COMETS is a software platform for performing computer simulations of 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. COMETS is built and maintained by the Daniel Segre Lab at Boston University.
Documentation on how to install and use COMETS is found at comets-manual.readthedocs.io.
COMETS can be downloaded from www.bu.edu/segrelab/comets/
We have developed both a Matlab and a python toolbox to interface the Comets software. How to use these toolboxes are described in the documentation.
- Matlab toolbox: github.com/segrelab/comets-toolbox
- Python toolbox: github.com/djbajic/COMETS-Python-Toolbox
If you use COMETS in you scientific work, please cite:
Harcombe, W. R., Riehl, W. J., Dukovski, I., Granger, B. R., Betts, A., Lang, A. H., Bonilla, G., Kar, A., Mehta, M., Marx, C. J. & Segré, D (2014). Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell reports, 7(4), 1104-1115.
Contributions are welcome and appreciated. Questions and discussions can be raised on Gitter. Issues should be discussed in this forum before they are raised on GitHub. For other questions contact us on email comets@bu.edu.