Genome-scale metabolic reconstructions have been leveraged to develop numerous computational methods for microbial system analysis and design. The incorporation of selected methods within software tools such as Constraint-Based Reconstruction and Analysis Toolbox (COBRA) allows experienced users to code specialized workflows to solve research-oriented problems. However, available tools are not well suited for typical industrial practitioners who desire GUI-based software tools that are easily understood and used.
In Silico Fermentation is developing a suite of free MATLAB GUI applications that enable industrial scientists and engineers to quickly access the power of metabolic modeling and simulation tools. Starting with genome-scale metabolic reconstruction(s) of the microbial strain(s) of interest, the metabolic modeling software allows the user to quickly define medium conditions, input strain-dependent metabolic parameters, simulate strain performance, and design improved mutant strains. The following applications have been released or are under development.
- MediumFBA – Integrated Medium Design and Flux Balance Analysis for Genome-Scale Metabolic Models (first release February 2024).
- InSilicoKO – In Silico Design of Knockout Strains for Metabolite Overproduction using Genome-Scale Metabolic Models (first release March 2023).
- SynComSim – Metabolic Simulation of Synthetic Microbial Communities using Genome-Scale Metabolic Models (first release anticipated February 2024).
- STBRsim – Dynamic Simulation of Stirred Tank Bioreactors Using Genome-Scale Metabolic Models (first anticipated summer 2024).
Please contact me by email if you would like to learn more about these metabolic modeling applications.
