| MCSim | |
| Logo Size: | 100px |
| Latest Release Version: | 6.2.0 |
| Programming Language: | C |
| Website: | https://www.gnu.org/software/mcsim |
GNU MCSim is a suite of simulation software. It allows one to design one's own statistical or simulation models,perform Monte Carlo simulations, and Bayesian inference through (tempered) Markov chain Monte Carlo simulations. The latest version allows parallel computing of Monte Carlo or MCMC simulations.
GNU MCSim is a simulation and statistical inference tool for algebraic or differential equation systems, optimized for performing Monte Carlo analysis. The software comprises a model generator and a simulation engine:
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 primary motivation for the work was to be able to quickly develop and easily maintain PBPK models. However, the syntax was defined with enough generality that many algebraic and first-order ordinary differential equations can be solved. The capability 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 UCSF 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 UC Berkeley Statistics Department. Additional code written by Ken Revzan allowed the definition and Bayesian calibration of hierarchical (multilevel) statistical models. At the time of these developments (around 1996) those capabilities 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 of the License, or (at your option) any later version.
The C source code is provided and can be compiled on any machine with a C compiler. The GNU Scientific Library needs to be also available on the target platform to use a few extra distributions in statistical models. To take advantage of the SBML translation capabilities, 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 (from version 6.2.0 on) a MPI library needs to be installed.
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