Journal Article

Snoopy—a unifying Petri net framework to investigate biomolecular networks

Christian Rohr, Wolfgang Marwan and Monika Heiner

in Bioinformatics

Volume 26, issue 7, pages 974-975
Published in print April 2010 | ISSN: 1367-4803
Published online February 2010 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btq050
Snoopy—a unifying Petri net framework to investigate biomolecular networks

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Summary: To investigate biomolecular networks, Snoopy provides a unifying Petri net framework comprising a family of related Petri net classes. Models can be hierarchically structured, allowing for the mastering of larger networks. To move easily between the qualitative, stochastic and continuous modelling paradigms, models can be converted into each other. We get models sharing structure, but specialized by their kinetic information. The analysis and iterative reverse engineering of biomolecular networks is supported by the simultaneous use of several Petri net classes, while the graphical user interface adapts dynamically to the active one. Built-in animation and simulation are complemented by exports to various analysis tools. Snoopy facilitates the addition of new Petri net classes thanks to its generic design.

Availability: Our tool with Petri net samples is available free of charge for non-commercial use at http://www-dssz.informatik.tu-cottbus.de/snoopy.html; supported operating systems: Mac OS X, Windows and Linux (selected distributions).

Contact: snoopy@informatik.tu-cottbus.de

Journal Article.  1227 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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