Comparing Petri net-based models of biological systems using Holmes

Abstract

Motivation The first and necessary step in systems approach to study biological phenomana is building a formal model. One of the possibilities is to construct a model based on Petri nets. They have an intuitive graphical representation on one hand, and on the other, can be analyzed using formal mathematical methods. Finding homologies or conserved processes playing important roles in various biological systems can be done by comparing models. The ones expressed as Petri nets are especially well-suited for such a comparison, but there is a lack of software tools for this task. Results To resolve this problem, a new analytical tool has been implemented in Holmes application and described in this paper. It offers four different comparison methods, i.e., the ones based on t-invariants, decomposition, graphlets and branching vertices. Availability and implementation Available at http://www.cs.put.poznan.pl/mradom/Holmes/holmes.html