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Bioinformatics Advance Access published online on March 28, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm107
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Cyclone : Java-based querying and computing with Pathway Genome Databases

François Le Fèvre , Serge Smidtas and Vincent Schächter

Computational Systems Biology Group, Genoscope/CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry Cedex, France.

To whom correspondence should be addressed. Vincent Schächter, E-mail: cyclone{at}genoscope.cns.fr


  Abstract

Summary: Cyclone aims at facilitating the use of BioCyc, a collection of Pathway/Genome Databases (PGDBs). Cyclone provides a fully extensible Java Object API to analyze and visualize these data. Cyclone can read and write PGDBs, and can write its own data in the CycloneML format. This format is automatically generated from the BioCyc ontology by Cyclone itself, ensuring continued compatibility. Cyclone objects can also be stored in a relational database CycloneDB. Queries can be written in SQL, and in an intuitive and concise object-oriented query language, HQL. In addition, Cyclone interfaces easily with Java software including the Eclipse IDE for HQL edition, the Jung API for graph algorithms or Cytoscape for graph visualization.

Availability: Cyclone is freely available under an open source license at: http://sourceforge.net/projects/nemo-cyclone

Supplementary data: for download and installation instructions, tutorials, use cases and examples, see http://nemo-cyclone.sourceforge.net

Associate Editor: Prof. Alfonso Valencia

Received on November 3, 2006; revised on March 12, 2007; accepted on March 13, 2007

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