ExperimentMeasurepH
ExperimentMeasurepH[Samples]⟹Protocol
generates a Protocol to measure pH of the provided Samples.
Measuring pH (log inverse concentration of H+ species) involves quantifying the hydrogen-ion activity (acidity or alkalinity) of an aqueous solution. To perform measurements, a probe is immersed into the sample solution. The probe consists of two combined electrodes, the hydrogen-ion selective glass electrode and the reference electrode. The voltage generated between the electrodes is directly proportional to the pH of the solution. The typical pH scale ranges from 0 to 14, where acidic solutions have a pH value below 7 (higher concentration of hydrogen ions), basic solutions have a pH value above 7 (lower concentration of hydrogen ions).
Experimental Principles
Figure 1.1: Procedural overview of a MeasurepH experiment. Step 1: Before each batch of samples, the pH probe is calibrated with calibration solutions of known pH. Step 2: Probe is immersed into the sample and pH is measured. Step 3: After the final sample measurement, the probe is rinsed with water, removed from the system, and stored.
Instrumentation
SevenExcellence (for pH)
Figure 2.1.1: Seven Excellence methods can be pre-programmed with Mothod Modules. pH probes are held with a holding arm for pH measurements of samples by submerging into samples or measuring on surface of samples.
Mettler Toledo InLab Micro
Figure 2.2.1: The probe is immersed in the test sample. pH is measured by measuring the generated voltage between two electrodes which directly proportional to the pH of the solution.
Mettler Toledo InLab Reach 225
Figure 2.3.1: The probe is immersed in the test sample. pH is measured by measuring the generated voltage between two electrodes which directly proportional to the pH of the solution.
Experiment Options
General
Instrument
For each member of 'items', the pH meter to be used for measurement.
Default Value: Automatic
Default Calculation: For each member of 'items', the pH meter chosen is based suitability to sample volume and container.
Pattern Description: An object of type or subtype Object[Instrument, pHMeter] or Model[Instrument, pHMeter]
Programmatic Pattern: ObjectP[{Object[Instrument, pHMeter], Model[Instrument, pHMeter]}] | Automatic
Index Matches to: experiment samples
Probe
The pH probe which is immersed in each sample for conductivity measurement.
Default Value: Automatic
Default Calculation: If the sample volume is small, a surface or microprobe will be chosen. Otherwise, set to the large immersion probe.
Pattern Description: An object of type or subtype Object[Part, pHProbe] or Model[Part, pHProbe] or Null.
Programmatic Pattern: (ObjectP[{Object[Part, pHProbe], Model[Part, pHProbe]}] | Automatic) | Null
Index Matches to: experiment samples
AcquisitionTime
The amount of time that data from the pH sensor should be acquired. 0 Second indicates that the pH sensor should be pinged instantaneously, collecting only 1 data point. When set, SensorNet pings the instrument in 1 second intervals. This option cannot be set for the non-SensorNet pH instruments since they only provide a single pH reading.
Default Value: Automatic
Default Calculation: Resolves to 5 Second if the probe is connected to our SensorNet system; otherwise, set to Null.
Pattern Description: Greater than or equal to 0 seconds and less than or equal to 30 minutes or Null.
Programmatic Pattern: (RangeP[0*Second, 30*Minute] | Automatic) | Null
Index Matches to: experiment samples
TemperatureCorrection
Defines the relationship between temperature and pH. Linear: Use for the temperature correction of medium and highly conductive solutions. NonLinear: Use for natural water (only for temperature between 0…36 °C). Off: The pH value at the current temperature is displayed.
Default Value: Automatic
Default Calculation: Set to Linear if the instrument is capable; otherwise, Null.
Pattern Description: Linear or Off or Null.
Programmatic Pattern: ((Linear | Off) | Automatic) | Null
Index Matches to: experiment samples
RecoupSample
Indicates if the transferred liquid used for pH measurement will be recouped or transferred back into the original container after pH measurement. If ProbeType->Immersion, the sample will be returned to the container before aliquotting occurred, if applicable, since aliquotting is automatically turned on for this measurement type.
Default Value: False
Default Calculation: Resolves to False unless explicitly set to True.
Pattern Description: True or False.
Programmatic Pattern: BooleanP
Index Matches to: experiment samples
NumberOfReplicates
The number of times to repeat the experiment on each provided 'item'. If specified, the recorded replicate measurements will be averaged for determining the final pH of the sample(s). Note that specifying NumberOfReplicates is identical to providing duplicated input.
Default Value: Null
Pattern Description: Greater than or equal to 2 and less than or equal to 10 in increments of 1 or Null.
