Object[Protocol, BioLayerInterferometry]
A protocol describing the sample, assay, and instrument parameters for a bio-layer interferometry experiment.
Organizational Information
Name
Name of this Object.
Format: Single
Class: String
Programmatic Pattern: _String
Pattern Description: A string.
ID
ID of this Object.
Format: Single
Class: String
Programmatic Pattern: _String
Pattern Description: The ID of this object.
Object
Object of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Protocol, BioLayerInterferometry, _String]
Pattern Description: The object reference of this object.
Type
Type of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Protocol, BioLayerInterferometry]
Pattern Description: Object[Protocol, BioLayerInterferometry]
Notebook
Notebook this object belongs to.
Format: Single
Class: Link
Programmatic Pattern: _Link
Pattern Description: An object of that matches ObjectP[Object[LaboratoryNotebook]].
Relation: Object[LaboratoryNotebook][Objects]
Author
The investigator who created this protocol.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[User][ProtocolsAuthored]
General
DateConfirmed
The date on which the protocol first entered processing or a backlog.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateEnqueued
The date on which the protocol was accepted and added to the queue.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateStarted
The date on which the protocol moved from the front of the queue to begin running in the lab.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateCompleted
The date on which the last step of this protocol's execution was finished.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateCanceled
The date on which the protocol was canceled and removed from the queue.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
Script
The script that created this protocol.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Notebook][Protocols]
SubprotocolScripts
All scripts generated by this protocol as a list of subprotocols.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Notebook, Script][ParentProtocol]
Site
The ECL site at which this protocol was executed.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Container, Site]
SamplesIn
Input samples for this analytical or preparative experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ContainersIn
Any containers containing this protocols' SamplesIn.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
NumberOfReplicates
Indicates the number of times the experiment is repeated with identical parameters.
Format: Single
Class: Integer
Programmatic Pattern: GreaterP[0, 1]
Status
The current status of the protocol.
Format: Single
Class: Expression
Programmatic Pattern: ProtocolStatusP
CheckpointProgress
A listing of all the checkpoints passed in the execution of this protocol.
Format: Multiple
[[1]] Name
Header: Name
Class: String
Programmatic Pattern: _String
[[2]] Start Time
Header: Start Time
Class: Date
Programmatic Pattern: _?DateObjectQ
[[3]] End Time
Header: End Time
Class: Date
Programmatic Pattern: _?DateObjectQ|Null
SubprotocolDescription
A short title indicating what this subprotocol accomplishes.
Format: Single
Class: String
Programmatic Pattern: _String
BatchedUnitOperations
The individual batches of the protocol, as they will be executed in the lab.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[UnitOperation][Protocol]
ReplacementProtocol
If this protocol was aborted due to technical reasons, links to the replacement protocol run in its place.
Format: Single
Class: Link
Programmatic Pattern: _Link
Sterile
Indicates if the protocol is performed in a sterile environment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
LiquidHandlingLog
The instrumentation trace file that monitored and recorded the execution of this robotic liquid handling.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[EmeraldCloudFile]
PooledSamplesIn
The members of SamplesIn gathered into the pools that are mixed in each AliquotContainer.
Format: Multiple
Class: Expression
Programmatic Pattern: {ObjectReferenceP[Object[Sample]]..}
NestedIndexMatchingSamplesIn
The members of SamplesIn gathered into the pools that are mixed in each AliquotContainer.
Format: Multiple
Class: Expression
Programmatic Pattern: {ObjectReferenceP[Object[Sample]]..}
InitialNitrogenPressure
The pressure data of the nitrogen gas source before starting the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
NitrogenPressureLog
The pressure log for the nitrogen gas source for the relevant section of the facility.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
InitialCO2Pressure
The pressure data of the CO2 gas source before starting the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
CO2PressureLog
The pressure log for the CO2 gas source for the relevant section of the facility.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
InitialArgonPressure
The pressure data of the argon gas source before starting the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
HoldOrder
Indicates if the queue position of this protocol should be strictly enforced, regardless of the available resources in the lab.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
Priority
Indicates if this protocol should be prioritized to start at the given StartDate, have dedicated operation for its entirety, and not be interrupted by other protocols.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
StartDate
The date at which this protocol should be prioritized to start.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
Branch
The git branch that this protocol should be run on.
Format: Single
Class: String
Programmatic Pattern: _String
Instrument
The device used for the BioLayerInterferometry protocol.
Format: Single
Class: Link
Programmatic Pattern: _Link
ExperimentType
The type of bio-layer interferometry assay performed in this protocol.
Format: Single
Class: Expression
Programmatic Pattern: Kinetics | Quantitation | EpitopeBinning | AssayDevelopment
BioProbes
The surface-functionalized fiber-optic probes used to measure analyte binding and dissociation in the bio-layer interferometry experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
ProbeRackPlate
The 96 well plate used to equilibrate probes in the probe rack.
