ExperimentMeasureDensity

ExperimentMeasureDensity[Objects]⟹Protocol

creates a MeasureDensity Protocol which determine the density of Objects.

Density measurement of liquid samples is performed via fixed volume weight measurement, or by a density meter. The fixed volume weight technique involves using an analytical balance to weigh a known volume of the sample, and calculating the density from the average sample masses divided by the known volume. The density meter uses Piezoelectric elements to excite the oscillation of the liquid sample in a hollow U-shaped glass tube, for which the oscillation frequency can be used to determine the density of the sample with very high resolution.

Experimental Principles

Figure 1.1: Procedural overview of a MeasureDensity experiment. Step 1 (Optional): The density of water and air are measured to verify how clean and dry the measurement tube is. Step 2: The sample is injected into the U-tube measurement chamber in the density meter instrument. Step 3: The density meter records the density of the sample at the specified Temperature using the U-tube oscillation technique. Step 4 (Optional): The sample is returned to its original container. Step 5: The U-tube is cleaned by the WashSolution (default is water), followed by the SecondaryWashSolution (default is ethanol) and the TertiaryWashSolution (default is acetone). The WashVolume (default of 10 mL) of each solution is sequentially flushed through the U-tube measurement chamber by the number of WashCycles (default is 1), followed by forced-air drying of the chamber prior to the next sample being measured.

Figure 1.2: Procedural overview of a MeasureDensity experiment. Step 1: A micropipette is used to transfer a known volume of the sample into a tared measurement container. Step 2: The sample in the measurement container is weighed. Step 3: The density is determined from the average sample mass and known volume.

Instrumentation

Mettler Toledo XP6

Figure 2.1.1: Items are transferred through an ionizer, which floods the local environment with positive and negative ions. This removes any static electricity that has built up on items and provides a more stable and accurate mass reading.The user must explicitly specify the Micro-Balance using the option Instrument -> Model[Instrument,Balance,"id:54n6evKx08XN"] if so desired.

DMA 5000 Density Meter

Figure 2.2.1: For ExperimentMeasureDensity using the DensityMeter method, samples are syringed into the U-shaped hollow glass tube which is heated or cooled to the specified Temperature. The measurement is performed by Piezo elements exciting the U-tube to oscillate, with ViscosityCorrection either on or off. The measured oscillation frequency is used to accurately determine the density of the samples, which are either recollected or disposed of if RecoupSample is True or False, respectively. The U-tube is cleaned by the WashSolution, which should be a good solvent for the sample (default is water), followed by the SecondaryWashSolution, which should be a good solvent for the WashSolution and evaporate quickly (default is ethanol) and the optional TertiaryWashSolution (default is acetone). The WashVolume (default of 10 mL) of each solution is sequentially flushed through the U-tube measurement chamber by the number of WashCycles (default is 1), followed by forced-air drying of the chamber prior to the next sample being measured.

Experiment Options

General

NumberOfReplicates

The number of times to repeat density measurement on each provided sample.

Default Value: 5

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

Programmatic Pattern: GreaterEqualP[1, 1] | Null

Method

The type of measurement performed to determine the density of the sample.

Default Value: Automatic

Default Calculation: Is automatically set to DensityMeter unless the volume is too low (below 2 mL) or the manual fixed volume weight method is specified.

Pattern Description: {DensityMeter, FixedVolumeWeight} or Automatic.

Programmatic Pattern: (DensityMethodP | Automatic) | Automatic

Index Matches to: experiment samples

Volume

The volume of the liquid that will be used for density measurement.

Default Value: Automatic

Default Calculation: Is automatically set to 2 Milliliter (if total sample volume is sufficient, to allow the more accurate density meter method) or 90% of the sample, whichever is smaller.

Pattern Description: Greater than or equal to 50 microliters and less than or equal to 2 milliliters.

Programmatic Pattern: RangeP[50*Microliter, 2*Milliliter] | Automatic

Index Matches to: experiment samples

Instrument

The instrument used to perform the density analysis.

Default Value: Automatic

Default Calculation: Is automatically set to DensityMeter unless the volume is too low (below 2 mL) or a manual method is specified (where a balance is automatically selected instead).

