Free Release of MediumFBAtutorial MATLAB Application

In Silico Fermentation is pleased to announce the release of MediumFBAtutorial, a free MATLAB application that provides two tutorials that demonstrate the use of our MediumFBA app for integrated medium design and flux balance analysis (FBA). Using genome-scale metabolic reconstructions from the AGORA resource, users are guided through an intuitive workflow in which they identify nutrients essential for in silico growth, use the developed media to perform FBA, and interpret the results of the FBA calculations. Each tutorial provides step-by-step instructions within the GUI to provide a totally self-contained training experience.

The first tutorial uses a metabolic reconstruction of the gut pathogen Clostridioides difficile to develop a glucose minimal medium containing essential amino acids and vitamins. The developed medium is used to perform FBA for prediction of secreted fermentation and amino acid degradation products. The second tutorial considers the medium design and FBA problems for five bacterial pathogens commonly associated with cystic fibrosis airway infections. A single glucose minimal medium that ensures monoculture growth of each pathogen is designed, and the developed medium is simulated with FBA to predict the growth rate and metabolic products of each pathogen in monoculture.

More information about MediumFBAtutorial and the freely downloadable application are available here.