Format: Single
Class: Link
Programmatic Pattern: _Link
RepeatMeasurements
The number of times that the indicated measurement type is performed on a each sample.
Format: Single
Class: Real
Programmatic Pattern: GreaterP[0, 1]
AcquisitionRate
The rate at which data points are recorded.
Format: Single
Class: Real
Unit: 1 hertz
Programmatic Pattern: 2 Hertz | 5 Hertz | 10 Hertz | 2. Hertz | 5. Hertz | 10. Hertz
PlateCover
The plate cover is used to prevent evaporation from the assay plate during the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
Temperature
The temperature of the 96-well plate in which the assay is conducted.
Format: Single
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterP[0 Kelvin] | Ambient
ProbeRackEquilibrationTime
The minimum amount of time for which bio-probes used in the assay are immersed in ProbeRackEquilibrationBuffer while in the probe rack, prior to use. All bio-probes used in this experiment remain immersed in the ProbeEquilibrationBufferSolution until required for the assay.
Format: Single
Class: Real
Unit: 1 minute
Programmatic Pattern: GreaterP[0 Minute]
ProbeRackEquilibrationBuffer
The buffer used to equilibrate bio-probes in the bio-probe rack.
Format: Single
Class: Link
Programmatic Pattern: _Link
StartDelay
The amount of time for which the assay plate is located in the instrument prior to beginning the assay.
Format: Single
Class: Real
Unit: 1 minute
Programmatic Pattern: GreaterEqualP[0 Minute]
StartDelayShake
Indicates if the assay 96 well plate is shaken during the start delay time.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
AssayPlate
The plate which contains input samples and other solutions used in the bio-layer interferometry experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
Standard
The standard solution used for reference in the assay.
Format: Single
Class: Link
Programmatic Pattern: _Link
LoadSolutions
The solution(s) used to load the probe surface with a specified ligand which interacts with the solution phase analyte.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
DevelopmentType
The type of assay development conducted in this experiment.
Format: Single
Class: Expression
Programmatic Pattern: ScreenDetectionLimit | ScreenBuffer | ScreenInteraction | ScreenLoading | ScreenRegeneration | ScreenActivation
DilutionNumberOfMixes
The number of times the DilutionMixVolume will be pipetted in and out of each dilution/solution prepared in this assay.
Format: Single
Class: Integer
Programmatic Pattern: GreaterP[0]
DilutionMixRate
The rate at which solution will be pipetted in and out to mix each dilution/solution prepared in this assay.
Format: Single
Class: Real
Unit: 1 microliter per second
Programmatic Pattern: Microliter
Hold[GreaterP[0 ----------]]
Second
DilutionMixVolume
The volume of solution which will be pipetted in and out to mix each dilution/solution prepared in this assay.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Microliter]
KineticsSampleFixedDilutions Plate
The plate(s) which are used to prepare dilutions that require volumes larger than 250 Microliter. Dilutions of smaller volumes occur on the assay plate.
Format: Single
Class: Link
Programmatic Pattern: _Link
KineticsSampleSerialDilutions Plate
The plate(s) which are used to prepare dilution series require volumes larger than 250 Microliter.
Format: Single
Class: Link
Programmatic Pattern: _Link
DevelopmentSampleFixed DilutionsPlate
The plate(s) which are used to prepare dilution series which include a dilution with volumes larger than 250 Microliter.
Format: Single
Class: Link
Programmatic Pattern: _Link
DevelopmentSampleSerial DilutionsPlate
The plate(s) which are used to prepare dilution series which include a dilution with volumes larger than 250 Microliter.
Format: Single
Class: Link
Programmatic Pattern: _Link
QuantitationParameters
The modifications on a basic quantitation experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: StandardCurve | StandardWell | BlankWell | AmplifiedDetection | EnzymeLinked
QuantitationStandardFixed DilutionsPlate
The plate(s) which are used to prepare dilution series which include a dilution with volumes larger than 250 Microliter.
Format: Single
Class: Link
Programmatic Pattern: _Link
QuantitationStandardSerial DilutionsPlate
The plate(s) which are used to prepare dilution series which include a dilution with volumes larger than 250 Microliter.
Format: Single
Class: Link
Programmatic Pattern: _Link
QuantitationEnzyme
The solution containing an enzyme used to amplify the singal from a bound analyte.
Format: Single
Class: Link
Programmatic Pattern: _Link
BinningType
The assay configuration for EpitopeBinning.
Format: Single
Class: Expression
Programmatic Pattern: PreMix | Sandwich | Tandem
InitialSequence
The sequential list of assay steps which are performed for the first sample measured by a given probe.
