Cain: Stochastic Simulations for Chemical Kinetics

News

August 5, 2009

Version 1.1 is released. It fixes issues with displaying online help and reading the record time from XML files.

July 29, 2009

Version 1.0 is released. It features:

Improved documentation.
Simple solvers for time inhomogeneous problems.
Histogram solvers that now record the mean and variance.
Improved job scheduling.
Improved file formats.
Refactoring to help future development.

April 23, 2009

Version 0.12 is released. I have improved the layout of the application by using splitters. I have corrected the documentation regarding the Mac OS X distribution. The MS Windows distribution now supports the MS Visual Studio 2008 compiler.

April 11, 2009

Version 0.11 is released. I have improved the user interface and the documentation. I have fixed an error in recording histogram output.

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.

Cain: Stochastic Simulations for Chemical Kinetics

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