Applying microbial systems principles to challenges ranging from renewable chemical production to microbiota-associated diseases
We are passionate about translating recent advances in microbial metabolic modeling to commercial practice. We believe that in silico modeling can accelerate innovation and expand applications of microbial technologies that benefit society.
About In Silico FermentationDevelopment and refinement of genome-scale metabolic reconstructions for in silico studies
Application of flux balance analysis and related techniques to predict growth and metabolic fluxes
Computational design of gene knockout and overexpression strains for optimized metabolite production
Dynamic metabolic modeling of fermentation processes to predict and optimize performance
Simulation of engineered and natural communities to study species interactions and collective behaviors
Development of educational and training tools to advance applications of metabolic modeling
Founder and Principal
October 3, 2026
In Silico Fermentation is pleased to announce the release of GEMrefine, a free MATLAB application that enables manual refinement and analysis of draft genome-scale metabolic reconstructions (GEMs) within a GUI environment. The main app allows the tabularization and search of all model, reactions and genes along with their relevant properties. Existing reactions and metabolites can […]
August 12, 2026
We are pleased to announce a significant update of our website. The content is more focused on our most active training and app development activities. Please check it out!
July 26, 2026
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 […]
