGFlowRateP | Automatic) | Null

    Absorbance Measurement

    NumberOfReadings

    Number of redundant readings taken by the detector to determine a single averaged absorbance reading.
    Default Value: Automatic
    Default Calculation: If an instrument capable of adjusting NumberOfReadings is selected, resolves to 100. Otherwise resolves to Null
    Pattern Description: Greater than or equal to 1 and less than or equal to 200 or Null.
    Programmatic Pattern: (RangeP[1, 200] | Automatic) | Null

    ReadDirection

    Indicate the plate path the instrument will follow as it measures absorbance in each well, for instance reading all wells in a row before continuing on to the next row (Row).
    Figure 3.2: Use the ReadDirection option to control how the plate reader scans the plate during each read cycle. Choosing a more efficient path will lead to a shorter DetectionInterval. Also note that you may want to consider dripping injectors if you're working with low viscosity injection samples.
    Default Value: Automatic
    Default Calculation: Resolves to Row if a plate reader capable of adjusting read direction is selected.
    Pattern Description: Row, Column, SerpentineRow, or SerpentineColumn or Null.
    Programmatic Pattern: (ReadDirectionP | Automatic) | Null

    RunTime

    The length of time for which absorbance measurements are made.
    Default Value: 45 minutes
    Pattern Description: Greater than or equal to 1 minute and less than or equal to 24 hours.
    Programmatic Pattern: RangeP[1*Minute, 24*Hour]

    ReadOrder

    Indicates if all measurements and injections are done for one well before advancing to the next (Serial) or in cycles in which each well is read once per cycle (Parallel).
    Default Value: Parallel
    Pattern Description: Serial or Parallel.
    Programmatic Pattern: ReadOrderP

    Wavelength

    The wavelength(s) at which absorbance is measured. All indicates that the full spectrum available to the plate reader is used.
    Default Value: Automatic
    Default Calculation: Automatically resolves to the wavelengths specified in the input samples' ExtinctionCoefficients field or 260 Nanometer if that field is not populated, for Serial ReadOrder or Matrix SamplingPattern. Otherwise automatically resolves to All.
    Pattern Description: All or a span from anything greater than or equal to 220 nanometers and less than or equal to 1000 nanometers to anything greater than or equal to 220 nanometers and less than or equal to 1000 nanometers or greater than or equal to 220 nanometers and less than or equal to 1000 nanometers or list of one or more greater than or equal to 220 nanometers and less than or equal to 1000 nanometers entries.
    Programmatic Pattern: (All | RangeP[220*Nanometer, 1000*Nanometer] | {RangeP[220*Nanometer, 1000*Nanometer]..} | RangeP[220*Nanometer, 1000*Nanometer] ;; RangeP[220*Nanometer, 1000*Nanometer]) | Automatic

    Injections

    PrimaryInjectionSample

    The sample to be injected in the first round of injections in order to introduce a time sensitive reagent/sample into the plate before/during absorbance measurement. The corresponding injection times and volumes can be set with PrimaryInjectionTime and PrimaryInjectionVolume.
    Default Value: Null
    Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample or Null.
    Programmatic Pattern: (ObjectP[{Object[Sample], Model[Sample]}] | _String) | Null
    Index Matches to: experiment samples

    PrimaryInjectionVolume

    The amount of the primary sample injected in the first round of injections.
    Default Value: Null
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 300 microliters or Null.
    Programmatic Pattern: RangeP[0.5*Microliter, 300*Microliter] | Null
    Index Matches to: experiment samples

    SecondaryInjectionSample

    The sample to be injected in the second round of injections. Set the corresponding injection times and volumes with SecondaryInjectionTime and SecondaryInjectionVolume.
    Default Value: Null
    Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample or Null.
    Programmatic Pattern: (ObjectP[{Object[Sample], Model[Sample]}] | _String) | Null
    Index Matches to: experiment samples

    SecondaryInjectionVolume

    The amount of the secondary sample injected in the second round of injections.
    Default Value: Null
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 300 microliters or Null.
    Programmatic Pattern: RangeP[0.5*Microliter, 300*Microliter] | Null
    Index Matches to: experiment samples

    PrimaryInjectionFlowRate

    The speed at which to transfer injection samples into the assay plate in the first round of injections.
    Default Value: Automatic
    Default Calculation: Defaults to 300 Microliter/Second if primary injections are specified.
    Pattern Description: 430 microliters per second, 400 microliters per second, 350 microliters per second, 300 microliters per second, 260 microliters per second, 220 microliters per second, 190 microliters per second, 170 microliters per second, 150 microliters per second, 135 microliters per second, 115 microliters per second, 100 microliters per second, 85 microliters per second, 65 microliters per second, or 50 microliters per second or Null.
    Programmatic Pattern: (BMGFlowRateP | Automatic) | Null

