Object[Protocol, Incubate]
A protocol to perform thermal incubation (with optional mixing) of a sample using a heating or cooling device.
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, Incubate, _String]
Pattern Description: The object reference of this object.
Type
Type of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Protocol, Incubate]
Pattern Description: Object[Protocol, Incubate]
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
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]
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]
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
Incubation
Thaw
For each member of SamplesIn, indicates if SamplesIn should be incubated until visibly liquid, before they are mixed and/or incubated.
Format: Multiple
Class: Boolean
Programmatic Pattern: BooleanP
ThawTimes
For each member of SamplesIn, the length of time that samples should be thawed.
Format: Multiple
Class: Real
Unit: 1 minute
Programmatic Pattern: GreaterEqualP[0 Minute]
MaxThawTimes
For each member of SamplesIn, the maximum duration of time for which the samples will be mixed, in an attempt to dissolve any solute, if the MixUntilDissolved option is chosen. Note this option only applies for mix type: Shake, Roll, Vortex or Sonicate.
Format: Multiple
Class: Real
Unit: 1 minute
Programmatic Pattern: GreaterEqualP[0 Minute]
ThawTemperatures
For each member of SamplesIn, the temperature at which the samples should be thawed.
Format: Multiple
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterEqualP[0 Kelvin]
ThawInstrument
For each member of SamplesIn, the instrument that will be used to thaw the sample.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Mix
For each member of SamplesIn, indicates the style of motion used to mix the sample.
Format: Multiple
Class: Boolean
Programmatic Pattern: BooleanP
MixTypes
For each member of SamplesIn, indicates the style of motion used to mix the sample.
Format: Multiple
Class: Expression
Programmatic Pattern: MixTypeP
MixUntilDissolved
For each member of SamplesIn, indicates if the mix should be continued up to the MaxTime or MaxNumberOfMixes (chosen according to the mix Type), in an attempt dissolve any solute.
Format: Multiple
Class: Boolean
Programmatic Pattern: BooleanP
Instruments
For each member of SamplesIn, the instrument used to perform the Mix and/or Incubation.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Model[Instrument, Roller] | Model[Instrument, OverheadStirrer] | Model[Instrument, Vortex] | Model[Instrument, Shaker] | Model[Instrument, BottleRoller] | Model[Instrument, Roller] | Model[Instrument, Sonicator] | Model[Instrument, HeatBlock] | Model[Instrument, Homogenizer] | Model[Instrument, Disruptor] | Model[Instrument, Nutator] | Model[Instrument, Thermocycler] | Model[Instrument, EnvironmentalChamber] | Model[Instrument, Pipette] | Object[Instrument, Roller] | Object[Instrument, OverheadStirrer] | Object[Instrument, Vortex] | Object[Instrument, Shaker] | Object[Instrument, BottleRoller] | Object[Instrument, Roller] | Object[Instrument, Sonicator] | Object[Instrument, HeatBlock] | Object[Instrument, Homogenizer] | Object[Instrument, Disruptor] | Object[Instrument, Nutator] | Object[Instrument, Thermocycler] | Object[Instrument, EnvironmentalChamber] | Object[Instrument, Pipette]
StirBars
For each member of SamplesIn, the stir bar that should be used to stir the sample.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Times
For each member of SamplesIn, the duration of time for which the samples will be mixed.
Format: Multiple
Class: Real
Unit: 1 minute
Programmatic Pattern: GreaterEqualP[0 Minute]
DutyCycles
For each member of SamplesIn, specifies how the homogenizer should mix the given sample via pulsation of the sonication horn. This duty cycle is repeated indefinitely until the specified Time/MaxTime has elapsed. This option can only be set when mixing via homogenization.
Format: Multiple
[On]
Header: On
Class: Real
Unit: 1 second
[Off]
Header: Off
Class: Real
Unit: 1 second
MixRates
For each member of SamplesIn, the frequency of rotation the mixing instrument should use to mix the samples.
Format: Multiple
Class: VariableUnit
Programmatic Pattern: GreaterEqualP[0 RPM] | GreaterEqualP[0 GravitationalAcceleration]
MixRateProfiles
For each member of SamplesIn, the frequency of rotation the mixing instrument should use to mix the samples, over the course of time.
