MonaLisa is a Petri net-based tool for modeling of biochemical networks. It comprises an editor supported by an intuitive visualization and animation, and various analysis techniques. The analysis focuses on invariant analysis, topological network analysis, knockout analysis, and other. It includes the computation of transition invariants (elementary modes), place invariants, Manatee invariants, maximal common transition sets (MCT-sets), t-clusters, minimal cut sets (MCS), degree distributions, cluster coefficient distributions, and other.
MonaLisa supports interfaces for different systems biology and graph-theoretic formats: SBML, KGML, PNT, APNN, MetaTool, and PNML.
MonaLisa was written in the Molecular Bioinformatics group of Prof. Dr. Ina Koch at Goethe University Frankfurt, Germany. Many students contributed to the current version (in temporal order): Jens Einloft, Jörg Ackermann, Joachim Nöthen, Pavel Balazki, Lilya Mirzoyan, Daniel Noll, Marcel Gehrmann, Marlena Meyer, Marius Kirchner, Lara Klemt, Tim Stadager.