ExperimentPellet
ExperimentPellet[Samples]⟹Protocol
generates a Protocol object to concentrate the denser, insoluble contents of a solution to the bottom of a given container via centrifugation, aspirate off the supernatant, optionally apply a wash solution that can be fed into multiple rounds of pelleting, and optionally add a resuspension solution to rehydrate the pellet.
ExperimentPellet is used to concentrate the denser, insoluble contents of a solution to the bottom of a given container via centrifugation, aspirate off the supernatant, optionally apply a wash solution that can be fed into multiple rounds of pelleting, and optionally add a resuspension solution to rehydrate the pellet.
Experimental Principles
Figure 1.1: Figure 1.1: Procedural overview of a Pelleting experiment.
Step 1: The SamplesIn are prepared according to any sample preparation options that are set. This may include any aliquots needed to get the SamplesIn into a centrifuge compatible container.
Step 2: The samples are centrifuged in order to form a pellet.
Step 3: (Optional) The supernatant is aspirated from the pelleted sample.
Step 4: (Optional) The pellet is resuspended using the specified ResuspensionSource and mixed.
Instrumentation
Avanti J-15R
Figure 2.1: Samples to be centrifuged are counterbalanced in available centrifuge bucket slots. The centrifuge spins the buckets around the axis of the main rotor, while applying optional heating or cooling. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.
Avanti J-15R with JA-10.100 Fixed Angle Rotor
Figure 2.2: Samples to be centrifuged are counterbalanced in available centrifuge rotor slots. The centrifuge spins the rotors around the axis of the main rotor, while applying optional heating or cooling. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.
Microfuge 16
Figure 2.3: Samples to be centrifuged are counterbalanced in available centrifuge slots. The centrifuge spins the samples around the axis of the rotor. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.
Beckman Coulter Microfuge 20R
Figure 2.4: Samples to be centrifuged are counterbalanced in available centrifuge bucket slots. The centrifuge spins the buckets around the axis of the main rotor, while applying optional heating or cooling. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.
Eppendorf 5920R
Figure 2.5: Samples to be centrifuged are counterbalanced in available centrifuge bucket slots. The centrifuge spins the buckets around the axis of the main rotor, while applying optional cooling to prevent a buildup of heat caused by the friction of spinning the rotor. As the samples spin, they are exposed to a centrifugal force that is significantly larger than typical gravitational acceleration. The samples can subsequently be collected at the end of the experiment.
Experiment Options
General
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.
WorkCell
The automated workstation with a collection of integrated instruments on which this unit operation will be will be performed if Preparation -> Robotic.
Centrifugation
Instrument
Default Calculation: Automatically set to a centrifuge that can attain the specified intensity, time, temperature, and sterility and (if possible) that is compatible with the sample in its current container.
Pattern Description: An object of type or subtype Model[Instrument, Centrifuge] or Object[Instrument, Centrifuge]
Programmatic Pattern: ObjectP[{Model[Instrument, Centrifuge], Object[Instrument, Centrifuge]}] | Automatic
Intensity
The rotational speed or the force that will be applied to the samples by centrifugation in order to create a pellet.
Default Calculation: Automatically set to one fifth of the maximum rotational rate of the centrifuge, rounded to the nearest attainable centrifuge precision.
Pattern Description: Greater than or equal to 0 revolutions per minute and less than or equal to 80000 revolutions per minute or greater than or equal to 0 standard accelerations due to gravity on the surface of the earth and less than or equal to 504000 standard accelerations due to gravity on the surface of the earth.
Programmatic Pattern: (RangeP[0*RPM, $MaxCentrifugeSpeed] | RangeP[0*GravitationalAcceleration, $MaxRelativeCentrifugalForce]) | Automatic
Time
Temperature
The temperature at which the centrifuge chamber will be held while the samples are being centrifuged.
Pattern Description: Ambient or greater than or equal to -10 degrees Celsius and less than or equal to 40 degrees Celsius.
Supernatant Aspiration
SupernatantVolume
Default Calculation: Automatically set based on Preparation: All for Preparation is Manual and half of the sample volume for Preparation is Robotic.
SupernatantDestination
The destination that the supernatant should be dispensed into, after aspirated from the source sample.
Default Calculation: SupernatantDestination is set to Waste if performing the aspiration manually using an aspirator. Otherwise, SupernatantDestination is set to an empty liquid handler container to dispense the supernatant into.
