| Cyclone: java-based querying and computing with Pathway/Genome databases. | |
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MedLine Citation:
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PMID: 17392333 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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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, Hibernate 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 INFORMATION: For download and installation instructions, tutorials, use cases and examples, see http://nemo-cyclone.sourceforge.net. |
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Authors:
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François Le Fèvre; Serge Smidtas; Vincent Schächter |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2007-03-28 |
Journal Detail:
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Title: Bioinformatics (Oxford, England) Volume: 23 ISSN: 1367-4811 ISO Abbreviation: Bioinformatics Publication Date: 2007 May |
Date Detail:
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Created Date: 2007-05-29 Completed Date: 2007-09-17 Revised Date: 2009-11-04 |
Medline Journal Info:
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Nlm Unique ID: 9808944 Medline TA: Bioinformatics Country: England |
Other Details:
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Languages: eng Pagination: 1299-300 Citation Subset: IM |
Affiliation:
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Computational Systems Biology Group, Genoscope/CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry Cedex, France. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Computational Biology Databases, Factual* Databases, Genetic* Metabolic Networks and Pathways Programming Languages* Software* |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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