Programmatic Pattern: RangeP[2, 10, 1] | Null
WashSolution
The solution that should be used to wash the pH probe between measurements. For Surface and Immersion probes, if WashSolution is not Model[Sample,"Milli-Q water"], probe with be washed with a wash bottle containing Milli-Q water and then washed in a clean 600ml beaker containing 400ml of Milli-Q water. If WashSolution is not Model[Sample,"Milli-Q water"], two aliquots of the wash solutions will be created. The probe will first be washed in a "dirty" solution and then washed in a "clean" solution.
Default Value: Model[Sample, Milli-Q water]
Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample.
Programmatic Pattern: ObjectP[{Object[Sample], Model[Sample]}] | _String
Calibration
LowCalibrationBuffer
The low pH buffer that should be used to calibrate the pH probe. Only SensorNet-based probes can have non-standard calibration buffers.
Default Value: Model[Sample, id:BYDOjvGjGxGr]
Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample.
Programmatic Pattern: ObjectP[{Object[Sample], Model[Sample]}] | _String
LowCalibrationBufferpH
The pH of the LowCalibrationBuffer that should be used to calibrate the pH probe. Only SensorNet-based probes can have non-standard calibration buffers.
Default Value: Automatic
Default Calculation: Resolves to the pH of the LowCalibrationBuffer, if known.
Pattern Description: Greater than or equal to 0 and less than or equal to 14.
Programmatic Pattern: RangeP[0, 14] | Automatic
MediumCalibrationBuffer
The medium pH buffer that should be used to calibrate the pH probe. This buffer is optional and may be set to Null if a calibration using two reference buffers (low and high) is desired). This option only applies to Surface and Immersion probes since Droplet probes must always use a three point calibration at pH 4, 7, and 10.
Default Value: Model[Sample, id:vXl9j57j7OVd]
Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample or Null.
Programmatic Pattern: (ObjectP[{Object[Sample], Model[Sample]}] | _String) | Null
MediumCalibrationBufferpH
The pH of the MediumCalibrationBuffer, if provided, that should be used to calibrate the pH probe. Only SensorNet-based probes can have non-standard calibration buffers.
Default Value: Automatic
Default Calculation: Resolves to the pH of the MediumCalibrationBuffer, if known.
Pattern Description: Greater than or equal to 0 and less than or equal to 14.
Programmatic Pattern: RangeP[0, 14] | Automatic
HighCalibrationBuffer
The medium pH buffer that should be used to calibrate the pH probe. This buffer is optional and may be set to Null if a calibration using two reference buffers (low and high) is desired). Only SensorNet-based probes can have non-standard calibration buffers.
Default Value: Model[Sample, id:n0k9mG8m8dMn]
Pattern Description: An object of type or subtype Object[Sample] or Model[Sample] or a prepared sample.
Programmatic Pattern: ObjectP[{Object[Sample], Model[Sample]}] | _String
HighCalibrationBufferpH
The pH of the HighCalibrationBuffer, if provided, that should be used to calibrate the pH probe. Only SensorNet-based probes can have non-standard calibration buffers.
Default Value: Automatic
Default Calculation: Resolves to the pH of the HighCalibrationBuffer, if known.
Pattern Description: Greater than or equal to 0 and less than or equal to 14.
Programmatic Pattern: RangeP[0, 14] | Automatic
Post Experiment
SamplesInStorageCondition
The non-default conditions under which the SamplesIn of this experiment should be stored after the protocol is completed. If left unset, SamplesIn will be stored according to their current StorageCondition.
Default Value: Null
Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, BacteriaIncubation, MammalianIncubation, TissueCultureCellsIncubation, MicrobialCellsIncubation, MicrobialCellsShakingIncubation, YeastCellsIncubation, YeastCellsShakingIncubation, ViralIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null
Index Matches to: experiment samples
Sample Prep Options
Sample Preparation
PreparatoryUnitOperations
Specifies a sequence of transferring, aliquoting, consolidating, or mixing of new or existing samples before the main experiment. These prepared samples can be used in the main experiment by referencing their defined name. For more information, please reference the documentation for ExperimentSampleManipulation.
Default Value: Null
Pattern Description: List of one or more unit Operation ManualSamplePreparation or RoboticSamplePreparation or unit Operation must match SamplePreparationP entries or Null.
Programmatic Pattern: {((ManualSamplePreparationMethodP | RoboticSamplePreparationMethodP) | SamplePreparationP)..} | Null
PreparatoryPrimitives
Specifies a sequence of transferring, aliquoting, consolidating, or mixing of new or existing samples before the main experiment. These prepared samples can be used in the main experiment by referencing their defined name. For more information, please reference the documentation for ExperimentSampleManipulation.
