Object[Protocol, DNASynthesis]
A protocol for phosphoramidite-based synthesis of DNA oligomers using a DNA synthesizer.
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, DNASynthesis, _String]
Pattern Description: The object reference of this object.
Type
Type of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Protocol, DNASynthesis]
Pattern Description: Object[Protocol, DNASynthesis]
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
ActivatorSolutionStorage Conditions
The non-default storage condition for the ActivatorSolutionStorageCondition once the experiment is set up.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
CapASolutionStorageConditions
The non-default storage condition for the CapASolutionStorageCondition once the experiment is set up.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
CapBSolutionStorageConditions
The non-default storage condition for the CapBSolutionStorageCondition once the experiment is set up.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
OxidationSolutionStorage Conditions
The non-default storage condition for the OxidationSolutionStorageCondition once the experiment is set up.
Format: Single
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
SecondaryOxidationSolution StorageConditions
The non-default storage condition for the SecondaryOxidationSolutionStorageCondition once the experiment is set up.
Format: Single
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
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
Synthesis
Strands
The sequence of monomers and modifications that make up the oligomers being synthesized.
Format: Multiple
Class: Expression
Programmatic Pattern: {StrandP..} | Null
StrandModels
The oligomer models that will be synthesized in this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Model[Sample]
Instrument
The synthesizer instrument used to conduct the synthesis.
Format: Single
Class: Link
Programmatic Pattern: _Link
Scale
The theoretical amount of reaction sites available for synthesis.
Format: Single
Class: Real
Unit: 1 micromole
Programmatic Pattern: GreaterEqualP[0 Micro Mole]
Columns
For each member of StrandModels, the solid support on which the synthesis of the strand is carried out.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
FinalSequences
Oligomer models that the final samples should have once the experiment was completed.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Model[Molecule, Oligomer]
Coupling
PhosphoramiditeDilution Manipulation
The set of instructions to transfer the phosphoramidite dilution solution to the undissolved phosphoramidites.
Format: Single
Class: Link
Programmatic Pattern: _Link
PhosphoramiditeMixingProtocol
The mix protocols used to dissolve the phosphoramidites.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Phosphoramidites
The phosphoramidite used for each monomer.
Format: Multiple
[[1]] Monomer Type
Header: Monomer Type
Class: Expression
Programmatic Pattern: SequenceP
[[2]] Phosphoramidite
Header: Phosphoramidite
Class: Link
Programmatic Pattern: _Link
PhosphoramiditeConcentrations
The phosphoramidite concentration used for each monomer.
Format: Multiple
[[1]] Monomer Type
Header: Monomer Type
Class: Expression
Programmatic Pattern: SequenceP
[[2]] Concentration
Header: Concentration
Class: Real
Unit: 1 molar
Programmatic Pattern: GreaterP[0 Molar]
PhosphoramiditeSolvents
The solvent used to dilute the phosphoramidite for each monomer.
Format: Multiple
[[1]] Monomer Type
Header: Monomer Type
Class: Expression
Programmatic Pattern: SequenceP
[[2]] Solvent
Header: Solvent
Class: Link
Programmatic Pattern: _Link
PhosphoramiditeCosolvents
The cosolvent used to dilute the phosphoramidite for each monomer, along with its ratio with respect to the corresponding PhosphoramiditeSolvent.
Format: Multiple
[[1]] Monomer Type
Header: Monomer Type
Class: Expression
Programmatic Pattern: SequenceP
[[2]] Cosolvent Fraction
Header: Cosolvent Fraction
Class: Real
Programmatic Pattern: RangeP[0., 1.]
[[3]] Solvent
Header: Solvent
Class: Link
Programmatic Pattern: _Link
SynthesisCycles
A list of synthesis cycle methods (controlling coupling conditions) for each monomer type.
