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R2011b Documentation → SimBiology
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Contents

Index

• Getting Started Guide

• SimBiology Overview

Features

Integrated Environment

• Integrating SimBiology Models into Your Existing Workflow

Existing Workflow in Experimental Research

Workflow Incorporating Mathematical Modeling

Workflow Using SimBiology Models for Mathematical Modeling

Using the SimBiology Desktop vs. the Command Line

• SimBiology and SBML

What Is SBML?

Importing from SBML Files

Exporting a SimBiology Model to SBML Format

• SimBiology Desktop Overview

What is the SimBiology Desktop?

Opening the Desktop

Using the Desktop Tools

Using the Desktop to Learn About the Command Line

• Understanding SimBiology Projects and Libraries

What Are SimBiology Projects?

What Are SimBiology Libraries?

• Managing SimBiology Projects and Libraries

Desktop Management and Navigation Aids

Models

Analysis Tasks

Data

Importing and Exporting Models, Tasks, and Data

Searching a Project

Generating a Report for a Project

Using Libraries

• About The Gene Regulation Model

Model Diagram

Model Reactions

Creating a SimBiology Model

Adding the Reaction for Transcription

Adding the Reaction for Translation

Adding the Reactions for Gene Regulation

Adding the Reactions for mRNA and Protein Degradation

• Simulating the Model

Properties — Alphabetical List

By Category

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

AbsoluteTolerance
Active
Amount
AmountUnits
Annotation
BoundaryCondition
BuiltInKineticLaws
BuiltInLibrary
BuiltInUnitPrefixes
BuiltInUnits
Capacity
CapacityUnits
Compartments
CompileOptions
Composition
ConstantAmount
ConstantCapacity
ConstantValue
Content
CovariateLabels
CovariateLabels (CovariateModel)
Data
DataCount
DataInfo
DataNames
DataSet
DefaultSpeciesDimension
DependentVarLabel
DependentVarUnits
DimensionalAnalysis
Dosed
DoseLabel
DoseUnits
DosingType
DurationParameterName
EliminationType
ErrorTolerance
Estimated
EventFcns
Events
Exponent
Expression (CovariateModel)
Expression (PKCovariateModel)
Expression (AbstractKineticLaw, KineticLaw)
FixedEffectDescription (CovariateModel)
FixedEffectNames (CovariateModel)
FixedEffectValues (CovariateModel)
GroupID
GroupLabel
GroupNames
HasLag
HasResponseVariable
IndependentVarLabel
IndependentVarUnits
InitialAmount
InitialAmountUnits
Inputs
Interval
KineticLaw
KineticLawName
LagParameter
LagParameterName
LogDecimation
MaxIterations
MaxStep
ModelName
Models
Multiplier
Name
Normalization
Notes
Observed
Offset
Outputs
Owner
ParameterInputFactors
ParameterNames (CovariateModel)
Parameters
ParameterVariableNames
ParameterVariables
Parent
PKCompartments
Products
RandomEffectNames (CovariateModel)
RandomState
Rate
RateUnits
RateLabel
Reactants
Reaction
ReactionRate
Reactions
RelativeTolerance
RepeatCount
Reversible
Rule
RuleType
Rules
RunInfo
RuntimeOptions
SensitivityAnalysis
SensitivityAnalysisOptions
SolverOptions
SolverType
Species
SpeciesInputFactors
SpeciesOutputs
SpeciesVariableNames
SpeciesVariables
StartTime
StatesToLog
Stoichiometry
StopTime
StopTimeType
Tag
TargetName
Trigger
Time
TimeUnits
Type
UnitConversion
UserData
UserDefinedKineticLaws
UserDefinedLibrary
UserDefinedUnitPrefixes
UserDefinedUnits
Value
ValueUnits
ZeroOrderDurationParameter

Property Reference

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