Programmatic Pattern: (Waste | (ObjectP[{Object[Sample], Object[Container], Model[Container]}] | _String)) | Automatic
Resuspension
Resuspension
ResuspensionSource
Default Calculation: Automatically set to Model[Sample, "Milli-Q water"] if any of the other Resuspension options are set.
Pattern Description: An object of type or subtype Model[Sample], Object[Sample], or Object[Container] or a prepared sample or Null.
Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample], Object[Container]}] | _String) | Automatic) | Null
ResuspensionVolume
The volume of ResuspensionSource that should be used to resuspend the pellet from the source sample.
Default Calculation: Automatically set to 1/4 of the source sample container's volume or the volume of the provided ResuspensionSource (whichever is smaller), if any of the other Resuspension options are set.
Resuspension Mix
ResuspensionMix
Default Calculation: Automatically set to True if any Mix related options are set. Otherwise, set to False.
ResuspensionMixType
Indicates the style of motion used to mix the sample. Options include Roll, Vortex, Sonicate, Pipette, Invert, Stir, Shake, Homogenize, Swirl, Disrupt, Nutate.
Default Calculation: Automatically sets based on the container of the sample and the Mix option. Specifically, if Mix is set to False, the option is set to Null. If MixInstrument is specified, the option is set based on the type of the Model[Instrument] or Object[Instrument] of the specified MixInstrument. If MixRate and Time are Null, when MixVolume is Null or larger than 50ml, the option is set to Invert, otherwise set to Pipette. If Amplitude, MaxTemperature, or DutyCycle is not Null, the option is set to Homogenizer. If MixRate is set, the option is set based on the type of the Model[Instrument] of the first instrument found by MixDevices that is compatible with the SamplesIn, Temperature, and MixRate.
Pattern Description: Roll, Vortex, Sonicate, Pipette, Invert, Stir, Shake, Homogenize, Swirl, Disrupt, or Nutate or Null.
ResuspensionMixUntilDissolved
Indicates if the mix should be continued up to the MaxTime or MaxNumberOfMixes (chosen according to the mix Type), in an attempt dissolve any solute.
ResuspensionMixInstrument
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: ((Null | ObjectP[Join[MixInstrumentModels, MixInstrumentObjects]]) | Automatic) | Null
ResuspensionMixStirBar
Default Calculation: If MixRate is above 1000 RPM, or if no compatible impeller can be found for the given stirrer, StirBar is automatically set to the largest compatible stir bar found. Here, a compatible impeller means that it can fit in the aperture of the sample's container, can reach the bottom of the sample's container, and is compatible with the stir instrument given; a compatible stir bar means that its width can fit in the aperture of the sample's container and that its length is not greater than the InternalDiameter of the sample's container. Otherwise set to Null.
Pattern Description: An object of type or subtype Model[Part, StirBar] or Object[Part, StirBar] or Null.
Programmatic Pattern: ((Null | ObjectP[{Model[Part, StirBar], Object[Part, StirBar]}]) | Automatic) | Null
ResuspensionMixTime
Default Calculation: Automatically set to 5 Minute for robotic preparation. For manual preparation, if Thaw is True, set to 0 Minute; else if MaxTime is specified, Time is automatically set to 1/3 of MaxTime; otherwise set to 15 Minute. As a special case in manual preparation, when LightExposure is not Null, Thaw is True, set to 0 Minute; else if TotalLightExposure is specified and LightExposureIntensity is not Null, Time is automatically set to TotalLightExposure/LightExposureIntensity; otherwise set to 1 Hour.
ResuspensionMixMaxTime
Maximum duration of time for which the samples are mixed, in an attempt to dissolve any solute, if the MixUntilDissolved option is chosen. Note this option only applies for mix type: Shake, Roll, Vortex or Sonicate.
Default Calculation: Automatically set to 5 Hour if MixUntilDissolved is True, when an applicable MixType is chosen, otherwise set to Null.
ResuspensionMixDutyCycle
The style how the homogenizer mixes the given sample via pulsation of the sonication horn. This duty cycle is repeated indefinitely until the specified Time/MaxTime has elapsed. This option can only be set when mixing via homogenization.
Default Calculation: Automatically set to {10 Millisecond, 10 Millisecond} if mixing by homogenization.