Format: Multiple
Class: Expression
Programmatic Pattern: _List
NumberOfMixes
For each member of SamplesIn, the number of times the samples should be mixed if mix Type: Pipette or Invert, is chosen.
Format: Multiple
Class: Integer
Programmatic Pattern: GreaterEqualP[0]
MaxNumberOfMixes
For each member of SamplesIn, the number of times the samples should be mixed if mix Type: Pipette or Invert, is chosen.
Format: Multiple
Class: Integer
Programmatic Pattern: GreaterEqualP[0]
MixVolumes
For each member of SamplesIn, the volume of the sample that should be pipetted up and down to mix if mix Type: Pipette, is chosen.
Format: Multiple
Class: Real
Unit: 1 milliliter
Programmatic Pattern: GreaterEqualP[0 Microliter]
Temperatures
For each member of SamplesIn, the temperature of the device that should be used to mix/incubate the sample. If mixing via homogenization, the pulse duty cycle of the sonication horn will automatically adjust if the measured temperature of the sample exceeds this set temperature.
Format: Multiple
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterEqualP[0 Kelvin]
TemperatureProfiles
For each member of SamplesIn, the temperature of the device, over the course of time, that should be used to mix/incubate the sample.
Format: Multiple
Class: Expression
Programmatic Pattern: _List
MaxTemperatures
For each member of SamplesIn, the maximum temperature that the sample should reach during mixing via homogenization or sonication. If the measured temperature is above this MaxTemperature, the homogenizer/sonicator will turn off until the measured temperature is 2C below the MaxTemperature, then it will automatically resume.
Format: Multiple
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterEqualP[0 Kelvin]
RelativeHumidities
For each member of SamplesIn, the amount of water vapor present in air that the samples will be exposed to during incubation, relative to the amount needed for saturation.
Format: Multiple
Class: Real
Unit: 1 percent
Programmatic Pattern: GreaterEqualP[0 Percent]
LightExposures
For each member of SamplesIn, the range of wavelengths of light that the incubated samples will be exposed to. Only available when incubating the samples in an environmental chamber with UVLight and VisibleLight control.
Format: Multiple
Class: Expression
Programmatic Pattern: EnvironmentalChamberLightTypeP
LightExposureIntensities
For each member of SamplesIn, the intensity of light that the incubated samples will be exposed to during the course of the incubation. UVLight exposure is measured in Watt/Meter^2 and Visible Light Intensity is measured in Lumen/Meter^2.
Format: Multiple
Class: VariableUnit
Programmatic Pattern: Watt Lumen
Hold[GreaterEqualP[0 ------] | GreaterEqualP[0 ------]]
2 2
Meter Meter
LightExposureStandards
During light exposure experiments, a set of samples that are placed in an opaque box to receive identical incubation conditions without exposure to light. This option can only be set if incubating other samples in an environmental stability chamber with light exposure.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
LightExposureStandardBox
The opaque box used to protect the LightExposureStandards during light exposure experiments.
Format: Single
Class: Link
Programmatic Pattern: _Link
OscillationAngles
For each member of SamplesIn, the angle of oscillation of the mixing motion when a wrist action shaker is used.
Format: Multiple
Class: Real
Unit: 1 degree
Programmatic Pattern: GreaterEqualP[0 AngularDegree]
Amplitudes
For each member of SamplesIn, the amplitude of the sonication horn when mixing via homogenization. When using a microtip horn (ex. for 2mL and 15mL tubes), the maximum amplitude is 70 Percent, as specified by the manufacturer, in order not to damage the instrument.
Format: Multiple
Class: Real
Unit: 1 percent
Programmatic Pattern: PercentP
AnnealingTime
For each member of SamplesIn, the minimum duration for which the SamplesIn should remain in the incubator allowing the system to settle to room temperature after the Time has passed.
Format: Multiple
Class: Real
Unit: 1 minute
Programmatic Pattern: TimeP
ResidualIncubation
For each member of SamplesIn, indicates if the incubation and/or mixing should continue after Time/MaxTime has finished while waiting to progress to the next step in the protocol.
Format: Multiple
Class: Boolean
Programmatic Pattern: BooleanP
ResidualTemperatures
For each member of SamplesIn, the temperature at which the sample(s) should remain incubating after Time has elapsed. This option can only be set if Preparation->Robotic.