Format: Single
Class: Expression
Programmatic Pattern: {BLIPrimitiveNameP..}
RepeatedSequence
The sequential list of assay steps which are repeated using the same probe for each requested sample or standard.
Format: Single
Class: Expression
Programmatic Pattern: {BLIPrimitiveNameP..}
AssayPrimitives
The sequential list of every assay step performed in this protocol.
PreMix solutions, and dilution series used for quantitation standard curves or kinetics association may be referred to by their solution name, as assigned in the PreMixSolutions, AnalyteDilutions, or QuantitationStandardDilutions fields.
When prepared as indicated in their respective sample manipulation primitives, these solutions appear as Objects.
Format: Single
Class: Expression
Programmatic Pattern: {ValidBLIPrimitiveP..}
AssayOverview
The bio-probe, assay number, and assay plate column associated with each assay step.
Format: Multiple
[[1]] Assay Number
Header: Assay Number
Class: Integer
Programmatic Pattern: GreaterP[0, 1]
[[2]] Assay Step
Header: Assay Step
Class: Integer
Programmatic Pattern: GreaterP[0, 1]
[[3]] Plate Column Number
Header: Plate Column Number
Class: Integer
Programmatic Pattern: RangeP[1, 12, 1]
[[4]] Probe Number
Header: Probe Number
Class: Integer
Programmatic Pattern: RangeP[1, 12, 1]
[[5]] Step Type
Header: Step Type
Class: Expression
Programmatic Pattern: BLIPrimitiveNameP
Replicate Experiments
Template
The protocol whose option selections should be selected as the default options for this protocol.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol][ProtocolsTemplated]
ProtocolsTemplated
Protocols which were generated using this protocol's options as a starting point for its option defaults.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol][Template]
Sample Preparation
PreparatoryUnitOperations
A list of transfers, consolidations, aliquots, mixes and dilutions that will be performed in the order listed to prepare samples for the experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: _ | _
PreparatoryPrimitives
A list of transfers, consolidations, aliquots, mixes and dilutions that will be performed in the order listed to prepare samples for the experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: _ | _
VolumeCheckSamplePrep
Indicates if any liquid samples prepared by using the PreparatoryUnitOperations option should have their volumes measured and updated before running the experiment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
IncubateSamplePreparation
For each member of SamplesIn, parameters describing how the input samples should be heated prior to any aliquoting or the start of the experiment.
Format: Multiple
[Incubate]
Header: Incubate
Class: Boolean
[IncubationTemperature]
Header: IncubationTemperature
Class: Real
Unit: 1 degree Celsius
[IncubationTime]
Header: IncubationTime
Class: Real
Unit: 1 second
[Mix]
Header: Mix
Class: Boolean
[MixType]
Header: MixType
Class: Expression
[MixUntilDissolved]
Header: MixUntilDissolved
Class: Boolean
[MaxIncubationTime]
Header: MaxIncubationTime
Class: Real
Unit: 1 second
[IncubationInstrument]
Header: IncubationInstrument
Class: Link
[AnnealingTime]
Header: AnnealingTime
Class: Real
Unit: 1 second
[IncubateAliquotContainer]
Header: IncubateAliquotContainer
Class: Expression
[IncubateAliquot]
Header: IncubateAliquot
Class: Real
Unit: 1 liter
[IncubateAliquotDestinationWell]
Header: IncubateAliquotDestinationWell
Class: Expression
CentrifugeSamplePreparation
For each member of SamplesIn, parameters describing how the input samples should be spun down prior to any aliquoting or the start of the experiment.
Format: Multiple
[Centrifuge]
Header: Centrifuge
Class: Boolean
[CentrifugeInstrument]
Header: CentrifugeInstrument
Class: Link
[CentrifugeIntensity]
Header: CentrifugeIntensity
Class: VariableUnit
[CentrifugeTime]
Header: CentrifugeTime
Class: Real
Unit: 1 minute
[CentrifugeTemperature]
Header: CentrifugeTemperature
Class: Real
Unit: 1 degree Celsius
[CentrifugeAliquotContainer]
Header: CentrifugeAliquotContainer
Class: Expression
[CentrifugeAliquot]
Header: CentrifugeAliquot
Class: Real
Unit: 1 liter
[CentrifugeAliquotDestinationWell]
Header: CentrifugeAliquotDestinationWell
Class: Expression
FilterSamplePreparation
For each member of SamplesIn, parameters describing how particulates should be separated from the input samples prior to any aliquoting or the start of the experiment.
