MCSim

GNU MCSim is a suite of simulation software. It allows users to design statistical or simulation models, perform Monte Carlo simulations, and Bayesian inference through Markov chain Monte Carlo simulations. The latest version allows parallel computing of Monte Carlo or MCMC simulations.

Description

The model generator facilitates structural model definition and maintenance, while keeping execution time short. The model is coded using a simple grammar, and the generator translates it into source code for C. Starting with version 5.3.0, models coded in Systems Biology Markup Language can also be used.
The simulation engine is a set of routines that are linked to the model to produce executable code. The result is that simulations of a structural model can be run under a variety of conditions.

Internally, the software uses the GNU Scientific Library for some of its numerical calculations.

The project began in 1991 in Berkeley when Don Maszle and Frederic Y. Bois translated in C and reorganized a program that Bois had developed at Harvard for his PhD thesis. The main motive for the work was to be able to quickly develop and easily maintain physiologically based pharmacokinetic modelling models. However, the syntax was defined with enough generality that many algebraic and first-order ordinary differential equations can be solved. The ability to perform efficient Monte Carlo simulations was added early on, for the research needs of the group. The code was made freely available from a server at UC Berkeley. Discussions with Stuart Beal at University of California, San Francisco School of Pharmacy, led the team to investigate the use of Markov chain Monte Carlo techniques for PBPK models' calibration. The corresponding code was developed by Maszle, during a project in collaboration with Andrew Gelman, then professor at University of California, Berkeley Statistics Department. Additional code written by Ken Revzan allowed the definition and Bayesian calibration of hierarchical statistical models. At the time of these developments, those abilities were unique for a freely distributed, easily accessible, very powerful and versatile software. Since then the software has been consistently maintained and extended.

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, or any later version, at user option.

The C source code is provided and can be compiled on any machine with a C compiler. The GNU Scientific Library must be available also on the target platform to use a few extra distributions in statistical models. To use the SBML translation abilities, the LibSBLM library should be installed. Starting with version 6.0.0, the Sundials Cvodes integrator is also used. To take advantage of parallel computation a Message Passing Interface library must be installed.