Object[Protocol, ThermalShift]
A protocol for measuring changes in thermal stability of one or more analytes in the presence of varying ligands or buffer conditions.
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, ThermalShift, _String]
Pattern Description: The object reference of this object.
Type
Type of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Protocol, ThermalShift]
Pattern Description: Object[Protocol, ThermalShift]
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 instrument used to ramp over the specified temperature range and record detected fluorescence.
Format: Single
Class: Link
Programmatic Pattern: _Link
ReactionVolume
The total volume of the reaction including the sample, any ligands, buffer, and detection reagent.
Format: Single
Class: Real
Unit: 1 milliliter
Programmatic Pattern: GreaterEqualP[0 Milli Liter]
DynamicLightScattering CapillaryLoading
The loading method for capillaries for DLS measurements.
Format: Single
Class: Expression
Programmatic Pattern: Null | Robotic | Manual
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]
Dilutions
For each member of SamplesIn, the collection of dilutions performed on each sample before instrument measurement. This is the volume of the sample and the volume of the diluent that will be mixed together for each concentration in the dilution curve.
Format: Multiple
Class: Expression
Programmatic Pattern: ListableP[{{GreaterEqualP[0 Microliter], GreaterEqualP[0 Microliter]}..} | None]
SerialDilutions
For each member of SamplesIn, the volume taken out of each sample and transferred serially and the volume of the Diluent it is mixed with at each step.
Format: Multiple
Class: Expression
Programmatic Pattern: ListableP[{{GreaterEqualP[0 Microliter], GreaterEqualP[0 Microliter]}..} | None]
Diluents
For each member of SamplesIn, the sample that is used to dilute each sample to a concentration series.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
DilutionContainers
The container or containers in which samples are diluted with the Diluent to make the concentration series.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
DilutionStorageConditions
The conditions under which any leftover samples from the DilutionCurve should be stored after the samples are transferred to the measurement plate.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
SampleDilutionPrimitives
A set of instructions specifying the loading and mixing of each sample and the Diluent in the DilutionContainers.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleManipulationP
DilutionSampleManipulation
The sample manipulation protocol used to generate sample dilution curves.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
DilutionMixVolumes
For each member of SamplesIn, the volume that is pipetted out and in of the dilution to mix the sample with the Diluent to make the DilutionCurve.
Format: Multiple
Class: Expression
Programmatic Pattern: ListableP[{(GreaterEqualP[0 Microliter] | None)..}]
DilutionNumberOfMixes
For each member of SamplesIn, the number of pipette out and in cycles that is used to mix the sample with the Diluent to make the DilutionCurve.
Format: Multiple
Class: Expression
Programmatic Pattern: ListableP[{(RangeP[0, 20, 1] | None)..}]
DilutionMixRates
For each member of SamplesIn, the speed at which the DilutionMixVolume is pipetted out and in of the dilution to mix the sample with the Diluent to make the DilutionCurve.
Format: Multiple
Class: Expression
Programmatic Pattern: Microliter Microliter
Hold[ListableP[{(RangeP[0.4 ----------, 250 ----------] | None)..}]]
Second Second
PoolingPrimitives
A set of instructions specifying the aliquoting of the experimental samples into the pooling plate prior to instrument analysis.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleManipulationP
PooledMixSamplePreparation
For each member of PooledSamplesIn, parameters describing how the pooled samples should be mixed prior to the start of the experiment.
Format: Multiple
[Mix]
Header: Mix
Class: Boolean
[MixType]
Header: MixType
Class: Expression
[NumberOfMixes]
Header: NumberOfMixes
Class: Integer
[MixVolume]
Header: MixVolume
Class: Real
Unit: 1 microliter
[Incubate]
Header: Incubate
Class: Boolean
NestedIndexMatchingMixSample Preparation
For each member of PooledSamplesIn, parameters describing how the pooled samples should be mixed prior to the start of the experiment.
Format: Multiple
[Mix]
Header: Mix
Class: Boolean
[MixType]
Header: MixType
Class: Expression
[NumberOfMixes]
Header: NumberOfMixes
Class: Integer
[MixVolume]
Header: MixVolume
Class: Real
Unit: 1 microliter
[Incubate]
Header: Incubate
Class: Boolean
PoolingSampleManipulation
The sample manipulation protocol used to pool samples prior to instrument measurement.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
SampleVolumes
For each member of PooledSamplesIn, the volume added to the assay reaction.
Format: Multiple
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterEqualP[0 Microliter]
Buffers
For each member of PooledSamplesIn, the sample used to bring each reaction to its ReactionVolume once all other components have been added.
Format: Multiple
Class: Expression
Programmatic Pattern: _Link | Null
BufferVolumes
For each member of PooledSamplesIn, the volume of buffer used to bring each reaction to its ReactionVolume once all other components have been added.
Format: Multiple
Class: Expression
Programmatic Pattern: GreaterEqualP[0 Microliter] | Null
DetectionReagents
For each member of PooledSamplesIn, the fluorescent dye that this experiment uses to monitor melting.
Format: Multiple
Class: Expression
Programmatic Pattern: _Link | Null
DetectionReagentVolumes
For each member of PooledSamplesIn, the volume of detection reagent added to the well.
