Free release of STBRsim Version 2.0
In Silico Fermentation is pleased to announce the free release of STBRsim Version 2.0, a MATLAB application that streamlines the development of dynamic metabolic models for bioreactor simulation.
Given a genome-scale metabolic model of the target strain, the App allows the definition of the growth medium, growth-limiting substrates and secreted products along with their uptake kinetics, growth inhibition effects involving extracellular substrates and products, bioreactor operating conditions including multiple stages for different liquid/gas feeding policies, dissolution and mass transfer parameters for dissolved gases, and initial conditions for extracellular variables. The App generates time-resolved predictions of biomass, substrate and product concentrations, liquid/gas phase volumes, and intracellular-extracellular transport fluxes. Dynamic simulations can be performed for different combinations of the user-defined model parameters and stored for plotting and comparison using an included visualization App.
STBRsim Version 2.0 offers several improvements over our most recent release. More information about the App and freely downloaded files are available here.
