newbiomassCOMETS 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 diffusion. For more information, see Harcombe et al., Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics, Cell Reports, 2014.



COMETS can be downloaded here.

Install and Run:

The instructions for installing and running COMETS are here.

User Manual:

How to start with COMETS and description of the layout and model files format is here.

Publications, Layouts and Models:

Examples of published layouts and models are here.

Software Development:

COMETS is open-source software. The code is available at: If you are interested in contributing to the development of COMETS, or have any questions about the code, please contact us: