# Links

Stochastic Simulations.

- The SBML (Systems Biology Markup Language) homepage has links to many software projects.
- Linda Petzold and her research group at UCSB (including Hong Li, Kevin Sanft, Min Roh, and Brian Drawert) study stochastic simulation methods and have developed StochKit.
- Darren Wilkinson, provides software and test models at his web site.
- DSMTS (Discrete Stochastic Models Test Suite) is a test suite in SBML format.
- SB.OS is a live DVD based on Ubuntu Linux that comes with a comprehensive list of Systems Biology Software.
- Dizzy is a chemical kinetics stochastic simulation software package written in Java.
- COPASI is a software application for simulation and analysis of biochemical networks.
- FERN (Framework for Evaluation of Reaction Networks) is an extensible and comprehensive framework for efficient simulations and analysis of chemical reaction networks written in Java.
- CellMC is an open source program generator that compiles a mesoscopic model of a biochemical reaction network, expressed as SBML, into an executable program that realizes SSA for that model; the program can then be run for any final simulation time and number of realizations.
- STOCKS is public domain (GNU GPL) software for stochastic simulations of biochemical processes.
- SimBiology provides graphical and programmatic tools for modeling, simulating, and analyzing biological systems.

Open-source software resources.

- SourceForge hosts a wealth of software projects.
- freshmeat maintains the Web's largest index of Unix and cross-platform software.

Software.

- Python is a simple, powerful, and extensible object-oriented programming language.
- The Enthought Python Distribution is a kitchen-sink-included distribution of Python.
- wxPython is a cross-platform GUI toolkit.
- Cain uses matplotlib, a 2D plotting library.
- Cain uses some icons from the Tango Desktop Project.