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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2018: 0.90

SCImago Journal Rank (SJR) 2018: 0.315

Open Access
Online
ISSN
1613-4516
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Volume 13, Issue 1

Issues

PetriScape - A plugin for discrete Petri net simulations in Cytoscape

Diogo Almeida
  • Computational Biology laboratory, Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, Odense, Denmark
  • Laboratorio de Genética Celular e Molecular, Univeridade Federal de Minas Gerais. Av.Antonio Carlos 6627, Belo Horizonte, Brazil
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Vasco Azevedo
  • Laboratory for DNA Polymorphism, Federal University of Pará.Rua Augusto Correa, 01, Belém, Brazil
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Artur Silva
  • Laboratorio de Genética Celular e Molecular, Univeridade Federal de Minas Gerais. Av. Antonio Carlos 6627, Belo Horizonte, Brazil
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Jan Baumbach
  • Corresponding author
  • Computational Biology laboratory, Department of Mathematics and Computer Science, University of Southern Denmark. Campusvej 55, Odense, Denmark
  • Email
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  • De Gruyter OnlineGoogle Scholar
Published Online: 2017-04-20 | DOI: https://doi.org/10.1515/jib-2016-284

Summary

Systems biology plays a central role for biological network analysis in the post-genomic era. Cytoscape is the standard bioinformatics tool offering the community an extensible platform for computational analysis of the emerging cellular network together with experimental omics data sets. However, only few apps/plugins/tools are available for simulating network dynamics in Cytoscape 3. Many approaches of varying complexity exist but none of them have been integrated into Cytoscape as app/plugin yet. Here, we introduce PetriScape, the first Petri net simulator for Cytoscape. Although discrete Petri nets are quite simplistic models, they are capable of modeling global network properties and simulating their behaviour. In addition, they are easily understood and well visualizable. PetriScape comes with the following main functionalities: (1) import of biological networks in SBML format, (2) conversion into a Petri net, (3) visualization as Petri net, and (4) simulation and visualization of the token flow in Cytoscape. PetriScape is the first Cytoscape plugin for Petri nets. It allows a straightforward Petri net model creation, simulation and visualization with Cytoscape, providing clues about the activity of key components in biological networks.

About the article

Published Online: 2017-04-20

Published in Print: 2016-03-01


Citation Information: Journal of Integrative Bioinformatics, Volume 13, Issue 1, Pages 1–6, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2016-284.

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© 2016 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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