Format: Multiple
Class: Expression
Programmatic Pattern: GreaterEqualP[0 Microliter] | Null
CapillaryStripPreparation Plate
The container in which the final assay reaction is assembled prior to loading the Uncle capillary strip.
Format: Single
Class: Link
Programmatic Pattern: _Link
PassiveReferenceDye
The passive fluorescence reference dye used to normalize fluorescence background fluctuations during melting.
Format: Single
Class: Link
Programmatic Pattern: _Link
PassiveReferenceDyeVolume
The volume of the passive fluorescence reference dye added to each well.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterEqualP[0 Microliter]
CapillaryStripLoading Primitives
A set of instructions specifying the transfer of the experimental samples into Uncle Uni capillary strips prior to instrument analysis.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleManipulationP
CapillaryStripLoadingSample Manipulation
The sample manipulation protocol used to load experimental samples into Uncle Uni capillary strips prior to instrument analysis.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
ContainersOutLoading Primitives
A set of instructions specifying the sample transfer of the experimental samples into the ContainersOut prior to storage.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleManipulationP
ContainersOutSample Manipulation
The sample manipulation protocol used to load experimental samples into the ContainersOut prior to storage.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
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
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]
DataFiles
The files containing the unprocessed data generated by the instrument.
Format: Multiple
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
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
Sample Loading
AssayContainers
The containers the samples are assayed in.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
PlateSeal
The optically transparent self-adhesive seal used to cover the assay plate wells during thermal cycling.
Format: Single
Class: Link
Programmatic Pattern: _Link
DynamicLightScatteringManual LoadingPlate
The plate from which samples are loaded onto assay capillaries manually. This plate is set for loading using an 8-channel multichannel pipette.
Format: Single
Class: Link
Programmatic Pattern: _Link
DynamicLightScatteringManual LoadingPipette
The multichannel pipette that is used to manually load samples onto assay capillaries manually. This plate is set for loading using an 8-channel multichannel pipette.
Format: Single
Class: Link
Programmatic Pattern: _Link
DynamicLightScatteringManual LoadingTips
The pipette tips that are used to manually load samples onto assay capillaries manually. This plate is set for loading using an 8-channel multichannel pipette.
Format: Single
Class: Link
Programmatic Pattern: _Link
DynamicLightScatteringManual LoadingTuples
The pipetting instructions used to manually load samples onto assay capillaries manually. This plate is set for loading using an 8-channel multichannel pipette.
Format: Multiple
[Sources]
Header: Sources
Class: Link
[SourceRow]
Header: SourceRow
Class: Expression
[Targets]
Header: Targets
Class: Link
[TargetRow]
Header: TargetRow
Class: Expression
[FirstWell]
Header: FirstWell
Class: Expression
[NumberOfWells]
Header: NumberOfWells
Class: Expression
Thermocycling
RunTime
The length of time for which the instrument is expected to run given the specified parameters.
Format: Single
Class: Real
Unit: 1 minute
Programmatic Pattern: GreaterEqualP[0 Minute]
MinTemperature
The low temperature of the melting or cooling curve.
Format: Single
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterP[0 Kelvin]
MaxTemperature
The high temperature of the melting or cooling curve.
Format: Single
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterEqualP[0 Kelvin]
TemperatureRampOrder
The order of temperature ramping to be performed in each cycle.
Format: Single
Class: Expression
Programmatic Pattern: ThermodynamicCycleP
EquilibrationTime
The time to hold the temperature at the thermocycling endpoints.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterEqualP[0 Second]
NumberOfCycles
The number of heating/cooling cycles to perform. Each heating or cooling phase is considered a half cycle.
Format: Single
Class: Real
Programmatic Pattern: GreaterP[0]
TemperatureRamping
The type of temperature ramp. Linear temperature ramps increase temperature at a constant rate given by TemperatureRampRate. Step temperature ramps increase the temperature by TemperartureRampStep and holds the temperature constant for TemperatureRampStepTime before increasing the temperature again.
Format: Single
Class: Expression
Programmatic Pattern: Linear | Step
TemperatureRampRate
The rate at which the temperature is changed in the course of one heating and/or cooling cycle.
Format: Single
Class: Real
Unit: 1 degree Celsius per second
Programmatic Pattern: 0 Celsius
Hold[GreaterEqualP[---------]]
Second
TemperatureResolution
The amount by which the temperature is changed between each data point and the next during the melting and/or cooling curves.
Format: Single
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterEqualP[0 Celsius]
NumberOfTemperatureRampSteps
The number of step changes in temperature for a heating or cooling cycle.
Format: Single
Class: Real
Programmatic Pattern: GreaterP[0]
StepHoldTime
The length of time samples are held at each temperature during a stepped temperature ramp.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterP[0 Second]
Detection
ExcitationWavelengths
For each member of PooledSamplesIn, the wavelength of light used to excite intrinsic or extrinsic fluorescence.
Format: Multiple
Class: Expression
Programmatic Pattern: GreaterEqualP[0 Nano Meter] | Null
StaticLightScattering ExcitationWavelengths
For each member of PooledSamplesIn, the wavelength(s) of light used to collect static light scattering data.
