Object[Protocol, PNASynthesis]
A protocol for synthesizing Peptide Nucleic Acid (PNA) oligomers.
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, PNASynthesis, _String]
Pattern Description: The object reference of this object.
Type
Type of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Protocol, PNASynthesis]
Pattern Description: Object[Protocol, PNASynthesis]
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
Primitives
For each member of StrandModels, a complete list of all chemical steps, including resin swelling, resin downloading, synthesis and cleavage, used to synthesize that strand.
Format: Multiple
Class: Expression
Programmatic Pattern: {SynthesisCycleStepP..}
Replicate Experiments
Template
The protocol whose option selections should be selected as the default options for this protocol.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol][ProtocolsTemplated]
ProtocolsTemplated
Protocols which were generated using this protocol's options as a starting point for its option defaults.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol][Template]
Sample Preparation
PreparatoryUnitOperations
A list of transfers, consolidations, aliquots, mixes and dilutions that will be performed in the order listed to prepare samples for the experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: _ | _
PreparatoryPrimitives
A list of transfers, consolidations, aliquots, mixes and dilutions that will be performed in the order listed to prepare samples for the experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: _ | _
VolumeCheckSamplePrep
Indicates if any liquid samples prepared by using the PreparatoryUnitOperations option should have their volumes measured and updated before running the experiment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
IncubateSamplePreparation
For each member of SamplesIn, parameters describing how the input samples should be heated prior to any aliquoting or the start of the experiment.
Format: Multiple
[Incubate]
Header: Incubate
Class: Boolean
[IncubationTemperature]
Header: IncubationTemperature
Class: Real
Unit: 1 degree Celsius
[IncubationTime]
Header: IncubationTime
Class: Real
Unit: 1 second
[Mix]
Header: Mix
Class: Boolean
[MixType]
Header: MixType
Class: Expression
[MixUntilDissolved]
Header: MixUntilDissolved
Class: Boolean
[MaxIncubationTime]
Header: MaxIncubationTime
Class: Real
Unit: 1 second
[IncubationInstrument]
Header: IncubationInstrument
Class: Link
[AnnealingTime]
Header: AnnealingTime
Class: Real
Unit: 1 second
[IncubateAliquotContainer]
Header: IncubateAliquotContainer
Class: Expression
[IncubateAliquot]
Header: IncubateAliquot
Class: Real
Unit: 1 liter
[IncubateAliquotDestinationWell]
Header: IncubateAliquotDestinationWell
Class: Expression
CentrifugeSamplePreparation
For each member of SamplesIn, parameters describing how the input samples should be spun down prior to any aliquoting or the start of the experiment.
Format: Multiple
[Centrifuge]
Header: Centrifuge
Class: Boolean
[CentrifugeInstrument]
Header: CentrifugeInstrument
Class: Link
[CentrifugeIntensity]
Header: CentrifugeIntensity
Class: VariableUnit
[CentrifugeTime]
Header: CentrifugeTime
Class: Real
Unit: 1 minute
[CentrifugeTemperature]
Header: CentrifugeTemperature
Class: Real
Unit: 1 degree Celsius
[CentrifugeAliquotContainer]
Header: CentrifugeAliquotContainer
Class: Expression
[CentrifugeAliquot]
Header: CentrifugeAliquot
Class: Real
Unit: 1 liter
[CentrifugeAliquotDestinationWell]
Header: CentrifugeAliquotDestinationWell
Class: Expression
FilterSamplePreparation
For each member of SamplesIn, parameters describing how particulates should be separated from the input samples prior to any aliquoting or the start of the experiment.
