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    • In Silico Fermentation MATLAB Apps Reach 2500 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 has surpassed 2500 downloads. 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 grapple with 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 (second release November 2025; 424 downloads).
    • InSilicoKO – In Silico Design of Knockout Strains for Metabolite Overproduction using Genome-Scale Metabolic Models (second release May 2024; 346 downloads).
    • STBRsim – Dynamic Simulation of Stirred Tank Bioreactors using Genome-Scale Metabolic Models (second release February 2025; 483 downloads)
    • SynComSim – Metabolic Simulation of Synthetic Microbial Communities using Genome-Scale Metabolic Models (first release September 2024; 346 downloads)
    • BacMicroSim – Metabolic Simulation of Bacterial Microbiomes using Genome-Scale Metabolic Models (first release September 2025; 429 downloads)
    • STBRtutorial – Understanding the Dynamic Behavior of Stirred Tank Bioreactors (first release January 2025; 370 downloads)
    • MediumFBAtutorial – Understanding In Silico Medium Design and Flux Balance Analysis (first release January 2026; 257 downloads)

    Next, we plan to release improved version of selected apps and to develop two new apps for genome-scale metabolic model refinement and fermentation data integration into stirred tank bioreactor models. Feel free to email us if you have any comments or suggestions about our app development program.