News | Downloading GNU MCSim | Documentation | Citation | Installation | Mailing lists | Contributed material and related links | Getting involved | Licensing

GNU MCSim

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

• design and run your own statistical or simulation models (using algebraic or differential equations),
• perform Monte Carlo stochastic simulations,
• do Bayesian inference through Markov Chain Monte Carlo simulations,
• formally optimize experimental designs.

News

January 8th, 2024 - GNU MCSim's future.

GNU MCSim is facing stiff competition from software like the R package Nimble or Stan. They offer much more flexibility for defining statistical models. We recommend that you check them. Nimble is faster (in our experience) for differential equation models. Both are pretty cool pieces of software. See this preprint and that preprint for extensive examples of simulations and inference for differential equation models with Nimble.

June 3rd, 2020 - Release of GNU MCSim version 6.2.0.

Version 6.2.0 offers various extensions, but most notably parallelization of Monte Carlo, SetPoints and MCMC simulations, if you have a multi-processor machine and MPI installed.

Downloading GNU MCSim

The latest version of GNU MCSim (and older versions) can be found on any GNU mirror.

You can also download it from the main GNU ftp server:

• via HTTP at http://ftp.gnu.org/gnu/mcsim/
• via FTP at ftp://ftp.gnu.org/gnu/mcsim/.

The gzipped tar archive contains:

• A User's Manual (in Texinfo, pdf 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

GNU MCSim development is hosted on savannah.gnu.org. See the MCSim project page on Savannah, where the latest development sources are publicly available.

Verifying GNU MCSim Signature

To verify the signature of the GNU MCSim tarball, please download both the mcsim-X.Y.Z.tar.gz and mcsim-X.Y.Z.tar.gz.sig files. The key used to sign the official releases can be found here.

The signature can be verified with the following steps:

gpg --import mcsim-keyring
gpg --verify mcsim-X.Y.Z.tar.gz.sig

Documentation

The User's manual 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.

Your can download a PDF version of the manual by clicking here.

Dr. Nan-Hung Hsieh (at Texas A&M) contributed a series of nice tutorial slides (PDF here) for GNU MCSim.

Citation

To cite GNU MCSim in publications you should refer to this page or to: Bois F., 2009, GNU MCSim: Bayesian statistical inference for SBML-coded systems biology models Bioinformatics, 25:1453-1454, doi: 10.1093/bioinformatics/btp162.

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, and its companion gslcblas) 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.

Version 6.0.0 and later releases can make use of the Sundial's CVODES integrator, if you install the CVODES library. You should use version 2.7.0 of that library. Later versions have restructured their files and will probably not work. We provide CVODES version 2.7.0 here. It is also distributed by Ubuntu (as of March 11, 2020), or you can fetch it from the archives of the Sundials web site.

Version 6.2.0 and later releases can take advantage of multi-processors machines to run parallel simulations. You need to install a MPI library (for example from the Open MPI project).

The user's manual (online here) provides detailed instructions for installation for several platforms.

The basic tools needed to build and run GNU MCSim are not available to most users of Windows systems. At least two simple options exists for them:

• The R software (http://www.r-project.org/), installed together with Rtools (this requires administrator's rights), can compile and run GNU MCSim models.

  Follow this link to download the corresponding scripts, code, and README detailed instructions file.

• Pr. W. Chiu, of Texas A&M, proposes an alternative using minGW. It requires no administrator's rights. However, only 32 bits code is generated (it is at bit slower).

  Follow this link to download the detailed instructions file.

Mailing lists

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.

Announcements about GNU MCSim and most other GNU software are made on info-gnu (archive). See also info-mcsim.

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.

You can also look at the same lists, GNU MCSim help, and GNU MCSim bug report, on the gmane portal which has spam control.

Contributed material and related links

• GNU MCSim older news

• 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. See the article "A mechanistic modeling framework for predicting metabolic interactions in complex mixtures", Environmental Health Perspectives, 2011; 119:1712-1718.

• Supplementary material containing all model and input files for simulated tempering demonstrations (2019).

• Report describing the OpenCAT model (PBPK model with multi-compartment gut) (2020).

• 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.)

• A Debian package of version 5.4.0, prepared by Bill Harris (mcsim_5.4.0-1_amd64.deb, 2.7 MB, 25/02/2012).

• A nice quick reference card, again by Bill.

Getting involved

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).

Development

For development sources, issue trackers, and other information, please see the GNU MCSim project page at savannah.gnu.org.

Maintainer

GNU MCSim is currently being maintained by Frederic Y. Bois. Please use the mailing lists for contact.

Licensing

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.