Format: Multiple
[Filtration]
Header: Filtration
Class: Boolean
[FiltrationType]
Header: FiltrationType
Class: Expression
[Filter]
Header: Filter
Class: Link
Relation: Object[Container] | Model[Container] | Object[Sample] | Model[Sample] | Object[Item] | Model[Item]
[FilterMaterial]
Header: FilterMaterial
Class: Expression
[FilterPoreSize]
Header: FilterPoreSize
Class: Real
Unit: 1 micrometer
[FilterContainerOut]
Header: FilterContainerOut
Class: Expression
[FilterInstrument]
Header: FilterInstrument
Class: Link
Relation: 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]
[FilterSyringe]
Header: FilterSyringe
Class: Link
[FilterHousing]
Header: FilterHousing
Class: Link
[FilterIntensity]
Header: FilterIntensity
Class: VariableUnit
[FilterTime]
Header: FilterTime
Class: Real
Unit: 1 minute
[FilterTemperature]
Header: FilterTemperature
Class: Real
Unit: 1 degree Celsius
[FilterSterile]
Header: FilterSterile
Class: Boolean
[FilterAliquotContainer]
Header: FilterAliquotContainer
Class: Expression
[FilterAliquot]
Header: FilterAliquot
Class: Real
Unit: 1 liter
[PrefilterMaterial]
Header: PrefilterMaterial
Class: Expression
[PrefilterPoreSize]
Header: PrefilterPoreSize
Class: Real
Unit: 1 micrometer
[FilterAliquotDestinationWell]
Header: FilterAliquotDestinationWell
Class: Expression
SamplePreparationProtocols
Protocols used to mix, centrifuge, incubate, and filter the SamplesIn prior to starting the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
PooledIncubateSample Preparation
For each member of PooledSamplesIn, parameters describing how the pooled samples should be incubated after aliquoting but prior to the start of the experiment.
Format: Multiple
[Incubate]
Header: Incubate
Class: Boolean
[IncubationTemperature]
Header: IncubationTemperature
Class: Real
Unit: 1 degree Celsius
[IncubationTime]
Header: IncubationTime
Class: Real
Unit: 1 second
[Mix]
Header: Mix
Class: Boolean
[MixType]
Header: MixType
Class: Expression
[MixUntilDissolved]
Header: MixUntilDissolved
Class: Boolean
[MaxIncubationTime]
Header: MaxIncubationTime
Class: Real
Unit: 1 second
[IncubationInstrument]
Header: IncubationInstrument
Class: Link
[AnnealingTime]
Header: AnnealingTime
Class: Real
Unit: 1 second
[IncubateAliquotContainer]
Header: IncubateAliquotContainer
Class: Expression
[IncubateAliquot]
Header: IncubateAliquot
Class: Real
Unit: 1 liter
[IncubateAliquotDestinationWell]
Header: IncubateAliquotDestinationWell
Class: Expression
NestedIndexMatchingIncubate SamplePreparation
For each member of NestedIndexMatchingSamplesIn, parameters describing how the pooled samples should be incubated after aliquoting but prior to the start of the experiment.
Format: Multiple
[Incubate]
Header: Incubate
Class: Boolean
[IncubationTemperature]
Header: IncubationTemperature
Class: Real
Unit: 1 degree Celsius
[IncubationTime]
Header: IncubationTime
Class: Real
Unit: 1 second
[Mix]
Header: Mix
Class: Boolean
[MixType]
Header: MixType
Class: Expression
[MixUntilDissolved]
Header: MixUntilDissolved
Class: Boolean
[MaxIncubationTime]
Header: MaxIncubationTime
Class: Real
Unit: 1 second
[IncubationInstrument]
Header: IncubationInstrument
Class: Link
[AnnealingTime]
Header: AnnealingTime
Class: Real
Unit: 1 second
[IncubateAliquotContainer]
Header: IncubateAliquotContainer
Class: Expression
[IncubateAliquot]
Header: IncubateAliquot
Class: Real
Unit: 1 liter
[IncubateAliquotDestinationWell]
Header: IncubateAliquotDestinationWell
Class: Expression
PooledCentrifugeSample Preparation
For each member of PooledSamplesIn, parameters describing how the pooled samples should be centrifuge after aliquoting and pooled mixing but prior to the start of the experiment.
Format: Multiple
[Centrifuge]
Header: Centrifuge
Class: Boolean
[CentrifugeInstrument]
Header: CentrifugeInstrument
Class: Link
[CentrifugeIntensity]
Header: CentrifugeIntensity
Class: VariableUnit
[CentrifugeTime]
Header: CentrifugeTime
Class: Real
Unit: 1 minute
[CentrifugeTemperature]
Header: CentrifugeTemperature
Class: Real
Unit: 1 degree Celsius
[CentrifugeAliquotContainer]
Header: CentrifugeAliquotContainer
Class: Expression
[CentrifugeAliquot]
Header: CentrifugeAliquot
Class: Real
Unit: 1 liter
[CentrifugeAliquotDestinationWell]
Header: CentrifugeAliquotDestinationWell
Class: Expression
NestedIndexMatchingCentrifuge SamplePreparation
For each member of PooledSamplesIn, parameters describing how the pooled samples should be centrifuge after aliquoting and pooled mixing but prior to the start of the experiment.
