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Biological points that Cyclone addresses
- Systems Biology.
Helps to understand how the whole cell works. Easy to manipulate large data sets and models.
- Computational Biology, Bioinformatics.
Java API allows users to run complex algorithms such as one coming from graph theory. Rank, cluster, find paths and flow distribution, compare results with randomly generated networks and make statistics, visualize graphs, search for subnetworks, analyse the topical updated data live, directly contained into Biocyc (with the help of Jung/Cytoscape).
- Biological annotation.
Helps to annotate the roles of the constituents of the system. Automates repetitive annotation tasks. Modify or implement new housekeeping functions for a PGDB add / update data from a given annotation database (e.g. multifun, cellular localization of gene products, Pubmed links...) delete / annotate pathways as part of a curation process keep that information even after annotation or BioCyc updates.

Scientific communications
Bioinformatics: Application notes.
ISMB 2006: Fortaleza, Brazil. May 8, 2006 Demo Submission Deadline
Pathway Tools User Group Meeting: Geneva, Switzerland. December 1, 2005 (PPT)

Projects that use Cyclone
Mage: Magnifying Genomes, Microbial genome Annotation System - AGC, Genoscope
MicroCyc: Microbial Genome Biochemical Pathways - AGC, Genoscope

Alternatives to query Biocyc
Representation SystemFRSRelational model
StorageOcelot, mySQL, OraclemySQLmySQL, Oracle, Sybase, pgSQL ...(more)
QueryLisp, (SQL)SQLOQL, (SQL), Java-Criteria
APILisp, Perl, Java-Java
Biocyc coverageFullPartialFull
ImportOcelot, BiocycSQLBiocyc, XML
ExportOcelotBiocyc, XML, GraphML, SIF

Alternatives to { Biocyc + Cyclone + Cytoscape }
Biocyc + Cyclone + CytoscapeaMazeSigPathReactomePatikaPathCaseIngenuity
Representation SystemFRS, XSDGeneralized Entity RelationshipXSD
StoragemySQL, Oracle, Sybase, pgSQL ...(more)JDO-compliantmySQL
InterfacePathwayTool Application, Web, Eclipse(JBoss)EclipseJava Application, WebWeb
Query languageOQL, (SQL), Java-CriteriaIglooQL(object)?PathfinderFields, Neighborhood
ImportBiocyc, XMLXML, BioWizard
ExportBioPax-L1, Biocyc, XML, GraphML, SIFBioPax-L1XMLBioPax-L2JPG, SVG, Biopax, SBML, XML
DistributionOpen Source GNU GPLFree for academicGNU GPLOpen Source
VisualizationPathway Tools Web, JaxFront, Cytoscape, Graph API-Jung, Cluster-APINoWebWeb, SkyPainterWeb, Java program
EditingPathway Tools, JaxFront,OQL-
Organisms205 organimsE.coli,Yeast,HumanHuman, Mouse, Rat, C-elegans, Yeast24 organisms including: Human, Mouse, Rat, C-elegans, Yeast, Arabidopsis, Drosophila, Subtilis, Tetraodon, S.pombe, SubtilisReactome, Uniprot, Entrez, GO, IntAct, HPRD, PubChemHuman, Mouse Rat

Other projects or api used by Cyclone
Hyperjaxb2 -Relational persistence for XML data, with JAXB and Hibernate. - many thanks to Aleksei Valikov
BioCyc Pathway Tools
Sun Java
Hibernate - is a powerful, high performance object/relational persistence and query service.
Jaxb - provides a convenient way to bind an XML schema to a representation in Java code.
Eclipse - is an open source community whose projects are focused on providing an extensible development platform and application frameworks for building software.
JBoss Eclipse IDE - Designed for use with the JBoss Enterprise Middleware System (JEMS), JBoss Eclipse IDE is a series of integrated Eclipse plug-ins for building quality software applications.
mySQL - a RDBMS.
JaxFront - to browse xml data.
Log4J - to log errors.
Javadoc - to document the project.
Sourceforge - to publish the project.

New: Webservice (beta)

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