    SecondaryInjectionFlowRate

    The speed at which to transfer injection samples into the assay plate in the second round of injections.
    Default Value: Automatic
    Default Calculation: Defaults to 300 Microliter/Second if secondary injections are specified.
    Pattern Description: 430 microliters per second, 400 microliters per second, 350 microliters per second, 300 microliters per second, 260 microliters per second, 220 microliters per second, 190 microliters per second, 170 microliters per second, 150 microliters per second, 135 microliters per second, 115 microliters per second, 100 microliters per second, 85 microliters per second, 65 microliters per second, or 50 microliters per second or Null.
    Programmatic Pattern: (BMGFlowRateP | Automatic) | Null

    InjectionSampleStorageCondition

    The non-default conditions under which any injection samples used by this experiment are stored after the protocol is completed.
    Default Value: Null
    Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, BacteriaIncubation, MammalianIncubation, TissueCultureCellsIncubation, MicrobialCellsIncubation, MicrobialCellsShakingIncubation, YeastCellsIncubation, YeastCellsShakingIncubation, ViralIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (SampleStorageTypeP | Disposal) | Null

    TertiaryInjectionSample

    The sample to be injected in the third round of injections. Note that only two unique samples can be injected in total. The corresponding injection times and volumes can be set with TertiaryInjectionTime and TertiaryInjectionVolume.
    Default Value: Null
    Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample or Null.
    Programmatic Pattern: (ObjectP[{Object[Sample], Model[Sample]}] | _String) | Null
    Index Matches to: experiment samples

    TertiaryInjectionVolume

    The amount of the tertiary sample injected in the third round of injections.
    Default Value: Null
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 300 microliters or Null.
    Programmatic Pattern: RangeP[0.5*Microliter, 300*Microliter] | Null
    Index Matches to: experiment samples

    QuaternaryInjectionSample

    The sample to be injected in the fourth round of injections. Note that only two unique samples can be injected in total. The corresponding injection times and volumes can be set with QuaternaryInjectionTime and QuaternaryInjectionVolume.
    Default Value: Null
    Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample or Null.
    Programmatic Pattern: (ObjectP[{Object[Sample], Model[Sample]}] | _String) | Null
    Index Matches to: experiment samples

    QuaternaryInjectionVolume

    The amount of the quaternary sample injected in the fourth round of injections.
    Default Value: Null
    Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 300 microliters or Null.
    Programmatic Pattern: RangeP[0.5*Microliter, 300*Microliter] | Null
    Index Matches to: experiment samples

    PrimaryInjectionTime

    The time at which the first round of injections starts.
    Default Value: Null
    Pattern Description: Greater than or equal to 1 second and less than or equal to 24 hours or Null.
    Programmatic Pattern: RangeP[1*Second, 24*Hour] | Null

    SecondaryInjectionTime

    The time at which the second round of injections starts.
    Default Value: Null
    Pattern Description: Greater than or equal to 1 second and less than or equal to 24 hours or Null.
    Programmatic Pattern: RangeP[1*Second, 24*Hour] | Null

    TertiaryInjectionTime

    The time at which the third round of injections starts.
    Default Value: Null
    Pattern Description: Greater than or equal to 1 second and less than or equal to 24 hours or Null.
    Programmatic Pattern: RangeP[1*Second, 24*Hour] | Null

    QuaternaryInjectionTime

    The time at which the fourth round of injections starts.
    Default Value: Null
    Pattern Description: Greater than or equal to 1 second and less than or equal to 24 hours or Null.
    Programmatic Pattern: RangeP[1*Second, 24*Hour] | Null

    Data Processing

    BlankAbsorbance

    For each members of SamplesIn, indicates if a corresponding blank measurement, which consists of a separate container (well, chamber, or cuvette) than SampleLink, will be performed, prior to measuring the absorbance of samples. If using Cuvettes, the BlankAbsorbance will be read at the same time as the SampleLink.
    Default Value: True
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP

    Blanks

    The object or source used to generate a blank sample (i.e. buffer only, water only, etc.) whose absorbance is subtracted as background from the absorbance readings of the SamplesIn to take accound for any artifacts.
    Default Value: Automatic
    Default Calculation: Automatically set to Null if BlankMeasurement is False. Otherwise, automatically set to the value of Solvent in SamplesIn. If Solvent not specfied, set to Model[Sample, "Milli-Q water"].
    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

