Object[Protocol, PAGE]
A polyacrylamide gel electrophoresis (PAGE) experiment which separate biological macromolecules acording to their electrophoretic mobility (a combination of size and charge).
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, PAGE, _String]
Pattern Description: The object reference of this object.
Type
Type of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Protocol, PAGE]
Pattern Description: Object[Protocol, PAGE]
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]
SampleVolumes
For each member of SamplesIn, the volume of sample that is mixed with the LoadingBuffer before a portion of the mixture, the SampleLoadingVolume, is loaded into the gel.
Format: Multiple
Class: Real
Unit: 1 microliter
Programmatic Pattern: VolumeP
LoadingBuffer
The buffer that is mixed with the input samples before a portion of the mixture, the SampleLoadingVolume, is loaded into the gel.
Format: Single
Class: Link
Programmatic Pattern: _Link
LoadingBufferVolumes
For each member of SamplesIn, the amount of LoadingBuffer that is mixed with a SampleVolume amount of the input sample before a portion of the mixture, the SampleLoadingVolume, is loaded into the gel.
Format: Multiple
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Microliter]
Ladder
The ladder that is run with samples on the gel.
Format: Single
Class: Link
Programmatic Pattern: _Link
LadderVolume
The volume of the Ladder that is mixed with the LoadingBuffer before a portion of the mixture, the SampleLoadingVolume, is loaded into the gel.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterEqualP[0 Microliter]
LadderLoadingBuffer
The buffer that is mixed with the Ladder before a portion of the mixture, the SampleLoadingVolume, is loaded into the gel.
Format: Single
Class: Link
Programmatic Pattern: _Link
LadderLoadingBufferVolume
The volume of the LadderLoadingBuffer that is mixed with the Ladder before a portion of the mixture, the SampleLoadingVolume, is loaded into the gel.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterEqualP[0 Microliter]
SampleLoadingVolume
The volume of dye-sample mixture that is loaded into each well.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: _?VolumeQ
LadderMixing
The protocol(s) used to mix the ladder sample(s) before transferring samples into the loading plate.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
LadderCentrifugations
The protocol(s) used to centrifuge the ladder sample(s) before transferring samples into the loading plate.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
LoadingPlate
The plate used to mix ladder, sample, and loading buffer before transferring to the lanes of the gels.
Format: Single
Class: Link
Programmatic Pattern: _Link
LoadingPlateManipulation
A sample manipulation protocol used to transfer the loading buffer, ladders and samples into the loading plate.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
LoadingPlateMixing
The protocol(s) used to mix the contents of the loading plate(s) after preparation.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
LoadingPlateCentrifugations
The protocol(s) used to centrifuge the contents of the loading plate(s) after preparation.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
PipetteTips
Pipette tips used to prepare the loading plate for the protocol.
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]
LadderData
Data for ladder lanes generated by 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
LadderStorageCondition
The storage condition under which the Ladder should be stored after its usage in the experiment.
Format: Single
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
Option Handling
ResolvedOptions
The final options used as parameters for this protocol, after automatic options are resolved.
Format: Single
Class: Compressed
Programmatic Pattern: {_Rule...}
UnresolvedOptions
The verbatim options originally input by the protocol author to generate this protocol, often with some options set to Automatic.
Format: Single
Class: Compressed
Programmatic Pattern: {_Rule...}
Computations
ParallelComputations
List of computational jobs generated and run in parallel to the execution of this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ComputationsOutstanding
Indicates if any of the computation jobs in ParallelComputations have not yet completed.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
ErroneousComputations
List of computational jobs generated and run in parallel to the execution of this protocol in which a warning or error was thown, or that did not finish.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Staining & Imaging
LoadingPlatePrimitives
A set of instructions specifying the transfers of the loading buffer, ladders, and samples into the loading plate.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleManipulationP
PostRunStaining
Indicates if the gel is incubated with the StainingSolution after electrophoresis in order to visualize the analytes.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
PrewashingSolution
The solution used to rinse the gel after electrophoresis before staining.
Format: Single
Class: Link
Programmatic Pattern: _Link
PrewashVolume
The amount of PrewashingSolution that is added to each gel after electrophoresis before staining.
Format: Single
Class: Real
Unit: 1 milliliter
Programmatic Pattern: GreaterEqualP[0 Milliliter]
PrewashingTime
The length of time the post-electrophoresis PrewashingSolution is incubated with the gel.