Programmatic Pattern: ((Null | {RangeP[0*Minute, 60*Hour], RangeP[0*Minute, 60*Hour]}) | Automatic) | Null
ResuspensionMixRate
Default Calculation: Automatically set to 300 RPM for robotic preparation. For manual preparation, MixRate is set to 20% of the MaxRotationRate if MixType is Stir, or otherwise is set to the average of MinRotationRate and MaxRotationRate of the instrument.
Programmatic Pattern: ((Null | (RangeP[$MinMixRate, $MaxMixRate] | RangeP[0*GravitationalAcceleration, 100*GravitationalAcceleration])) | Automatic) | Null
ResuspensionMixRateProfile
The frequency of rotation of the mixing instrument used to mix the samples, over the course of time.
Programmatic Pattern: ((Null | {{RangeP[0*Minute, $MaxExperimentTime], RangeP[$MinMixRate, $MaxMixRate] | RangeP[0*GravitationalAcceleration, 100*GravitationalAcceleration]}..}) | Automatic) | Null
ResuspensionNumberOfMixes
Default Calculation: If MaxNumberOfMixes is specified, automatically set to 1/3 of MaxNumberOfMixes (round to integer); else if MixUntilDissolved->True, automatically set to 25; otherwise set to 15.
Pattern Description: Greater than or equal to 1 and less than or equal to 50 in increments of 1 or Null.
ResuspensionMaxNumberOfMixes
The maximum number of times for which the samples are mixed, in an attempt to dissolve any solute, if the MixUntilDissolved option is chosen. Note this option only applies for mix type: Pipette or Invert.
Default Calculation: When MixUntilDissolved->True, automatically set to 2*NumberOfMixes if it is Numeric (specified or automatically set); if not, set to 50.
Pattern Description: Greater than or equal to 1 and less than or equal to 250 in increments of 1 or Null.
ResuspensionMixVolume
Default Calculation: For robotic preparation, automatically set to 970 Microliter or sample volume informed by the field Volume of the sample, whichever is smaller. For manual preparation, automatically set to 50 Milliliter or half of the sample volume informed by the field Volume of the sample, whichever is smaller.
Pattern Description: Greater than or equal to 0.5 microliters and less than or equal to 50 milliliters or Null.
ResuspensionMixTemperature
The temperature of the device that is used to mix/incubate the sample. If mixing via homogenization, the pulse duty cycle of the sonication horn is automatically adjusted if the measured temperature of the sample exceeds this set temperature.
Default Calculation: Automatically set to 40 Celsius if AnnealingTime is specified, if not, set to Ambient.
Pattern Description: Ambient or greater than or equal to -20 degrees Celsius and less than or equal to 500 degrees Celsius or Null.
Programmatic Pattern: ((Null | (RangeP[$MinIncubationTemperature, $MaxIncubationTemperature] | Ambient)) | Automatic) | Null
ResuspensionMixTemperatureProfile
Programmatic Pattern: ((Null | {{RangeP[0*Minute, $MaxExperimentTime], RangeP[$MinTemperatureProfileTemperature, $MaxTemperatureProfileTemperature]}..}) | Automatic) | Null
ResuspensionMixMaxTemperature
The maximum temperature that the sample is allowed to reach during mixing via homogenization or sonication. If the measured temperature is above this MaxTemperature, the homogenizer/sonicator turns off until the measured temperature is 2C below the MaxTemperature, then it automatically resumes.
Pattern Description: Greater than or equal to 0 degrees Celsius and less than or equal to 100 degrees Celsius or Null.
ResuspensionMixOscillationAngle
Pattern Description: Greater than or equal to 0 degrees and less than or equal to 15 degrees or Null.
ResuspensionMixAmplitude
The amplitude of the sonication horn when mixing via homogenization. When using a microtip horn (ex. for 2mL and 15mL tubes), the maximum amplitude is 70 Percent, as specified by the manufacturer, in order not to damage the instrument.
Pattern Description: Greater than or equal to 10 percent and less than or equal to 100 percent or Null.
ResuspensionMixFlowRate
The speed at which liquid is aspirated and dispensed in a liquid before it is aspirated. This option can only be set if Preparation->Robotic.
Default Calculation: Automatically set to 100 Microliter/Second when mixing by pipetting if Preparation->Robotic.
Pattern Description: MixFlowRate speed at which liquid should be drawn up into the pipette tip or Null.
