Genome-scale metabolic reconstructions have emerged as powerful computational platforms for analyzing and engineering microbial metabolism. Researchers typically develop their own workflows by writing customized code around general-purpose functions available within software tools such as the Constraint-Based Reconstruction and Analysis Toolbox (COBRA). The development of effective and robust workflows can be challenging due to incompatibility between component functions, difficulty in integrating user-designed codes, and the substantial overhead associated with code development and testing. As a result, the power of metabolic modeling has been largely limited to domain experts.
To address these challenges, In Silico Fermentation has been developing a suite of free MATLAB GUI apps that enable academic researchers and industrial practitioners to quickly access the power of metabolic modeling and associated simulation methods. Starting with genome-scale metabolic reconstruction(s) of the microbial strain(s) of interest, our apps allows the user to quickly refine metabolic pathways, define medium conditions, input strain-dependent metabolic parameters, simulate strain performance, interrogate strain interactions, and design improved mutant strains. The following five research apps have been released and the six app in under development.
- MediumFBA – Integrated Medium Design and Flux Balance Analysis for Genome-Scale Metabolic Models (second release November 2025).
- 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 (second release February 2025)
- SynComSim – Metabolic Simulation of Synthetic Microbial Communities using Genome-Scale Metabolic Models (first release September 2024)
- BacMicroSim – Simulation of Bacterial Microbiomes Using Community Read Data and Genome-Scale Metabolic Models (first release September 2025)
- GEMrefine – Interactive Refinement and Analysis of Genome-Scale Metabolic Models (first release expected Fall 2026)
These apps have been designed to allow seamless integration such that available metabolic models can be rapidly used for pathway refinement, medium design, metabolite production prediction, knockout strain design, fermentation process simulation, community composition prediction, and community interaction interrogation.
Please contact us by email if you would like to learn more about these research-oriented apps.
