compuGUT: An in silico platform for simulating intestinal fermentation | Zendy

Arun S. Moorthy | Zendy; Hermann J. Eberl | Zendy

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compuGUT: An in silico platform for simulating intestinal fermentation

Author(s) -

Arun S. Moorthy,

Hermann J. Eberl

Publication year - 2017

Publication title -

softwarex

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.528

H-Index - 21

ISSN - 2352-7110

DOI - 10.1016/j.softx.2017.06.004

Subject(s) - in silico , computer science , computational biology , biology , genetics , gene

The microbiota inhabiting the colon and its effect on health is a topic of significant interest. In this paper, we describe the compuGUT — a simulation tool developed to assist in exploring interactions between intestinal microbiota and their environment. The primary numerical machinery is implemented in C, and the accessory scripts for loading and visualization are prepared in bash (LINUX) and R. SUNDIALS libraries are employed for numerical integration, and googleVis API for interactive visualization. Supplementary material includes a concise description of the underlying mathematical model, and detailed characterization of numerical errors and computing times associated with implementation parameters

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