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    • In Silico Fermentation MATLAB Apps Reach 1000 Downloads

    We are pleased to report that our suite of free MATLAB applications that provide state-of-the-art microbial metabolic modeling and simulation tools have reached a milestone of 1,000 downloads. We develop these free apps by modifying and generalizing proprietary modeling tools we have developed for industrial clients. Our hope is that these apps will allow industrial practitioners, academic researchers, and biotechnology educators to take full advantage of the power of metabolic modeling without the need to understand the associated mathematical complexities and code implementation details.

    To date, the following apps have been released:

    • MediumFBA – Integrated Medium Design and Flux Balance Analysis for Genome-Scale Metabolic Models (first release February 2024).
    • InSilicoKO – In Silico Design of Knockout Strains for Metabolite Overproduction using Genome-Scale Metabolic Models (second release May 2024).
    • STBRsim – Dynamic Simulation of Stirred Tank Bioreactors Using Genome-Scale Metabolic Models (first release August 2024)
    • SynComSim – Metabolic Simulation of Synthetic Microbial Communities using Genome-Scale Metabolic Models (first release anticipated October 2024)
    • STBRtutorial – Understanding the Dynamic Behavior of Stirred Tank Bioreactors (first release January 2025)

    In 2025, we plan to release improved version of these five apps and to develop new apps for metabolic modeling research and education. Feel free to email us if you have any comments or suggestions about our app development program.