Format: Multiple
[Filtration]
Header: Filtration
Class: Boolean
[FiltrationType]
Header: FiltrationType
Class: Expression
[Filter]
Header: Filter
Class: Link
Relation: Object[Container] | Model[Container] | Object[Sample] | Model[Sample] | Object[Item] | Model[Item]
[FilterMaterial]
Header: FilterMaterial
Class: Expression
[FilterPoreSize]
Header: FilterPoreSize
Class: Real
Unit: 1 micrometer
[FilterContainerOut]
Header: FilterContainerOut
Class: Expression
[FilterInstrument]
Header: FilterInstrument
Class: Link
Relation: Model[Instrument, FilterBlock] | Object[Instrument, FilterBlock] | Model[Instrument, PeristalticPump] | Object[Instrument, PeristalticPump] | Model[Instrument, VacuumPump] | Object[Instrument, VacuumPump] | Model[Instrument, Centrifuge] | Object[Instrument, Centrifuge] | Model[Instrument, SyringePump] | Object[Instrument, SyringePump]
[FilterSyringe]
Header: FilterSyringe
Class: Link
[FilterHousing]
Header: FilterHousing
Class: Link
[FilterIntensity]
Header: FilterIntensity
Class: VariableUnit
[FilterTime]
Header: FilterTime
Class: Real
Unit: 1 minute
[FilterTemperature]
Header: FilterTemperature
Class: Real
Unit: 1 degree Celsius
[FilterSterile]
Header: FilterSterile
Class: Boolean
[FilterAliquotContainer]
Header: FilterAliquotContainer
Class: Expression
[FilterAliquot]
Header: FilterAliquot
Class: Real
Unit: 1 liter
[PrefilterMaterial]
Header: PrefilterMaterial
Class: Expression
[PrefilterPoreSize]
Header: PrefilterPoreSize
Class: Real
Unit: 1 micrometer
[FilterAliquotDestinationWell]
Header: FilterAliquotDestinationWell
Class: Expression
SamplePreparationProtocols
Protocols used to mix, centrifuge, incubate, and filter the SamplesIn prior to starting the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
PooledIncubateSample Preparation
For each member of PooledSamplesIn, parameters describing how the pooled samples should be incubated after aliquoting but prior to the start of the experiment.
Format: Multiple
[Incubate]
Header: Incubate
Class: Boolean
[IncubationTemperature]
Header: IncubationTemperature
Class: Real
Unit: 1 degree Celsius
[IncubationTime]
Header: IncubationTime
Class: Real
Unit: 1 second
[Mix]
Header: Mix
Class: Boolean
[MixType]
Header: MixType
Class: Expression
[MixUntilDissolved]
Header: MixUntilDissolved
Class: Boolean
[MaxIncubationTime]
Header: MaxIncubationTime
Class: Real
Unit: 1 second
[IncubationInstrument]
Header: IncubationInstrument
Class: Link
[AnnealingTime]
Header: AnnealingTime
Class: Real
Unit: 1 second
[IncubateAliquotContainer]
Header: IncubateAliquotContainer
Class: Expression
[IncubateAliquot]
Header: IncubateAliquot
Class: Real
Unit: 1 liter
[IncubateAliquotDestinationWell]
Header: IncubateAliquotDestinationWell
Class: Expression
NestedIndexMatchingIncubate SamplePreparation
For each member of NestedIndexMatchingSamplesIn, parameters describing how the pooled samples should be incubated after aliquoting but prior to the start of the experiment.
Format: Multiple
[Incubate]
Header: Incubate
Class: Boolean
[IncubationTemperature]
Header: IncubationTemperature
Class: Real
Unit: 1 degree Celsius
[IncubationTime]
Header: IncubationTime
Class: Real
Unit: 1 second
[Mix]
Header: Mix
Class: Boolean
[MixType]
Header: MixType
Class: Expression
[MixUntilDissolved]
Header: MixUntilDissolved
Class: Boolean
[MaxIncubationTime]
Header: MaxIncubationTime
Class: Real
Unit: 1 second
[IncubationInstrument]
Header: IncubationInstrument
Class: Link
[AnnealingTime]
Header: AnnealingTime
Class: Real
Unit: 1 second
[IncubateAliquotContainer]
Header: IncubateAliquotContainer
Class: Expression
[IncubateAliquot]
Header: IncubateAliquot
Class: Real
Unit: 1 liter
[IncubateAliquotDestinationWell]
Header: IncubateAliquotDestinationWell
Class: Expression
PooledCentrifugeSample Preparation
For each member of PooledSamplesIn, parameters describing how the pooled samples should be centrifuge after aliquoting and pooled mixing but prior to the start of the experiment.
