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 (second release May 2024).
- STBRsim – Dynamic Simulation of Stirred Tank Bioreactors Using Genome-Scale Metabolic Models (first release August 2024)
- SynComSim – Metabolic Simulation of Synthetic Microbial Communities using Genome-Scale Metabolic Models (first release anticipated October 2024)
These four applications have been designed to allow seamless integration of metabolic modeling tasks such that available metabolic models can be rapidly used for knockout strain design, fermentation process simulation and community interaction prediction.
Please contact me by email if you would like to learn more about these metabolic modeling applications.
