Object[Protocol, AbsorbanceSpectroscopy]
A protocol for reading plate well absorbances in a plate reader.
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, AbsorbanceSpectroscopy, _String]
Pattern Description: The object reference of this object.
Type
Type of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Protocol, AbsorbanceSpectroscopy]
Pattern Description: Object[Protocol, AbsorbanceSpectroscopy]
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
Methods
Indicates the vessel in which an absorbance assay will be performed. Microfluidic is a low volume chamber with fixed path length. Cuvette is a square container with transparent sides that measures absorbance at a fixed path length. PlateReader uses a wells in a plate which does not have a fixed path length.
Format: Single
Class: Expression
Programmatic Pattern: AbsorbanceMethodP
MicrofluidicChipLoading
The loading method for microfluidic chips.
Format: Single
Class: Expression
Programmatic Pattern: Robotic | Manual
MicrofluidicChipManipulation
A sample manipulation protocol used to transfer samples into the microfluidic chips used to house sample for absorbance measurement.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
MicrofluidicChipManualLoading Manipulation
A sample manipulation protocol used to manually transfer unspotted samples into the microfluidic chips used to house sample for absorbance measurement.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
MicrofluidicChipRetry Manipulation
A sample manipulation protocol used to manually transfer unspotted samples into the microfluidic chips used to house sample for absorbance measurement.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
MagnifyingGlass
The magnifying glass used to verify microfluidic chip spotting.
Format: Single
Class: Link
Programmatic Pattern: _Link
MoatManipulation
The sample manipulations protocol used to transfer buffer into the moat wells.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
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]
AssayPlatePrep
The protocol used to prepare the input samples prior to absorbance measurements.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
EquilibrationTime
The length of time for which the samples incubate at the requested temperature prior to measuring the absorbance.
Format: Single
Class: Real
Unit: 1 minute
Programmatic Pattern: GreaterEqualP[0 Minute]
MoatSize
The number of concentric perimeters of wells filled with MoatBuffer in order to slow evaporation of inner assay samples.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
MoatBuffer
The sample each moat well is filled with in order to slow evaporation of inner assay samples.
Format: Single
Class: Link
Programmatic Pattern: _Link
MoatVolume
The volume which each moat well is filled with in order to slow evaporation of inner assay samples.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterEqualP[0 Microliter]
TemperatureProbe
The part used to monitor the temperature of the reference cuvette during absorbance measurement.
Format: Single
Class: Link
Programmatic Pattern: _Link
Cuvettes
For each member of SamplesIn, the cuvette in which the reaction is mixed and assayed.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
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]
BlankAbsorbance
The absorbance measured from the container with buffer alone.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
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
CuvetteWasher
The cuvette washer instrument used to wash cuvettes after the absorbance thermodynamics experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
RecoupSample
For each member of SamplesIn, indicates if the aliquot used to measure the absorbance should be returned to source container after each reading.
Format: Multiple
Class: Boolean
Programmatic Pattern: BooleanP
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
InjectionStorageCondition
The storage conditions under which any injections samples used in this experiment should be stored after their usage in this 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
Absorbance Measurement
Temperature
Indicates the temperature the samples will held at prior to measuring absorbance and during data acquisition within the instrument.
Format: Single
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterEqualP[0 Kelvin]
TemperatureMonitor
The integrated detector on the spectrophotometer used to monitor temperature during the experiment. Possibilities include 'CuvetteBlock', indicating that a temperature sensor in the heater/chiller block will be monitored, and 'ImmersionProbe', indicating that a temperature sensor in a buffer-filled cuvette will be monitored.
Format: Single
Class: Expression
Programmatic Pattern: TemperatureMonitorTypeP
Instrument
The instrument to shine light through the sample and measure the absorbance according to AbsorbanceMethod.
Format: Single
Class: Link
Programmatic Pattern: _Link
NumberOfReadings
Number of redundant readings taken by the detector to determine a single averaged absorbance reading.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
ReadDirection
The plate path the instrument follows as it measures absorbance in each well, for instance reading all wells in a row before continuing on to the next row (Row).
Format: Single
Class: Expression
Programmatic Pattern: ReadDirectionP
RetainCover
Indicates if the plate seal or lid on the assay container should not be taken off during measurement thereby decreasing evaporation. When this option is set to True, injections cannot be performed as it's not possible to inject samples through the cover. When using the Cuvette Method, automatically set to True.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
SpectralBandwidth
Indicates the physical size of the slit from which light passes out from the monochromator. The smaller the bandwidth, the greater the resolution in measurements.
Format: Single
Class: Real
Unit: 1 nanometer
Programmatic Pattern: GreaterP[0 Nanometer]
AcquisitionMix
For each member of SamplesIn, indicates whether the samples within the cuvette are mixed with a stir bar during data acquisition.