Format: Single
Class: Real
Unit: 1 minute
Programmatic Pattern: GreaterEqualP[0 Minute]
StainingSolution
The solution used to stain the gel in order to visualize the analytes.
Format: Single
Class: Link
Programmatic Pattern: _Link
StainVolume
The amount of StainingSolution that is added to each gel after electrophoresis.
Format: Single
Class: Real
Unit: 1 milliliter
Programmatic Pattern: GreaterEqualP[0 Milliliter]
StainingTime
The length of time the post-electrophoresis stain is incubated with the gel.
Format: Single
Class: Real
Unit: 1 minute
Programmatic Pattern: GreaterEqualP[0 Minute]
RinsingSolution
The solution used to rinse the gels after stain incubation.
Format: Single
Class: Link
Programmatic Pattern: _Link
RinseVolume
The amount of RinsingSolution that is added to each gel after staining to remove .
Format: Single
Class: Real
Unit: 1 milliliter
Programmatic Pattern: GreaterEqualP[0 Milliliter]
RinsingTime
The length of time the post-electrophoresis RinsingSolution is incubated with the gel after the StainingSolution.
Format: Single
Class: Real
Unit: 1 minute
Programmatic Pattern: GreaterEqualP[0 Minute]
StainReservoir
The reservoir plate used to store staining solution and rinsing solution, if required.
Format: Single
Class: Link
Programmatic Pattern: _Link
RinseReservoir
The reservoir plate used to store additional RinsingSolution, if required.
Format: Single
Class: Link
Programmatic Pattern: _Link
SecondaryRinseReservoir
The reservoir plate used to store PrewashingSolution and additional RinsingSolution, if required.
Format: Single
Class: Link
Programmatic Pattern: _Link
WasteReservoir
The reservoir plate used for collecting buffer waste.
Format: Single
Class: Link
Programmatic Pattern: _Link
SecondaryWasteReservoir
The reservoir plate used for collecting buffer waste.
Format: Single
Class: Link
Programmatic Pattern: _Link
GelBufferTransferVessel
The vessel used to transfer gel buffer from a source bottle to the gel.
Format: Single
Class: Link
Programmatic Pattern: _Link
ReservoirBufferTransferVessel
The vessel used to transfer reservoir buffer from a source bottle into the cassette reservoirs.
Format: Single
Class: Link
Programmatic Pattern: _Link
ExcitationWavelength
The wavelength of light used to excite the gel for a fluorescence image.
Format: Single
Class: Real
Unit: 1 nanometer
Programmatic Pattern: GreaterP[0 Meter Nano]
ExcitationBandwidth
The range in wavelengths centered around the excitation wavelength that the excitation filter allows to pass through at 50% of the maximum transmission.
Format: Single
Class: Real
Unit: 1 nanometer
Programmatic Pattern: GreaterP[0 Meter Nano]
EmissionWavelength
The wavelength at which fluorescence emitted from the gel is captured for a fluorescence image.
Format: Single
Class: Real
Unit: 1 nanometer
Programmatic Pattern: GreaterP[0 Meter Nano]
EmissionBandwidth
The range in wavelengths centered around the emission wavelength that the emission filter allows to pass through at 50% of the maximum transmission.
Format: Single
Class: Real
Unit: 1 nanometer
Programmatic Pattern: GreaterP[0 Meter Nano]
LowExposureTime
The shortest length of time for which a camera shutter stayed open for each gel image.
Format: Single
Class: Real
Unit: 1 millisecond
Programmatic Pattern: GreaterP[0 Milli Second]
MediumLowExposureTime
The second shortest length of time for which a camera shutter stayed open for each gel image.
Format: Single
Class: Real
Unit: 1 millisecond
Programmatic Pattern: GreaterP[0 Milli Second]
MediumHighExposureTime
The second longest amount of time for which a camera shutter stayed open for each gel image.
Format: Single
Class: Real
Unit: 1 millisecond
Programmatic Pattern: GreaterP[0 Milli Second]
HighExposureTime
The longest amount of time for which a camera shutter stayed open for each gel image.
Format: Single
Class: Real
Unit: 1 millisecond
Programmatic Pattern: GreaterP[0 Milli Second]
ExposureTime
The amount of time for which a camera shutter stayed open for each gel image.
