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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:

News

May 5th, 2018 - Release of GNU MCSim version 6.0.1.

Version 6.0.1 fixes minor problems of version 6.0.0. Version 6.0.0 brought several major extensions: The Jacobian matrix of your model's derivatives can be used by the Lsodes integrator instead of numerical differentiation. The Sundials library Cvodes integrator can be called in a Integrate specification. The vector notation can now be used in input simulation files. If you use the GNU Scientific Library (recommended), the very long-period "Mersenne twister" random number generator is used. Two new distributions, Normal_cv and TruncNormal_cv, can be used to draw normal random variates with specified mean and coefficient of variation.

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:

The gzipped tar archive contains:

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

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.

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 expected later releases can make use of the Sundial's Cvodes integrator, if you install the Sundials library.

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:

Mailing lists

GNU MCSim has the following mailing lists:

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

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.

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