chaste-sbml

chaste-sbml reads an SBML model and generates the corresponding Chaste C++ classes, allowing you to import SBML models into a Chaste simulation.

Getting started

• Installation
  • User install
  • Developer install
• First steps
  • Generate code from an SBML file
  • Selecting a model type
  • Getting the base classes
• Using generated code
  • Project layout
  • Project setup
  • Using the classes in a simulation

Tutorials

• Tutorial: Goldbeter 1991
  • 1. Get the model
  • 2. Generate the code
  • 3. Review the ODE system
  • 4. Review the SRN wrapper
  • 5. Build and run
  • Next steps
• Tutorial: Tyson-Novak 2001
  • 1. Generate the code
  • 2. Function definitions
  • 3. Events
  • 4. Cell cycle
  • 5. Build and run
  • Things to check

Reference

• Command-line options
  • Positional argument
  • General options
  • Generation options
  • Copying the base classes
  • Time units
• Anatomy of generated code
  • What gets generated
  • The class hierarchy
  • The ODE system
  • The wrapper (SRN / cell-cycle)
  • Events
  • The placeholder test
  • The base classes
• SBML feature support
  • SBML levels and packages
  • Model components
  • Rules
  • Events
  • Time and units
  • MathML
  • Explicitly unsupported constructs
  • SBML Test Suite results