Format: Multiple
[Centrifuge]
Header: Centrifuge
Class: Boolean
[CentrifugeInstrument]
Header: CentrifugeInstrument
Class: Link
[CentrifugeIntensity]
Header: CentrifugeIntensity
Class: VariableUnit
[CentrifugeTime]
Header: CentrifugeTime
Class: Real
Unit: 1 minute
[CentrifugeTemperature]
Header: CentrifugeTemperature
Class: Real
Unit: 1 degree Celsius
[CentrifugeAliquotContainer]
Header: CentrifugeAliquotContainer
Class: Expression
[CentrifugeAliquot]
Header: CentrifugeAliquot
Class: Real
Unit: 1 liter
[CentrifugeAliquotDestinationWell]
Header: CentrifugeAliquotDestinationWell
Class: Expression
FilteredSamples
Samples corresponding to filtered eluents of SamplesIn generated during sample preparation and intended for use in this experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Sample]
ProbeRackPlatePrimitives
A set of instructions specifying loading of the probe rack plate with the required solutions.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleManipulationP
ProbeRackPlateManipulation
A sample manipulation protocol used to load the probe rack plate with buffer.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
AssayPlatePrimitives
A set of instructions specifying the loading of the assay plate with the required solutions.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleManipulationP
AssayPlateManipulation
A sample manipulation protocol used to load the assay plate.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
KineticsSampleDiluent
For each member of SamplesIn, the solution that is used to dilute the sample to generate the dilution series used for a Kinetics assay.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
KineticsSampleFixedDilutions
For each member of SamplesIn, the linear dilutions series for use in a Kinetics assay given as {SampleAmount, DiluentVolume, DilutionName}, where DilutionName is the integer used to reference this solution in the AssayPrimitives.
Format: Multiple
Class: Expression
Programmatic Pattern: {({GreaterEqualP[0 Microliter], GreaterEqualP[0 Microliter], _String | ObjectP[{Model[Sample], Object[Sample]}]} | Null)...}
KineticsSampleFixedDilutions Primitives
Instructions specifying preparation of a linear dilution series.
Format: Multiple
Class: Expression
Programmatic Pattern: Null | SampleManipulationP
KineticsSampleFixedDilutions Manipulation
The specific sub-protocol performed to generate fixed dilutions for a Kinetics assay.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
KineticsSampleSerialDilutions
For each member of SamplesIn, the serial dilutions series for use in a Kinetics assay given as {TransferAmount, DiluentVolume, DilutionName}, where DilutionName is the integer used to reference this solution in the AssayPrimitives.
Format: Multiple
Class: Expression
Programmatic Pattern: {({GreaterEqualP[0 Microliter], GreaterEqualP[0 Microliter], _String | ObjectP[{Model[Sample], Object[Sample]}]} | Null)...}
KineticsSampleSerialDilutions Primitives
Instructions specifying preparation of dilution series.
Format: Multiple
Class: Expression
Programmatic Pattern: Null | SampleManipulationP
KineticsSampleSerialDilutions Manipulation
The specific sub-protocol performed to perform dilutions for association measurement.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
DevelopmentSampleDiluent
For each member of SamplesIn, the solution that is used to dilute the input samples for ScreenDetectionLimit experiments.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
DevelopmentSampleFixed Dilutions
For each member of SamplesIn, the linear dilutions series for the input samples for use in a Development assay given as {SampleAmount, DiluentVolume, DilutionName}, where DilutionName is the integer used to reference this solution in the AssayPrimitives.
Format: Multiple
Class: Expression
Programmatic Pattern: {({GreaterEqualP[0 Microliter], GreaterEqualP[0 Microliter], _String | ObjectP[{Model[Sample], Object[Sample]}]} | Null)...}
DevelopmentSampleFixed DilutionsPrimitives
Instructions specifying preparation of a linear dilution series.
Format: Multiple
Class: Expression
Programmatic Pattern: Null | SampleManipulationP
DevelopmentSampleFixed DilutionsManipulation
The specific sub-protocol performed to generate linear dilutions.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
DevelopmentSampleSerial Dilutions
For each member of SamplesIn, the serial dilutions series for use in a Development assay given as {TransferAmount, DiluentVolume, DilutionName}, where DilutionName is the integer used to reference this solution in the AssayPrimitives.
