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Learn more about SimBiology
• Getting Started Guide
• Introduction
• SimBiology Overview
Features
Integrated Environment
Expected Users
Required Software
Optional Software
Related Software
• 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
• Getting Started Using the SimBiology Desktop
• 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
• Getting Started Using the Command Line
• 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
See Also
• Simulating the Model with a Stochastic Solver
More Examples of Using the Command Line
• User's Guide
• Modeling
• What is a Model?
• Model Modifiers
• Representing a Model and Model Modifiers in SimBiology
• Example - Creating A Model That Changes a Species Amount Using an Event
• Example - Creating A Model That Changes a Parameter Value Using a Variant
• Example - Creating A Model That Uses a User-Defined Function in an Expression
• Structural Analysis
Overview of Structural Analysis
• Verifying a Model
Example - Verifying a Model
• Determining Conserved Moieties
Example - Determining Conserved Moieties
• Determining the Adjacency Matrix for a Model
• Determining the Stoichiometry Matrix for a Model
• Simulation and Analysis
• Overview of Simulation and Analysis
• Simulating Models
• Example - Simulating a Model and Viewing Results
• Calculating Sensitivities
• Example - Calculating Sensitivities
• Estimating Parameters
• Example - Estimating Parameters Using sbioparamestim
• Accelerating Model Simulations and Analyses
• Pharmacokinetic Modeling
• Pharmacokinetic Modeling Functionality
• Importing Data - Supported Files and Data Types
• Importing Data
• Creating Pharmacokinetic Models
• Parameter Fitting in Pharmacokinetic Models
• Fitting Pharmacokinetic Model Parameters
• Creating Reaction Rates
• Defining Reaction Rates with Mass Action Kinetics
• Defining Reaction Rates with Enzyme Kinetics
• Creating Rate Rules
Using Rate Rules When the Rate of Change Is Constant
Using Rate Rules When the Rate of Change Is Exponential
Using Rate Rules When the Rate of Change Is Determined by Another Species
Using Rate Rules To Express Differential Rate Equations as Rules
• Models Used in Examples
• Minimal Cascade Model for a Mitotic Oscillator
• Model of the Yeast Heterotrimeric G Protein Cycle
• Model of M-Phase Control in Xenopus Oocyte Extracts
• Method Reference
Objects
Abstract Kinetic Laws
Compartments
Configuration Sets
Covariate Analysis
Events
Kinetic Laws
Parameters
Pharmacokinetic Modeling
PKCovariate Analysis
Reactions
RepeatDose
Root
Rules
ScheduleDose
SimData
Species
Units and Unit Prefixes
Variants
• Using Object Methods
• Property Reference
Abstract Kinetic Law
CovariateModel
NMFileDef
PKCompartment
PKData
PKCovariateModel
PKModelDesign
PKModelMap
Unit
Unit Prefix
Variant
• Using Object Properties
• Functions
Examples
• Release Notes
Symbols 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
By Category
Alphabetical List