Default Value: Null
Pattern Description: List of one or more a primitive with head Define, Transfer, Mix, Aliquot, Consolidation, FillToVolume, Incubate, Filter, Wait, Centrifuge, or Resuspend entries or Null.
Programmatic Pattern: {SampleManipulationP..} | Null
Preparatory Incubation
Incubate
Indicates if the SamplesIn should be incubated at a fixed temperature prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).
Default Value: Automatic
Default Calculation: Resolves to True if any of the corresponding Incubation options are set. Otherwise, resolves to False.
Pattern Description: True or False.
Programmatic Pattern: BooleanP | Automatic
Index Matches to: experiment samples
IncubationTemperature
Temperature at which the SamplesIn should be incubated for the duration of the IncubationTime prior to starting the experiment.
Default Value: Automatic
Pattern Description: Ambient or greater than or equal to -20 degrees Celsius and less than or equal to 500 degrees Celsius or Null.
Programmatic Pattern: ((Ambient | RangeP[$MinIncubationTemperature, $MaxIncubationTemperature]) | Automatic) | Null
Index Matches to: experiment samples
IncubationTime
Duration for which SamplesIn should be incubated at the IncubationTemperature, prior to starting the experiment.
Default Value: Automatic
Pattern Description: Greater than or equal to 1 minute and less than or equal to 72 hours or Null.
Programmatic Pattern: (RangeP[1*Minute, $MaxExperimentTime] | Automatic) | Null
Index Matches to: experiment samples
Mix
Indicates if this sample should be mixed while incubated, prior to starting the experiment.
Default Value: Automatic
Default Calculation: Automatically resolves to True if any Mix related options are set. Otherwise, resolves to False.
Pattern Description: True or False or Null.
Programmatic Pattern: (BooleanP | Automatic) | Null
Index Matches to: experiment samples
MixType
Indicates the style of motion used to mix the sample, prior to starting the experiment.
Default Value: Automatic
Default Calculation: Automatically resolves based on the container of the sample and the Mix option.
Pattern Description: Roll, Vortex, Sonicate, Pipette, Invert, Stir, Shake, Homogenize, Swirl, Disrupt, or Nutate or Null.
Programmatic Pattern: (MixTypeP | Automatic) | Null
Index Matches to: experiment samples
MixUntilDissolved
Indicates if the mix should be continued up to the MaxIncubationTime or MaxNumberOfMixes (chosen according to the mix Type), in an attempt dissolve any solute. Any mixing/incubation will occur prior to starting the experiment.
Default Value: Automatic
Default Calculation: Automatically resolves to True if MaxIncubationTime or MaxNumberOfMixes is set.
Pattern Description: True or False or Null.
Programmatic Pattern: (BooleanP | Automatic) | Null
Index Matches to: experiment samples
MaxIncubationTime
Maximum duration of time for which the samples will be mixed while incubated in an attempt to dissolve any solute, if the MixUntilDissolved option is chosen. This occurs prior to starting the experiment.
Default Value: Automatic
Default Calculation: Automatically resolves based on MixType, MixUntilDissolved, and the container of the given sample.
Pattern Description: Greater than or equal to 1 minute and less than or equal to 72 hours or Null.
Programmatic Pattern: (RangeP[1*Minute, $MaxExperimentTime] | Automatic) | Null
Index Matches to: experiment samples
IncubationInstrument
The instrument used to perform the Mix and/or Incubation, prior to starting the experiment.
Default Value: Automatic
Default Calculation: Automatically resolves based on the options Mix, Temperature, MixType and container of the sample.
Pattern Description: An object of type or subtype Model[Instrument, Roller], Object[Instrument, Roller], Model[Instrument, OverheadStirrer], Object[Instrument, OverheadStirrer], Model[Instrument, Vortex], Object[Instrument, Vortex], Model[Instrument, Shaker], Object[Instrument, Shaker], Model[Instrument, BottleRoller], Object[Instrument, BottleRoller], Model[Instrument, Roller], Object[Instrument, Roller], Model[Instrument, Sonicator], Object[Instrument, Sonicator], Model[Instrument, HeatBlock], or Object[Instrument, HeatBlock] or Null.
Programmatic Pattern: (ObjectP[{Model[Instrument, Roller], Object[Instrument, Roller], Model[Instrument, OverheadStirrer], Object[Instrument, OverheadStirrer], Model[Instrument, Vortex], Object[Instrument, Vortex], Model[Instrument, Shaker], Object[Instrument, Shaker], Model[Instrument, BottleRoller], Object[Instrument, BottleRoller], Model[Instrument, Roller], Object[Instrument, Roller], Model[Instrument, Sonicator], Object[Instrument, Sonicator], Model[Instrument, HeatBlock], Object[Instrument, HeatBlock]}] | Automatic) | Null
Index Matches to: experiment samples
AnnealingTime
Minimum duration for which the SamplesIn should remain in the incubator allowing the system to settle to room temperature after the IncubationTime has passed but prior to starting the experiment.
