cdanielmachado
commented
5 years ago 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).
Greetings Daniel,
I was wondering if you could school me a bit on the specifics of --no-community-biomass, --split-pool, and --init.
As I understand it: a common biomass objective function is output during a merge and thus during simulation they will grow at the same rate; while the --no-community-biomass option allows for species growth a different rates during simulations. But then, the carveme docs it says that with the --split-pool option "...simulation results are the same...", the same as the default output, or the no-community-biomass option?
If i use --init and --split-pool, are the metabolites in the chosen medium what goes in the 'pool'?