Cyclone: java-based querying and computing with Pathway/Genome databases

F. L. Fevre, S. Smidtas, V. Schachter
2007 Bioinformatics  
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
more » ... n 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:
doi:10.1093/bioinformatics/btm107 pmid:17392333 fatcat:qm3z2w46rnf4leeum5f4ssqix4