Default Value: Automatic
Pattern Description: Greater than or equal to 0 minutes and less than or equal to 72 hours or Null.
Programmatic Pattern: (RangeP[0*Minute, $MaxExperimentTime] | Automatic) | Null
Index Matches to: experiment samples
IncubateAliquotContainer
The desired type of container that should be used to prepare and house the incubation samples which should be used in lieu of the SamplesIn for the experiment.
Default Value: Automatic
Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.
Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
Index Matches to: experiment samples
IncubateAliquotDestinationWell
The desired position in the corresponding IncubateAliquotContainer in which the aliquot samples will be placed.
Default Value: Automatic
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
Pattern Description: Any well from A1 to H12 or Null.
Programmatic Pattern: (WellPositionP | Automatic) | Null
Index Matches to: experiment samples
IncubateAliquot
The amount of each sample that should be transferred from the SamplesIn into the IncubateAliquotContainer when performing an aliquot before incubation.
Default Value: Automatic
Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.
Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.
Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null
Index Matches to: experiment samples
Preparatory Centrifugation
Centrifuge
Indicates if the SamplesIn should be centrifuged prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).
Default Value: Automatic
Default Calculation: Resolves to True if any of the corresponding Centrifuge options are set. Otherwise, resolves to False.
Pattern Description: True or False.
Programmatic Pattern: BooleanP | Automatic
Index Matches to: experiment samples
CentrifugeInstrument
The centrifuge that will be used to spin the provided samples prior to starting the experiment.
Default Value: Automatic
Pattern Description: An object of type or subtype Model[Instrument, Centrifuge] or Object[Instrument, Centrifuge] or Null.
Programmatic Pattern: (ObjectP[{Model[Instrument, Centrifuge], Object[Instrument, Centrifuge]}] | Automatic) | Null
Index Matches to: experiment samples
CentrifugeIntensity
The rotational speed or the force that will be applied to the samples by centrifugation prior to starting the experiment.
Default Value: Automatic
Pattern Description: Greater than 0 revolutions per minute or greater than 0 standard accelerations due to gravity on the surface of the earth or Null.
Programmatic Pattern: ((GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration]) | Automatic) | Null
Index Matches to: experiment samples
CentrifugeTime
The amount of time for which the SamplesIn should be centrifuged prior to starting the experiment.
Default Value: Automatic
Pattern Description: Greater than 0 minutes or Null.
Programmatic Pattern: (GreaterP[0*Minute] | Automatic) | Null
Index Matches to: experiment samples
CentrifugeTemperature
The temperature at which the centrifuge chamber should be held while the samples are being centrifuged prior to starting the experiment.
Default Value: Automatic
Pattern Description: Ambient or greater than or equal to -10 degrees Celsius and less than or equal to 40 degrees Celsius or Null.
Programmatic Pattern: ((Ambient | RangeP[-10*Celsius, 40*Celsius]) | Automatic) | Null
Index Matches to: experiment samples
CentrifugeAliquotContainer
The desired type of container that should be used to prepare and house the centrifuge samples which should be used in lieu of the SamplesIn for the experiment.
Default Value: Automatic
Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.
Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
Index Matches to: experiment samples
CentrifugeAliquotDestinationWell
The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
Default Value: Automatic
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
Pattern Description: Any well from A1 to H12 or Null.
Programmatic Pattern: (WellPositionP | Automatic) | Null
Index Matches to: experiment samples
CentrifugeAliquot
The amount of each sample that should be transferred from the SamplesIn into the CentrifugeAliquotContainer when performing an aliquot before centrifugation.
Default Value: Automatic
Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.
Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.
Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null
Index Matches to: experiment samples
Preparatory Filtering
Filtration
Indicates if the SamplesIn should be filter prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).
Default Value: Automatic
Default Calculation: Resolves to True if any of the corresponding Filter options are set. Otherwise, resolves to False.
Pattern Description: True or False.
Programmatic Pattern: BooleanP | Automatic
Index Matches to: experiment samples
FiltrationType
The type of filtration method that should be used to perform the filtration.
Default Value: Automatic
Default Calculation: Will automatically resolve to a filtration type appropriate for the volume of sample being filtered.
Pattern Description: PeristalticPump, Centrifuge, Vacuum, Syringe, or AirPressure or Null.
Programmatic Pattern: (FiltrationTypeP | Automatic) | Null
Index Matches to: experiment samples
FilterInstrument
The instrument that should be used to perform the filtration.