    BlankVolumes

    The amount of liquid of the Blank that should be transferred out and used to blank measurements. Set BlankVolume to Null to indicate blanks should be read inside their current containers.
    Default Value: Automatic
    Default Calculation: If BlankMeasurement is True, automatically set to the value of AssayVolume if that was specified, or maximum volume of the container otherwise.
    Pattern Description: Greater than or equal to 1 microliter and less than or equal to 4000 microliters or Null.
    Programmatic Pattern: (RangeP[1*Microliter, 4000*Microliter] | Automatic) | Null
    Index Matches to: experiment samples

    Sampling

    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

    SamplingPattern

    Indicates where in the well measurements are taken.
    Figure 3.3: Ring sampling allows multiple measurements over a band with a specified diameter. The specified number of flashes will be equally divided over the ring and a higher number will yield to increased sampling (as seen in A). The average value of all measurements will be returned as a single data point. Spiral sampling follows the same principle as ring sampling, but covers a larger part of the well as it takes spiraling inward measurements. Again the number of flashes determines if the well is highly sampled (A) or lightly (B). Use Matrix sampling to scan over a NxN grid of points. Note that points on the border of the well will not be measured.
    Default Value: Automatic
    Default Calculation: When using the BMG plate readers, automatically set to Matrix if SamplingDimension is specified or Ring if SamplingDistance is specified. Otherwise set to Center.
    Pattern Description: Matrix, Spiral, Ring, or Center or Null.
    Programmatic Pattern: (PlateReaderSamplingP | Automatic) | Null

    Post Experiment

    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, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, BacteriaIncubation, MammalianIncubation, TissueCultureCellsIncubation, MicrobialCellsIncubation, MicrobialCellsShakingIncubation, YeastCellsIncubation, YeastCellsShakingIncubation, ViralIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
    Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | 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 ExperimentSampleManipulation.
    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

    PreparatoryPrimitives

    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 ExperimentSampleManipulation.
    Default Value: Null
    Pattern Description: List of one or more a primitive with head Define, Transfer, Mix, Aliquot, Consolidation, FillToVolume, Incubate, Filter, Wait, Centrifuge, or Resuspend entries or Null.
    Programmatic Pattern: {SampleManipulationP..} | 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, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, Silica, or HLB 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, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, Silica, or HLB 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, 0.1 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, 0.1 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 ConcentrationFactor 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, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, BacteriaIncubation, MammalianIncubation, TissueCultureCellsIncubation, MicrobialCellsIncubation, MicrobialCellsShakingIncubation, YeastCellsIncubation, YeastCellsShakingIncubation, ViralIncubation, 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 or Null.
    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: 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

Example Calls

    Absorbance Wavelength

    Specify which wavelengths at which to measure the absorbance with the Wavelength option:
    To indicate instead a range of wavelengths to read, use a Span:
    If you would like to collect the full spectrum obtainable by the plate reader, set Wavelength to All:

    Injections

    To specify injections, use the InjectionSample, InjectionVolume, and InjectionTime options. The sample and volume options are index matched to the input samples allowing you to control the wells which receive injections and the volumes of those injections. In the example below, all the input samples will receive the first injection after 20 minutes. At the 40 minute mark the first sample will receive a second injection of 75uL, the second sample will receive 25uL, and the third sample will not receive a second injection:

    Plate Reader Mixing

    The assay plate can be mixed during readings by specifying any of the PlateReaderMix options if using the PHERAstar, CLARIOstar, or Omega:

Preferred Input Containers

    The plate readers can read standard SBS shallow well plates.
    The plate readers can object samples from samples in 2mL, 15mL and 50 mL tubes while recording kinetic signal.

Data Processing

    Plot the data generated from a single trajectory or a combined set of trajcetories overlaid into a single plot:
    If three-dimensional data is obtained, multiple PlotTypes are possible. Consider using PlotType -> ListPlot3D or ContourPlot.
    If three-dimensional data is obtained but the traces of specific wavelengths are desired, specify the Wavelength option and set PlotType -> ListLinePlot.