Format: Multiple
Class: Boolean
Programmatic Pattern: BooleanP
NominalAcquisitionMixRate
Indicates the target/set rate at which the samples within the cuvette are mixed with a stir bar during data acquisition.
Format: Single
Class: Real
Unit: 1 revolution per minute
Programmatic Pattern: GreaterP[0 RPM]
ActualAcquisitionMixRate
Indicates the final rate at which the samples within the cuvette were able to be stably mixed at with a stir bar during data acquisition.
Format: Single
Class: Real
Unit: 1 revolution per minute
Programmatic Pattern: GreaterP[0 RPM]
AdjustMixRate
When using a stir bar, if specified AcquisitionMixRate does not provide a uniform or consistent circular rotation of the magnetic bar, indicates if mixing should continue up to MaxStirAttempts in attempts to stir the samples. If stir bar is wiggling, decrease AcquisitionMixRate by AcquisitionMixRateIncrements and check if the stir bar is still wiggling. If it does, decrease by AcquisitionMixRateIncrements again. If still wiggling, repeat decrease process until MaxStirAttempts. If the stir bar is not moving/stationary, increase the AcquisitionMixRate by AcquisitionMixRateIncrements and check if the stir bar is still stationary. If it does, increase by AcquisitionMixRateIncrements again. If still stationary, repeat increase process until MaxStirAttempts. Mixing will occur during data acquisition.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
MinAcquisitionMixRate
Sets the lower limit stirring rate to be decreased to for sample mixing in the cuvette when attempting to mix the samples with a stir bar.
Format: Single
Class: Real
Unit: 1 revolution per minute
Programmatic Pattern: GreaterEqualP[0 RPM]
MaxAcquisitionMixRate
Sets the upper limit stirring rate to be decreased to for sample mixing in the cuvette when attempting to mix the samples with a stir bar.
Format: Single
Class: Real
Unit: 1 revolution per minute
Programmatic Pattern: GreaterEqualP[0 RPM]
AcquisitionMixRateIncrements
Indicates the value to increase or decrease the mixing rate by in a stepwise fashion while attempting to mix the samples with a stir bar.
Format: Single
Class: Real
Programmatic Pattern: GreaterEqualP[0 RPM]
MaxStirAttempts
For each member of SamplesIn, indicates the maximum number of attempts to mix the samples with a stir bar. One attempt designates each time AdjustMixRate changes the AcquisitionMixRate (i.e. each decrease/increase is equivalent to 1 attempt.
Format: Single
Class: Real
Programmatic Pattern: GreaterEqualP[1, 1]
StirringError
Indicates if uniform stirring was not achieved within the cuvette after MaxStirAttempts during the setup of the assay.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
StirBar
For each member of SamplesIn, indicates the stir bar inserted into the cuvette to mix the sample during data acquisition.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
SamplingPattern
Specifies the pattern or set of points that are sampled within each well and averaged together to form a single data point. Ring indicates measurements will be taken in a circle concentric with the well with a diameter equal to the SamplingDistance. Spiral indicates readings will spiral inward toward the center of the well. Matrix reads a grid of points within a circle whose diameter is the SamplingDistance.
Format: Single
Class: Expression
Programmatic Pattern: PlateReaderSamplingP
SamplingDistance
When SamplingPattern->Matrix, SamplingDistance is the length of the square that will be measured within the well diameter; SamplingDimension is an integer representing the number of squares forming a grid within the SamplingDistance.
Format: Single
Class: Real
Unit: 1 millimeter
Programmatic Pattern: GreaterEqualP[0 Millimeter]
SamplingDimension
When SamplingPattern->Matrix, SamplingDistance is the length of the square that will be measured within the well diameter; SamplingDimension is an integer representing the number of squares forming a grid within the SamplingDistance.
Format: Single
Class: Integer
Programmatic Pattern: GreaterP[0]
Analysis & Reports
QuantifyConcentration
Indicates if the concentration of the samples should be determined. Automatically calls AnalyzeAbsorbanceConcentration to update the concentration of analytes on completion of the experiment.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
QuantificationWavelength
The wavelength at which quantification analysis is performed to determine concentration.
Format: Single
Class: Real
Unit: 1 nanometer
Programmatic Pattern: GreaterP[0 Nanometer]
QuantifyConcentrations
For each member of SamplesIn, indicates if the concentration of the samples should be determined. Automatically calls AnalyzeAbsorbanceConcentration to update the concentration of analytes on completion of the experiment..
