Free Release of SynComSim MATLAB Application

In Silico Fermentation has been developing freely downloadable MATLAB applications that streamline the utilization of microbial metabolic modeling methods. Our previous three applications, MediumFBA, InSilicoKO and STBRsim, already have over 400 downloads since the first release in February, 2024.

Now we are pleased to announce the release of SynComSim, a free MATLAB application that enables rapid development, simulation and analysis of synthetic communities models realizable through in vitro cell cultures. Given genome-scale metabolic reconstructions of the community strains, the GUI tool generates predictions of the community growth rate and strain abundances, nutrient uptake and product secretion rates, and metabolite crossfeeding rates. All predictions are resolved on both a community and strain-by-strain basis.

The workflow allows the definition of the growth medium (compatible with MediumFBA), the crossfed metabolites, and excluded strains to mimic strain dropout experiments. Community simulations can be performed for different combinations of the user-defined model parameters and stored for plotting and comparison using the included visualization App.

More information about SynComSim and the freely downloadable application are available here.