GNU MCSim Simulation Software

New: MCSim now simulates SBML models:

Yeast glycolysis model, JDesigner view Simulated time course of the model's chemical species

Example (left) of SBML model (yeast glycolysis, renderred by JDesigner) and
GNU MCSim simulated time course of the model's chemical species (right).
This is from "GNU MCSim: Bayesian statistical inference for SBML-coded
systems biology models" published in Bioinformatics
(Bioinformatics, 1 June 2009; 25: 1453 - 1454). Supplementary material
for that work, demonstrating MCMC sampling, optimal design and multilevel
modeling, can be found here.

What is GNU MCSim?

GNU MCSim is a simulation package, written in C, which allows you to:

design your own statistical or simulation models (eventually dynamic, via ODEs),
perform Monte Carlo stochastic simulations,
do Bayesian inference through Markov Chain Monte Carlo simulations.

GNU MCSim is GNU Software (see the license below).

Browse the User's Manual online

You may want to read the User's Manual online before attempting to use GNU MCSim.
Check also the User's Manual update file provided with the source code for last minute updates and tips.

How do I get GNU MCSim?

Download version 5.3.1 of MCSim (MCSim-v5.3.1.tar.gz, 1.19 MB, 03/03/2009)

We provide a gzipped tar archive which contains:

A User's Manual (in Texinfo and HTML formats)
The ASCII source code of the Mod program (to preprocess your models)
The ASCII source code of the GNU MCSim routines (to link with your models)
Examples of model and simulation files

Older versions can be obtained here.
You can also get the latest raw source code and additional information (on how to contribute, etc.) on GNU's Savannah

Installation

To install GNU MCSim, you will need a C compiler and linker to compile the sources and obtain executables.
Versions 5.0.0 and above also requires the GNU Scientific Library (gsl) to be installed.
For Unix or Linux machines we recommend GNU gcc.
For other machines, standard C compilers should work.
The user's manual (online here) provides detailed instructions for installation for several platforms.
In addition, for Windows systems, the following patch may help.

Contacts

You can contact us by e-mail (fredomatic[on]free.fr) for more information, comments about this page, or if you need further help.

Public Lists

Three public mailing list on GNU MCSim are available. We recommend using the gmane portal which has spam control
- GNU MCSim info list (http://lists.gnu.org/archive/html/info-mcsim)
- GNU MCSim help list (http://blog.gmane.org/gmane.comp.gnu.mcsim)
- GNU MCSim bug report list (http://blog.gmane.org/gmane.comp.gnu.mcsim.bugs)

Validation report

A PDF software validation report for version 5.0.0 can be found here. (The bug with the half-normal distribution it mentions has been fixed in version 5.1.0 and later versions.)

Links

GNU MCSim-related links .

License

GNU MCSim is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.