Format: Multiple
Class: Boolean
Programmatic Pattern: BooleanP
QuantificationWavelengths
For each member of SamplesIn, the wavelength at which quantification analysis is performed to determine concentration.
Format: Multiple
Class: Real
Unit: 1 nanometer
Programmatic Pattern: GreaterP[0 Nanometer]
QuantificationAnalytes
For each member of SamplesIn, the substance whose concentration is measured by this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: 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] | Model[Species]
QuantificationAnalyses
Analyses performed using AnalyzeAbsorbanceConcentration to determine the concentration of samples in this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Sensor Information
NitrogenPurge
Indicates if the experiment is run under purge with dry nitrogen gas to avoid condensation of moisture and blocking of the cuvette windows at low temperatures.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
Sample Loading
MicrofluidicChipManualLoading Pipette
The multichannel pipette that is used to manually load samples onto microfluidic chips manually.
Format: Single
Class: Link
Programmatic Pattern: _Link
MicrofluidicChipManualLoading Tips
The pipette tips that are used to manually load samples onto microfluidic chips.
Format: Single
Class: Link
Programmatic Pattern: _Link
MicrofluidicChipManualLoading Tuples
The pipetting instructions used to manually load samples onto microfluidic chips.
Format: Multiple
[Sources]
Header: Sources
Class: Link
[Destinations]
Header: Destinations
Class: Link
[SourceWell]
Header: SourceWell
Class: Expression
[DestinationWell]
Header: DestinationWell
Class: Expression
Blanking
BlankContainers
Indicates the container that BlankVolume should be transferred to for measuring absorbance of the SamplesIn. If BlankVolume is Null, indicates the blanks should be read inside their current containers.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
BlankContainerManipulation
A sample manipulation protocol used to transfer blanks into the plates used to house sample for absorbance measurement.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
Blanks
For each member of SamplesIn, the object or source used to generate a blank sample (i.e. buffer only, water only, etc.) whose absorbance is subtracted as background from the absorbance readings of the SamplesIn to take accound for any artifacts.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
BlankVolumes
For each member of Blanks, the volume of that sample that should be used for blank measurements.
Format: Multiple
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Microliter]
Injections
PrimaryInjections
For each member of SamplesIn, a description of the first injection into the assay plate.
Format: Multiple
[[1]] Injected Sample
Header: Injected Sample
Class: Link
Programmatic Pattern: _Link
[[2]] Amount Injected
Header: Amount Injected
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterEqualP[0 Micro Liter]|Null
SecondaryInjections
For each member of SamplesIn, a description of the second injection into the assay plate.
Format: Multiple
[[1]] Injected Sample
Header: Injected Sample
Class: Link
Programmatic Pattern: _Link
[[2]] Amount Injected
Header: Amount Injected
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterEqualP[0 Micro Liter]|Null
PrimaryInjectionFlowRate
The speed at which samples are transferred from the injection containers into the assay plate during the first round of injection.
Format: Single
Class: Real
Unit: 1 microliter per second
Programmatic Pattern: 0 (Micro Liter)
Hold[GreaterEqualP[---------------]]
Second
SecondaryInjectionFlowRate
The speed at which samples are transferred from the injection containers into the assay plate during the first round of injection.
Format: Single
Class: Real
Unit: 1 microliter per second
Programmatic Pattern: 0 (Micro Liter)
Hold[GreaterEqualP[---------------]]
Second
InjectionSample
The sample loaded into the first injector position on the instrument.
Format: Single
Class: Link
Programmatic Pattern: _Link
SecondaryInjectionSample
The sample loaded into the second injector position on the instrument.
Format: Single
Class: Link
Programmatic Pattern: _Link
Mixing
PlateReaderMix
Indicates if the assay plate is agitated inside the plate reader chamber prior to absorbance reads.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
PlateReaderMixRate
The frequency at which the plate is agitated inside the plate reader chamber prior to absorbance reads.
Format: Single
Class: Real
Unit: 1 revolution per minute
Programmatic Pattern: GreaterEqualP[0 RPM]
PlateReaderMixTime
The the length of time for which the plate is agitated inside the plate reader chamber prior to absorbance reads.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterEqualP[0 Second]
PlateReaderMixMode
The mode of shaking which should be used to mix the plate.
Format: Single
Class: Expression
Programmatic Pattern: MechanicalShakingP
Injector Cleaning
PrimaryPreppingSolvent
The primary solvent with which the injectors are washed prior to running the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
SecondaryPreppingSolvent
The secondary solvent with which the injectors are washed prior to running the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
PrimaryFlushingSolvent
The primary solvent with which to wash the injectors after running the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
SecondaryFlushingSolvent
The secondary solvent with which to wash the injectors after running the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
Last modified on Mon 26 Sep 2022 15:43:48