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 […]
Early this month, In Silico Fermentation released MediumFBA version1.0, a freely downloadable MATLAB application for genome-scale metabolic modeling. MediumFBA is a GUI tool which generates growth media that ensure monoculture growth of all strains through a simple and intuitive workflow. We are gratified that MediumFBA already has over 60 downloads. Based on initial user feedback, […]
In Silico Fermentation is pleased to announce the release of MediumFBA version1.0, a freely downloadable MATLAB application that integrates the medium design and flux balance analysis (FBA) problems to facilitate in silico metabolic analyses. MediumFBA is a GUI tool which generates growth media that ensure monoculture growth of all strains where the metabolic properties of […]
Flux Balance Analysis (FBA) has proven to be a very valuable tool for predicting microbial metabolism. However, FBA neglects dynamic process behavior and does not provide predictions of extracellular variables. Both these capabilities are critical for fermentation process modeling. Dynamic flux balance modeling is a powerful extension that combines steady-state cell metabolism with extracellular dynamics […]
Microbiota metabolic modeling is a powerful complementary tool to experimentation for interrogating microbial communities involved in human disease. One of my recent review papers overviews some of the capabilities, accomplishments and challenges associated with bacterial community modeling. In Silico Fermentation offers metabolic modeling tools to simulate, analyze and manipulate host-associated microbiota involved in human health […]
Fermentation modeling is no simple task. Key to any successful project is to determine the desired level of modeling detail, selecting an appropriate model structure, executing well-designed experiments, performing model parameter estimation using the available data, conducting model validation studies, deploying the model for real-time use, training operations staff, and maintaining the model application. It […]
In Silico Fermentation was created to support the biotechnology and biomedical industries by providing consulting services, applied research, and educational training on microbial systems and processes. The company was founded by Dr. Mike Henson following his 28-year academic career as a vehicle to translate recent advances in metabolic modeling to industrial practice. A novel computational […]
