Cyclone

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The Group

The Cyclone Group is an informal group of people working on and developing the Cyclone Package. The current set of members is listed below with some of their notable contributions.

Francois LE FEVRE Original developments of the main application, integration of useful libraries such as hibernate, jaxb, hyperjaxb, javadoc, log4J, global support. Biocyc and Cyclone Guru.
Serge SMIDTAS Original developments of the import/export to Biocyc function, standalone application, rev. engineering, logo, documentation, website, publication.
Maxime DUROT Development of parts not included in the distributed version of Cyclone (CPM models)	Benjamin PINAUD Beta test & Web services (in development).	Mathias HEINIG Uses TutorialEx5()
Vincent SCHACHTER Comments and suggestions along the whole development of the project.

History

Cyclone has been written by the Genoscope team called NEMO: NEtwork MOdeling Team for use in its projects but it has become so popular that many have asked us to publish it (Biocyc Genova Meeting). The Cyclone software was inspired by BioCyc , Javacyc and aMaze.
We wanted to make some changes, updates and use the power of object oriented programming, but Biocyc was implemented in Lisp. So Cyclone started out as just a Java API of Biocyc, originally called HyperCyc then OoCyc. Along the way, it has had numerous cleanups and other modifications, a process simplified by the elegance of Java language.
In 2004, the first version was running and then several stable-yet-pre-1.0 versions were released. Then the project continued to mature, and in 2006 the project became Open Source. We are proud now to present you the best version of Cyclone ever released. Today, a small community of bioinformattians is developing Cyclone.

Future work

Cyclone is an Open Source project. So any future development depends on the contributions that will be made by its user community. Certainly working patches have greater chances to become implemented quickly than feature requests, but please do not hesitate to submit you suggestions. Some things we're thinking about include a KeggClone, a more developed Graph and Cluster Toolbox for Cyclone and a GenoLink extension.
Export Biocyc data into Biopax Level-2 and 3.
Improve translation scheme between FRS and Java classes, map complete inheritance hierarchy, generate associations directly instead of using Ids, cardinality constraints.
Software platform dedicated to multi-CBM management: Basic constraint-based model management, representation of sets of environments, representation of perturbation sets, generation of corresponding models, pluggable analysis modules (topological analyses, phenotype predictions...).

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