MP-GeneticSynth: Inferring Biological Network Regulations from Time Series

Summary: MP-GeneticSynth is a Java tool for discovering the logic and regulation mechanisms responsible for observed biological dy-namics in terms of finite difference recurrent equations. The software makes use of: i) Metabolic P systems as a modeling framework, ii) an evolutionary approach to discover flux regulation functions as linear combinations of given primitive functions, iii) a suitable reformulation of the least squares method to estimate function parameters consi-dering simultaneously all the reactions involved in complex dynamics. The tool is available as a plugin for the virtual laboratory MetaPlab. It has graphical and interactive interfaces for data preparation, a priori knowledge integration, and flux regulator analysis