Programmatic Pattern: ((Null | RangeP[0.4*(Microliter/Second), 500*(Microliter/Second)]) | Automatic) | Null
ResuspensionMixPosition
The location from which liquid should be mixed by pipetting. This option can only be set if Preparation->Robotic.
ResuspensionMixPositionOffset
The distance from the center of the well that liquid will aspirated/dispensed while mixing the sample. When specifying a Z Offset, the Z Offset is calculated either as the height below the top of the well, the height above the bottom of the well, or the height below the detected liquid level, depending on value of the AspirationPosition option (Top|Bottom|LiquidLevel). When an AspirationAngle is specified, the AspirationPositionOffset is measured in the frame of reference of the tilted labware (so that wells that are further away from the pivot point of the tilt are in the same frame of reference as wells that are close to the pivot point of the tilt). This option can only be set if Preparation->Robotic.
Default Calculation: Automatically set to 2 Millimeter if MixType->Pipette and Preparation->Robotic.
Programmatic Pattern: ((Null | (GreaterEqualP[0*Millimeter] | Coordinate[{DistanceP, DistanceP, GreaterEqualP[0*Millimeter]}])) | Automatic) | Null
ResuspensionMixCorrectionCurve
The relationship between a target volume and the corrected volume that needs to be aspirated or dispensed to reach the target volume. This option can only be set if Preparation->Robotic.
Default Calculation: Automatically set to correction curve set in the PipettingMethod for the Object[Sample] if MixType->Pipette and Preparation->Robotic.
Programmatic Pattern: ((Null | {{RangeP[0*Microliter, 1000*Microliter], RangeP[0*Microliter, 1250*Microliter]}..}) | Automatic) | Null
ResuspensionMixTips
Default Calculation: If MixType->Pipette, automatically set to the preferred tips determined by TransferDevices with given MixVolume, as well as TipType and TipMaterial if specified, and it is also checked that the tips can reach the bottom of the container.
Programmatic Pattern: ((Null | ObjectP[{Model[Item, Tips], Object[Item, Tips]}]) | Automatic) | Null
ResuspensionMixTipType
Default Calculation: If Tips is specified, automatically set to the field TipType of the Model[Item, Tips] or the Model of Object[Item,Tips]. Otherwise, set to Null.
ResuspensionMixTipMaterial
The material of the pipette tips used to aspirate and dispense the requested volume during the transfer.
Default Calculation: If Tips is specified, automatically set to the field Material of the Model[Item, Tips] or the Model of Object[Item,Tips]. Otherwise, set to Null.
Pattern Description: {ABS, PLA, Acrylic, AmorphousFluoropolymer, CPVC, CTFE, Cycloolefine, COC, Delrin, ECTFE, EPDM, ETFE, EVA, FEP, FFKM, HDPE, Hypalon, LDPE, NaturalRubber, NBR, Neoprene, Nitrile, Noryl, Nylon, PEEK, PEI, Perlast, PharmaPure, Polycarbonate, Polyester, Polyethylene, Polyisoprene, Polyolefin, Polyoxymethylene, Polypropylene, Polysulfone, Polystyrene, Polyurethane, PVC, PCTFE, PETG, PF, PFA, PPS, PTFE, PVDF, SEBS, Silicone, Styrofoam, SyntheticRubber, TFM, TPE, Tygon, UVPlastic, UVXPO, Viton}, {Aluminum, Alloy, AnodisedAluminum, Brass, Bronze, CarbonSteel, CastIron, Chrome, Copper, Elgiloy, Gold, Hastelloy, Lead, Magnesium, Molybdenum, MP35N, MP35NHPS, Nickel, Niobium, Platinum, Silver, Steel, StainlessSteel, Titanium, Tungsten, Zinc}, {Cellulose, Cotton, Polyethylene, Polypropylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, AgaroseResin, CobaltResin, Silica, HLB, AnoporeAlumina}, {Silica, Alumina, ResinParticlesWithLatexMicroBeads, CrossLinkedDextranBeads, CrossLinkedPolystyrene, AerisCoreShell, KinetexCoreShell, CrossLinkedAgarose, Vydac218MS, JordiGel, Styrene, SilicaCompositeTWIN, BEH, CSH, HSS, CarboPacPA1, CarboPacPA10, BEH}, AluminiumOxide, ZirconiumOxide, Ceramic, Epoxy, EpoxyResin, GlassyCarbon, {BorosilicateGlass, Glass, OpticalGlass}, Graphite, Porcelain, Oxidizer, {Cardboard, Wood}, {Agate, Quartz, UVQuartz, ESQuartz, FusedQuartz, IRQuartz}, Ruby, Sapphire, Silicon, Viton, or {VacuumMeltedStainlessSteel} or Null.