Default Value: Automatic
Default Calculation: Will automatically resolved to an instrument appropriate for the filtration type.
Pattern Description: An object of type or subtype Model[Instrument, FilterBlock], Object[Instrument, FilterBlock], Model[Instrument, PeristalticPump], Object[Instrument, PeristalticPump], Model[Instrument, VacuumPump], Object[Instrument, VacuumPump], Model[Instrument, Centrifuge], Object[Instrument, Centrifuge], Model[Instrument, SyringePump], or Object[Instrument, SyringePump] or Null.
Programmatic Pattern: (ObjectP[{Model[Instrument, FilterBlock], Object[Instrument, FilterBlock], Model[Instrument, PeristalticPump], Object[Instrument, PeristalticPump], Model[Instrument, VacuumPump], Object[Instrument, VacuumPump], Model[Instrument, Centrifuge], Object[Instrument, Centrifuge], Model[Instrument, SyringePump], Object[Instrument, SyringePump]}] | Automatic) | Null
Index Matches to: experiment samples
Filter
The filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.
Default Value: Automatic
Default Calculation: Will automatically resolve to a filter appropriate for the filtration type and instrument.
Pattern Description: An object of type or subtype Model[Container, Plate, Filter], Model[Container, Vessel, Filter], or Model[Item, Filter] or Null.
Programmatic Pattern: (ObjectP[{Model[Container, Plate, Filter], Model[Container, Vessel, Filter], Model[Item, Filter]}] | Automatic) | Null
Index Matches to: experiment samples
FilterMaterial
The membrane material of the filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.
Default Value: Automatic
Default Calculation: Resolves to an appropriate filter material for the given sample is Filtration is set to True.
Pattern Description: Cellulose, Cotton, Polyethylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, Silica, or HLB or Null.
Programmatic Pattern: (FilterMembraneMaterialP | Automatic) | Null
Index Matches to: experiment samples
PrefilterMaterial
The material from which the prefilter filtration membrane should be made of to remove impurities from the SamplesIn prior to starting the experiment.
Default Value: Automatic
Default Calculation: By default, no prefiltration is performed on samples, even when Filter->True.
Pattern Description: Cellulose, Cotton, Polyethylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, Silica, or HLB or Null.
Programmatic Pattern: (FilterMembraneMaterialP | Automatic) | Null
Index Matches to: experiment samples
FilterPoreSize
The pore size of the filter that should be used when removing impurities from the SamplesIn prior to starting the experiment.
Default Value: Automatic
Default Calculation: Resolves to an appropriate filter pore size for the given sample is Filtration is set to True.
Pattern Description: 0.008 micrometers, 0.1 micrometers, 0.22 micrometers, 0.45 micrometers, 1. micrometer, 1.1 micrometers, 2.5 micrometers, 6. micrometers, 20. micrometers, 30. micrometers, or 100. micrometers or Null.
Programmatic Pattern: (FilterSizeP | Automatic) | Null
Index Matches to: experiment samples
PrefilterPoreSize
The pore size of the filter; all particles larger than this should be removed during the filtration.
Default Value: Automatic
Default Calculation: By default, no prefiltration is performed on samples, even when Filter->True.
Pattern Description: 0.008 micrometers, 0.1 micrometers, 0.22 micrometers, 0.45 micrometers, 1. micrometer, 1.1 micrometers, 2.5 micrometers, 6. micrometers, 20. micrometers, 30. micrometers, or 100. micrometers or Null.
Programmatic Pattern: (FilterSizeP | Automatic) | Null
Index Matches to: experiment samples
FilterSyringe
The syringe used to force that sample through a filter.
Default Value: Automatic
Default Calculation: Resolves to an syringe appropriate to the volume of sample being filtered, if Filtration is set to True.
Pattern Description: An object of type or subtype Model[Container, Syringe] or Object[Container, Syringe] or a prepared sample or Null.
Programmatic Pattern: ((ObjectP[{Model[Container, Syringe], Object[Container, Syringe]}] | _String) | Automatic) | Null
Index Matches to: experiment samples
FilterHousing
The filter housing that should be used to hold the filter membrane when filtration is performed using a standalone filter membrane.
Default Value: Automatic
Default Calculation: Resolve to an housing capable of holding the size of the membrane being used, if filter with Membrane FilterType is being used and Filtration is set to True.
Pattern Description: An object of type or subtype Model[Instrument, FilterHousing], Object[Instrument, FilterHousing], Model[Instrument, FilterBlock], or Object[Instrument, FilterBlock] or Null.
Programmatic Pattern: (ObjectP[{Model[Instrument, FilterHousing], Object[Instrument, FilterHousing], Model[Instrument, FilterBlock], Object[Instrument, FilterBlock]}] | Automatic) | Null
Index Matches to: experiment samples
FilterIntensity
The rotational speed or force at which the samples will be centrifuged during filtration.