Format: Single
Class: Real
Unit: 1 millisecond
Programmatic Pattern: GreaterP[0 Milli Second]
ReservoirPlateManipulation
A sample manipulation protocol used to transfer the stain and rinse solutions into the stain reservoir.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
ReservoirPlatePrimitives
A set of instructions specifying the transfers of individual components required to prepare the stain and rinse solutions.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleManipulationP
Denaturation
SampleDenaturing
Indicates if the mixtures of input samples and loading buffer are heated prior electrophoresis.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
DenaturingTemperature
The temperature which the mixture of input samples and loading buffer is heated to before prior to electrophoresis.
Format: Single
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterEqualP[0 Celsius]
DenaturingTime
The duration for which the mixture of input samples and loading buffer is heated to DenaturingTemperature prior to electrophoresis.
Format: Single
Class: Real
Unit: 1 minute
Programmatic Pattern: GreaterEqualP[0 Minute]
LoadingPlateDenaturation
An incubation protocol used to denature the mixture of input samples and loading buffer present in the LoadingPlate after the LoadingPlateManipulation.
Format: Single
Class: Link
Programmatic Pattern: _Link
Running the Gel
PrimaryPipetteTips
Pipette tips used by the Instrument to load the contents of the LoadingPlate into the Gels.
Format: Single
Class: Link
Programmatic Pattern: _Link
SecondaryPipetteTips
If necessary, an additional set of pipette tips used by the Instrument to load the contents of the LoadingPlate into the Gels.
Format: Single
Class: Link
Programmatic Pattern: _Link
Gels
For each member of SamplesIn, the electrophoresis gel that the sample is run on.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
GelModel
The model of the type of gel that the samples are separated on.
Format: Single
Class: Link
Programmatic Pattern: _Link
GelMaterial
The polymer material that the gel is composed of.
Format: Single
Class: Expression
Programmatic Pattern: GelMaterialP
GelPercentage
The polymer density of the gel by percent weight.
Format: Single
Class: Real
Unit: 1 percent
Programmatic Pattern: GreaterP[0 Percent]
CrosslinkerRatio
The weight ratio of acrylamide monomer to bis-acrylamide crosslinker used to prepare the gel.
Format: Single
Class: Real
Programmatic Pattern: GreaterP[0]
DenaturingGel
Indicates if the gel contains additives that disrupt the secondary structure of macromolecules.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
NumberOfGels
The number of gels run during this experiment.
Format: Single
Class: Integer
Programmatic Pattern: GreaterP[0, 1]
NumberOfLanes
The number of gel lanes run during this experiment.
Format: Single
Class: Integer
Programmatic Pattern: RangeP[1, 80, 1]
GelBuffer
The buffer used to wet the gels during electrophoresis.
Format: Single
Class: Link
Programmatic Pattern: _Link
ReservoirBuffer
The buffer used to fill the end reservoirs of the gel cassettes.
Format: Single
Class: Link
Programmatic Pattern: _Link
Instrument
The instrument used to apply current for this electrophoresis experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
SeparationTime
The amount of time a voltage is applied across the gel.
Format: Single
Class: Real
Unit: 1 minute
Programmatic Pattern: GreaterP[0 Minute]
Voltage
The voltage of the current applied to the gel during the run.
Format: Single
Class: Real
Unit: 1 volt
Programmatic Pattern: GreaterP[0 Volt]
DutyCycle
The percentage of each power cycle that voltage is applied to the gel.
Format: Single
Class: Real
Unit: 1 percent
Programmatic Pattern: RangeP[0 Percent, 100 Percent, 1 Percent, Inclusive -> Right]
CycleDuration
The time duration of each power cycle applied to the gel. If duty cycle is less than 100%, this is the period over which the voltage switches on and off once.
Format: Single
Class: Real
Unit: 1 microsecond
Programmatic Pattern: GreaterP[0 Micro Second]
NumberOfRinses
The number of times the RinsingSolution will be added to each gel, incubated for the RinsingTime, and removed, before the gel images are taken.
Format: Single
Class: Integer
Programmatic Pattern: GreaterP[0, 1]
Instrument Setup
GelBufferVolume
The volume of buffer that is used to wet the gels during eletrophoresis.
Format: Single
Class: Real
Unit: 1 milliliter
Programmatic Pattern: GreaterP[0 Milliliter]
ReservoirBufferVolume
The volume of buffer that is poured into each of the end reservoirs of the gel cassettes.
Format: Single
Class: Real
Unit: 1 milliliter
Programmatic Pattern: GreaterP[0 Milliliter]
Last modified on Mon 26 Sep 2022 15:43:51