Cain: Stochastic Simulations for Chemical Kinetics

News

September 27, 2011

Version 1.9 is released. It features:

Fixes for inhomogeneous models.
Added documentation.

September 5, 2011

Version 1.8 is released. It features:

Improved export of time series data.
Examples from "Stochastic Approaches for Systems Biology."

June 24, 2011

Version 1.7 is released. It features:

Re-organization of the source code.
Bug fixes in the tau-leaping solver.
Improved handling of SBML files.

December 20, 2010

Version 1.6 is released. It features:

Significance testing for transient solutions.
Improved handling of SBML files.
Examples from the DSMTS in the documentation.

September 25, 2010

Version 1.5 is released. It features:

Support for events.
Expanded documentation.
Bug fixes.

Introduction

Cain performs stochastic and deterministic simulations of chemical reactions. It can spawn multiple simulation processes to utilize multi-core computers. It stores models, simulation parameters, and simulation results in an XML format. In addition, SBML models can be imported and exported. The models and simulation parameters can be read from input files or edited within the program.

The GUI (Graphical User Interface) shown below is written in Python and uses the wxPython toolkit. The solvers are implemented as command line executables, written in C++, which are driven by Cain. This makes it easy to launch batch jobs. It also simplifies the process of adding new solvers. Cain offers a variety of solvers:

Gillespie's direct method.
Gillespie's first reaction method.
Gibson and Bruck's next reaction method.
Tau-leaping.
Hybrid direct/tau-leaping.
ODE integration.

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.
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.

http://www.its.caltech.edu/~sean/,

/ Last Modified: June 24, 2011