Default Value: Automatic
Default Calculation: Will automatically resolve to 2000 GravitationalAcceleration if FiltrationType is Centrifuge and Filtration is True.
Pattern Description: Greater than 0 revolutions per minute or greater than 0 standard accelerations due to gravity on the surface of the earth or Null.
Programmatic Pattern: ((GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration]) | Automatic) | Null
Index Matches to: experiment samples
FilterTime
The amount of time for which the samples will be centrifuged during filtration.
Default Value: Automatic
Default Calculation: Will automatically resolve to 5 Minute if FiltrationType is Centrifuge and Filtration is True.
Pattern Description: Greater than 0 minutes or Null.
Programmatic Pattern: (GreaterP[0*Minute] | Automatic) | Null
Index Matches to: experiment samples
FilterTemperature
The temperature at which the centrifuge chamber will be held while the samples are being centrifuged during filtration.
Default Value: Automatic
Default Calculation: Will automatically resolve to 22 Celsius if FiltrationType is Centrifuge and Filtration is True.
Pattern Description: Greater than or equal to 4 degrees Celsius or Null.
Programmatic Pattern: ((Alternatives[GreaterEqualP[4*Celsius]]) | Automatic) | Null
Index Matches to: experiment samples
FilterContainerOut
The desired container filtered samples should be produced in or transferred into by the end of filtration, with indices indicating grouping of samples in the same plates, if desired.
Default Value: Automatic
Default Calculation: Automatically set as the PreferredContainer for the Volume of the sample. For plates, attempts to fill all wells of a single plate with the same model before using another one.
Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or {Index, Container} or Null.
Programmatic Pattern: (((ObjectP[{Model[Container], Object[Container]}] | _String) | {GreaterEqualP[1, 1] | Automatic, (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
Index Matches to: experiment samples
FilterAliquotDestinationWell
The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
Default Value: Automatic
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
Pattern Description: Any well from A1 to H12 or Null.
Programmatic Pattern: (WellPositionP | Automatic) | Null
Index Matches to: experiment samples
FilterAliquotContainer
The desired type of container that should be used to prepare and house the filter samples which should be used in lieu of the SamplesIn for the experiment.
Default Value: Automatic
Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.
Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null
Index Matches to: experiment samples
FilterAliquot
The amount of each sample that should be transferred from the SamplesIn into the FilterAliquotContainer when performing an aliquot before filtration.
Default Value: Automatic
Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.
Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.
Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null
Index Matches to: experiment samples
FilterSterile
Indicates if the filtration of the samples should be done in a sterile environment.
Default Value: Automatic
Default Calculation: Resolve to False if Filtration is indicated. If sterile filtration is desired, this option must manually be set to True.
Pattern Description: True or False or Null.
Programmatic Pattern: (BooleanP | Automatic) | Null
Index Matches to: experiment samples
Aliquoting
Aliquot
Indicates if aliquots should be taken from the SamplesIn and transferred into new AliquotSamples used in lieu of the SamplesIn for the experiment. Note that if NumberOfReplicates is specified this indicates that the input samples will also be aliquoted that number of times. Note that Aliquoting (if specified) occurs after any Sample Preparation (if specified).
Default Value: Automatic
Pattern Description: True or False.
Programmatic Pattern: BooleanP | Automatic
Index Matches to: experiment samples
AliquotAmount
The amount of a sample that should be transferred from the input samples into aliquots.
Default Value: Automatic
Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container if a liquid, or the current Mass or Count if a solid or counted item, respectively.
Pattern Description: All or Count or Count or Mass or Volume or Null.
Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | RangeP[1*Milligram, 20*Kilogram] | GreaterP[0*Unit, 1*Unit] | GreaterP[0., 1.] | All) | Automatic) | Null
Index Matches to: experiment samples
TargetConcentration
The desired final concentration of analyte in the AliquotSamples after dilution of aliquots of SamplesIn with the ConcentratedBuffer and BufferDiluent which should be used in lieu of the SamplesIn for the experiment.
Default Value: Automatic
Default Calculation: Automatically calculated based on aliquot and buffer volumes.
Pattern Description: Greater than 0 molar or greater than 0 grams per liter or Null.
Programmatic Pattern: ((GreaterP[0*Molar] | GreaterP[(0*Gram)/Liter]) | Automatic) | Null
Index Matches to: experiment samples
TargetConcentrationAnalyte
The substance whose final concentration is attained with the TargetConcentration option.
Default Value: Automatic
Default Calculation: Automatically set to the first value in the Analytes field of the input sample, or, if not populated, to the first analyte in the Composition field of the input sample, or if none exist, the first identity model of any kind in the Composition field.
