Free Release of STBRsim MATLAB Application

In Silico Fermentation has been developing freely downloadable MATLAB applications that facilitate the implementation of metabolic modeling methods. Our first two applicationsMediumFBA and InSilicoKO, already have over 300 downloads since their initial release in February, 2024.

Now we are pleased to announce the release of STBRsim, a free MATLAB application that streamlines the development of dynamic metabolic models for bioreactor simulation. Given a genome-scale metabolic reconstruction of the target strain, the GUI tool generates dynamic predictions of extracellular variables including biomass, substrate and product concentrations and liquid/gas phase volumes for user-specified reactor conditions and liquid/gas feeding strategies.

The workflow allows the definition of the growth medium (compatible with MediumFBA), growth-limiting substrates and secreted products along with their Michaelis-Menten uptake kinetics, bioreactor operating conditions such as multiple stages for different liquid/gas feeding policies, dissolution and mass transfer parameters for dissolved gases, and initial conditions for the extracellular variables. Dynamic 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 STBRsim and the freely downloadable application are available here.