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 […]

In Silico Fermentation has been developing freely downloadable MATLAB applications that streamline the utilization of microbial metabolic modeling methods. Our previous three applications, MediumFBA, InSilicoKO and STBRsim, already have over 400 downloads since the first release in February, 2024. Now we are pleased to announce the release of SynComSim, a free MATLAB application that enables […]

Last month, In Silico Fermentation released STBRsim version1.0, a freely downloadable MATLAB application for Stirred Tank BioReactor (STBR) simulation using genome-scale metabolic models. STBRsim is a GUI tool that generates dynamic predictions of extracellular variables including biomass, substrate and product concentrations and liquid/gas phase volumes for user-specified reactor conditions and liquid/gas feeding strategies. Based on […]

In Silico Fermentation has been developing freely downloadable MATLAB applications that facilitate the implementation of metabolic modeling methods. Our first two applicationsMediumFBA and InSilicoKO, already have over 300 downloads since their initial release in February, 2024. Now we are pleased to announce the release of STBRsim, a free MATLAB application that streamlines the development of […]

In Silico Fermentation is pleased to announce the release of InSilicoKO version 2.0, a freely downloadable MATLAB application for the computational design of knockout strains for metabolite overproduction based on genome-scale metabolic reconstructions. The GUI tool provides a simple and intuitive workflow that allows the user to generate reaction/gene knockouts that maximize the secretion of […]