Format: Multiple
Class: Expression
Programmatic Pattern: {({GreaterEqualP[0 Microliter], GreaterEqualP[0 Microliter], _String | ObjectP[{Model[Sample], Object[Sample]}]} | Null)...}
DevelopmentSampleSerial DilutionsPrimitives
Instructions specifying preparation of dilution series.
Format: Multiple
Class: Expression
Programmatic Pattern: Null | SampleManipulationP
DevelopmentSampleSerial DilutionsManipulation
The specific sub-protocol performed to perform dilutions for association measurement.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
QuantitationStandardFixed DilutionsPrimitives
Instructions specifying the transfer of solutions to create the Quantitation standard linear dilutions.
Format: Multiple
Class: Expression
Programmatic Pattern: Null | SampleManipulationP
QuantitationStandardFixed DilutionsManipulation
The specific subprotocol performed to create the Quantitation standard linear dilutions.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
QuantitationStandardSerial DilutionsPrimitives
Instructions specifying the transfer of solutions to create the Quantitation standard serial dilutions.
Format: Multiple
Class: Expression
Programmatic Pattern: Null | SampleManipulationP
QuantitationStandardSerial DilutionsManipulation
The specific subprotocol performed to create the Quantitation standard serial dilutions.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
AntigenSolution
The solution containing antigen used in an epitope binning assay and to create PreMix solutions.
Format: Single
Class: Link
Programmatic Pattern: _Link
PreMixDiluent
The solution used to lower the concentration in generating PreMix solutions used in some epitope binning assays.
Format: Single
Class: Link
Programmatic Pattern: _Link
PreMixSolutions
For each member of SamplesIn, the PreMix solutions required to perform a PreMix type Epitope Binning assay. The Antibody solutions are the input samples, and the solution is referred to in the AssayStepPrimitives by the Solution Name. The form of this field is: {Antibody Amount, Antigen Amount, Diluent Amount, Solution Name}, where Solution Name is the string used to reference this solution in the AssayPrimitives.
Format: Multiple
Class: Expression
Programmatic Pattern: {GreaterEqualP[0 Microliter], GreaterEqualP[0 Microliter], GreaterEqualP[0 Microliter], _String | ObjectP[{Model[Sample], Object[Sample]}]}
PreMixSolutionsPrimitives
Instructions specifying the PreMix solution preparation.
Format: Multiple
Class: Expression
Programmatic Pattern: Null | SampleManipulationP
PreMixSolutionsManipulation
The specific subprotocol performed to create the PreMix solutions.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
PlateLayout
The layout of solutions in the assay plate, grouped by column. Nulls represent empty wells.
Format: Multiple
[[1]] A
Header: A
Class: Expression
[[2]] B
Header: B
Class: Expression
[[3]] C
Header: C
Class: Expression
[[4]] D
Header: D
Class: Expression
[[5]] E
Header: E
Class: Expression
[[6]] F
Header: F
Class: Expression
[[7]] G
Header: G
Class: Expression
[[8]] H
Header: H
Class: Expression
Aliquoting
AliquotSamplePreparation
For each member of AliquotSamples, parameters describing how aliquots should be drawn from the input samples after initial sample preparation in order to create new aliquot samples upon which aliquot preparation and the experiment should proceed.
Format: Multiple
[Aliquot]
Header: Aliquot
Class: Boolean
[AliquotAmount]
Header: AliquotAmount
Class: Expression
[TargetConcentration]
Header: TargetConcentration
Class: Expression
[AssayVolume]
Header: AssayVolume
Class: Real
Unit: 1 milliliter
[AliquotContainer]
Header: AliquotContainer
Class: Expression
[AssayBuffer]
Header: AssayBuffer
Class: Link
[BufferDiluent]
Header: BufferDiluent
Class: Link
[BufferDilutionFactor]
Header: BufferDilutionFactor
Class: Real
[ConcentratedBuffer]
Header: ConcentratedBuffer
Class: Link
[DestinationWell]
Header: DestinationWell
Class: Expression
[TargetConcentrationAnalyte]
Header: TargetConcentrationAnalyte
Class: Expression
[AliquotSampleLabel]
Header: AliquotSampleLabel
Class: String
AliquotProtocols
Protocols used to create AliquotSamples prior to starting the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol]
AliquotPreparationProtocols
Protocols used to mix, centrifuge, incubate, and filter the AliquotSamples prior to starting the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol]
AliquotSamples
Samples corresponding to aliquots of SamplesIn generated during sample preparation and intended for use in this experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Sample]
AliquotContainers
Containers that hold AliquotSamples generated during sample preparation and intended for use in this experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
SaveAliquots
Indicates if the AliquotSamples should be stored after the experiment, rather than being discarded.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
ConsolidateAliquots
Indicates if identical aliquots should be consolidated in a single sample.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
AliquotPreparation
Indicates if the aliquotting should occur manually or on a robotic liquid handler.