Format: Multiple
[Centrifuge]
Header: Centrifuge
Class: Boolean
[CentrifugeInstrument]
Header: CentrifugeInstrument
Class: Link
[CentrifugeIntensity]
Header: CentrifugeIntensity
Class: VariableUnit
[CentrifugeTime]
Header: CentrifugeTime
Class: Real
Unit: 1 minute
[CentrifugeTemperature]
Header: CentrifugeTemperature
Class: Real
Unit: 1 degree Celsius
[CentrifugeAliquotContainer]
Header: CentrifugeAliquotContainer
Class: Expression
[CentrifugeAliquot]
Header: CentrifugeAliquot
Class: Real
Unit: 1 liter
[CentrifugeAliquotDestinationWell]
Header: CentrifugeAliquotDestinationWell
Class: Expression
NestedIndexMatchingCentrifuge SamplePreparation
For each member of PooledSamplesIn, parameters describing how the pooled samples should be centrifuge after aliquoting and pooled mixing but prior to the start of the experiment.
Format: Multiple
[Centrifuge]
Header: Centrifuge
Class: Boolean
[CentrifugeInstrument]
Header: CentrifugeInstrument
Class: Link
[CentrifugeIntensity]
Header: CentrifugeIntensity
Class: VariableUnit
[CentrifugeTime]
Header: CentrifugeTime
Class: Real
Unit: 1 minute
[CentrifugeTemperature]
Header: CentrifugeTemperature
Class: Real
Unit: 1 degree Celsius
[CentrifugeAliquotContainer]
Header: CentrifugeAliquotContainer
Class: Expression
[CentrifugeAliquot]
Header: CentrifugeAliquot
Class: Real
Unit: 1 liter
[CentrifugeAliquotDestinationWell]
Header: CentrifugeAliquotDestinationWell
Class: Expression
FilteredSamples
Samples corresponding to filtered eluents of SamplesIn generated during sample preparation and intended for use in this experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Sample]
Aliquoting
AliquotSamplePreparation
For each member of AliquotSamples, parameters describing how aliquots should be drawn from the input samples after initial sample preparation in order to create new aliquot samples upon which aliquot preparation and the experiment should proceed.
Format: Multiple
[Aliquot]
Header: Aliquot
Class: Boolean
[AliquotAmount]
Header: AliquotAmount
Class: Expression
[TargetConcentration]
Header: TargetConcentration
Class: Expression
[AssayVolume]
Header: AssayVolume
Class: Real
Unit: 1 milliliter
[AliquotContainer]
Header: AliquotContainer
Class: Expression
[AssayBuffer]
Header: AssayBuffer
Class: Link
[BufferDiluent]
Header: BufferDiluent
Class: Link
[BufferDilutionFactor]
Header: BufferDilutionFactor
Class: Real
[ConcentratedBuffer]
Header: ConcentratedBuffer
Class: Link
[DestinationWell]
Header: DestinationWell
Class: Expression
[TargetConcentrationAnalyte]
Header: TargetConcentrationAnalyte
Class: Expression
[AliquotSampleLabel]
Header: AliquotSampleLabel
Class: String
AliquotProtocols
Protocols used to create AliquotSamples prior to starting the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol]
AliquotPreparationProtocols
Protocols used to mix, centrifuge, incubate, and filter the AliquotSamples prior to starting the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol]
AliquotSamples
Samples corresponding to aliquots of SamplesIn generated during sample preparation and intended for use in this experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Sample]
AliquotContainers
Containers that hold AliquotSamples generated during sample preparation and intended for use in this experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
SaveAliquots
Indicates if the AliquotSamples should be stored after the experiment, rather than being discarded.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
ConsolidateAliquots
Indicates if identical aliquots should be consolidated in a single sample.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
AliquotPreparation
Indicates if the aliquotting should occur manually or on a robotic liquid handler.
Format: Single
Class: Expression
Programmatic Pattern: PreparationMethodP
AliquotVolumes
For each member of SamplesIn, the volume transferred from the sample into the aliquot sample which is used in lieu of the initial sample for the experiment.
Format: Multiple
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterP[0 Micro Liter]
AliquotMasses
For each member of SamplesIn, the mass of a solid transferred from the sample into the aliquot sample which is used in lieu of the initial sample for the experiment.
Format: Multiple
Class: Real
Unit: 1 milligram
Programmatic Pattern: GreaterP[0 Milligram]
AliquotAmounts
For each member of SamplesIn, the amount transferred from the sample into the aliquot sample which is used in lieu of the initial sample for the experiment.
