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Information


Unique identifier OMICS_21412
Name GNU MCSim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 5.6.6
Stability Stable
Maintained Yes

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http://ftp.gnu.org/gnu/mcsim/

GNU MCSim citations

 (6)
library_books

Multi level and hybrid modelling approaches for systems biology

2017
Comput Struct Biotechnol J
PMCID: 5565741
PMID: 28855977
DOI: 10.1016/j.csbj.2017.07.005

[…] are pretty effective for inferring the parameter values of complex models, in particular when ODEs are used as formalism, which is often the case in systems biology studies. In , the authors present GNU MCSim, a numerical simulation tool able to perform Bayesian statistical inference for algebraic or differential equation systems. This tool supports different kinds of simulations, including simpl […]

library_books

High Throughput Analysis of Ovarian Cycle Disruption by Mixtures of Aromatase Inhibitors

2017
Environ Health Perspect
PMCID: 5744692
PMID: 28886606
DOI: 10.1289/EHP742

[…] he prediction of oral bioavailability (F) and the total body clearance rate constant (Ke), respectively (see Supplemental Material, “PK modules of ACD/Labs”; see also Table S1 and Figures S2 and S3). GNU MCSim v5.6.5 (www.gnu.org/software/mcsim) () was used to build the ovarian cycle model. R v3.1.1 (R Development Core Team) with the parallel, deSolve, and EnvStats packages was used for database p […]

library_books

An Individual Based Model of Zebrafish Population Dynamics Accounting for Energy Dynamics

2015
PLoS One
PMCID: 4418570
PMID: 25938409
DOI: 10.1371/journal.pone.0125841

[…] DEB model parameters calibrations were performed using GNU MCSim software [], which is a program for the statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo (MCMC). Details are provided in the supporting information (). The pa […]

library_books

Hamiltonian Monte Carlo methods for efficient parameter estimation in steady state dynamical systems

2014
BMC Bioinformatics
PMCID: 4262080
PMID: 25066046
DOI: 10.1186/1471-2105-15-253

[…] -Hastings [, ] algorithms are among the most popular choices for this task (see e.g. [, ]). Variants of these core algorithms are also widely available in parameter estimation software packages, e.g. GNU MCSIM[], or the MCMCSTAT MATLAB toolbox [].The speed of convergence of the Markov chain is crucial for the efficiency of the MCMC approach. Finding a good tuning of the Markov chain’s transition d […]

library_books

A Computational Model to Predict Rat Ovarian Steroid Secretion from In Vitro Experiments with Endocrine Disruptors

2013
PLoS One
PMCID: 3543310
PMID: 23326527
DOI: 10.1371/journal.pone.0053891

[…] Cell Designer 4.2 was used to produce . Model simulations, MCMC simulations for model calibration, and flux analyses were performed with GNU MCSim v5.4.0 . Statistical analyses and plots were performed with R, version 2.14.0 . […]

call_split

A Mechanistic Modeling Framework for Predicting Metabolic Interactions in Complex Mixtures

2011
Environ Health Perspect
PMCID: 3261979
PMID: 21835728
DOI: 10.1289/ehp.1103510
call_split See protocol

[…] ns describing the joint transport and metabolism of the four substances (“global model,” in the following) was automatically generated from the individual SBML metabolic pathway files and compiled by GNU MCSim (version 5.3.1; http://www.gnu.org/software/mcsim/). The transport terms, based on the PBPK template presented above, were generated for each chemical species placed outside the liver cell c […]

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