Cyclone

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Alternatives

Alternatives to query Biocyc

	PathwayTools	Biowarehouse	Cyclone
Representation System	FRS	Relational model
Storage	Ocelot, mySQL, Oracle	mySQL	mySQL, Oracle, Sybase, pgSQL ...(more)
Query	Lisp, (SQL)	SQL	OQL, (SQL), Java-Criteria
API	Lisp, Perl, Java	-	Java
Biocyc coverage	Full	Partial	Full
Import	Ocelot, Biocyc	SQL	Biocyc, XML
Export	Ocelot		Biocyc, XML, GraphML, SIF

Alternatives to { Biocyc + Cyclone + Cytoscape }

	Biocyc + Cyclone + Cytoscape	aMaze	SigPath	Reactome	Patika	PathCase	Ingenuity
Representation System	FRS, XSD	Generalized Entity Relationship	XSD
Storage	mySQL, Oracle, Sybase, pgSQL ...(more)		JDO-compliant	mySQL
Interface	PathwayTool Application, Web, Eclipse(JBoss)	Eclipse	Java Application, Web	Web
Query language	OQL, (SQL), Java-Criteria	IglooQL(object)	?	Pathfinder	Fields, Neighborhood
API	Java		Java	Perl
Import	Biocyc, XML		XML, BioWizard
Export	BioPax-L1, Biocyc, XML, GraphML, SIF	BioPax-L1	XML	BioPax-L2	JPG, SVG, Biopax, SBML, XML
Distribution	Open Source GNU GPL	Free for academic	GNU GPL	Open Source
Visualization	Pathway Tools Web, JaxFront, Cytoscape, Graph API-Jung, Cluster-API	No	Web	Web, SkyPainter	Web, Java program
Editing	Pathway Tools, JaxFront,OQL	-
Organisms	205 organims	E.coli,Yeast,Human	Human, Mouse, Rat, C-elegans, Yeast	24 organisms including: Human, Mouse, Rat, C-elegans, Yeast, Arabidopsis, Drosophila, Subtilis, Tetraodon, S.pombe, Subtilis	Reactome, Uniprot, Entrez, GO, IntAct, HPRD, PubChem		Human, Mouse Rat

Elsewhere

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)

Projets that use Cyclone

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

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.

Bibliography

The E. coli EcoCyc Database: No Longer Just a Metabolic Pathway Database
Karp P.D., Arnaud M., Collado-Vides J., Ingraham J., Paulsen I.T., Saier M.H. Jr.
ASM News 70(1): 25-30. 2004.

MetaCyc: a multiorganism database of metabolic pathways and enzymes
Cynthia J. Krieger, and Peter D. Karp
Nucleic Acids Research, 32(1):D438-42 2004.

The Pathway Tools Software
P. Karp, S. Paley, and P. Romero,
Bioinformatics 18:S225-32 2002.

Evaluation of computational metabolic-pathway predictions for H. pylori
S. Paley and P. Karp
Bioinformatics 18(5):705-14 2002.

Abstract Querying and computing with BioCyc databases
Krummenacker M, Paley S, Mueller L, Yan T, Karp PD.
Bioinformatics. 15;21(16):3454-5. 2005.

The Generic Frame Protocol
P. D. Karp, K. Myers, and T. Gruber,
in Proceedings of the 1995 International Joint Conference on Artificial Intelligence, pp. 768--774, 1995.

Pipeline 2

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