Visualization and analysis of functional modules in biochem. networks
MonaLisa uses Petri net representation to model and analyse biochemical networks. Here, all reactions of a pathway are modeled by their metabolites and reactions. These are represetend by different kind of vertices, metabolites as circles and reactions as rectangles. The Petri net formalism offers a rich variety of mathematical anaylisis aproaches to check the model for structual faults or to identify biological modules. Furthermore, MonaLisa can visualize the computed results, so that a quick visual inspection is possible. This will help especially for handeling big models.
This is a collection of code snippets, utilities and scripts I have written over decades as a technologist. I'm releasing them here to the public in the hopes that someone will find them as useful as I have.