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 mod to perform random graph simulations.
The newest code for the model generator mod (see http://cvs.savannah.gnu.org/viewvc/mcsim/mod/?root=mcsim) now accept the "-G" option to generate random graph from specified through a "script.txt" file.
GNU MCSim can now generate C code to work with R deSolve package.
The latest version
of the model generator "mod" can now
generate C code directly usable with the R package deSolve. Simply use the "-R" option for that.
Follow this link for a couple of examples. You need to have R and its deSolve package installed.
Version 5.5.0 also fixes a potential security problem at the installation phase
(originating from automake).
Downloading GNU MCSim
The latest version of GNU MCSim (5.5.0) can be found on the main GNU ftp server: http://ftp.gnu.org/gnu/mcsim/ (via HTTP) and ftp://ftp.gnu.org/gnu/mcsim/ (via FTP). It can also be found on the GNU mirrors; please use a mirror if possible.The gzipped tar archive 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 also be obtained on the GNU ftp mirrors and main page.
Documentation for GNU MCSim is available online, as is documentation for most GNU software. You may also find more information about GNU MCSim by running info mcsim, or by looking at /usr/share/mcsim/doc, or similar directories on your system.
Check also the User's Manual update file provided with the source code for last minute updates and tips.
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).
Versions above 5.4.0 also prefers libSBML v4.2.0 or above to be installed, but that is not needed if you do not want to read SBML model files.
The user's manual (online here) provides detailed instructions for installation for several platforms.
In addition, for Windows systems, the following instructions and associated patch may help (if anything can help).
GNU MCSim has the following mailing lists:
- bug-mcsim is used to discuss most aspects of GNU MCSim, including development and enhancement requests, as well as bug reports.
- help-mcsim is for general user help and discussion.
Security reports that should not be made immediately public can be sent directly to the maintainer. If there is no response to an urgent issue, you can escalate to the general security mailing list for advice.
Contributed material and 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.
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.)
Development of GNU MCSim, and GNU in general, is a volunteer effort, and you can contribute. For information, please read How to help GNU. If you'd like to get involved, it's a good idea to join the discussion mailing list (see above).
- For development sources, issue trackers, and other information, please see the GNU MCSim project page at savannah.gnu.org.
- GNU MCSim is currently being maintained by Frederic Y. Bois. Please use the mailing lists for contact.
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.