COMETS is a software platform for performing computer simulations of metabolism in spatially structured microbial communities. It is based on stoichiometric modeling of the genome-scale metabolic network of individual microbial species (using dynamic flux balance analysis), and on a discrete approximation of convection-diffusion equations.
The newest version of COMETS, which was developed as a partnership between researchers at Boston University, Yale University and the University of Minnesota is fully described in the following paper:
Dukovski, Bajić, Chacón, Quintin, et al.: A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS), Nature Protocols (2021) https://doi.org/10.1038/s41596-021-00593-3.
The first version of COMETS became publicly available in 2014, and was associated with the following paper: Harcombe et al., Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics, Cell Reports, 2014.