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

Reference9 articles.

1. A graph distance metric based on the maximal common subgraph;Bunke;Pattern Recogn. Lett,1998

2. On functional module detection in metabolic networks;Koch;Metabolites,2013

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3