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[Analysis, Kinetics, _String]

Pattern Description: The object reference of this object.

Type

Type of this Object.

Format: Single

Class: Expression

Programmatic Pattern: Object[Analysis, Kinetics]

Pattern Description: Object[Analysis, Kinetics]

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 person who ran the analysis.

Format: Single

Class: Link

Programmatic Pattern: _Link

Relation: Object[User]

General

UnresolvedOptions

The initial options entered into the analysis function that generated this object, along with the default values for any unspecified options.

Format: Single

Class: Compressed

Programmatic Pattern: {_Rule...}

ResolvedOptions

The final options used by the analysis function, after automatic options have been determined from the input and unresolved options.

Format: Single

Class: Compressed

Programmatic Pattern: {_Rule...}

Reference

The objects containing the source data used in this analysis.

Format: Multiple

Class: Link

Programmatic Pattern: _Link

ReferenceField

The field in the Reference object containing the source data.

Format: Single

Class: Expression

Programmatic Pattern: FieldP[Output -> Short]

Species

All of the participating reagents involved in the ReactionMechanism.

Format: Multiple

Class: Expression

Programmatic Pattern: ReactionSpeciesP

FitMechanism

A ReactionMechanism containing some unkonwn kinetic rates, which is fitted by this analysis.

Format: Single

Class: Compressed

Programmatic Pattern: ReactionMechanismP

TrainingData

The data that the kinetic rates are fitted to.

Format: Multiple

[[1]] Initial State

Header: Initial State

Class: Expression

Programmatic Pattern: StateFormatP

[[2]] Injections

Header: Injections

Class: Expression

Programmatic Pattern: InjectionsFormatP|{}

[[3]] Trajectory

Header: Trajectory

Class: Expression

Programmatic Pattern: TrajectoryFormatP

[[4]] InitialVolume

Header: InitialVolume

Class: Expression

Programmatic Pattern: VolumeP

StandardCurve

Standard curve fitting analysis characterizing the relationship between concentration and fluorescence.

Format: Single

Class: Link

Programmatic Pattern: _Link

Relation: Object[Analysis, Fit][PredictedValues]

KineticsEquations

The equations that are fitted to sovle for the Rates.

Format: Multiple

Class: Expression

Programmatic Pattern: KineticsEquationP

Analysis & Reports

Rates

The unknown rate variables from the InitialMechanism along with their fitted values.

Format: Multiple

[[1]] Rate Variable Name

Header: Rate Variable Name

Class: Expression

Programmatic Pattern: _Symbol

[[2]] Fitted Value

Header: Fitted Value

Class: Real

Programmatic Pattern: NumericP

RatesStandardDeviation

The standard deviation of the fitted rate values.

Format: Multiple

[[1]] Rate Variable Name

Header: Rate Variable Name

Class: Expression

Programmatic Pattern: _Symbol

[[2]] Standard Deviation

Header: Standard Deviation

Class: Real

Programmatic Pattern: NumericP

RatesDistribution

The distribution of the fitted rate values.

Format: Multiple

[[1]] Rate Variable Name

Header: Rate Variable Name

Class: Expression

Programmatic Pattern: _Symbol

[[2]] Distribution

Header: Distribution

Class: Expression

Programmatic Pattern: QuantityDistributionP[]

ReactionMechanism

The fully specified ReactionMechanism that best fits the training data, which is the initial ReactionMechanism with the fitted rates substituted in for the unknown rates.

Format: Single

Class: Compressed

Programmatic Pattern: ReactionMechanismP

PredictedTrajectories

The kinetic trajectories predicted by the fitted model when simulated with the intial states and injections specified in the TrainingData.

Format: Single

Class: Compressed

Programmatic Pattern: {TrajectoryP...}

NumberOfIterations

The number of steps required to by the optimizer to solve for the kinetic rates, which is a measure of how difficult the fitting was.

Format: Single

Class: Integer

Programmatic Pattern: GreaterEqualP[0, 1]

Residual

The minimum value of the objective function, which is achieved at the solution of the optimization problem (i.e. the fitted rates). This is a measure of how well the fitted model matches the training data.

Format: Single

Class: Real

Programmatic Pattern: NumericP

Statistical Information

SumSquaredError

Sum of squared errors across all training trajectories and predicted trajectories.

Format: Single

Class: Real

Programmatic Pattern: GreaterEqualP[0]