Pattern Description: An object of type or subtype Model[Instrument, DensityMeter], Object[Instrument, DensityMeter], Model[Instrument, Balance], or Object[Instrument, Balance]

Programmatic Pattern: ObjectP[{Model[Instrument, DensityMeter], Object[Instrument, DensityMeter], Model[Instrument, Balance], Object[Instrument, Balance]}] | Automatic

Index Matches to: experiment samples

RecoupSample

Indicates if the transferred liquid used for density measurement will be recouped (transferred back into the original container) or discarded.

Default Value: Automatic

Default Calculation: Is automatically set to False for samples with at least 100mL of volume (5mL for density meter), and to True for samples with less than 100mL of volume (5mL for density meter).

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Index Matches to: experiment samples

Method

Temperature

Indicates the desired temperature used for density measurement (refers to the temperature inside the instrument chamber during measurement only).

Default Value: Automatic

Default Calculation: Is automatically set to 20 Celsius unless a different temperature is given.

Pattern Description: Greater than or equal to 0 degrees Celsius and less than or equal to 100 degrees Celsius or Null.

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

Index Matches to: experiment samples

ViscosityCorrection

Determines if viscosity correction should be automatically applied during density meter measurement to provide the most accurate result.

Default Value: Automatic

Default Calculation: Is automatically set to true unless false is specified (usually for comparison to older instrument results).

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Index Matches to: experiment samples

WashSolution

The solution used to perform the washing of the previous sample out of the instrument chamber (should be a good solvent for the sample).

Default Value: Automatic

Default Calculation: Is automatically set to Milli-Q water unless a specific solvent is chosen.

Pattern Description: Water, Hexanes, or Automatic or Null.

Programmatic Pattern: ((Water | Hexanes | Automatic) | Automatic) | Null

Index Matches to: experiment samples

SecondaryWashSolution

A fast-evaporating solution used to remove traces of the first wash solution and facilitate drying the instrument chamber (should be a good solvent for the first wash solution).

Default Value: Automatic

Default Calculation: Is automatically set to 95 % ethanol unless a specific solvent is chosen.

Pattern Description: Ethanol, Acetone, or Automatic or Null.

Programmatic Pattern: ((Ethanol | Acetone | Automatic) | Automatic) | Null

Index Matches to: experiment samples

TertiaryWashSolution

A fast-evaporating solution used to remove traces of the second wash solution and facilitate drying the instrument chamber.

Default Value: Automatic

Default Calculation: Is automatically set to acetone unless a specific solvent is chosen.

Pattern Description: Ethanol, Acetone, or Automatic or Null.

Programmatic Pattern: ((Ethanol | Acetone | Automatic) | Automatic) | Null

Index Matches to: experiment samples

WashVolume

The volume of each wash solution used for primary and secondary washing in between each sample run.

Default Value: Automatic

Default Calculation: Is automatically set to 10 mL unless a higher number is chosen (typically for samples more difficult to clean out of the chamber).

Pattern Description: Greater than or equal to 10 milliliters and less than or equal to 50 milliliters in increments of 10 milliliters or Null.

Programmatic Pattern: (RangeP[10*Milliliter, 50*Milliliter, 10*Milliliter] | Automatic) | Null

Index Matches to: experiment samples

WashCycles

Number of wash cycles (using primary, secondary and tertiary wash solutions once per cycle) to perform in between each sample run.

Default Value: Automatic

Default Calculation: Is automatically set to 1 unless a higher number is chosen (typically for samples more difficult to clean out of the chamber) up to a maximum of 3 cycles.

Pattern Description: Greater than or equal to 1 and less than or equal to 3 in increments of 1 or Null.

Programmatic Pattern: (RangeP[1, 3, 1] | Automatic) | Null

Index Matches to: experiment samples

AirWaterCheck

If AirWaterCheck sets to be True, the density meter measures density of water and air before measuring the density of sample. This verifies how clean and dry the measuring tube is.

Default Value: Automatic

Default Calculation: Is automatically set to False if Method is set to DensityMeter.

