Object[Protocol, AgaroseGelElectrophoresis]
An agarose gel electrophoresis experiment which separates 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, AgaroseGelElectrophoresis, _String]
Pattern Description: The object reference of this object.
Type
Type of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Protocol, AgaroseGelElectrophoresis]
Pattern Description: Object[Protocol, AgaroseGelElectrophoresis]
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
Scale
Indicates whether the run is meant to preparatively purify the samples or meant to analyze the purity of the samples.
Format: Single
Class: Expression
Programmatic Pattern: PurificationScaleP
Instrument
The instrument used to apply current for this electrophoresis experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
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 Primary and SecondaryLoadingDye before the mixture is loaded into the gel.
Format: Multiple
Class: Real
Unit: 1 microliter
Programmatic Pattern: VolumeP
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 all lanes for featuring the sample in the Ladder field generated by this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
DataFile
The compressed folder containing the raw and processed data generated by the instrument, as well as method information.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[EmeraldCloudFile]
Troubleshooting
TroubleshootingReports
Reports for errors that require troubleshooting associated with the execution of this top-level protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Resources
AwaitingResources
Indicates if this protocol is awaiting the arrival of items before it can be begun or continued.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
ShippingMaterials
Indicates the transactions, and the specific products or samples therein, that must be received before this protocol can be begun or continued.
Format: Multiple
[[1]] Transaction
Header: Transaction
Class: Link
Programmatic Pattern: _Link
[[2]] Required Product
Header: Required Product
Class: Link
Programmatic Pattern: _Link
HazardousWaste
The types of waste generated by this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
DispenserContainers
Containers gathered as destinations for any resources obtained from a chemical dispenser.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
GasSources
A list of containers that supplied gas to instruments in this protocol through plumbing connections.
Format: Multiple
[[1]] Gas Type
Header: Gas Type
Class: Expression
Programmatic Pattern: GasP
[[2]] Source Container
Header: Source Container
Class: Link
Programmatic Pattern: _Link
Relation: Object[Container]
[[3]] Supplied Instrument
Header: Supplied Instrument
Class: Link
Programmatic Pattern: _Link
Relation: Object[Instrument]
Cleaning
WasteGenerated
For each type of waste generated by this protocol, the total amount (in grams) generated during the conduct of the protocol.
Format: Multiple
[Waste]
Header: Waste
Class: Link
Relation: Model[Sample]
[Weight]
Header: Weight
Class: Real
Unit: 1 gram
Storage Information
StoragePrice
The total monthly price for warehousing all user owned items associated with this protocol in an ECL facility under the storage conditions specified by each item.
Format: Single
Class: Real
Unit: 1 US dollar per month
Programmatic Pattern: USD
Hold[GreaterEqualP[0 -----]]
Month
Sample Storage
SamplesInStorage
For each member of SamplesIn, The storage conditions under which any input samples to this experiment should be stored after their usage in this experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
AliquotStorage
For each member of AliquotSamples, The storage conditions under which any aliquot samples generated by this experiment should be stored after the protocol is completed.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
SamplesOutStorage
For each member of SamplesOut, the storage conditions under which any output samples generated by this experiment should be stored after the protocol is completed.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
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
Loading
PrimaryLoadingDyes
For each member of SamplesIn, the first dye solution that is mixed with the input sample, SecondaryLoadingDye, and LoadingDilutionBuffer according to the SampleVolumes, LoadingDilutionBufferVolumes, and LoadingDyeVolumes fields.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
SecondaryLoadingDyes
For each member of SamplesIn, the second dye solution that is mixed with the input sample, PrimaryLoadingDye, and LoadingDilutionBuffer according to the SampleVolumes, LoadingDilutionBufferVolumes, and LoadingDyeVolumes fields.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
LoadingDyeVolumes
For each member of SamplesIn, the amount of loading dye that is mixed with the sample and loading buffer according to the SampleVolumes, LoadingDilutionBufferVolumes, and LoadingDyeVolumes fields.
Format: Multiple
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Microliter]
LoadingDilutionBuffers
For each member of SamplesIn, the buffer that is mixed with the sample and loading dye according to the SampleVolumes, LoadingDilutionBufferVolumes, and LoadingDyeVolumes fields.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
LoadingDilutionBufferVolumes
For each member of SamplesIn, the amount loading buffer that is mixed with the sample and loading dye according to the SampleVolumes, LoadingDilutionBufferVolumes, and LoadingDyeVolumes fields.
Format: Multiple
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
LoadingPlate
The plate used to mix ladder, sample, and loading dye before transferring to the lanes of the gels.
Format: Single
Class: Link
Programmatic Pattern: _Link
LoadingPlatePrimitives
A set of instructions specifying the transfers of the loading dye, ladders, and samples into the loading plate.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleManipulationP
LoadingPlateManipulation
A sample manipulation protocol used to transfer the loading dye, ladders and samples into the loading plate.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
LoadingPlateMix
An incubation protocol used to mix the contents of the LoadingPlate after the LoadingPlateManipulation.
Format: Single
Class: Link
Programmatic Pattern: _Link
LoadingPlateCentrifugation
A centrifuge protocol used to get rid of any air bubbles present in the LoadingPlate introduced by the LoadingPlateMix.
Format: Single
Class: Link
Programmatic Pattern: _Link
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
Ladder
The ladder to be run with samples on the gel.
