Object[Simulation, PrimerSet]
A simulation to generate ideal sets of nucleic acid primers and beacons for use in a qPCR experiment given a particular target gene sequence or transcript sequence.
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[Simulation, PrimerSet, _String]
Pattern Description: The object reference of this object.
Type
Type of this Object.
Format: Single
Class: Expression
Programmatic Pattern: Object[Simulation, PrimerSet]
Pattern Description: Object[Simulation, PrimerSet]
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]
Status
The current status of the simulation.
Format: Single
Class: Expression
Programmatic Pattern: ProtocolStatusP
Author
The person who requested this simulation.
Format: Single
Class: Link
Programmatic Pattern: _Link
Relation: Object[User][SimulationsAuthored]
DateConfirmed
The date on which the simulation first entered processing or a backlog.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateEnqueued
The date on which the simulation first entered processing or a backlog.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateStarted
Date when this simulation was started.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateCompleted
Date when this simulation was completed.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
DateCanceled
Date when this simulation was canceled.
Format: Single
Class: Date
Programmatic Pattern: _?DateObjectQ
TimeElapsed
The time that was required to complete the simulation.
Format: Computable
Programmatic Pattern: GreaterEqualP[0 Day]
Expression: SafeEvaluate[{Field[DateCompleted], Field[DateStarted]}, Computables`Private`timeElapsed[Field[DateCompleted], Field[DateStarted]]]
Option Handling
UnresolvedOptions
The unresolved options entered into the simulation function that generated this object.
Format: Single
Class: Compressed
Programmatic Pattern: {_Rule...}
ResolvedOptions
The options resolved automatically by this simulation or entered by the requestor.
Format: Single
Class: Compressed
Programmatic Pattern: {_Rule...}
General
Target
The model of the RNA transcript that the simulation seeks to detect and amplified via PCR in this primer set simulation.
Format: Single
Class: Link
Programmatic Pattern: _Link
TargetName
The name (e.g. gene name or transcript name) of the target sequence being detected and amplified.
Format: Single
Class: String
Programmatic Pattern: _String
TargetSequence
The sequence of the transcript target being detected and amplified.
Format: Single
Class: String
Programmatic Pattern: SequenceP
MinPrimerLength
The minimum allowed length of the primers simulated.
Format: Single
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
MaxPrimerLength
The maxmimum allowed length of the primers simulated.
Format: Single
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
MinAmpliconLength
The minimum allowed length of the qPCR amplicon sequence.
Format: Single
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
MaxAmpliconLength
The maximum allowed length of the qPCR amplicon sequence.
Format: Single
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
PrimerConcentration
The concentration of the primer to be used in the simulation.
Format: Single
Class: Real
Unit: 1 micromolar
Programmatic Pattern: GreaterEqualP[0 Molar Micro]
ProbeConcentration
The concentration of the probe/beacon to be used in the simulation.
Format: Single
Class: Real
Unit: 1 micromolar
Programmatic Pattern: GreaterEqualP[0 Molar Micro]
TargetConcentration
The concentration of the target sequence to be used in the simulation.
Format: Single
Class: Real
Unit: 1 femtomolar
Programmatic Pattern: GreaterEqualP[0 Molar Micro]
AnnealingTime
The simulated annealing time for the primer pairs in each binding reaction.
Format: Single
Class: Real
Unit: 1 second
Programmatic Pattern: GreaterEqualP[0 Second]
AnnealingTemperature
The temperature at which annealing took place in the simulation for each binding reaction.
Format: Single
Class: Real
Unit: 1 degree Celsius
Programmatic Pattern: GreaterP[0 Kelvin]
MinBeaconStemLength
The minimum allowed beacon stem length that the simulation can use. The beacons are chosen to optimally bind to the Target between the forward and reverse primers.
Format: Single
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
MaxBeaconStemLength
The maximum allowed beacon stem length that the simulation can use. The beacons are chosen to optimally bind to the Target between the forward and reverse primers.
Format: Single
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
Orientation
Indicates whether the beacon probe binds to the sense strand or the antisense strand.
Format: Single
Class: Expression
Programmatic Pattern: PrimerSetOrientationP
NumberOfCandidates
The number of top primer sets the simulation will pass onto each round of ranking for beacon binding.