Format: Single
Class: Expression
Programmatic Pattern: PreparationMethodP
AliquotVolumes
For each member of SamplesIn, the volume transferred from the sample into the aliquot sample which is used in lieu of the initial sample for the experiment.
Format: Multiple
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Micro Liter]
AliquotMasses
For each member of SamplesIn, the mass of a solid transferred from the sample into the aliquot sample which is used in lieu of the initial sample for the experiment.
Format: Multiple
Class: Real
Unit: 1 milligram
Programmatic Pattern: GreaterP[0 Milligram]
AliquotAmounts
For each member of SamplesIn, the amount transferred from the sample into the aliquot sample which is used in lieu of the initial sample for the experiment.
Format: Multiple
Class: VariableUnit
Programmatic Pattern: GreaterP[0 Milliliter] | GreaterP[0 Milligram] | GreaterP[0 Unit, 1 Unit]
TargetConcentrations
For each member of SamplesIn, the final concentration of analyte in the aliquot sample which is used in lieu of the initial sample for the experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: Milligram
Hold[GreaterP[0 Micro Molar] | GreaterP[0 ----------]]
Milliliter
AssayVolumes
For each member of SamplesIn (or PooledSamplesIn), the total volume of the reaction mixture which is used in lieu of the initial sample for the experiment.
Format: Multiple
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterEqualP[0 Micro Liter]
AssayBuffers
For each member of SamplesIn (or PooledSamplesIn), the final buffers used to generate AliquotSamples by aliquoting SamplesIn.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ConcentratedBuffers
For each member of SamplesIn (or PooledSamplesIn), the concentrated buffer source which is added to the AliquotSamples to obtain 1x buffer concentration after dilution of the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
BufferDilutionFactors
For each member of SamplesIn (or PooledSamplesIn), he dilution factor by which the concentrated buffer is diluted in preparing the AliquotSamples to obtain a 1x buffer concentration after dilution of the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Multiple
Class: Real
Programmatic Pattern: GreaterP[0]
BufferDiluents
For each member of SamplesIn (or PooledSamplesIn), the diluent used to dilute the concentration of the concentrated buffer in preparing the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ConcentratedBuffer
The concentrated buffer source which is added to each of the AliquotSamples to obtain 1x buffer concentration after dilution of the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
BufferDilutionFactor
The dilution factor by which the concentrated buffer is diluted in preparing the AliquotSamples to obtain a 1x buffer concentration after dilution of the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Single
Class: Integer
Programmatic Pattern: GreaterP[0]
BufferDiluent
The diluent used to dilute the concentration of the concentrated buffer in preparing the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
AssayBuffer
The desired buffer for the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
Sample Post-Processing
PostProcessingProtocols
Protocols used to perform post-processing such as sample imaging or volume measurement.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol]
ImageSample
Indicates if the samples that are modified in the course of the experiment are imaged after running the experiment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
MeasureVolume
Indicates if the volume of the liquid samples modified in the course of the experiment are measured after running the experiment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
MeasureWeight
Indicates if the weight of the solid samples modified in the course of the experiment are measured after running the experiment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
Measure
Indicates if the volume/weight of the samples modified in the course of the experiment are measured after running the experiment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
Storage
Indicates the conditions under which any samples generated by this experiment are stored after the protocol is completed.
Format: Single
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
SaveAssayPlate
Indicates if the assay plate was saved or discarded after the assay was completed.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
RecoupSample
For each member of SamplesIn, indicates if the samples used in this experiment are transferred back into the original container upon completion of the assay.
Format: Multiple
Class: Expression
Programmatic Pattern: BooleanP
RecoupSamplePrimitives
For each member of SamplesIn, instructions specifying the transfer of the sample back into the original container after completion of the assay.
Format: Multiple
Class: Expression
Programmatic Pattern: Null | {SampleManipulationP...}
RecoupSampleManipulation
For each member of SamplesIn, the specific subprotocol performed to transfer the sample back into the origin container after completion of the assay.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
Experimental Results
Data
Any primary data generated by this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
SamplesOut
Any preparative samples generated by the protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ContainersOut
Any containers holding SamplesOut generated by this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
EnvironmentalData
Measurements of environmental conditions (temperature and humidity) recorded during the execution of this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
MethodFile
The file containing the run information.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[EmeraldCloudFile]
DataFile
The file containing the unprocessed data generated by the instrument.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[EmeraldCloudFile]
Troubleshooting
TroubleshootingReports
Reports for errors that require troubleshooting associated with the execution of this top-level protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Resources
AwaitingResources
Indicates if this protocol is awaiting the arrival of items before it can be begun or continued.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
ShippingMaterials
Indicates the transactions, and the specific products or samples therein, that must be received before this protocol can be begun or continued.
