Integrated Environment

  Expected Users

  Required Software

  Optional Software

  Related Software

  Compiler Setup

  Existing Workflow in Experimental Research

  Workflow Incorporating Mathematical Modeling

  Workflow Using SimBiology Models for Mathematical Modeling

  What Is SBML?

  Importing from SBML Files

  Exporting a SimBiology Model to SBML Format

• SimBiology Desktop Overview

  Opening the Desktop

  Using the Desktop Tools

  Using the Desktop to Learn About the Command Line

  What Are SimBiology Projects?

  What Are SimBiology Libraries?

  Desktop Management and Navigation Aids

  Working with Models in the Desktop

  Working with Analysis Tasks in the Desktop

  Working with Data in the Desktop

  Importing and Exporting Models, Tasks, and Data from the Desktop

  Searching a Project from the Desktop

  Generating a Report for a Project from the Desktop

  Using Libraries from the Desktop

• About The Gene Regulation Model

  Model Reactions

  See Also

  See Also

  Typical Workflow

  See Also

  Simulating a Model

  Plotting Simulation Results

  Interpreting Simulation Results

  Configuring Stop Time and Other Simulation Settings

  Choosing a Simulation Solver

  SUNDIALS Solvers

  Stochastic Solvers

  See Also

  Overview

  Loading the Example Model

  Configuring Simulation Settings

  Simulating the Model

  Plotting Simulation Results

  Extracting Data for Analysis

  About Calculating Sensitivities

  Model Requirements for Calculating Sensitivities

  Setting SolverOptions Properties for Calculating Sensitivities

  Calculating Sensitivities of a Model and Viewing Results

  See Also

  References

  Overview

  Loading and Configuring the Model for Sensitivity Analysis

  Performing Sensitivity Analysis

  Extracting and Plotting Sensitivity Data

  About Parameter Estimation

  Estimating Parameters of a Model

  Specifying Solver Type and Options for Parameter Estimation

  See Also

  About Individual and Population Fitting

  Overview

  Loading the Example Model

  Defining Experimental Data

  Simulating the G Protein Model

  Estimating the kGd Parameter in the G Protein Model

  Simulating and Plotting Results Using the Estimated Parameter

  Estimating Other Parameters in the G Protein Model

  What Is Acceleration?

  What Simulations and Analyses Can Be Accelerated?

  When to Accelerate Simulations and Analyses

  Prerequisites for Accelerating Simulations and Analyses

  Accelerating a Simulation or Analysis

  Troubleshooting Accelerated Simulations and Analyses