Format: Single
Class: Link
Programmatic Pattern: _Link
LadderFrequency
The frequency the ladder will be loaded to be run with samples on each gel in Analytical experiments.
Format: Single
Class: Expression
Programmatic Pattern: First | FirstAndLast | Null
LadderVolume
The volume of the Ladder that is mixed with the LadderLoadingDyes 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]
LadderLoadingDyes
The dye solutions that are mixed with the Ladder before a portion of the mixture, the SampleLoadingVolume, is loaded into the gel.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
LadderLoadingDyeVolume
The volume each LadderLoadingDyes 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]
LadderStorageCondition
The non-default conditions under which any ladder used by this experiment should be stored after the protocol is completed. If left unset, the ladder will be stored according to their Models' DefaultStorageCondition.
Format: Single
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
Separation
DestinationPlate
The plate used to collect the the samples if Scale is set to Preparative.
Format: Single
Class: Link
Programmatic Pattern: _Link
Gels
For each member of SamplesIn, the electrophoresis gel that the sample was run on.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
GelModel
The Model of the Gel that the samples are run through in this protocol.
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]
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: GreaterP[0, 1]
SeparationTime
If Scale is Analytical, the amount of time that Voltage is applied across the Gel. If Scale is Preparative, the maximum amount of time that Voltage is applied across the Gel before the run is stopped. The actual separation time may be shorter if all bands have been extracted before the SeparationTime has been reached.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterP[0 Second]
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
If Scale is Analytical, the percentage of each power cycle that Voltage is applied across the gel. If Scale is Preparative, the maximum percentage of each power cycle that Voltage is applied across 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]
AutomaticPeakDetections
For each member of SamplesIn, indicates if, when Scale -> Preparative, the instrument software will automatically detect and collect the largest peak present between the corresponding MinPeakDetectionSize and MaxPeakDetectionSize.
Format: Multiple
Class: Expression
Programmatic Pattern: BooleanP
MinPeakDetectionSizes
For each member of SamplesIn, the lower bound, in base pairs, of the range the instrument software searches for a peak to collect when the Scale is Preparative and the corresponding member of AutomaticPeakDetections is True.
Format: Multiple
Class: Real
Unit: 1 Basepairs
Programmatic Pattern: GreaterP[0 BasePair]
MaxPeakDetectionSizes
For each member of SamplesIn, the upper bound, in base pairs, of the range the instrument software searches for a peak to collect when the Scale is Preparative and the corresponding member of AutomaticPeakDetections is True.
Format: Multiple
Class: Real
Unit: 1 Basepairs
Programmatic Pattern: GreaterP[0 BasePair]
CollectionSizes
For each member of SamplesIn, the size of the sample, in base paris, to collect in the ExtractionVolume when Scale is Preparative and the corresponding member of AutomaticPeakDetections is False.
Format: Multiple
Class: Real
Unit: 1 Basepairs
Programmatic Pattern: GreaterP[0 BasePair]
MinCollectionRangeSizes
For each member of SamplesIn, the lower bound, in base pairs, of the range of Oligomers to collect in the ExtractionVolume when the corresponding member of AutomaticPeakDetections is True and the corresponding member of CollectionSizes is Null.
Format: Multiple
Class: Real
Unit: 1 Basepairs
Programmatic Pattern: GreaterP[0 BasePair]
MaxCollectionRangeSizes
For each member of SamplesIn, the upper bound, in base pairs, of the range of Oligomers to collect in the ExtractionVolume when the corresponding member of AutomaticPeakDetections is True and the corresponding member of CollectionSizes is Null.
Format: Multiple
Class: Real
Unit: 1 Basepairs
Programmatic Pattern: GreaterP[0 BasePair]
ExtractionVolume
The total volume of sample-containing buffer that is removed from the gel for each input sample. The ExtractionVolume is either centered around the largest peak between the MinPeakDetectionSize and MaxPeakDetectionSize, centered around the CollectionSize, or spans the MinCollectionRangeSize and MaxCollectionRangeSize, depending on the method of peak selection chosen.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Microliter]
Imaging
ExposureTimes
The amounts of time for which a camera shutter stays open for each set of gel images.
Format: Multiple
Class: Real
Unit: 1 millisecond
Programmatic Pattern: GreaterP[0 Milli Second]
ExcitationWavelengths
The wavelengths of light used to excite the gel for fluorescence images.
Format: Multiple
Class: Real
Unit: 1 nanometer
Programmatic Pattern: GreaterP[0 Meter Nano]
ExcitationBandwidths
For each member of ExcitationWavelengths, the range in wavelengths centered around the ExcitationWavelength that the excitation filter allows through at 50% of the maximum transmission.
Format: Multiple
Class: Real
Unit: 1 nanometer
Programmatic Pattern: GreaterP[0 Meter Nano]
EmissionWavelengths
The wavelengths at which fluorescence emitted from the gels was for fluorescence images.
Format: Multiple
Class: Real
Unit: 1 nanometer
Programmatic Pattern: GreaterP[0 Meter Nano]
EmissionBandwidths
For each member of EmissionWavelengths, the range in wavelengths centered around the EmissionWavelength that the emission allows to pass through at 50% of the maximum transmission.
Format: Multiple
Class: Real
Unit: 1 nanometer
Programmatic Pattern: GreaterP[0 Meter Nano]
Last modified on Mon 26 Sep 2022 15:43:48