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ECL`

ExperimentCircularDichroism

ExperimentCircularDichroism[Samples]⟹Protocol

generates a Protocol object for measuring the differential absorption of left and right circularly polarized light of the Samples.

    
Circular Dichroism (CD, aka Electronic Circular Dichroism (ECD)) measures how samples differentially absorb left and right circularly polarized light radiation, either at a specific wavelength or over a range of wavelengths. In UV-Vis experiment (e.g., ExperimentAbsorbanceSpectroscopy, ExperimentUVMelting etc), samples are exposed to the unpolarized light, where its electric and magnetic fields perpendicular oscillate in all directions perpendicular to the propagation direction of the light. In circularly polarized light, the electric field vector rotates around the propagation direction at a constant magnitude, resulting in the electric field vector appearing to trace a circle throughout one wave frequency. Optically active chiral molecules will preferentially absorb one direction of the circularly polarized light. The difference in absorption of the left and right circularly polarized light can be measured and quantified as absorption bands. CD spectroscopy can probe the secondary structure composition of polypeptides/proteins and determine the tertiary structure class of globular proteins.
    

Experimental Principles

    Figure 1.1: Procedural overview of a CircularDichroism experiment using an Ekko CD plate reader.Step 1:Samples and blanks are loaded to the plate for reading.Step 2 (optional):the sample volume will be measured by the supersonic method to calculate the pathlength.Step 3:Samples are loaded to the instrument.Step 4:The circular dichroism of samples is measured as ellipticity,based on differential absorption of the left and right circularly polarized light of samples.Step 5:Data is plotted and visualized.

Instrumentation

    Ekko

    Figure 2.1.1: In an Ekko CD Microplate Reader, a Xenon Lamp emits the full-spectrum light. The light is then split and diffracted into several beams by passing a grating monochromator to emit non-polarized light. The non-polarized light then passes the polarizer to generate linear polarized light. The linear polarized light then passes through the photoelastic modulator to create both left- and right-hand circular polarized light. Finally, the differential absorbed circularly polarized light. The transmitted light is then directed through a prism that splits the beam into wavelengths from 185 nm to 900 nm as measured by the detector.

Experiment Options

    General

    Instrument

    The plate reader that is used for measuring circular dichroism spectroscopy or circular dichroism intensity at specific wavelengths.
    Default Value: Model[Instrument, PlateReader, Ekko]
    Pattern Description: An object of type or subtype Model[Instrument, PlateReader] or Object[Instrument, PlateReader]
    Programmatic Pattern: ObjectP[{Model[Instrument, PlateReader], Object[Instrument, PlateReader]}]

    PreparedPlate

    Indicates if the plate containing the samples for the CircularDichroism experiment has been previously prepared that does not need to run sample preparation steps.
    Default Value: False
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP

    Optics

    RetainCover

    Indicates if the plate seal or lid on the assay container is left on during measurement to decrease evaporation. It is strongly recommended not to retain a cover because Circular Dichroism can only read from top.
    Default Value: False
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP

    DetectionWavelength

    The specific wavelength(s) which should be used to measure absorbance in the samples.
    Default Value: Automatic
    Default Calculation: Automatically resolves based on the EnantiomericExcessWavelength first: If EnantiomericExcessWavelength is specified, resolved to be the same as EnantiomericExcessWavelength. If EnantiomericExcessWavelength is blank, this option resolves based on Analytes option: if Analytes are specified as biomacromolecules (Proteins, Peptides, Oligomers), resolves this option to Span[200 Nanometer, 400 Nanometer]; Else resolved to Span[300 Nanometer, 800 Nanometer].
    Pattern Description: Multiple or Range or Single.
    Programmatic Pattern: (RangeP[185*Nanometer, 850*Nanometer] | RangeP[185*Nanometer, 850*Nanometer] ;; RangeP[185*Nanometer, 850*Nanometer] | {RangeP[185*Nanometer, 850*Nanometer]..}) | Automatic
    Index Matches to: experiment samples

    StepSize

    This option determines how often the spectrophotometer will record an circular dichroism absorbance measurement, if the sample was scanned in a range of wavelength. For example, a step size of 2 nanometer indicates that the spectrophotometer will collect circular dichroism absorbance data for every 2 nanometer within the wavelength range.
    Default Value: Automatic
    Default Calculation: Automatically resolves to 1 Nanomer if the DetectionWavelength is resolved as a range values. Otherwise will resove to Null.
    Pattern Description: Greater than or equal to 0.5 nanometers and less than or equal to 5 nanometers or Null.
    Programmatic Pattern: (RangeP[0.5*Nanometer, 5*Nanometer] | Automatic) | Null
    Index Matches to: experiment samples

