Abstract
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.
C. W. Lorton, J. L. Proctor and M. K. Roh—Co-first author.
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References
CMS Documentation. http://idmod.org/docs/cms/
CMS Repository. https://github.com/InstituteforDiseaseModeling/IDM-CMS
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Acknowledgements
JLP, MKR, CWL, and PW would like to thank Bill and Melinda Gates for their active support of the Institute for Disease Modeling and their sponsorship through the Global Good Fund. The authors would also like to thank Mandy Izzo for her assistance illustrating Fig. 1.
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Lorton, C.W., Proctor, J.L., Roh, M.K., Welkhoff, P.A. (2019). Compartmental Modeling Software: A Fast, Discrete Stochastic Framework for Biochemical and Epidemiological Simulation. In: Bortolussi, L., Sanguinetti, G. (eds) Computational Methods in Systems Biology. CMSB 2019. Lecture Notes in Computer Science(), vol 11773. Springer, Cham. https://doi.org/10.1007/978-3-030-31304-3_18
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