Format: Multiple
Class: VariableUnit
Programmatic Pattern: GreaterP[0 Milliliter] | GreaterP[0 Milligram] | GreaterP[0 Unit, 1 Unit]
TargetConcentrations
For each member of SamplesIn, the final concentration of analyte in the aliquot sample which is used in lieu of the initial sample for the experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: Milligram
Hold[GreaterP[0 Micro Molar] | GreaterP[0 ----------]]
Milliliter
AssayVolumes
For each member of SamplesIn (or PooledSamplesIn), the total volume of the reaction mixture which is used in lieu of the initial sample for the experiment.
Format: Multiple
Class: Real
Unit: 1 microliter
Programmatic Pattern: GreaterEqualP[0 Micro Liter]
AssayBuffers
For each member of SamplesIn (or PooledSamplesIn), the final buffers used to generate AliquotSamples by aliquoting SamplesIn.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ConcentratedBuffers
For each member of SamplesIn (or PooledSamplesIn), the concentrated buffer source which is added to the AliquotSamples to obtain 1x buffer concentration after dilution of the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
BufferDilutionFactors
For each member of SamplesIn (or PooledSamplesIn), he dilution factor by which the concentrated buffer is diluted in preparing the AliquotSamples to obtain a 1x buffer concentration after dilution of the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Multiple
Class: Real
Programmatic Pattern: GreaterP[0]
BufferDiluents
For each member of SamplesIn (or PooledSamplesIn), the diluent used to dilute the concentration of the concentrated buffer in preparing the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ConcentratedBuffer
The concentrated buffer source which is added to each of the AliquotSamples to obtain 1x buffer concentration after dilution of the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
BufferDilutionFactor
The dilution factor by which the concentrated buffer is diluted in preparing the AliquotSamples to obtain a 1x buffer concentration after dilution of the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Single
Class: Integer
Programmatic Pattern: GreaterP[0]
BufferDiluent
The diluent used to dilute the concentration of the concentrated buffer in preparing the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
AssayBuffer
The desired buffer for the AliquotSamples which are used in lieu of the SamplesIn for the experiment.
Format: Single
Class: Link
Programmatic Pattern: _Link
Sample Post-Processing
PostProcessingProtocols
Protocols used to perform post-processing such as sample imaging or volume measurement.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol]
ImageSample
Indicates if the samples that are modified in the course of the experiment are imaged after running the experiment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
MeasureVolume
Indicates if the volume of the liquid samples modified in the course of the experiment are measured after running the experiment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
MeasureWeight
Indicates if the weight of the solid samples modified in the course of the experiment are measured after running the experiment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
Measure
Indicates if the volume/weight of the samples modified in the course of the experiment are measured after running the experiment.
Format: Single
Class: Expression
Programmatic Pattern: BooleanP
Storage
Indicates the conditions under which any samples generated by this experiment are stored after the protocol is completed.
Format: Single
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
Experimental Results
Data
Any primary data generated by this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
SamplesOut
Any preparative samples generated by the protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ContainersOut
Any containers holding SamplesOut generated by this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
EnvironmentalData
Measurements of environmental conditions (temperature and humidity) recorded during the execution of this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Data][Protocol]
Troubleshooting
TroubleshootingReports
Reports for errors that require troubleshooting associated with the execution of this top-level protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Resources
AwaitingResources
Indicates if this protocol is awaiting the arrival of items before it can be begun or continued.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
ShippingMaterials
Indicates the transactions, and the specific products or samples therein, that must be received before this protocol can be begun or continued.
Format: Multiple
[[1]] Transaction
Header: Transaction
Class: Link
Programmatic Pattern: _Link
[[2]] Required Product
Header: Required Product
Class: Link
Programmatic Pattern: _Link
HazardousWaste
The types of waste generated by this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
DispenserContainers
Containers gathered as destinations for any resources obtained from a chemical dispenser.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
GasSources
A list of containers that supplied gas to instruments in this protocol through plumbing connections.
