Table 1.

Examples of bioinformatic resources and computational tools.

Database	URL	Reference
DATA RESOURCES: DATABASES FOR ONTOLOGIES, GENOMICS, PROTEOMICS, SIGNALING PATHWAYS, AND INTERACTION NETWORKS
KEGG	http://www.genome.jp/kegg/	Kanehisa et al. (2012)
Human Gene Expression Index	http://www.biotechnologycenter.ora/hio/	Haverty et al. (2002)
TRED	http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=home	Jiang et al. (2007)
GELBANK	http://gelbank.anl.gov/	Babnigg and Giometti (2004)
X Tandem	http://www.theapm.orq/TANDEM/	Craig et al. (2004)
PRIDE	ftp://ftp.ebi.ac.uk/pub/databases/pride/	Jones and Cote (2008)
PANTHER	http://www.pantherdb.ora/	Mi and Thomas (2009)
GenMAPP2	http://www.aenmapp.ora/	Salomonis et al. (2007)
Reactome	http://www.reactome.org/	Croft et al. (2011)
TRANSPATH	http://www.aenexplain.com/transpath	Krull et al. (2006)
IntAct	http://www.ebi.ac.uk/intact/index.isp	Kerrien et al. (2012)
MIPSMPPI	http://mips.gsf.de/proj/ppi/	Pagel et al. (2005)
aMAZE	http://www.amaze.ulb.ac.be	Lemer et al. (2004)
GeneNet	http://wwwmgs.bionet.nsc.ru/mgs/gnw/qenenet/.	Ananko et al. (2002)
GO – Gene Ontology	http://www.geneontoloav.ora/GO.downloads.shtml	Harris et al. (2004)
SO – Sequence Ontology	http://obo.sourceforge.net/cgi-bin/detail.cgi?seauence
PhenomicDB	http://www.phenomicdb.de	Kahraman et al. (2005)
DATA ANALYSIS TOOLS: NETWORK ANALYSIS, SIMULATION, AND/OR MODEL ASSESSMENT
MATLAB Simulink toolbox	http://www.mathworks.com/products/simulink/	Ullah et al. (2006)
Virtual Cell	http://www.nrcam.uchc.edu	Moraru et al. (2002)
JWS online	http://iii.biochem.sun.ac.za/index.html	Olivier and Snoep (2004)
Ingenuity Pathway Analysis	http://www.ingenuity.com/products/pathways_analysis.html	Jimenez-Marin et al. (2009)
NetBuilder	http://homepaqesstca.hertsac.uk/~erdqmjs/NetBuilder%20home/NetBuilder/
Copasi	http://www.copasi.ora/	Mendes et al. (2009)
E-cell	http://www.e-cell.org/	Takahashi et al. (2003)
Cell Designer	http://www.celldesianer.ora/	Van Hemert and Dickerson (2010)
Cellware	http://www.bii.a-star.edu.sq/research/sbq/cellware/index.asp	Dhar et al. (2004)
SimCell	http://wishart.biology.ualberta.ca/SimCell	Tretter and Gebicke-Haerter (2012)
NETWORK VISUALIZATION TOOLS
Cytoscape	http://www.cytoscape.org/	Shannon et al. (2003)
BioLayout	http://www.biolayout.org	Theocharidis et al. (2009)
Cobweb	http://bioinformatics.charite.de/cobweb/ cobweb	von Eichborn et al. (2011)