Format: Multiple
[[1]] Monomer Type
Header: Monomer Type
Class: Expression
Programmatic Pattern: SequenceP
[[2]] Method
Header: Method
Class: Link
Programmatic Pattern: _Link
Relation: Object[Method]
ActivatorSolution
The solution that activates the phosphoramidite prior to coupling by protonating the diisopropylamino group of the phosphoramidite, thereby making the diisopropylamino group a good leaving group that is readily displaced by the 5' hydroxyl group on the growing oligomer.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ActivatorSolutionDesiccants
For each member of ActivatorSolution, the desiccant used to keep the activator solution dry.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ActivatorVolume
The volume of activator solution used to activate the phosphoramidite prior to coupling.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Micro Liter]
PhosphoramiditeDesiccants
For each member of PhosphoramiditePlacements, the desiccants, used to keep the phosphoramidite solution dry, added as the phosphoramidite bottle is loaded onto the instrument.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Washing
WashSolution
The solvent used for washing the solid supports between reagent additions.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
WashSolutionDesiccants
For each member of WashSolution, the desiccant used to keep the wash solution dry.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
NumberOfInitialWashes
The number of washes at the start of the synthesis.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
InitialWashTime
Amount of time that the solid supports are incubated with wash solution at the start of the synthesis.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterEqualP[0 Second]
InitialWashVolume
The volume of each wash at the start of the synthesis.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Micro Liter]
NumberOfFinalWashes
The number of washes at the end of the synthesis.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
FinalWashTime
Amount of time that the solid supports are incubated with wash solution at the end of the synthesis.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterEqualP[0 Second]
FinalWashVolume
The volume of each wash at the end of the synthesis.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Micro Liter]
Deprotection
DeprotectionSolution
The solution used to remove the trityl protecting group.
Format: Single
Class: Link
Programmatic Pattern: _Link
NumberOfDeprotections
The number of times that the deprotection solution is added to the solid support after each cycle.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
DeprotectionTime
Amount of time that the solid supports are incubated with deprotection solution.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterEqualP[0 Second]
DeprotectionVolume
The volume of deprotection solvent used in each deprotection iteration.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Micro Liter]
FinalDeprotection
For each member of StrandModels, indicates if a final deprotection (detritylation) step is done following the last synthesis cycle.
Format: Multiple
Class: Expression
Programmatic Pattern: BooleanP
NumberOfDeprotectionWashes
The number of times the solid support is washed after deprotection.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
DeprotectionWashTime
The amount of time that the solid supports are incubated with wash solution following deprotection.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterEqualP[0 Second]
DeprotectionWashVolume
The volume of each post-deprotection wash.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Micro Liter]
Capping
CapASolution
The solution (used in conjunction with Cap B Solution) used to cap unreacted sites by acetylating free hydroxy sites.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
CapBSolution
The solution (used in conjunction with Cap A Solution) used to cap unreacted sites by acetylating free hydroxy sites.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
NumberOfCappings
The number of capping iterations.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
CapTime
Amount of time that the solid supports are incubated with Cap A solution and Cap B solution.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterEqualP[0 Second]
CapAVolume
The volume of Cap A solution used in each capping iteration.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Micro Liter]
CapBVolume
The volume of Cap B solution used in each capping iteration.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Micro Liter]
Oxidation
OxidationSolution
The solution used to oxidize the DNA backbone, thereby converting the phosphite triester to a more stable phosphate triester.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
NumberOfOxidations
The number of oxidation iterations.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
OxidationTime
Amount of time that the solid supports are incubated with oxidation solution.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterEqualP[0 Second]
OxidationVolume
The volume of oxidation solution used in each oxidation iteration.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Micro Liter]
NumberOfOxidationWashes
The number of washes following oxidation.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
OxidationWashTime
Amount of time that the solid supports are incubated with wash solution following oxidation.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterEqualP[0 Second]
OxidationWashVolume
The volume of wash solution for each post-oxidation wash.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Micro Liter]
SecondaryOxidationSolution
The solution used to oxidize the DNA backbone, thereby converting the phosphite triester to a more stableform; used by the secondary set of cycle parameters.
