References

Brenner S., cited from R.Bradford, 2009. Salk Signals, 5(2):12-17.

Finney A., 2004. http://sbml.org/wiki/Semantic_Test_Suite
Le Novère N. et al, Moodie S., Sorokin A., Hucka M., Shreiber F., Mi H., Demir E., Wegner K., Aladjem M., imalaratne S., Bergman F.T., Gauges R., Ghazal P., Hideya K., Li L., Matsuoka Y., Villéger A., Calzone L., Courtot M., Dogrusoz U., Freeman T., Funahashi A., Ghosh S., Jouraku K., Kim S., Kolpakov F., Luna A., Sahle S., Watterson S., Goryanin I., Kell D.B., Kohn K., Kitano H., 2009. The Systems Biology Graphical Notation. Nature biotechnology, submitted.

Hucka M. et al., 2003. The Systems Biology Markup Language (SBML): A Medium for Representation and Exchange of Biochemical Network Models. Bioinformatics, 19, 524-531.

Lee E.A., 2001. Overview of the Ptolemy Project. Technical Memorandum UCB/ERL M01/11, University of California, Berkeley.

Lloyd CM, Halstead MD, Nielsen PF, 2004. CellML: its future, present and past. Lloyd C.M. et al., 2004. Progress in Biophysics and Molecular Biology, 85, 433-450.

Patterson M. and Spiteri R.J., 2003. http://www.netlib.org/ode/odeToJava.tgz

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