Format: Single
Class: Integer
Programmatic Pattern: GreaterEqualP[0, 1]
Simulation Results
Models
The top primer sets generated by this simulation.
Format: Multiple
Class: Link
Programmatic Pattern: _Link
TopForwardPrimers
The forward primers from the simulation that exhibited the strongest binding to the target sequence.
Format: Multiple
[[1]] Binding Position Start
Header: Binding Position Start
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
[[2]] Binding Position End
Header: Binding Position End
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
[[3]] Primer Sequence
Header: Primer Sequence
Class: Expression
Programmatic Pattern: StrandP
[[4]] Unbound Primer Concentration
Header: Unbound Primer Concentration
Class: Real
Unit: 1 micromolar
Programmatic Pattern: GreaterEqualP[0 Molar]
[[5]] Bound Primer Concentration
Header: Bound Primer Concentration
Class: Real
Unit: 1 micromolar
Programmatic Pattern: GreaterEqualP[0 Molar]
TopBeacons
The beacons from the simulation that exhibited the strongest binding to the target sequence and folding upon themselves.
Format: Multiple
[[1]] Binding Position Start
Header: Binding Position Start
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
[[2]] Binding Position End
Header: Binding Position End
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
[[3]] Beacon Sequence
Header: Beacon Sequence
Class: Expression
Programmatic Pattern: StrandP
[[4]] Unbound Beacon Concentration
Header: Unbound Beacon Concentration
Class: Real
Unit: 1 micromolar
Programmatic Pattern: ConcentrationP
[[5]] Bound Beacon Concentration at Annealing Temperature
Header: Bound Beacon Concentration at Annealing Temperature
Class: Real
Unit: 1 micromolar
Programmatic Pattern: ConcentrationP
[[6]] Bound Beacon Concentration at Melting Temperature
Header: Bound Beacon Concentration at Melting Temperature
Class: Real
Unit: 1 micromolar
Programmatic Pattern: ConcentrationP
[[7]] Beacon Stem Length
Header: Beacon Stem Length
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
PrimerPairs
The positions of the primer pairs from the simulation that exhibited the strongest target sequence binding.
Format: Multiple
[[1]] Forward Start Position
Header: Forward Start Position
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
[[2]] Forward End Position
Header: Forward End Position
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
[[3]] Reverse Start Position
Header: Reverse Start Position
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
[[4]] Reverse End Position
Header: Reverse End Position
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
ForwardPrimers
The forward primers from the simulation of all potential primers binding to the target sequence.
Format: Multiple
[[1]] Binding Position Start
Header: Binding Position Start
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
[[2]] Binding Position End
Header: Binding Position End
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
[[3]] Primer Sequence
Header: Primer Sequence
Class: Expression
Programmatic Pattern: StrandP
[[4]] Unbound Primer Concentration
Header: Unbound Primer Concentration
Class: Real
Unit: 1 micromolar
Programmatic Pattern: ConcentrationP
[[5]] Bound Primer Concentration
Header: Bound Primer Concentration
Class: Real
Unit: 1 micromolar
Programmatic Pattern: ConcentrationP
ForwardPrimerSequences
The sequences of the forward primers resulting from simulating the interactions between the primers, probe, and target sequence.
Format: Multiple
Class: Expression
Programmatic Pattern: _?StrandQ
ForwardPrimerPositions
The positions of the forward primers resulting from simulating the interactions between the primers, probe, and target sequence.
Format: Multiple
[[1]] Start Position
Header: Start Position
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
[[2]] End Position
Header: End Position
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
ForwardPrimerConcentrations
The concentrations of the forward primers resulting from simulating the interactions between the primers, probe, and target sequence.
Format: Multiple
Class: Real
Unit: 1 micromolar
Programmatic Pattern: GreaterEqualP[0 Molar Micro]
ReversePrimerSequences
The sequences of the reverse primers resulting from simulating the interactions between the primers, probe, and target sequence.
Format: Multiple
Class: Expression
Programmatic Pattern: StrandP
ReversePrimerPositions
The positions of the reverse primers resulting from simulating the interactions between the primers, probe, and target sequence.