Format: Single
Class: Link
Programmatic Pattern: _Link
SecondaryNumberOfOxidations
The number of oxidation iterations for the secondary set of cycle parameters.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
SecondaryOxidationTime
Amount of time that the solid supports are incubated with secondary oxidation solution.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterEqualP[0 Second]
SecondaryOxidationVolume
The volume of the secondary oxidation solution used in each oxidation iteration specified in the secondary set of the cycle parameters.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Micro Liter]
SecondaryNumberOfOxidation Washes
The number of washes following oxidation for the secondary set of the cycle parameters.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
SecondaryOxidationWashTime
Amount of time that the solid supports are incubated with wash solution following oxidation for the secondary set of the cycle parameters.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterEqualP[0 Second]
SecondaryOxidationWashVolume
The volume of wash solution for each post-oxidation wash for the secondary set of the cycle parameters.
Format: Single
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Micro Liter]
SecondaryCyclePositions
Positions that should use the secondary cycle parameters (Lower Case).
Format: Multiple
Class: Expression
Programmatic Pattern: ListableP[_Integer]
Cleavage
Cleavage
For each member of StrandModels, indicates if the oligomer will be cleaved and filtered from the solid support after synthesis.
Format: Multiple
Class: Expression
Programmatic Pattern: BooleanP
CleavageMethods
For each member of StrandModels, the cleavage method specifying conditions used to cleave the oligomer from the solid support.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Method]
CleavageSolutions
For each member of StrandModels, the solution used to cleave the oligomer from the solid-phase support.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
CleavageTimes
For each member of StrandModels, the time that the oligomer will be incubated in cleavage solution.
Format: Multiple
Class: Real
Unit: 1 hour
Programmatic Pattern: GreaterEqualP[0 Hour]
CleavageTemperatures
For each member of StrandModels, the temperature at which the oligomer will be incubated in cleavage solution.
Format: Multiple
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterEqualP[0 Celsius]
CleavageSolutionVolumes
For each member of StrandModels, the volume of cleavage solution in which the oligomer is cleaved.
Format: Multiple
Class: Real
Unit: 1 milliliter
Programmatic Pattern: GreaterEqualP[0 Milli Liter]
CleavageWashVolumes
For each member of StrandModels, volume of solvent used to wash the solid support following cleavage. The wash filtrate is pooled with the filtered cleavage solution.
Format: Multiple
Class: Real
Unit: 1 milliliter
Programmatic Pattern: GreaterEqualP[0 Milli Liter]
CleavageWashSolutions
For each member of StrandModels, the solvent used to wash the solid support following cleavage. The wash filtrate is pooled with the filtered cleavage solution.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
CleavageIncubations
The thermal incubation protocols used to cleave the oligomers from the solid support.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
StorageSolvents
For each member of StrandModels, the solution that the uncleaved oligomer (still on the solid support) is stored in following synthesis.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
StorageSolventVolumes
For each member of StrandModels, the amount of solvent that the uncleaved oligomer (still on the solid support) is stored in post-synthesis.
Format: Multiple
Class: Real
Unit: 1 milliliter
Programmatic Pattern: GreaterEqualP[0 Milliliter]
Filters
The filters used to filter oligomers and cleavage solution from the solid support post-cleavage.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Sample] | Model[Sample] | Object[Container] | Model[Container] | Object[Item] | Model[Item]
CleavageSolutionManipulation
The set of instructions specifying the transfers of cleavage solution to the solid support.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
FilterTransferManipulation
The set of instructions specifying the transfers of cleaved oligomers and cleavage solution from the solid support to a filter.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
ResinWashManipulation
The set of instructions specifying the transfers of cleavage wash solution to the solid support.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
FilterWashManipulation
The set of instructions specifying the transfers of cleavage wash solution from the solid support to a filter.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
CleavageEvaporationProtocol
The set of instructions specifying the evaporation of the cleavage solution and cleavage wash solution from the cleaved oligomers.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
StorageSolventManipulation
The set of instructions specifying the transfers of storage solution to uncleaved oligomers (still attached to the solid support).
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
EvaporationInstruments
The devices used to remove cleavage solvents and dry the synthesized material after cleavage incubation.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
CleavageIncubationInstruments
The devices used to incubate oligomer solution with cleavage solution.
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]
Qualifications & Maintenance
SynthesizerWashSolution
The solution used to clean the synthesizer.
Format: Single
Class: Link
Programmatic Pattern: _Link
Last modified on Mon 26 Sep 2022 15:43:49