Representing and Comparing Metabolic Pathways as Petri Nets with MPath2PN and CoMeta

We present two tools, MPath2PN and CoMeta, which are part of an ongoing project for representing and comparing metabolic pathways as Petri Nets. MPath2PN is intended to support an automatic translation of metabolic pathways from the major biological databases into corresponding Petri nets expressed in the input formalisms for Petri net tools. CoMeta is devised to compare metabolic pathways of different organisms through their Petri net representation produced by MPath2PN. CoMeta automatically takes the data from the KEGG database and, in the comparison, it con- siders both homology of reactions and behavioural aspects of the pathways as expressed by the T-invariants of the underlying Petri nets.