Format: Multiple
[[1]] Gas Type
Header: Gas Type
Class: Expression
Programmatic Pattern: GasP
[[2]] Source Container
Header: Source Container
Class: Link
Programmatic Pattern: _Link
Relation: Object[Container]
[[3]] Supplied Instrument
Header: Supplied Instrument
Class: Link
Programmatic Pattern: _Link
Relation: Object[Instrument]
Cleaning
WasteGenerated
For each type of waste generated by this protocol, the total amount (in grams) generated during the conduct of the protocol.
Format: Multiple
[Waste]
Header: Waste
Class: Link
Relation: Model[Sample]
[Weight]
Header: Weight
Class: Real
Unit: 1 gram
Storage Information
StoragePrice
The total monthly price for warehousing all user owned items associated with this protocol in an ECL facility under the storage conditions specified by each item.
Format: Single
Class: Real
Unit: 1 US dollar per month
Programmatic Pattern: USD
Hold[GreaterEqualP[0 -----]]
Month
Sample Storage
SamplesInStorage
For each member of SamplesIn, The storage conditions under which any input samples to this experiment should be stored after their usage in this experiment.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
AliquotStorage
For each member of AliquotSamples, The storage conditions under which any aliquot samples generated by this experiment should be stored after the protocol is completed.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
SamplesOutStorage
For each member of SamplesOut, the storage conditions under which any output samples generated by this experiment should be stored after the protocol is completed.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleStorageTypeP | Disposal
Option Handling
ResolvedOptions
The final options used as parameters for this protocol, after automatic options are resolved.
Format: Single
Class: Compressed
Programmatic Pattern: {_Rule...}
UnresolvedOptions
The verbatim options originally input by the protocol author to generate this protocol, often with some options set to Automatic.
Format: Single
Class: Compressed
Programmatic Pattern: {_Rule...}
Computations
ParallelComputations
List of computational jobs generated and run in parallel to the execution of this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ComputationsOutstanding
Indicates if any of the computation jobs in ParallelComputations have not yet completed.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
ErroneousComputations
List of computational jobs generated and run in parallel to the execution of this protocol in which a warning or error was thown, or that did not finish.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Synthesis
Strands
The sequence of monomers and modifications that make up the oligomers being synthesized.
Format: Multiple
Class: Expression
Programmatic Pattern: {StrandP..} | Null
StrandModels
Oligomers that will be synthesized by this protocol.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Model[Sample]
CleavedStrandModels
The oligomers that will undergo cleavage following the end of the synthesis.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Model[Sample]
UncleavedStrandModels
The oligomers that will be left covalently attached to their resins support following the end of the synthesis.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Model[Sample]
Scale
For each member of StrandModels, the amount of the synthesis reagents employed by this synthesis.
Format: Multiple
Class: Real
Unit: 1 micromole
Programmatic Pattern: GreaterP[0 Micromole]
SynthesisStrategy
The protecting group strategy for solid phase peptide synthesis cycles.
Format: Single
Class: Expression
Programmatic Pattern: PeptideSynthesisStrategyP
Instrument
The synthesizer instrument used to conduct the synthesis.
Format: Single
Class: Link
Programmatic Pattern: _Link
Resin
For each member of StrandModels, the resin sample used for solid support for the synthesis.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Instrument Setup
FumeHood
The fume hood used to conduct sample manipulations of hazardous chemicals.
Format: Single
Class: Link
Programmatic Pattern: _Link
Resin Swelling
SwellResin
For each member of StrandModels, indicates if the resin is swollen in swell solution prior to first synthesis cycle.
Format: Multiple
Class: Expression
Programmatic Pattern: BooleanP
SwellSolution
The solution used to swell the resin prior to the start of synthesis to increase the accessibility of active sites.
Format: Single
Class: Link
Programmatic Pattern: _Link
SwellPurgeTime
The length of time that for which the swell solution is purged into the reaction vessels.
Format: Single
Class: Real
Unit: 1 hour
Programmatic Pattern: GreaterEqualP[0 Minute]
Downloading
TargetLoadings
For each member of Resin, the target amount of active sites per gram of downloaded resin.
Format: Multiple
Class: Real
Unit: 1 mole per gram
Programmatic Pattern: 0 Mole
Hold[GreaterEqualP[------]]
Gram
DownloadResins
Indicates if the resins are downloaded prior to the start of the synthesis.