Pattern Description: An object of type or subtype Model[Molecule], Model[Molecule, cDNA], Model[Molecule, Oligomer], Model[Molecule, Transcript], Model[Molecule, Protein], Model[Molecule, Protein, Antibody], Model[Molecule, Carbohydrate], Model[Molecule, Polymer], Model[Resin], Model[Resin, SolidPhaseSupport], Model[Lysate], Model[ProprietaryFormulation], Model[Virus], Model[Cell], Model[Cell, Mammalian], Model[Cell, Bacteria], Model[Cell, Yeast], Model[Tissue], Model[Material], or Model[Species] or Null.
Programmatic Pattern: (ObjectP[IdentityModelTypes] | Automatic) | Null
Index Matches to: experiment samples
AssayVolume
The desired total volume of the aliquoted sample plus dilution buffer.
Default Value: Automatic
Default Calculation: Automatically determined based on Volume and TargetConcentration option values.
Pattern Description: Greater than or equal to 1 microliter and less than or equal to 20 liters or Null.
Programmatic Pattern: (RangeP[1*Microliter, 20*Liter] | Automatic) | Null
Index Matches to: experiment samples
ConcentratedBuffer
The concentrated buffer which should be diluted by the BufferDilutionFactor in the final solution (i.e., the combination of the sample, ConcentratedBuffer, and BufferDiluent). The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.
Default Value: Automatic
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null
Index Matches to: experiment samples
BufferDilutionFactor
The dilution factor by which the concentrated buffer should be diluted in the final solution (i.e., the combination of the sample, ConcentratedBuffer, and BufferDiluent). The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.
Default Value: Automatic
Default Calculation: If ConcentratedBuffer is specified, automatically set to the ConcentrationFactor of that sample; otherwise, set to Null.
Pattern Description: Greater than or equal to 1 or Null.
Programmatic Pattern: (GreaterEqualP[1] | Automatic) | Null
Index Matches to: experiment samples
BufferDiluent
The buffer used to dilute the aliquot sample such that ConcentratedBuffer is diluted by BufferDilutionFactor in the final solution. The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.
Default Value: Automatic
Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is specified; otherwise, resolves to Null.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null
Index Matches to: experiment samples
AssayBuffer
The buffer that should be added to any aliquots requiring dilution, where the volume of this buffer added is the difference between the AliquotAmount and the total AssayVolume.
Default Value: Automatic
Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is not specified; otherwise, resolves to Null.
Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.
Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null
Index Matches to: experiment samples
AliquotSampleStorageCondition
The non-default conditions under which any aliquot samples generated by this experiment should be stored after the protocol is completed.
Default Value: Automatic
Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, BacteriaIncubation, MammalianIncubation, TissueCultureCellsIncubation, MicrobialCellsIncubation, MicrobialCellsShakingIncubation, YeastCellsIncubation, YeastCellsShakingIncubation, ViralIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.
Programmatic Pattern: ((SampleStorageTypeP | Disposal) | Automatic) | Null
Index Matches to: experiment samples
DestinationWell
The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.
Default Value: Automatic
Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.
Pattern Description: Any well from A1 to H12 or list of one or more any well from A1 to H12 or any well from A1 to H12 entries or Null.
Programmatic Pattern: ((WellPositionP | {((Automatic | Null) | WellPositionP)..}) | Automatic) | Null
AliquotContainer
The desired type of container that should be used to prepare and house the aliquot samples, with indices indicating grouping of samples in the same plates, if desired. This option will resolve to be the length of the SamplesIn * NumberOfReplicates.
Default Value: Automatic
Default Calculation: Automatically set as the PreferredContainer for the AssayVolume of the sample. For plates, attempts to fill all wells of a single plate with the same model before aliquoting into the next.
Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or Automatic or Null or {Index, Container} or list of one or more an object of type or subtype Model[Container] or Object[Container] or a prepared sample or Automatic or Null entries or list of one or more Automatic or Null or {Index, Container} entries or Null.
Programmatic Pattern: (((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null) | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | {((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null))..} | {({GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | (Automatic | Null))..}) | Automatic) | Null
AliquotPreparation
Indicates the desired scale at which liquid handling used to generate aliquots will occur.
Default Value: Automatic
Default Calculation: Automatic resolution will occur based on manipulation volumes and container types.
Pattern Description: Manual or Robotic or Null.
Programmatic Pattern: (PreparationMethodP | Automatic) | Null
ConsolidateAliquots
Indicates if identical aliquots should be prepared in the same container/position.
Default Value: Automatic
Pattern Description: True or False or Null.