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Index Matches to: experiment samples

Post Experiment

SamplesInStorageCondition

The non-default conditions under which the SamplesIn of this experiment should be stored after the protocol is completed. If left unset, SamplesIn will be stored according to their current StorageCondition.

Default Value: Null

Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, BacteriaIncubation, MammalianIncubation, TissueCultureCellsIncubation, MicrobialCellsIncubation, MicrobialCellsShakingIncubation, YeastCellsIncubation, YeastCellsShakingIncubation, ViralIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.

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

Index Matches to: experiment samples

Sample Prep Options

Sample Preparation

PreparatoryUnitOperations

Specifies a sequence of transferring, aliquoting, consolidating, or mixing of new or existing samples before the main experiment. These prepared samples can be used in the main experiment by referencing their defined name. For more information, please reference the documentation for ExperimentSampleManipulation.

Default Value: Null

Pattern Description: List of one or more unit Operation ManualSamplePreparation or RoboticSamplePreparation or unit Operation must match SamplePreparationP entries or Null.

Programmatic Pattern: {((ManualSamplePreparationMethodP | RoboticSamplePreparationMethodP) | SamplePreparationP)..} | Null

PreparatoryPrimitives

Default Value: Null

Pattern Description: List of one or more a primitive with head Define, Transfer, Mix, Aliquot, Consolidation, FillToVolume, Incubate, Filter, Wait, Centrifuge, or Resuspend entries or Null.

Programmatic Pattern: {SampleManipulationP..} | Null

Preparatory Incubation

Incubate

Indicates if the SamplesIn should be incubated at a fixed temperature prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).

Default Value: Automatic

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

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Index Matches to: experiment samples

IncubationTemperature

Temperature at which the SamplesIn should be incubated for the duration of the IncubationTime prior to starting the experiment.

Default Value: Automatic

Pattern Description: Ambient or greater than or equal to -20 degrees Celsius and less than or equal to 500 degrees Celsius or Null.

Programmatic Pattern: ((Ambient | RangeP[$MinIncubationTemperature, $MaxIncubationTemperature]) | Automatic) | Null

Index Matches to: experiment samples

IncubationTime

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

Default Value: Automatic

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

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

Index Matches to: experiment samples

Mix

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

Default Value: Automatic

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

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Index Matches to: experiment samples

MixType

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

Default Value: Automatic

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

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

Programmatic Pattern: (MixTypeP | Automatic) | Null

Index Matches to: experiment samples

MixUntilDissolved

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

Default Value: Automatic

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

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Index Matches to: experiment samples

MaxIncubationTime

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

Default Value: Automatic

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

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

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

Index Matches to: experiment samples

IncubationInstrument

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

Default Value: Automatic

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

Pattern Description: An object of type or subtype Model[Instrument, Roller], Model[Instrument, OverheadStirrer], Model[Instrument, Vortex], Model[Instrument, Shaker], Model[Instrument, BottleRoller], Model[Instrument, Roller], Model[Instrument, Sonicator], Model[Instrument, HeatBlock], Model[Instrument, Homogenizer], Model[Instrument, Disruptor], Model[Instrument, Nutator], Model[Instrument, Thermocycler], Model[Instrument, EnvironmentalChamber], Model[Instrument, Pipette], Object[Instrument, Roller], Object[Instrument, OverheadStirrer], Object[Instrument, Vortex], Object[Instrument, Shaker], Object[Instrument, BottleRoller], Object[Instrument, Roller], Object[Instrument, Sonicator], Object[Instrument, HeatBlock], Object[Instrument, Homogenizer], Object[Instrument, Disruptor], Object[Instrument, Nutator], Object[Instrument, Thermocycler], Object[Instrument, EnvironmentalChamber], or Object[Instrument, Pipette] or Null.

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

Index Matches to: experiment samples

AnnealingTime

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

Default Value: Automatic

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

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

Index Matches to: experiment samples

IncubateAliquotContainer

The desired type of container that should be used to prepare and house the incubation samples which should be used in lieu of the SamplesIn for the experiment.

