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 industrial 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 materials and training tools to advance applications of metabolic modeling
Founder and Principal
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 […]
March 19, 2026
In Silico Fermentation is pleased to announce our first training course focused on genome-scale metabolic reconstructions and their use for constraint-based metabolic analysis. The training focuses on developing a functional knowledge of metabolic reconstructions and more in-depth understanding of flux balance analysis (FBA) and its most important variants. Key concepts are demonstrated through computational exercises […]
January 11, 2026
In Silico Fermentation is pleased to announce the release of MediumFBAtutorial, a free MATLAB application that provides two tutorials that demonstrate the use of our MediumFBA app for integrated medium design and flux balance analysis (FBA). Using genome-scale metabolic reconstructions from the AGORA resource, users are guided through an intuitive workflow in which they identify […]
