Understanding SteadyCom/SteadierCom

[ryan-boobybiome]

I'm attempting to model community growth and individual growth/abundance for a set of models using the older SteadierCom implementation (based on some work I've been doing with designmc). My issue is that other than the example in designmc there is no documentation that I can find for the function and I'm not sure which parameters I need to modify or even exactly what each parameter does.

As a consequence I get communities where only a single bacteria appears to have any abundance. But when I modify the growth parameter the same community will have several bacteria with abundances. Likewise I may also get infeasible solutions or run into the CPLEX issue as described here.

I can also look at the exchange reactions for some metabolites of interest after optimising for community growth but again I'm unsure about the interpretation of the associated values i.e. are they uptake or secretion values?

Could you please provide some advice on using the function and interpretation of results or point me at the relevant literature.
Thanks

[cdanielmachado]

We have a new package here: https://github.com/cdanielmachado/steadiercom

The instructions are not yet super detailed. We are also working on a manuscript, that should be ready sometime soon.