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 provides the tabularization and search of all metabolites, reactions and genes along with their associated properties. Existing reaction and metabolite properties […]

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!

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 […]

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 […]

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 […]

We are pleased to announce the free release of MediumFBA version 2.0, a a MATLAB application that integrates the medium design and flux balance analysis (FBA) problems to allow more efficient analysis of metabolic models. Originally released in February 2024, MediumFBA generates growth media that ensure monoculture growth of all included strains, where the metabolic […]

In Silico Fermentation has been developing freely downloadable MATLAB applications that streamline the utilization of microbial metabolic modeling methods. To date, we have released four research oriented apps (MediumFBA, InSilicoKO, STBRsim, SynComSim), and one educationally focused app (STBRtutorial). Now we are pleased to announce the release of BacMicroSim, a free MATLAB application that enables rapid […]

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 […]

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 500 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 […]

In Silico Fermentation is pleased to announce the release of STBRtutorial, a free MATLAB application that provides two step-by-step tutorials that demonstrate how operating policies affect stirred tank bioreactor (STBR) dynamic behavior. Using a simplified metabolic model of Escherichia coli central metabolism, students are guided through an intuitive workflow in which they consider important aspects […]