ResuspensionMixMultichannelMix
Default Calculation: Automatically set to True if there are multiple samples that are mixed via pipette, if MixType->Pipette.
ResuspensionMixDeviceChannel
The channel of the work cell that should be used to perform the pipetting mixing. This option can only be set if Preparation->Robotic and MixType->Pipette.
Default Calculation: Automatically set to SingleProbe1 if MultichannelMix->False. Otherwise, set to the appropriate channel to perform the transfer, if Preparation->Robotic and MixType->Pipette.
Pattern Description: MultiProbeHead, SingleProbe1, SingleProbe2, SingleProbe3, SingleProbe4, SingleProbe5, SingleProbe6, SingleProbe7, or SingleProbe8 or Null.
ResuspensionMixResidualIncubation
Indicates if the incubation and/or mixing should continue after Time/MaxTime has finished while waiting to progress to the next step in the protocol.
Default Calculation: Automatically set to True if Temperature is non-Ambient and the samples being incubated have non-ambient TransportTemperature.
ResuspensionMixResidualTemperature
The temperature at which the sample(s) should remain incubating after Time has elapsed. This option can only be set if Preparation->Robotic.
Default Calculation: Automatically set to Temperature if ResidualIncubation is True and Preparation->Robotic.
Pattern Description: Ambient or Null or greater than or equal to 0 degrees Celsius and less than or equal to 105 degrees Celsius.
ResuspensionMixResidualMix
Indicates that the sample(s) should remain shaking at the ResidualMixRate after Time has elapsed. This option can only be set if Preparation->Robotic.
ResuspensionMixResidualMixRate
When mixing by shaking, this is the rate at which the sample(s) remains shaking after Time has elapsed. This option can only be set if Preparation->Robotic.
Pattern Description: Greater than or equal to 30 revolutions per minute and less than or equal to 2500 revolutions per minute or Null.
ResuspensionMixPreheat
Indicates if the incubation position is brought to Temperature before exposing the Sample to it. This option can only be set if Preparation->Robotic.
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.
Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
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.
Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
Transfer Technique
SterileTechnique
Indicates if sterilized instruments and aseptic transfer environments must be used for the transfer. Aseptic transfer environments include biosafety cabinets as TransferEnvironment, or bioSTAR and microbioSTAR Hamilton enclosures as WorkCell. Please consult the ExperimentTransfer documentation for a full diagram of SterileTechnique that is employed by operators.
Default Calculation: Automatically set to True if the samples being transferred contain tissue culture or microbial components, or require aseptic techniques.
Model Input
PreparedModelContainer
Indicates the container in which a Model[Sample] specified as input to the experiment function will be prepared.
Default Calculation: If PreparedModelAmount is set to All and when the input model has a product associated with both Amount and DefaultContainerModel populated, automatically set to the DefaultContainerModel value in the product. Otherwise set to Model[Container, Vessel, "2mL Tube"].
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.
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.
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 Calculation: Resolves to True if any of the corresponding Incubation options are set. Otherwise, resolves to False.
IncubationTemperature
Temperature at which the SamplesIn should be incubated for the duration of the IncubationTime prior to starting the experiment.
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
IncubationTime
Duration for which SamplesIn should be incubated at the IncubationTemperature, prior to starting the experiment.
Mix
Default Calculation: Automatically resolves to True if any Mix related options are set. Otherwise, resolves to False.
MixType
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.
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 Calculation: Automatically resolves to True if MaxIncubationTime or MaxNumberOfMixes is set.
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 Calculation: Automatically resolves based on MixType, MixUntilDissolved, and the container of the given sample.
IncubationInstrument
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.
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.
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.
Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
IncubateAliquotDestinationWell
The desired position in the corresponding IncubateAliquotContainer in which the aliquot samples will be placed.
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
IncubateAliquot
The amount of each sample that should be transferred from the SamplesIn into the IncubateAliquotContainer when performing an aliquot before incubation.
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.
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 Calculation: Resolves to True if any of the corresponding Centrifuge options are set. Otherwise, resolves to False.
CentrifugeInstrument
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
CentrifugeIntensity
The rotational speed or the force that will be applied to the samples by centrifugation prior to starting the experiment.