Default Value: Automatic

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

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

Index Matches to: experiment samples

IncubateAliquotDestinationWell

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

Default Value: Automatic

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

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

Programmatic Pattern: (WellPositionP | Automatic) | Null

Index Matches to: experiment samples

IncubateAliquot

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

Default Value: Automatic

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

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

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

Index Matches to: experiment samples

Preparatory Centrifugation

Centrifuge

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

Default Value: Automatic

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

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Index Matches to: experiment samples

CentrifugeInstrument

The centrifuge that will be used to spin the provided samples prior to starting the experiment.

Default Value: Automatic

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

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

Index Matches to: experiment samples

CentrifugeIntensity

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

Default Value: Automatic

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

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

Index Matches to: experiment samples

CentrifugeTime

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

Default Value: Automatic

Pattern Description: Greater than 0 minutes or Null.

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

Index Matches to: experiment samples

CentrifugeTemperature

The temperature at which the centrifuge chamber should be held while the samples are being centrifuged prior to starting the experiment.

Default Value: Automatic

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

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

Index Matches to: experiment samples

CentrifugeAliquotContainer

The desired type of container that should be used to prepare and house the centrifuge samples which should be used in lieu of the SamplesIn for the experiment.

Default Value: Automatic

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

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

Index Matches to: experiment samples

CentrifugeAliquotDestinationWell

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

Default Value: Automatic

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

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

Programmatic Pattern: (WellPositionP | Automatic) | Null

Index Matches to: experiment samples

CentrifugeAliquot

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

Default Value: Automatic

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

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

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

Index Matches to: experiment samples

Preparatory Filtering

Filtration

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

Default Value: Automatic

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

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Index Matches to: experiment samples

FiltrationType

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

Default Value: Automatic

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

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

Programmatic Pattern: (FiltrationTypeP | Automatic) | Null

Index Matches to: experiment samples

FilterInstrument

The instrument that should be used to perform the filtration.

Default Value: Automatic

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

Pattern Description: An object of type or subtype Model[Instrument, FilterBlock], Object[Instrument, FilterBlock], Model[Instrument, PeristalticPump], Object[Instrument, PeristalticPump], Model[Instrument, VacuumPump], Object[Instrument, VacuumPump], Model[Instrument, Centrifuge], Object[Instrument, Centrifuge], Model[Instrument, SyringePump], or Object[Instrument, SyringePump] or Null.

Programmatic Pattern: (ObjectP[{Model[Instrument, FilterBlock], Object[Instrument, FilterBlock], Model[Instrument, PeristalticPump], Object[Instrument, PeristalticPump], Model[Instrument, VacuumPump], Object[Instrument, VacuumPump], Model[Instrument, Centrifuge], Object[Instrument, Centrifuge], Model[Instrument, SyringePump], Object[Instrument, SyringePump]}] | Automatic) | Null

Index Matches to: experiment samples

Filter

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

Default Value: Automatic

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

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

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

Index Matches to: experiment samples

FilterMaterial

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

Default Value: Automatic

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

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

Programmatic Pattern: (FilterMembraneMaterialP | Automatic) | Null

Index Matches to: experiment samples

PrefilterMaterial

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

Default Value: Automatic

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

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

Programmatic Pattern: (FilterMembraneMaterialP | Automatic) | Null

Index Matches to: experiment samples

FilterPoreSize

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

Default Value: Automatic

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

Pattern Description: 0.008 micrometers, 0.1 micrometers, 0.22 micrometers, 0.45 micrometers, 1. micrometer, 1.1 micrometers, 2.5 micrometers, 6. micrometers, 20. micrometers, 30. micrometers, or 100. micrometers or Null.

Programmatic Pattern: (FilterSizeP | Automatic) | Null

Index Matches to: experiment samples

PrefilterPoreSize

The pore size of the filter; all particles larger than this should be removed during the filtration.

Default Value: Automatic

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

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.

Index Matches to: experiment samples

TargetConcentration

The desired final concentration of analyte in the AliquotSamples after dilution of aliquots of SamplesIn with the ConcentratedBuffer and BufferDiluent which should be used in lieu of the SamplesIn for the experiment.

