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Web sites:

BioModels database - http://www.ebi.ac.uk/biomodels-main
BioPAX - Biological Pathways Exchenge - http://www.biopax.org

CellML - http://www.cellml.org

Eclipse platform - http://www.eclipse.org

Lucene - full-featured text search engine - http://lucene.apache.org/

SBGN - Systems Biology Graphic Notation - http://www.sbgn.org

SBML - Systems Biology Markup Language - http://www.sbml.org