--split-pool (not an issue, just a question) about carveme

[cdanielmachado]

Hi, sure no problem.

The --no-community-biomass will not create a common biomass reaction that sums the growth of all the species. The user must then decide how to formulate an objective function for the community.

The split-pool option creates an extracellular compartment for each species, which is connected to the common pool (instead of than transporting compounds directly between the intracellular environment and the common pool). This doesn't really change anything simulation-wise, it just adds an additional layer of exchange reactions that facilitate tracking of the cross-feeding interactions.

The --init option initializes the compounds in the common pool (i.e. what is available to everyone).