Format: Multiple
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterEqualP[0 Kelvin]
ResidualMix
For each member of SamplesIn, indicates that the sample(s) should remain shaking at the ResidualMixRate after Time has elapsed. This option can only be set if Preparation->Robotic.
Format: Multiple
Class: Boolean
Programmatic Pattern: BooleanP
ResidualMixRates
For each member of SamplesIn, indicates the rate at which the sample(s) should remain shaking after Time has elapsed, when mixing by shaking. This option can only be set if Preparation->Robotic.
Format: Multiple
Class: Real
Unit: 1 revolution per minute
Programmatic Pattern: GreaterEqualP[0 RPM]
Preheat
For each member of SamplesIn, indicates if the incubation position should be brought to Temperature before exposing the Sample to it. This option can only be set if Preparation->Robotic.
Format: Multiple
Class: Boolean
Programmatic Pattern: BooleanP
FullyThawed
Boolean that indicate if our samples are fully thawed.
Format: Multiple
Class: Boolean
Programmatic Pattern: BooleanP
InvertFullyDissolved
For the samples that are to be mixed via inversion until they are fully dissolved, booleans that indicate whether the samples were fully dissolved after mixing.
Format: Multiple
Class: Boolean
Programmatic Pattern: BooleanP
PipetteFullyDissolved
For the samples that are to be mixed via pipette until they are fully dissolved, booleans that indicate whether the samples were fully dissolved after mixing.
Format: Multiple
Class: Boolean
Programmatic Pattern: BooleanP
VortexFullyDissolved
Indicates if all components in the solution appear fully dissolved by visual inspection. This field is applicable only if MixUntilDissolved is true. This field stores booleans for all vortex runs.
Format: Multiple
Class: Expression
Programmatic Pattern: MultipleChoiceAnswerP
DisruptFullyDissolved
Indicates if all components in the solution appear fully dissolved by visual inspection. This field is applicable only if MixUntilDissolved is true. This field stores booleans for all vortex runs.
Format: Multiple
Class: Expression
Programmatic Pattern: MultipleChoiceAnswerP
NutateFullyDissolved
Indicates if all components in the solution appear fully dissolved by visual inspection. This field is applicable only if MixUntilDissolved is true. This field stores booleans for all nutation runs.
Format: Multiple
Class: Expression
Programmatic Pattern: MultipleChoiceAnswerP
ShakeFullyDissolved
Indicates if all components in the solution appear fully dissolved by visual inspection. This field is applicable only if MixUntilDissolved is true. This field stores booleans for all vortex runs.
Format: Multiple
Class: Expression
Programmatic Pattern: MultipleChoiceAnswerP
RollFullyDissolved
Indicates if all components in the solution appear fully dissolved by visual inspection. This field is applicable only if MixUntilDissolved is true. This field stores booleans for all roller runs.
Format: Multiple
Class: Expression
Programmatic Pattern: MultipleChoiceAnswerP
StirFullyDissolved
Indicates if all components in the solution appear fully dissolved by visual inspection. This field is applicable only if MixUntilDissolved is true. This field stores booleans for all stirring runs.
Format: Multiple
Class: Expression
Programmatic Pattern: MultipleChoiceAnswerP
SonicateFullyDissolved
For the samples that are to be mixed via sonicate until they are fully dissolved, booleans that indicate whether the samples were fully dissolved after mixing.
Format: Multiple
Class: Expression
Programmatic Pattern: MultipleChoiceAnswerP
SonicationTemperatureData
A field used to record the current temperature of the sonication bath when the samples are placed in the water bath for sonication (for samples that are to be heated while sonicated).
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
HomogenizeFullyDissolved
For the samples that are to be mixed via homogenization until they are fully dissolved, booleans that indicate whether the samples were fully dissolved after mixing.
Format: Multiple
Class: Expression
Programmatic Pattern: MultipleChoiceAnswerP
SwirlFullyDissolved
For the samples that are to be mixed via swirling until they are fully dissolved, booleans that indicate whether the samples were fully dissolved after mixing.
Format: Multiple
Class: Boolean
Programmatic Pattern: BooleanP
Last modified on Mon 26 Sep 2022 15:43:50