    Sample Preparation

    ReadPlate

    The plate that is loaded with input samples then inserted into the CircularDichroism plater reader instrument.
    Default Value: Automatic
    Default Calculation: Is automatically set to Model[Container, Plate, "Hellma Black Quartz Microplate"].
    Pattern Description: An object of type or subtype Model[Container, Plate] or Object[Container, Plate] or a prepared sample.
    Programmatic Pattern: (ObjectP[{Model[Container, Plate], Object[Container, Plate]}] | _String) | Automatic

    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.
    Default Value: Automatic
    Pattern Description: Greater than or equal to 1 in increments of 1 or Null.
    Programmatic Pattern: (GreaterEqualP[1, 1] | Automatic) | Null

    MoatSize

    Indicates the number of concentric perimeters of wells to leave as empty or filled with MoatBuffer. Quartz plates have high birefringence in the outer ring of wells. So the circular dichroism data collected in the outer ring of wells have noise levels. With MoatSize == 2 (default value), the protocol will ignore the outer ring of wells in the plate.
    Figure 3.1: Use the moat options, MoatBuffer, MoatVolume and MoatSize to create an outer ring of wells (moat wells) filled with buffer or leave as empty wells. For quartz plate, since the plate's outer ring is not recommended to be sued for circular dichroism. Empty moat well will auto prevent using those wells. Moat wells with the buffer have been shown to decrease evaporation during long reads.
    Default Value: Automatic
    Default Calculation: Automatically set to 2 if ReadPlate is made by quartz (e.g. Model[Container, Plate, "Hellma Black Quartz Microplate"] and Object[Container,Plate] with this Model). Otherwise will resolve to 0.
    Pattern Description: Greater than or equal to 0 in increments of 1.
    Programmatic Pattern: GreaterEqualP[0, 1] | Automatic

    MoatBuffer

    Indicates the sample to use to fill each moat well. If the moat well is intended to be empty, specify this option as Null.
    Default Value: Automatic
    Default Calculation: Automatically set to Null if RetainCover is False. Otherwise resolve to automatically Milli-Q water.
    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

    MoatVolume

    Indicates the volume to add to to each moat well.
    Default Value: Automatic
    Default Calculation: Automatically set to the minimum volume of the assay plate if MoatBuffer is specified. Otherwise resolves to 0.
    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

    SampleVolume

    The volume that is taken from each input sample and aliquoted onto the read plate.
    Default Value: Automatic
    Default Calculation: Is automatically set based on the smallest volume value of all SamplesIn and the RecommendedFillVolume of the ReadPlate, whichever is smaller.
    Pattern Description: Greater than or equal to 50 microliters and less than or equal to 2000 microliters.
    Programmatic Pattern: RangeP[50*Microliter, 2000*Microliter] | Automatic
    Index Matches to: experiment samples

    CalculatingMolarEllipticitySpectrum

    Decide if the data will be transfered to molar ellipticity after the protocol is finished. If True, the Analyte and AnalyteConcentration option will set a single value for each of SamplesIn.
    Default Value: Automatic
    Default Calculation: If the analyte concentration is specified, this option resolved to True, otherwise resolve to False.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic
    Index Matches to: experiment samples

    Data Processing

    NitrogenPurge

    Indicates if the experiment is run under purge with dry nitrogen gas to avoid condensation of ozone generated by the light source.
    Default Value: True
    Pattern Description: True or False or Null.
    Programmatic Pattern: BooleanP | Null

    EmptyAbsorbance

    Indicates if a empty well will be scan to check the container's backgound signal at the begining of the experiment.
    Default Value: False
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP

    BlankAbsorbance

    Indicates if blank samples are prepared to account for the background signal when reading absorbance of the assay samples.
    Default Value: True
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP

    Blanks

    The source used to generate a blank sample whose absorbance is subtracted as background from the absorbance readings of the input sample.
    Default Value: Automatic
    Default Calculation: Automatically set to Null if BlankAbsorbance is False, otherwise 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 volume of the blank that should be transferred out and used for blank measurements. Set BlankVolumes to Null to indicate blanks should be read inside their current containers.
    Default Value: Automatic
    Default Calculation: Automatically set to Null if BlankAbsorbance is False or to the SampleVolume of the samples if BlankAbsorbance is True.
    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
    Index Matches to: experiment samples

    ReadDirection

    Indicate the plate path the instrument will follow as it measures circular dichroism 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: Row
    Pattern Description: Row, Column, SerpentineRow, or SerpentineColumn or Null.
    Programmatic Pattern: ReadDirectionP | Null

