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Genome-scale stoichiometric modeling of metabolism has become a standardsystems biology tool for modeling cellular physiology and growth. Extensions ofthis approach are also emerging as a valuable avenue for predicting,understanding and designing microbial communities. COMETS (Computation OfMicrobial Ecosystems in Time and Space) was initially developed as an extensionof dynamic flux balance analysis, which incorporates cellular and moleculardiffusion, enabling simulations of multiple microbial species in spatiallystructured environments. Here we describe how to best use and apply the mostrecent version of this platform, COMETS 2, which incorporates a more accuratebiophysical model of microbial biomass expansion upon growth, as well asseveral new biological simulation modules, including evolutionary dynamics andextracellular enzyme activity. COMETS 2 provides user-friendly Python andMATLAB interfaces compatible with the well-established COBRA models andmethods, and comprehensive documentation and tutorials, facilitating the use ofCOMETS for researchers at all levels of expertise with metabolic simulations.This protocol provides a detailed guideline for installing, testing andapplying COMETS 2 to different scenarios, with broad applicability to microbialcommunities across biomes and scales.

Computation Of Microbial Ecosystems in Time and Space (COMETS): An open source collaborative platform for modeling ecosystems metabolism