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PetriScape - A plugin for discrete Petri net simulations in Cytoscape

Almeida, Diogo ; Azevedo, Vasco ; Silva, Artur ; Baumbach, Jan

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)

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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.

Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Almeida, Diogo ; Azevedo, Vasco ; Silva, Artur ; Baumbach, Jan  (2016)  PetriScape - A plugin for discrete Petri net simulations in Cytoscape. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 13(1), 2016

Online-Journal: http://journal.imbio.de/article.php?aid=284
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2016/5423

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