    AverageTime

    The time on data collection for each measurment points. The collected data are averaged for this period of time and export as the result data point for this wavelength.
    Default Value: 1 second
    Pattern Description: Greater than or equal to 0.06 seconds and less than or equal to 18 seconds or Null.
    Programmatic Pattern: RangeP[0.06*Second, 18*Second] | Null

    Enatiomeric Excess Measurement

    EnantiomericExcessMeasurement

    Indicates if the experiment will be used to determined enantiomeric excess of SamplesIn.
    Default Value: Automatic
    Default Calculation: Automatically set to False. Unless EnantiomericExcessWavelength or EnantiomericExcessStandards is specified by users.
    Pattern Description: True or False.
    Programmatic Pattern: BooleanP | Automatic

    EnantiomericExcessWavelength

    Indicates if the wavelength will be used to determined enantiomeric excess of SamplesIn.
    Default Value: Automatic
    Default Calculation: Automatically set to Null if EnantiomericExcessMeasurement is set to False. For EnantiomericExcessMeasurement is True, If DetectionWavelength is specified as a list of single wavelengths, automatically set to the samme as DetectionWavelengh. Else, automatically set to the shortest wavelength specified in the input samples' ExtinctionCoefficients field, and 260 Nanometer if that field is not populated.
    Pattern Description: Multiple or Single or Null.
    Programmatic Pattern: ((RangeP[185*Nanometer, 850*Nanometer] | {RangeP[185*Nanometer, 850*Nanometer]..}) | Automatic) | Null

    EnantiomericExcessStandards

    Indicate samples with a known EnantiomericExcess values and the corresponding value. Preferrable to have optical pure isomers (with +100% and -100% in enantiomeric excess) and one racemic sample (0% in enantiomeric excess). The blank sample can be used as the racemic sample. Will throw an error message if not enough sample (<=3) is specified as SamplesIn.
    Default Value: Automatic
    Default Calculation: Automatically set to Null if EnantiomericExcessMeasurement is set to False. If EnantiomericExcessMeasurement is True, the first two SamplesIn will be set as Sample, with -100% and 100% Enantiomeric Excess Value, respectively. The blank sample (if any) or the 3rd SamplesIn will be set as the Sample with 0% Enantiomeric Excess Value.
    Pattern Description: List of one or more {Sample, Enantiomeric Excess Value} entries or Null.
    Programmatic Pattern: ({{(ObjectP[{Object[Sample], Model[Sample]}] | _String) | Automatic, RangeP[-100*Percent, 100*Percent] | Automatic}..} | Automatic) | Null

    Sample Information

    Analyte

    The compound of interest that is present in the given samples, will be used to determine the other settings for the plate reader (e.g. DetectionWavelength) and will be used to caluclate the molar epplicity.
    Default Value: Automatic
    Default Calculation: If populated, will set to the fist user-specified Analyte field in the Object[Sample]. Otherwise, will set to the fist larger compounds in the sample, in the order of Proteins, Peptides, Oligomers, then other small molecules. Otherwise, set Null.
    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

    AnalyteConcentrations

    The known concentration of the Analyte for each of the SamplesIn.
    Default Value: Automatic
    Default Calculation: Automatically set to the based on the concentration of Analyte, if any.
    Pattern Description: Greater than 0 molar or Null.
    Programmatic Pattern: (GreaterP[0*Molar] | Automatic) | Null
    Index Matches to: experiment samples

    Post Experiment

    ContainerOut

    The container in which the samples in the read plate are transferred into after the experiment.
    Default Value: Automatic
    Default Calculation: Is automatically set to Null if the SamplesOutStorageCondition is set to Disposal. If the SamplesOutStorageCondition is not Disposal, this option resolves based on the reusability of the ReadPlate: if the ReadPlate is reusable (Reusable->True for its Model), this option resolved to be Null, otherwise is resolved to Model[Container,Plate,"96-well 1mL Deep Well Plate"].
    Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or Null.
    Programmatic Pattern: ((ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic) | 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, Oven} 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, Oven} or Disposal or Null.
    Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null
    Index Matches to: experiment samples

    Model Input

    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 200 Microliter.
    Pattern Description: All or Count or Count or Mass or Volume or Null.
    Programmatic Pattern: ((Null | (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

    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 the input model has a product associated with both Amount and DefaultContainerModel populated, automatically set to the DefaultContainerModel value in the product. Otherwise, automatically set to Model[Container, Plate, "Hellma Black Quartz Microplate"].
    Pattern Description: An object of type or subtype Model[Container] or Null.
    Programmatic Pattern: ((Null | ObjectP[Model[Container]]) | 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, Oven} 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: 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

    Basics

    Measuring the circular dichroism in specific wavelength range or at some specific wavelengths
    Use BlankAbsorbance and EmptyAbsorbance options to generate protocol without blank and and empty well scans.
    Use Blanks and BlankVolume options to specify the unique blank buffer during the experiment.