Default Value: Automatic

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

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

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

Index Matches to: experiment samples

TargetConcentrationAnalyte

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

Default Value: Automatic

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

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

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

Index Matches to: experiment samples

AssayVolume

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

Default Value: Automatic

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

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

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

Index Matches to: experiment samples

ConcentratedBuffer

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

Default Value: Automatic

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

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

Index Matches to: experiment samples

BufferDilutionFactor

The dilution factor by which the concentrated buffer should be diluted in the final solution (i.e., the combination of the sample, ConcentratedBuffer, and BufferDiluent). The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.

Default Value: Automatic

Default Calculation: If ConcentratedBuffer is specified, automatically set to the ConcentrationFactor of that sample; otherwise, set to Null.

Pattern Description: Greater than or equal to 1 or Null.

Programmatic Pattern: (GreaterEqualP[1] | Automatic) | Null

Index Matches to: experiment samples

BufferDiluent

The buffer used to dilute the aliquot sample such that ConcentratedBuffer is diluted by BufferDilutionFactor in the final solution. The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.

Default Value: Automatic

Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is specified; otherwise, resolves to Null.

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

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

Index Matches to: experiment samples

AssayBuffer

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

Default Value: Automatic

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

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

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

Index Matches to: experiment samples

AliquotSampleStorageCondition

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

Default Value: Automatic

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

Index Matches to: experiment samples

DestinationWell

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

Default Value: Automatic

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

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

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

AliquotContainer

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

Default Value: Automatic

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

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

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

AliquotPreparation

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

Default Value: Automatic

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

Pattern Description: Manual or Robotic or Null.

Programmatic Pattern: (PreparationMethodP | Automatic) | Null

ConsolidateAliquots

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

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Protocol Options

Organizational Information

Template

A template protocol whose methodology should be reproduced in running this experiment. Option values will be inherited from the template protocol, but can be individually overridden by directly specifying values for those options to this Experiment function.

Default Value: Null

Pattern Description: An object of type or subtype Object[Protocol] or an object of type or subtype of Object[Protocol] with UnresolvedOptions, ResolvedOptions specified or Null.

Programmatic Pattern: (ObjectP[Object[Protocol]] | FieldReferenceP[Object[Protocol], {UnresolvedOptions, ResolvedOptions}]) | Null

Name

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

Default Value: Null

Pattern Description: A string or Null.

Programmatic Pattern: _String | Null

Post Experiment

MeasureWeight

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

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

MeasureVolume

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

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

ImageSample

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

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Example Calls

Density Measurement

ExperimentMeasureDensity can only be performed on liquid samples that have volume information already provided. This is to ensure the sample has enough material available to conduct a reliable density measurement. The Volume option controls how much sample volume will be measured out and weighed to determine density. For the FixedVolumeWeight method the minimum volume required to measure the density of a sample is 50 microliters, with the maximum volume used to measure the density of a sample being 1.5 milliliters, while the DensityMeter method uses 2 milliliters. By default, the experiment will use 2 milliliters for the DensityMeter method if there is sufficient volume, or for the FixedVolumeWeight method 800 microliters or 90% of the specified sample will be used, whichever is smaller.

This experiment operates by transferring material from your sample into a tared container on a balance (for the FixedVolumeWeight method) or injecting into the density meter (for the DensityMeter method). In order to avoid consuming your samples during this process, you can use the RecoupSample option to save any material used by the experiment. Any recouped material will be transferred back into its original container. The RecoupSample option will default to True for any samples with less than 100 milliliters (for FixedVolumeWeight)or 5 Milliliters (for DensityMeter). For samples with greater than 100 milliliters (FixedVolumeWeight) or 5 milliliters (DensityMeter) of volume, RecoupSample will default to False.

To measure the density of several samples with the same method for all samples, specify a single Method.

To measure the density of samples at non-ambient temperature for samples using the DensityMeter method, specify a Temperature between 0 and 100 Celsius.

To measure the density of air, water and air before measuring the density of each sample, set AirWaterCheck to True. This verifies how clean and dry the measuring tube is.

To measure the density of low-volume samples, you can specify the FixedVolumeWeight Method, with a low Volume, and RecoupSample set to True.

Measure the density of samples using a mix of different methods.

Preferred Input Containers

Any tube, bottle, or plate with sufficient volume is acceptable, as transfers into appropriate tared containers (FixedVolumeWeight Method) or the instrument (DensityMeter Method) are always required.

