MonaLisa

MonaLisa is a Petri net based tool for the analysis of biochemical networks. It comprises an editor supported by an intuitive visualization and animation, and various analysis techniques, focusing on network decomposition, knockout analysis. It includes the computation of elementary modes (T-invariants), P-invariants, Maximal common transition sets (MCT-sets), T-clusters, minimal cut sets (MCS), degree distribution and, cluster coefficient distribution.

MonaLisa supports interfaces for different systems biology and graph-theoretic formats SBML, KGML, PNT, APNN, MetaTool, and PNML.