Format: Multiple
Class: Expression
Programmatic Pattern: BooleanP
DownloadedStrandModels
The oligomers that will undergo resin downloading using the C terminal monomer of their sequence prior to the start of the synthesis.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Model[Sample]
DownloadMonomers
For each member of DownloadedStrandModels, the monomer sample used to download the resin when preloading the resin.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Monomer Activation
DownloadActivationSolution
A mix of preactivation and base solutions used to activate the monomers for coupling when preloading the resin.
Format: Single
Class: Link
Programmatic Pattern: _Link
MonomerPreactivations
For each member of StrandModels, indicates if the monomer is preactivated in a separate reaction vessel, in the reaction vessel with the resin, or not at all.
Format: Multiple
Class: Expression
Programmatic Pattern: PreactivationTypeP
SynthesisMonomers
A list of all monomers samples used to synthesize the sequence.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
PreactivationVessels
The vessel used to preactivate the monomers for that strand's synthesis.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
ActivationSolution
A mix of preactivation and base solutions used to activate the monomers for coupling.
Format: Single
Class: Link
Programmatic Pattern: _Link
Deprotonation
Deprotonation
For each member of StrandModels, indicates if a deprotonation step is performed between the coupling steps.
Format: Multiple
Class: Expression
Programmatic Pattern: BooleanP
DeprotonationSolution
The deprotonation solution used to neutralize the resin prior to the coupling step.
Format: Single
Class: Link
Programmatic Pattern: _Link
Deprotection
DeprotectionSolution
The deprotection solution used to remove protecting groups from the growing strand during the deprotection step.
Format: Single
Class: Link
Programmatic Pattern: _Link
InitialDeprotection
For each member of StrandModels, indicates if an initial deprotection step is done are part of resin download.
Format: Multiple
Class: Expression
Programmatic Pattern: BooleanP
FinalDeprotection
For each member of StrandModels, indicates if a final deprotection step is done following last synthesis cycle.
Format: Multiple
Class: Expression
Programmatic Pattern: BooleanP
Capping
InitialCapping
For each member of StrandModels, indicates if an initial capping step is done prior to the first synthesis cycle.
Format: Multiple
Class: Expression
Programmatic Pattern: BooleanP
FinalCapping
For each member of StrandModels, indicates if a final capping step is done following last synthesis cycle.
Format: Multiple
Class: Expression
Programmatic Pattern: BooleanP
CappingSolution
The capping solution used to cap any remaining uncoupled sites from growing further during the synthesis to aid in later purification of the truncations.
Format: Single
Class: Link
Programmatic Pattern: _Link
Coupling
DoubleCoupling
The cycle at which the synthesis begins to double couple by exposing each resin to fresh coupling for two consecutive incubations.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
DoubleCouplings
The cycle at which the synthesis begins to double couple by exposing each resin to fresh coupling for two consecutive incubations.
Format: Multiple
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
Washing
WashSolution
The primary solution used for washing the resin between reagent additions.
Format: Single
Class: Link
Programmatic Pattern: _Link
PrimaryResinShrinkSolution
The sample of primary shrink solution used to shrink the resin prior to cleavage.
Format: Single
Class: Link
Programmatic Pattern: _Link
SecondaryResinShrinkSolution
The sample of secondary shrink solution used to shrink the resin prior to cleavage.
Format: Single
Class: Link
Programmatic Pattern: _Link
Cleavage
Cleavage
For each member of StrandModels, indicates if the oligomer will be cleaved from the resin after synthesis.
Format: Multiple
Class: Expression
Programmatic Pattern: BooleanP
CleavageSolution
The solution used to cleave the strands from the resins post synthesis resin.
Format: Single
Class: Link
Programmatic Pattern: _Link
CollectionVessels
For each member of CleavedStrandModels, ihe temporary vessel used to collect the cleavage strands prior to trituration.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
WashSyringe
The syringe used to dispense cleavage swell solutions into reaction vessels during cleavage.
Format: Single
Class: Link
Programmatic Pattern: _Link
WashNeedle
The needle installed onto the syringe used to dispense cleavage swell solution into reaction vessels during cleavage.
