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Article


Title

Comparing Petri net-based models of biological systems using Holmes

Authors

[ 1 ] Instytut Informatyki, Wydział Informatyki i Telekomunikacji, Politechnika Poznańska | [ P ] employee

Scientific discipline (Law 2.0)

[2.3] Information and communication technology

Year of publication

2022

Published in

Bioinformatics

Journal year: 2022 | Journal volume: vol. 38 | Journal number: iss. 19

Article type

scientific article

Publication language

english

Abstract

EN 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.

Date of online publication

17.08.2022

Pages (from - to)

4652 - 4653

DOI

10.1093/bioinformatics/btac540

URL

https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btac540/6670618?redirectedFrom=fulltext

Ministry points / journal

200.0

Impact Factor

6.931 [List 2021]

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