Programmatic Pattern: (BooleanP | Automatic) | Null
Protocol Options
Organizational Information
Template
A template protocol whose methodology should be reproduced in running this experiment. Option values will be inherited from the template protocol, but can be individually overridden by directly specifying values for those options to this Experiment function.
Default Value: Null
Pattern Description: An object of type or subtype Object[Protocol] or an object of type or subtype of Object[Protocol] with UnresolvedOptions, ResolvedOptions specified or Null.
Programmatic Pattern: (ObjectP[Object[Protocol]] | FieldReferenceP[Object[Protocol], {UnresolvedOptions, ResolvedOptions}]) | Null
Name
A object name which should be used to refer to the output object in lieu of an automatically generated ID number.
Default Value: Null
Pattern Description: A string or Null.
Programmatic Pattern: _String | Null
Post Experiment
MeasureWeight
Indicates if any solid samples that are modified in the course of the experiment should have their weights measured and updated after running the experiment. Please note that public samples are weighed regardless of the value of this option.
Default Value: Automatic
Pattern Description: True or False or Null.
Programmatic Pattern: (BooleanP | Automatic) | Null
MeasureVolume
Indicates if any liquid samples that are modified in the course of the experiment should have their volumes measured and updated after running the experiment. Please note that public samples are volume measured regardless of the value of this option.
Default Value: Automatic
Pattern Description: True or False or Null.
Programmatic Pattern: (BooleanP | Automatic) | Null
ImageSample
Indicates if any samples that are modified in the course of the experiment should be freshly imaged after running the experiment. Please note that public samples are imaged regardless of the value of this option.
Default Value: Automatic
Pattern Description: True or False or Null.
Programmatic Pattern: (BooleanP | Automatic) | Null
Example Calls
Measurement
To measure with a particular pH meter, set the Instrument option:
To measure with a specific pH probe, the option can be set accordingly:
The custom reference solutions can be defined.These solution calibrate the pH measuring device preceding measurement:
The duration of measurement can be defined for Immersion probes in order to acquire the entire pH spectrum for the specified time:
Preferred Input Containers
2mL Tube
15mL Tube
50mL Tube
1L Glass Bottle
2L Glass Bottle
5L Glass Bottle
10L Polypropylene Carboy
20L Polypropylene Carboy
Warnings and Errors
Messages (23)
AcquisitionTimeConflict (3)
Return an error for when AcquisitionTime is specified and ProbeType->Droplet:
Return an error for when AcquisitionTime is specified and the instrument is incapatible:
Return an error for when AcquisitionTime is specified and the Probe is something that can't be measured:
CertainpHCalibrationRequired (1)
SevenExcellence system cannot be used without non-standard pH calibrants:
ConflictingInstrumentProbeType (1)
Return an error for when the specified Instrument and ProbeType conflict:
ConflictingReferencepHValues (1)
Return an error for when the specified CalibrationBufferpH is different from what is in the model:
DeprecatedInstrumentModel (1)
Return an error for when a deprecated instrument is specified:
DiscardedSamples (1)
Return an error for a discarded sample:
DropletAliquotConflict (1)
Return a warning for InstrumentType==Droplet and Aliquot==False:
EmptyContainers (1)
Return an error for a container without a sample:
IncompatibleInstrument (1)
Return an error when the Instrument is specified, Aliquot is false, and the Container is too big:
IncompatibleSample (2)
Return an error for a sample incapable of measurement:
Return an error for a sample too acidic for measurement:
IncompatibleSampleInstrument (1)
Return an error when the sample to be measured is chemically incompatible with the specified instrument:
InsufficientVolume (1)
Return an error for too low sample volume, thereby incapable of measurement:
LowAndHighpHValuesMustBeSpecified (1)
Return an error for when both Low and High CalibrationBufferpH values are Null:
MediumCalibrationOptionsRequiredTogether (1)
Return an error for when one of MediumCalibrationBufferpH,MediumCalibrationBuffer is specified and the other Null:
NoAvailableInstruments (1)
Return $Failed when a container with too low of liquid volume is enqueued without aliquot:
NoVolume (1)
Return an error for samples that do not have a volume:
pHProbeConflict (2)
Return an error when the Probe is incompatible for the given instrument:
Return an error when the Probe is set Null, but the instrument requires it:
RecoupSampleAliquotConflict (1)
Return an error when RecoupSample is True but Aliquot is false:
TemperatureCorrectionConflict (1)
Return an error when TemperatureCorrection is incompatible for the given instrument:
Possible Issues
Samples Compatibility
This experiment is compatible only with aqueous solutions, and won't work with organics.
Volume Consumption
When using the surface probe 50 microliters will be taken from the sample and cannot be recouped.
Last modified on Thu 28 Apr 2022 15:09:43