MAGMA: Microbial and Algal Growth Modeling Application

Kinetic modeling of biochemical reactions and bioreactor systems can enhance and quantify knowledge gained from cell culture experiments and has many applications in bioprocess design and optimization. The Microbial and Algal Growth Modeling Application (MAGMA) is a user-friendly MATLAB-based software for streamlining the development of kinetic models for various bioreactor systems. This study details the MAGMA workflow by demonstrating the creation of kinetic models with systems of ordinary differential equations (ODEs), model fitting by solving inverse problems, statistical evaluation of model fitting quality, and visual display of simulation results. Two case studies (microalgae growth and Rhodococcus jostii plastic fermentation) have been provided to validate MAGMA applicability. It also includes a proof-of-concept for utilizing OpenAI GPT-4o's graph interpretation capability to automate tabulation of time course culture data from figures/plots in relevant literature, which can be used to calibrate model parameters. MAGMA is open source and compiled with MATLAB Runtime.