RT Journal Article
SR Electronic
T1 Compartmental Modeling Software: a fast, discrete stochastic framework for biochemical and epidemiological simulation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 609172
DO 10.1101/609172
A1 Christopher W. Lorton
A1 Joshua L. Proctor
A1 Min K. Roh
A1 Philip A. Welkhoff
YR 2019
UL http://biorxiv.org/content/early/2019/04/19/609172.abstract
AB The compartmental modeling software (CMS) is an open source computational framework that can simulate discrete, stochastic reaction models which are often utilized to describe complex systems from epidemiology and systems biology. In this article, we report the computational requirements, the novel input model language, the available numerical solvers, and the output file format for CMS. In addition, the CMS code repository also includes a library of example model files, unit and regression tests, and documentation. Two examples, one from systems biology and the other from computational epidemiology, are included that highlight the functionality of CMS. We believe the creation of computational frameworks such as CMS will advance our scientific understanding of complex systems as well as encourage collaborative efforts for code development and knowledge sharing.