Warnings and Errors

    Messages  (38)

    AbsorbanceKineticsTooManySamples  (1)

    Print a message and returns $Failed if there are too many samples and blanks for a single run:

    AbsorbanceSamplingCombinationUnavailable  (1)

    SamplingDimension is only supported when SamplingPattern->Matrix:

    AliquotRequired  (1)

    If the sample must be aliquoted but no aliquot options are specified, throw a warning telling the user:

    BlankAliquotRequired  (1)

    Returns $Failed if the blank needs to be aliquoted into a new container but no blank volume was given:

    BlanksContainSamplesIn  (1)

    If the specified Blanks option contains samples that are also inputs, throw an error and return $Failed:

    BlankStateWarning  (1)

    If the blanks have a state of non-liquid, a warning is given:

    CoveredInjections  (1)

    As injections are made into the top of the plate, RetainCover cannot be set to True:

    DiscardedSamples  (1)

    Throw an error if one or multiple of the input samples are discarded:

    DuplicateName  (1)

    If the specified Name option already exists as a protocol object, throw an error and return $Failed:

    IncompatibleBlankOptions  (3)

    Returns an error if BlankAbsorbance -> False and Blanks is specified:

    Returns an error if BlankAbsorbance -> False and BlankVolumes is set:

    Returns an error if BlankAbsorbance -> True and Blanks -> Null:

    InjectionSampleStateError  (1)

    Print a message and returns $Failed if there are non-liquid injection samples:

    InsufficientBlankSpace  (2)

    Gives a warning if samples needs to be aliquoted because there's not enough room in the assay container. Note that by specifying a constant value for the blank volume, it becomes possible to avoid the aliquot:

    Prints a message and returns $Failed if Aliquot->False and samples need to be aliquoted because there's not enough room in the assay container:

    InvalidBlankContainer  (1)

    Throws an error because no blank volume has been specified but blank Buffer 1 is in a 50mL tube and must be transferred into the assay container to be read:

    InvalidInput  (1)

    Throw an error if one or multiple of the input samples are discarded:

    InvalidSimultaneousInjections  (1)

    Print a message and returns $Failed if subsequent injections are set to occur at the same time using same pump or unsupported plate reader:

    MixingParametersConflict  (1)

    Throws an error if PlateReaderMix cannot be resolved because one mixing parameter was specified and another was set to Null:

    MixingParametersRequired  (1)

    Throws an error if PlateReaderMix->True and PlateReaderMixTime has been set to Null:

    MixingParametersUnneeded  (1)

    Throws an error if PlateReaderMix->False and PlateReaderMixTime has been specified:

    MultipleWavelengthsUnsupported  (1)

    Due to limitations of the instrumentation, readings at multiple wavelengths are not possible in serial mode:

    NotEqualBlankVolumesWarning  (1)

    Print a warning message if the blank volume is not equal to the volume of the sample:

    ObjectDoesNotExist  (1)

    Throw an error and return early if an input object doesn't exist:

    RepeatedPlateReaderSamples  (2)

    Prints a warning if aliquots will be generated in order to make repeat readings of the same sample:

    Throws an error if the same sample is repeated multiple times and Aliquot->False since repeat readings are performed by reading multiple aliquots of the same sample:

    ReplicateAliquotsRequired  (2)

    Prints a warning if aliquots will be generated in order to make replicate readings:

    Throws an error if replicates are specified and Aliquot->False since replicates are performed by reading multiple aliquots of the same sample:

    SamplingPatternMismatch  (1)

    When using an instrument capable of sampling the SamplingPattern can't be set to Null:

    SinglePlateRequired  (2)

    Gives a warning if samples need to be consolidated into a single plate:

    Prints a message and returns $Failed if samples are in multiple plates and must be aliquoted in order to consolidate them into a single plate:

    SkippedInjectionError  (1)

    Print a message and returns $Failed if any injections are skipped:

    SpanWavelengthOrder  (1)

    If Wavelength is a span, a warning is thrown if it is specified as high-wavelength;;low-wavelength:

    TooManyWavelength  (1)

    Due to limitations of the instrumentation, the number of discrete wavelengths cannot exceed 8:

    UnnecessaryBlankTransfer  (1)

    Specifying a blank volume indicates that an aliquot of the blank should be taken and read. Gives a warning if this is set to happen even though the blank is already in a valid container:

    UnsupportedInstrumentSamplingPattern  (1)

    The Omega can't sample wells using a Matrix pattern:

    UnsupportedPlateReader  (2)

    Returns an error if the specified plate reader model is deprecated:

    Returns an error if the specified plate reader object is retired:

Possible Issues

    Blank samples are transferred to assay plate

    When blank samples are prepared to account for the background signal, they are transferred to the plate where all the assay samples are in. If the assay samples are measured in their source plate, the blank samples are transferred to the source plate as well.
Last modified on Mon 19 Dec 2022 11:22:07
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