Format: Multiple
Class: Expression
Programmatic Pattern: {GreaterEqualP[0 Nano Meter]..} | {Null..}
EmissionWavelengths
For each member of PooledSamplesIn, the wavelength at which fluorescence emission is detected.
Format: Multiple
Class: Expression
Programmatic Pattern: GreaterEqualP[0 Nano Meter] | Null
MinEmissionWavelengths
For each member of PooledSamplesIn, the minimum wavelength at which fluorescence emission is detected.
Format: Multiple
Class: Expression
Programmatic Pattern: GreaterEqualP[0 Nano Meter] | Null
MaxEmissionWavelengths
For each member of PooledSamplesIn, the maximum wavelength at which fluorescence emission is detected.
Format: Multiple
Class: Expression
Programmatic Pattern: GreaterEqualP[0 Nano Meter] | Null
FluorescenceLaserPower
For each member of PooledSamplesIn, the UV laser power filter used.
Format: Multiple
Class: Expression
Programmatic Pattern: LaserPowerFilterP
StaticLightScatteringLaser Power
For each member of PooledSamplesIn, the Blue laser power filter used.
Format: Multiple
Class: Expression
Programmatic Pattern: LaserPowerFilterP
OptimizeFluorescenceLaser Power
For each member of PooledSamplesIn and all corresponding dilutions, indicates if the fluorescence laser power filter is adjusted prior to sample measurement.
Format: Multiple
Class: Boolean
Programmatic Pattern: BooleanP
OptimizeStaticLightScattering LaserPower
For each member of PooledSamplesIn and all corresponding dilutions, indicates if the static light scattering laser power filter is matched to the optimal fluorescence laser power prior to sample measurement.
Format: Multiple
Class: Boolean
Programmatic Pattern: BooleanP
LaserOptimizationEmission WavelengthRange
For each member of PooledSamplesIn and all corresponding dilutions, the wavelength(s) of the sample's spectra used to evaluate optimal laser setting.
Format: Multiple
Class: Expression
Programmatic Pattern: {GreaterP[0 Nanometer]..} | Null
LaserOptimizationTarget EmissionIntensityRange
For each member of PooledSamplesIn and all corresponding dilutions, the intensity range, expressed as a counts, used to evaluate optimal laser setting.
Format: Multiple
Class: Expression
Programmatic Pattern: {GreaterP[0]..} | Null
FluorescenceLaserPower OptimizationResult
Indicates if the fluorescence laser power filter optimization was successful. "FailureLowSignal" indicates the laser power could not be optimized because signal intensity at 100% laser power is lower than the LaserOptimizationTargetEmissionIntensityRange. "FailureSignalSaturation" indicates the laser power could not be optimized because signal intensity at 13% laser power is higher than the LaserOptimizationTargetEmissionIntensityRange.
Format: Multiple
Class: Expression
Programmatic Pattern: LaserOptimizationResultP
DynamicLightScattering
Indicates if a DLS measurement of each sample is made before and after the thermal ramping.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
DynamicLightScattering Measurements
Indicates if a DLS measurement of each sample is made before thermal ramping, after thermal ramping, or both before and after thermal ramping.
Format: Multiple
Class: Expression
Programmatic Pattern: Before | After
DynamicLightScattering MeasurementTemperatures
Indicates the temperatures at which each DLS measurement is made.
Format: Multiple
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: RangeP[15 Celsius, 95 Celsius]
NumberOfDynamicLight ScatteringAcquisitions
For each DLS measurement, the number of series of speckle patterns that are each collected over the AcquisitionTime to create the measurement's autocorrelation curve.
Format: Single
Class: Integer
Programmatic Pattern: GreaterP[0, 1]
DynamicLightScattering AcquisitionTime
For each DLS measurement, the length of time that each acquisition generates speckle patterns to create the measurement's autocorrelation curve.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterP[0 Second]
AutomaticDynamicLight ScatteringLaserSettings
Indicates if the DynamicLightScatteringLaserPower and DynamicLightScatteringDiodeAttenuation are automatically set at the beginning of the assay by the Instrument to levels ideal for the samples.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
DynamicLightScatteringLaser Power
The percent of the max dynamic light scattering laser power that is used to make DLS measurements. The laser level is optimized at run time by the instrument software when AutomaticDynamicLightScatteringLaserSettings is True and LaserLevel is Null.
Format: Single
Class: Real
Unit: 1 percent
Programmatic Pattern: GreaterP[0 Percent]
DynamicLightScatteringDiode Attenuation
The percent of scattered light signal that is allowed to reach the avalanche photodiode for DLS measurements. The attenuator level is optimized at run time by the instrument software when AutomaticDynamicLightScatteringLaserSettings is True and DiodeAttenuation is Null.
Format: Single
Class: Real
Unit: 1 percent
Programmatic Pattern: GreaterP[0 Percent]
Analysis & Reports
DynamicLightScatteringLoading Analyses
Analyses that determine properly loaded dynamic light scattering samples.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Analysis][Reference]
Last modified on Mon 26 Sep 2022 15:43:51