Frequently Asked Questions

  1. General Questions

1.1 What language is COMETS written in? COMETS is written in Java.

1.2 What can COMETS do? We use COMETS to simulate complex microbial ecosystems. The simulations are based on models of microbial metabolism, and are fully spatio-temporal.

1.3 How do I run COMETS? Once COMETS is installed, it can be started from command line with:

comets_scr comets_script.txt

where comets_script.txt is a custom script listing the input files. It can also be started using the Matlab or Python toolbox. Double click on the desktop icon will start the COMETS GUI. For more information please see the User Manual:

  1. Installation

2.1 What do I need to install, before I install COMETS? Before you install COMETS, you need to have Java and the optimizer Gurobi installed as well. You can install Java from here: and Gurobi from here:

2.2 How do I install COMETS? Please read the installation instructions.

2.3 How can I uninstall COMETS? Run the uninstaller from the directory where COMETS was installed. On Windows, uninstall it from the Control Panel.

2.4 How can I install the toolboxes? Please read the installation instructions.

  1. Applications

3.1 Where should I start? Where can I find example runs? Example runs can be found here:

3.2 How long is a COMETS run? It depends on the complexity of the spatial layout. A single step of a typical E. coli model may take milliseconds. A complex run of a layout with linear size of several centimeters, simulated time of several hours, consisting of several genome scale models may take days to finish.

3.3 How many species can I run? It depends on your resources, most importantly the total available memory. Tens of species on a ten by ten spatial grid with several hours of simulated time will take several days to finish.

3.4 How big system can I simulate? Similar to question 3.3, depends on your resources. Five to ten species running for several simulated hours on a four by four centimeters (400 by 400 spatial grid points) simulated layout will take several days to finish.

3.5 What can the Matlab and Python toolboxes do? The Matlab and Python toolboxes are convenient interfaces to the COMETS input/output. Using the toolboxes you can prepare the input files and visualize the results.

3.6 Where can I find examples of COMETS simulations using the toolboxes? Example runs can be found here:

  1. Troubleshooting

4.1 Something went wrong, where can I find troubleshooting help? The User Manual is a good place to look for the answers: Also, you can ask us COMETS related questions in the COMETS forum: