GNU MCSim Simulation Software

News: GNU MCSim version 5.4.0 is now available.
It is distributed under GPL version 3.

Highlight: A public domain generic PBPK model developed in GNU MCSim:

Schematic representation of a PBPK model for a woman.
The various organs or tissues are linked by blood flow. The parameters involved are
compartment volumes, blood flows, tissue affinity constants (or partition coefficients),
tissue affinity constants (or partition coefficients), and specific absorption, diffusion, metabolic,
and excretion rate constants. The whole life of the woman can be described, with time varying parameters.
The model is not specific of a particular chemical.
The GNU MCSim code for that model is freely available here.
(A cheap male version here...)

Variant PBPK model for a pregant woman and fetus:

Generic PBPK model for a pregnant woman

Gestation and lactation periods are adjustable and can be freely programmed.
The model is not specific of a particular chemical.
Get the GNU MCSim code for the pregant model 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 5.4.0 of MCSim (mcsim-5.4.0.tar.gz, 1.8 MB, 29/01/2011)

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. For any machine we recommend the GNU gcc compiler, but standard C compilers should also work.
Versions 5.0.0 up to 5.3.1 required GNU Scientific Library (gsl) to be installed. With version 5.4.0, GNU gsl becomes optional (but recommended).
Version 5.4.0 also prefers libSBML v4.2.0 or above to be installed.
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 (fbois[on]member.fsf.org) 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 and applications

GNU MCSim-related links.

Supplementary material for the article "GNU MCSim: Bayesian statistical inference for SBML-coded systems biology models" Bioinformatics, 1 June 2009; 25: 1453 - 1454. That paper demonstrates the application of GNU MCSim MCMC sampling, optimal design and multilevel modeling to SBML models.

Supplementary material containing all model and input files for predicting interactions between benzene, toluene, ethylbenzene and xylene via PBPK and systems biology coupling.

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 3 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.