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, and other. 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, cluster coefficient distribution.
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Bioinformatics. 2013 Jun 1;29(11):1469-70. doi: 10.1093/bioinformatics/btt165. Epub 2013 Apr 5.
MonaLisa–visualization and analysis of functional modules in biochemical networks.
Einloft J, Ackermann J, Nöthen J, Koch I.