compuGUT: An in silico platform for simulating intestinal fermentation

Abstract

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. Keywords: Anaerobic digestion, Large intestine, Linux, Mathematical modeling, Microbiota simulation