Format: Multiple
[[1]] Transaction
Header: Transaction
Class: Link
Programmatic Pattern: _Link
[[2]] Required Product
Header: Required Product
Class: Link
Programmatic Pattern: _Link
HazardousWaste
The types of waste generated by this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
DispenserContainers
Containers gathered as destinations for any resources obtained from a chemical dispenser.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
GasSources
A list of containers that supplied gas to instruments in this protocol through plumbing connections.
Format: Multiple
[[1]] Gas Type
Header: Gas Type
Class: Expression
Programmatic Pattern: GasP
[[2]] Source Container
Header: Source Container
Class: Link
Programmatic Pattern: _Link
Relation: Object[Container]
[[3]] Supplied Instrument
Header: Supplied Instrument
Class: Link
Programmatic Pattern: _Link
Relation: Object[Instrument]
Cleaning
WasteGenerated
For each type of waste generated by this protocol, the total amount (in grams) generated during the conduct of the protocol.
Format: Multiple
[Waste]
Header: Waste
Class: Link
Relation: Model[Sample]
[Weight]
Header: Weight
Class: Real
Unit: 1 gram
Storage Information
StoragePrice
The total monthly price for warehousing all user owned items associated with this protocol in an ECL facility under the storage conditions specified by each item.
Format: Single
Class: Real
Unit: 1 US dollar per month
Programmatic Pattern: USD
Hold[GreaterEqualP[0 -----]]
Month
Sample Storage
SamplesInStorage
For each member of SamplesIn, The storage conditions under which any input samples to this experiment should be stored after their usage in this experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
AliquotStorage
For each member of AliquotSamples, The storage conditions under which any aliquot samples generated by this experiment should be stored after the protocol is completed.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
SamplesOutStorage
For each member of SamplesOut, the storage conditions under which any output samples generated by this experiment should be stored after the protocol is completed.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
StandardStorageCondition
The storage condition under which Standard should be stored after its usage in the experiment.
Format: Single
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
LoadSolutionsStorage Conditions
The storage condition under which LoadSolutions should be stored after their usage in the experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
QuantitationStandardStorage Condition
The storage condition under which QuantitationStandard should be stored after its usage in the experiment.
Format: Single
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
QuantitationEnzymeStorage Condition
The storage condition under which QuantitationEnzyme should be stored after its usage in the experiment.
Format: Single
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
AntigenSolutionStorage Condition
The storage condition under which AntigenSolution should be stored after its usage in the experiment.
Format: Single
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
Option Handling
ResolvedOptions
The final options used as parameters for this protocol, after automatic options are resolved.
Format: Single
Class: Compressed
Programmatic Pattern: {_Rule...}
UnresolvedOptions
The verbatim options originally input by the protocol author to generate this protocol, often with some options set to Automatic.
Format: Single
Class: Compressed
Programmatic Pattern: {_Rule...}
Computations
ParallelComputations
List of computational jobs generated and run in parallel to the execution of this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ComputationsOutstanding
Indicates if any of the computation jobs in ParallelComputations have not yet completed.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
ErroneousComputations
List of computational jobs generated and run in parallel to the execution of this protocol in which a warning or error was thown, or that did not finish.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Standard Curve
QuantitationStandard
The solution with a known amount of analyte, which is used to generate a standard curve for the quantitation of analyte concentration in the input samples.
Format: Single
Class: Link
Programmatic Pattern: _Link
QuantitationStandardDiluent
The solution which is used to dilute the QuantitationStandardSolution to create a standard curve.
Format: Single
Class: Link
Programmatic Pattern: _Link
QuantitationStandardFixed Dilutions
The list of dilutions of QuantitationStandardSolution with QuantitationStandardDiluent. These fixed dilutions are used to create a standard curve for a Quantitation assay.
Format: Multiple
[[1]] Standard Amount
Header: Standard Amount
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterEqualP[0 Microliter]
[[2]] Diluent Volume
Header: Diluent Volume
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterEqualP[0 Microliter]
[[3]] Solution Name
Header: Solution Name
Class: Expression
QuantitationStandardSerial Dilutions
The list of dilutions of QuantitationStandardSolution with QuantitationStandardDiluent. These serial dilutions are used to create a standard curve for a Quantitation assay.
Format: Multiple
[[1]] Transfer Amount
Header: Transfer Amount
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterEqualP[0 Microliter]
[[2]] Diluent Volume
Header: Diluent Volume
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterEqualP[0 Microliter]
[[3]] Solution Name
Header: Solution Name
Class: Expression
Last modified on Mon 26 Sep 2022 15:43:49