Warnings and Errors

Messages (17)

InvalidAirWaterCheck (1)

An error is thrown if AirWaterCheck is provided with the FixedVolumeWeight method (this option is only compatible with the DensityMeter method):

InvalidSecondaryWashSolution (1)

An error is thrown if a SecondaryWashSolution is provided with the FixedVolumeWeight method (this option is only compatible with the DensityMeter method):

InvalidTemperature (1)

An error is thrown if a Temperature is provided with the FixedVolumeWeight method (this option is only compatible with the DensityMeter method):

InvalidTertiaryWashSolution (1)

An error is thrown if a TertiaryWashSolution is provided with the FixedVolumeWeight method (this option is only compatible with the DensityMeter method):

InvalidViscosityCorrection (1)

An error is thrown if ViscosityCorrection is provided with the FixedVolumeWeight method (this option is only compatible with the DensityMeter method):

InvalidWashCycles (1)

An error is thrown if WashCycles is provided with the FixedVolumeWeight method (this option is only compatible with the DensityMeter method):

InvalidWashSolution (1)

An error is thrown if a WashSolution is provided with the FixedVolumeWeight method (this option is only compatible with the DensityMeter method):

InvalidWashVolume (1)

An error is thrown if a WashVolume is provided with the FixedVolumeWeight method (this option is only compatible with the DensityMeter method):

MeasureDensityIncompatibleInstrument (1)

An error is thrown if an incompatible instrument is selected:

MeasureDensityIncompatibleVolume (1)

An error is thrown if a Volume other than 2 Milliliter is provided with the DensityMeter method (the measurement chamber has a fixed volume, requiring 2 Milliliter for accurate measurement):

MeasureDensitySolidSample (1)

An error is thrown if a sample is solid (only liquid samples can be have their density measured with ExperimentMeasureDensity):

MeasureDensityVentilatedSamples (1)

An error is thrown if a ventilated sample is specified to be measured with the DensityMeter method:

MeasureDensityVolumeTooLow (1)

An error is thrown if a sample does not have sufficient volume to be measured (at least 50 Microliter is required to measure density):

MeasureDensityVolumeUnknown (1)

An error is thrown if a sample has no volume information:

AmbientTemperatureMeasurement (2)

A Warning is thrown if the samples should be transport chilled but the measurement is taken at ambient temperature:

A Warning is thrown if the samples should be transport warmed but the measurement is taken at ambient temperature:

ModelDensityNotUpdated (1)

A Warning is thrown if the samples' Model already has Density information and will not have their Density updated from the current experiment (only the Object[Sample] will have its density updated):

Possible Issues

Very large number of samples

If ExperimentMeasureDensity is called with >200 SamplesIn in the same experiment, the duration of the experiment may be quite long. Consider splitting up the call into multiple experiments with <200 samples in each.

Very viscous samples

If ExperimentMeasureDensity is called with highly viscous SamplesIn and DensityMeter selected as the Method, by default ViscosityCorrection is set to True and the measurement will proceed at the default temperature (20.0 C) and try to correct for the viscosity to maintain accuracy of the measurement. To reduce the possibility of viscosity affecting the measurement, consider setting the Temperature to a higher value to reduce the effects of the viscosity on the measurement.

Incompatible wash solutions

If ExperimentMeasureDensity is called with DensityMeter selected as the Method, by default the WashSolution is set to water, and the SecondaryWashSolution is set to ethanol. If your sample is not soluble in these solutions, please choose alternatives to ensure your sample is fully removed from the measurement chamber following measurement and no cross-contamination occurs. The first WashSolution should be a good solvent for your sample, and the SecondaryWashSolution should be a good solvent for the first WashSolution and evaporate quickly (acetone is a good alternative for ethanol).

Volatile samples

If ExperimentMeasureDensity is called with FixedVolumeWeight selected as the Method with small volumes of volatile solvents, the accuracy of the measurement may be impacted. For the highest accuracy, if volume permits, consider using the DensityMeter method for volatile samples.

Last modified on Tue 10 Jan 2023 14:49:43