Format: Single
Class: Link
Programmatic Pattern: _Link
CleavageSyringes
The syringes used to dispense cleavage solution into reaction vessels during cleavage.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
WashNeedles
The needles installed onto the syringes used to dispense cleavage solution into reaction vessels during cleavage.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
CleavageNeedles
The needles installed onto the syringes used to dispense cleavage solution into reaction vessels during cleavage.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
VacuumManifold
The vacuum manifold used to conduct the cleavage and trituration part of this protocol.
Format: Single
Class: Link
Programmatic Pattern: _Link
Pipette
The pipette controller used to transfer resin from reaction vessels into cleavage syringes.
Format: Single
Class: Link
Programmatic Pattern: _Link
PipetteTips
Pipette tips used for the protocol.
Format: Single
Class: Link
Programmatic Pattern: _Link
Trituration
TriturationPrimitives
A set of instructions specifying the transfers required to add trituration solution to the cleavage vessels.
Format: Multiple
Class: Expression
Programmatic Pattern: SampleManipulationP
TriturationManipulations
Sample manipulations protocols used to add trituration solution to the cleavage vessels.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Protocol, SampleManipulation]
TriturationSolution
The solution used to purify the PNA strands after cleavage from the resin by using the solubility differences between PNA strands, which should crash out of solution and impurities which remain soluble.
Format: Single
Class: Link
Programmatic Pattern: _Link
TriturationVolume
The volume of TriturationSolution that used to crash the strands out of solution during trituration.
Format: Single
Class: Real
Unit: 1 milliliter
Programmatic Pattern: GreaterEqualP[0 Micro Liter]
TriturationTime
The length of time for which the cleaved strands will be triturated with TriturationSolution.
Format: Single
Class: Real
Unit: 1 minute
Programmatic Pattern: GreaterEqualP[0 Minute]
TriturationTemperature
The temperature at which the cleaved strands are triturated with TriturationSolution.
Format: Single
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterEqualP[0 Kelvin]
TriturationCentrifugationTime
The length of time for which the insoluble cleaved strands are spun down and pelleted during each trituration cycle.
Format: Single
Class: Real
Unit: 1 minute
Programmatic Pattern: GreaterEqualP[0 Minute]
TriturationCentrifugation Force
The centrifugal force at which the insoluble cleaved strands are spun down and pelleted during each trituration cycle.
Format: Single
Class: Real
Unit: 1 standard acceleration due to gravity on the surface of the earth
Programmatic Pattern: GreaterEqualP[0 GravitationalAcceleration]
TriturationCentrifugationRate
The centrifuge rate for which the insoluble cleaved strands are spun down and pelleted during each trituration cycle.
Format: Single
Class: Real
Unit: 1 revolution per minute
Programmatic Pattern: GreaterEqualP[0 RPM]
NumberOfTriturationCycles
The number of times the cleaved PNA strands are triturated with TriturationSolution.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
TriturationMixing
The mix protocols that will be executed during trituration to resuspend the pellet into the trituration solution.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
TriturationCentrifuging
The centrifuge protocols that will be executed during trituration to pellet the strands prior to decanting of supernatant.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Resuspension
ResuspensionBuffer
The buffer used to resuspend the strands after cleavage from the resin.
Format: Single
Class: Link
Programmatic Pattern: _Link
ResuspensionVolumes
For each member of CleavedStrandModels, the volume of resuspension buffer used to resuspend the strand after cleavage from the resin.
Format: Multiple
Class: Real
Unit: 1 milliliter
Programmatic Pattern: GreaterEqualP[0 Micro Liter]
Resin Storage
StorageSolution
The sample or model of solution used to store any uncleaved resin samples.
Format: Single
Class: Link
Programmatic Pattern: _Link
StorageVolumes
For each member of UncleavedStrandModels, the volume of storage solution in which to store the resin.
Format: Multiple
Class: Real
Unit: 1 milliliter
Programmatic Pattern: GreaterEqualP[0 Micro Liter]
Monomer Recovery
RecoupMonomers
Indicates if any leftover monomer solutions will be stored at the conclusion of the synthesis.
Format: Single
Class: Boolean
Programmatic Pattern: BooleanP
RecoupedMonomers
For each member of SynthesisMonomers, the leftover monomer solution transferred to a new container for storage.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
Relation: Object[Sample]
Last modified on Mon 26 Sep 2022 15:43:51