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
CentrifugeTime
CentrifugeTemperature
The temperature at which the centrifuge chamber should be held while the samples are being centrifuged prior to starting the experiment.
Pattern Description: Ambient or greater than or equal to -10 degrees Celsius and less than or equal to 40 degrees Celsius or Null.
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.
Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
CentrifugeAliquotDestinationWell
The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
CentrifugeAliquot
The amount of each sample that should be transferred from the SamplesIn into the CentrifugeAliquotContainer when performing an aliquot before centrifugation.
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.
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 Calculation: Resolves to True if any of the corresponding Filter options are set. Otherwise, resolves to False.
FiltrationType
Default Calculation: Will automatically resolve to a filtration type appropriate for the volume of sample being filtered.
FilterInstrument
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
Filter
The filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.
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
FilterMaterial
The membrane material of the filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.
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.
PrefilterMaterial
The material from which the prefilter filtration membrane should be made of to remove impurities from the SamplesIn prior to starting the experiment.
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.
FilterPoreSize
The pore size of the filter that should be used when removing impurities from the SamplesIn prior to starting the experiment.
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.
PrefilterPoreSize
The pore size of the filter; all particles larger than this should be removed during the filtration.
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.
FilterSyringe
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
FilterHousing
The filter housing that should be used to hold the filter membrane when filtration is performed using a standalone filter membrane.
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
FilterIntensity
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
FilterTime
Default Calculation: Will automatically resolve to 5 Minute if FiltrationType is Centrifuge and Filtration is True.
FilterTemperature
The temperature at which the centrifuge chamber will be held while the samples are being centrifuged during filtration.
Default Calculation: Will automatically resolve to 22 Celsius if FiltrationType is Centrifuge and Filtration is True.
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 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
FilterAliquotDestinationWell
The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
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.
Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
FilterAliquot
The amount of each sample that should be transferred from the SamplesIn into the FilterAliquotContainer when performing an aliquot before filtration.
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.
FilterSterile
Default Calculation: Resolve to False if Filtration is indicated. If sterile filtration is desired, this option must manually be set to True.
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).
AliquotAmount
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.
Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | RangeP[1*Milligram, 20*Kilogram] | GreaterP[0*Unit, 1*Unit] | GreaterP[0., 1.] | All) | Automatic) | Null
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.
TargetConcentrationAnalyte
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.
AssayVolume
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.
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.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
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 Calculation: If ConcentratedBuffer is specified, automatically set to the ConcentratedBufferDilutionFactor of that sample; otherwise, set to Null.
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 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.
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 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.
AliquotSampleStorageCondition
The non-default conditions under which any aliquot samples generated by this experiment should be stored after the protocol is completed.
Pattern Description: {AmbientStorage, EnclosedAmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
DestinationWell
The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
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 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
Default Calculation: Automatic resolution will occur based on manipulation volumes and container types.
ConsolidateAliquots
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.
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.
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.
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.
ImageSample
Example Calls
Warnings and Errors
Messages (9)
LabelingDiscardedSupernatant (1)
LabelsCannotBeNullForCollectedSupernatant (1)
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
Manual Pellet Exclusive Options
Those options are only available for manual pellet experiment: SupernatantTransferInstrument, ResuspensionMixUntilDissolved, ResuspensionMixMaxTemperature, ResuspensionMixAmplitude, ResuspensionMixMaxTime, ResuspensionMixUntilDissolved, ResuspensionInstrument, ResuspensionMaxNumberOfMixes, ResuspensionMixDutyCycle.
Limited Option Choices for Robotic Pellet
For Robotic Pellet primitives, Temperature, Instrument and ResuspensionMixType support fewer options than Manual Pritimives: 1. The Temperature needs to be Ambient; 2. The Instrument needs to be Model[Instrument, Centrifuge, "VSpin"]; 3. The ResuspensionMixType is either Shake or Pipette.
Can Remove All SupernatantVolume in Manual Pellet Primitive
For pellet experiment, if All is specified in SupernatantVolume, all solvent will be removed after the centrifugation. However, since "All" can only be judged by a lab operator, robotic pellet primitive does not include All as the choice for SupernatantVolume. Therefore, if removing all solution after the centrifugation is desired, please try using manual pellet primitives.
Lack of Pellet Formation
Last modified on Thu 4 Sep 2025 16:25:27