    Molar Ellipticity

    The resulting spectra are in ellipticity (mdeg). To generate data in molar ellipticity, specify the CalculatingMolarEllipticitySpectrum, Analyte, AnalyteConcentration in order to auto calculate the molar ellipticity in resulting spectra.

    Enantiomeric Excess

    To calculate the enantiomeric excess of an unknown sample, submit two standard samples and the unknown samples. Specify each standard sample with their known enantiomeric excess value in the EnantiomericExcessStandards option and specify which wavelengths should be used to calculate the enantiomeric excess in unknown samples EnantiomericExcessWavelengths option.

Preferred Input Containers

    All data collection is preferred to use a quartz plate. Note the quartz plates are reusable, so samples need to be transferred to ContainerOut to save the sample after the experiment.
    Data collection at a visible wavelength region (400 nm to 900 nm) can use standard SBS shallow well plates.

Data Processing

    The data can be viewed by PlotCircularDichroism:

Warnings and Errors

    Messages  (27)

    CircularDichroismContainerOutStorageConditionMismatch  (1)

    ContainrOut can only be Null if all samples are going to be disposed after the experiment:

    CircularDichroismDetectionWavelengthIncompatibleForReadPlate  (1)

    Use quartz plate for low wavelength detection:

    CircularDichroismDuplicateDestinationWell  (1)

    DestinationWell can not be same:

    CircularDichroismEnantiomericExcessWavelengthsNotCovered  (1)

    The specified analyte should be in sample's composition:

    CircularDichroismInconsistentAnalyteConcentration  (1)

    The specified AnalyteConcentaion are consistent with what are calculated from sample's composition:

    CircularDichroismInvalidDestinationWellLength  (1)

    DestinationWell should have same length with total sample we are gonna measure (including NumberOfReplicates):

    CircularDichroismInvalidDetectionWavelength  (1)

    EnantiomericExcessStandards should be one of the SamplesIn or specified in PreparatoryUnitOperations:

    CircularDichroismNeedMoreEnatiomericExcessStandards  (1)

    Need at least two EnantiomericExcessStandards:

    CircularDichroismNeedMoreSamplesForEnantiomericExcessMeasurement  (1)

    EnantiomericExcessStandards should be one of the SamplesIn or specified in PreparatoryUnitOperations:

    CircularDichroismQuartzPlateCannotRetainCover  (1)

    If we using a quartz plate as the read plate, RetainCover cannot be true:

    CircularDichroismRequiredBlankOption  (1)

    If BlankAbsorbance -> True, the blank related options cannot be Null:

    CircularDichroismSampleVolumeNotValid  (1)

    Sample should have enougth volume for this experiment:

    CircularDichroismTooManySamples  (1)

    One readplate should have enough wells to incorporate all the sample with replicates, blank wells and the well for the empty well:

    CircularDichroismUnknownEnatiomericExcessStandards  (1)

    EnantiomericExcessStandards should be one of the SamplesIn or specified in PreparatoryUnitOperations:

    CircularDichroismUnNeededBlankOption  (1)

    If BlankAbsorbance -> False, the blank related options can only be Null:

    CircularDirchroismQuartzPlateNeedMoat  (1)

    If using quartz plate as the Readplate, moatsize should be larger than or equals 2:

    CircularDirchroismUnknownAnalytes  (1)

    The specified analyte should be in sample's composition:

    DiscardedSamples  (1)

    Discarded samples cannot be used:

    IncompatibleInstrumentForCircularDichroism  (1)

    Instrument specified can measure circular dichroism:

    IncompatibleReadPlateForCircularDichroism  (1)

    Readplate specified can measure circular dichroism:

    NeedConcentrationForMolarEllipticity  (1)

    If calculate molar ellipticity, the analyte concentration needs to be specified:

    ObjectDoesNotExist  (6)

    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 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 sample that does not exist (ID form):

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

Possible Issues

    Absorbance Saturation

    Similar to UV-Vis spectroscopy, if the absorbance intensity is higher than 1 Abs Unit at a wavelength or a wavelength range, the ellipticity (mdeg) collected at those wavelengths are inaccurate.
Last modified on Wed 3 Sep 2025 14:58:10

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