Format: Multiple
[[1]] Start Position
Header: Start Position
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
[[2]] End Position
Header: End Position
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
ReversePrimerConcentrations
The concentrations of the reverse primers resulting from simulating the interactions between the primers, probe, and target sequence.
Format: Multiple
Class: Real
Unit: 1 micromolar
Programmatic Pattern: GreaterEqualP[0 Molar Micro]
Beacons
The beacons from the simulation of all potential primers binding to the target sequence.
Format: Multiple
[[1]] Binding Position Start
Header: Binding Position Start
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[1 Nucleotide]
[[2]] Binding Position End
Header: Binding Position End
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[1 Nucleotide]
[[3]] Beacon Sequence
Header: Beacon Sequence
Class: Expression
Programmatic Pattern: StrandP
[[4]] Unbound Beacon Concentration
Header: Unbound Beacon Concentration
Class: Real
Unit: 1 micromolar
Programmatic Pattern: ConcentrationP
[[5]] Bound Beacon Concentration at Annealing Temperature
Header: Bound Beacon Concentration at Annealing Temperature
Class: Real
Unit: 1 micromolar
Programmatic Pattern: ConcentrationP
[[6]] Bound Beacon Concentration at Melting Temperature
Header: Bound Beacon Concentration at Melting Temperature
Class: Real
Unit: 1 micromolar
Programmatic Pattern: ConcentrationP
[[7]] Beacon Stem Length
Header: Beacon Stem Length
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
BeaconSequences
The sequences of the beacons resulting from simulating the interactions between the primers, probe, and target sequence.
Format: Multiple
Class: Expression
Programmatic Pattern: StrandP
BeaconPositions
The positions of the beacons resulting from simulating the interactions between the primers, probe, and target sequence.
Format: Multiple
[[1]] Start Position
Header: Start Position
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
[[2]] End Position
Header: End Position
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
BeaconConcentrations
The concentrations of the beacons resulting from simulating the interactions between the primers, probe, and target sequence.
Format: Multiple
Class: Real
Unit: 1 micromolar
Programmatic Pattern: GreaterEqualP[0 Molar Micro]
BeaconStemLengths
The final beacon hairpin stem lengths chosen by the simulation. These stem lengths correspond to the beacon sequences in the BeaconSequences field.
Format: Multiple
Class: Integer
Unit: 1 Nucleotides
Programmatic Pattern: GreaterEqualP[0 Nucleotide]
PrimerDimerConcentrations
The primer dimer concentrations resulting from simulating the interactions between the primers, probe, and target sequence.
Format: Multiple
Class: Real
Unit: 1 micromolar
Programmatic Pattern: GreaterEqualP[0 Molar Micro]
PrimerProbeSets
A list of the transposed results of the primer set generation simulation function, with each primer.
Format: Computable
Header: ['Forward Primer Positions', 'Forward Primer Sequence', 'Forward Primer Concentration', 'Reverse Primer Positions', 'Reverse Primer Sequence', 'Reverse Primer Concentration', 'Beacon Position', 'Beacon Sequence', 'Beacon Concentration', 'Primer Dimer Concentration', 'Beacon Stem Length']
Programmatic Pattern: {{{GreaterEqualP[1, 1], GreaterEqualP[1, 1]}, StrandP, NumericP, {GreaterEqualP[1, 1], GreaterEqualP[1, 1]}, StrandP, GreaterEqualP[0], {GreaterEqualP[1, 1], GreaterEqualP[1, 1]}, StrandP, GreaterEqualP[0], GreaterEqualP[0], GreaterEqualP[0, 1]}..}
Expression: SafeEvaluate[{Field[ForwardPrimerPositions], Field[ForwardPrimerSequences], Field[ForwardPrimerConcentrations], Field[ReversePrimerSequences], Field[ReversePrimerConcentrations], Field[ReversePrimerPositions]}, Computables`Private`primerProbeSets[Field[ForwardPrimerPositions], Field[ForwardPrimerSequences], Field[ForwardPrimerConcentrations], Field[ReversePrimerPositions], Field[ReversePrimerSequences], Field[ReversePrimerConcentrations], Field[BeaconPositions], Field[BeaconSequences], Field[BeaconConcentrations], Field[PrimerDimerConcentrations], Field[BeaconStemLengths]]]
Last modified on Mon 26 Sep 2022 15:43:53