Comparing Petri net-based models of biological systems using Holmes
Author:
Szawulak Bartłomiej1ORCID,
Radom Marcin12ORCID,
Formanowicz Piotr1ORCID
Affiliation:
1. Institute of Computing Science, Poznan University of Technology , Poznan 60-965, Poland
2. Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan 61-704, Poland
Abstract
Abstract
Motivation
The first and necessary step in systems approach to study biological phenomena 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 article. 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
Supplementary information
Supplementary data are available at Bioinformatics online.
Funder
Poznan University of Technology
Publisher
Oxford University Press (OUP)
Subject
Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability
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