H. Kitano, S. Ghosh, and Y. Matsuoka, Social engineering for virtual 'big science' in systems biology, Nature Chemical Biology, vol.26, issue.6, pp.323-326, 2011.
DOI : 10.1038/nchembio.574

S. Ghosh, Y. Matsuoka, and H. Kitano, Connecting the dots: role of standardization and technology sharing in biological simulation, Drug Discovery Today, vol.15, issue.23-24, pp.1024-1031, 2010.
DOI : 10.1016/j.drudis.2010.10.001

E. Barillot, L. Calzone, P. Hupé, J. Vert, and A. Zinovyev, Computational systems biology of cancer, 2012.

H. Ooi, G. Schneider, T. Lim, Y. Chan, B. Eisenhaber et al., Biomolecular Pathway Databases, Methods Mol Biol, vol.609, pp.129-144, 2010.
DOI : 10.1007/978-1-60327-241-4_8

G. Joshi-tope, M. Gillespie, I. Vastrik, D. Eustachio, P. Schmidt et al., Reactome: a knowledgebase of biological pathways, Nucleic Acids Research, vol.33, issue.Database issue, pp.428-432, 2005.
DOI : 10.1093/nar/gki072

M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno, and M. Hattori, The KEGG resource for deciphering the genome, Nucleic Acids Research, vol.32, issue.90001, pp.277-280, 2004.
DOI : 10.1093/nar/gkh063

P. Thomas, A. Kejariwal, M. Campbell, H. Mi, K. Diemer et al., PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification, Nucleic Acids Research, vol.31, issue.1, pp.334-341, 2003.
DOI : 10.1093/nar/gkg115

R. Elkon, R. Vesterman, N. Amit, I. Ulitsky, I. Zohar et al., SPIKE ??? a database, visualization and analysis tool of cellular signaling pathways, BMC Bioinformatics, vol.9, issue.1, p.110, 2008.
DOI : 10.1186/1471-2105-9-110

A. Pico, T. Kelder, M. Van-iersel, K. Hanspers, B. Conklin et al., WikiPathways: Pathway Editing for the People, PLoS Biology, vol.19, issue.7, p.184, 2008.
DOI : 10.1371/journal.pbio.0060184.g002

M. Krull, S. Pistor, N. Voss, A. Kel, I. Reuter et al., TRANSPATH(R): an information resource for storing and visualizing signaling pathways and their pathological aberrations, Nucleic Acids Research, vol.34, issue.90001, pp.546-551, 2006.
DOI : 10.1093/nar/gkj107

URL : https://hal.archives-ouvertes.fr/hal-00314881

R. Caspi, T. Altman, J. Dale, K. Dreher, C. Fulcher et al., The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases, Nucleic Acids Research, vol.38, issue.Database, pp.473-479, 2010.
DOI : 10.1093/nar/gkp875

M. Stobbe, S. Houten, G. Jansen, A. Van-kampen, and P. Moerland, Critical assessment of human metabolic pathway databases: a stepping stone for future integration, BMC Systems Biology, vol.5, issue.1, p.165, 2011.
DOI : 10.1093/nar/gki711

L. Calzone, A. Gelay, A. Zinovyev, F. Radvanyi, and E. Barillot, A comprehensive modular map of molecular interactions in RB/E2F pathway, Molecular Systems Biology, vol.4, p.173, 2008.
DOI : 10.1016/S0092-8674(00)80625-X

D. Nicholson, A Lifetime of Metabolism, Cellular and Molecular Life Sciences, vol.63, issue.1, pp.1-5, 2006.
DOI : 10.1007/s00018-005-5500-x

K. Kohn, Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems, Molecular Biology of the Cell, vol.10, issue.8, pp.2703-2734, 1999.
DOI : 10.1091/mbc.10.8.2703

H. Kitano, A. Funahashi, Y. Matsuoka, and K. Oda, Using process diagrams for the graphical representation of biological networks, Nature Biotechnology, vol.33, issue.8, pp.961-966, 2005.
DOI : 10.1016/S1478-5382(03)02370-9

N. Novère, M. Hucka, H. Mi, S. Moodie, F. Schreiber et al., The Systems Biology Graphical Notation, Nature Biotechnology, vol.267, issue.8, pp.735-741, 2009.
DOI : 10.1038/nbt.1558

M. Hucka, A. Finney, H. Sauro, H. Bolouri, J. Doyle et al., The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, vol.19, issue.4, pp.524-531, 2003.
DOI : 10.1093/bioinformatics/btg015

E. Demir, M. Cary, S. Paley, K. Fukuda, C. Lemer et al., The BioPAX community standard for pathway data sharing, Nature Biotechnology, vol.35, issue.9, pp.935-942, 2010.
DOI : 10.1038/nbt.1666

A. Bauer-mehren, L. Furlong, and F. Sanz, Pathway databases and tools for their exploitation: benefits, current limitations and challenges, Molecular Systems Biology, vol.18, p.290, 2009.
DOI : 10.1093/bioinformatics/btm553

URL : http://doi.org/10.1038/msb.2009.47

L. Flórez, C. Lammers, R. Michna, and J. Stülke, CellPublisher: a web platform for the intuitive visualization and sharing of metabolic, signalling and regulatory pathways: Fig. 1., Bioinformatics, vol.26, issue.23, pp.2997-2999, 2010.
DOI : 10.1093/bioinformatics/btq585

N. Kono, K. Arakawa, R. Ogawa, N. Kido, K. Oshita et al., Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API, PLoS ONE, vol.36, issue.11, p.7710, 2009.
DOI : 10.1371/journal.pone.0007710.s001

URL : http://doi.org/10.1371/journal.pone.0007710

K. Dahlquist, N. Salomonis, K. Vranizan, S. Lawlor, and B. Conklin, GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways, Nature Genetics, vol.31, issue.1, pp.19-20, 2002.
DOI : 10.1038/ng0502-19

M. Van-iersel, T. Kelder, A. Pico, K. Hanspers, S. Coort et al., Presenting and exploring biological pathways with PathVisio, BMC Bioinformatics, vol.9, issue.1, p.399, 2008.
DOI : 10.1186/1471-2105-9-399

T. Czauderna, C. Klukas, and F. Schreiber, Editing, validating and translating of SBGN maps, Bioinformatics, vol.26, issue.18, pp.2340-2341, 2010.
DOI : 10.1093/bioinformatics/btq407

Y. Matsuoka, S. Ghosh, N. Kikuchi, and H. Kitano, Payao: a community platform for SBML pathway model curation, Bioinformatics, vol.26, issue.10, pp.1381-1383, 2010.
DOI : 10.1093/bioinformatics/btq143

K. Kandasamy, S. Keerthikumar, R. Raju, K. Prasad, T. Ramachandra et al., PathBuilder--open source software for annotating and developing pathway resources, Bioinformatics, vol.25, issue.21, pp.2860-2862, 2009.
DOI : 10.1093/bioinformatics/btp453

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781757

A. Zinovyev, E. Viara, L. Calzone, and E. Barillot, BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks, Bioinformatics, vol.24, issue.6, pp.876-877, 2008.
DOI : 10.1093/bioinformatics/btm553

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/24/6/876

E. Bonnet, L. Calzone, D. Rovera, G. Stoll, E. Barillot et al., BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats, BMC Systems Biology, vol.7, issue.1, p.18, 2013.
DOI : 10.1038/ng1923

URL : https://hal.archives-ouvertes.fr/inserm-00820930

E. Bonnet, L. Calzone, D. Rovera, G. Stoll, E. Barillot et al., Practical Use of BiNoM: A Biological Network Manager Software, Methods Mol Biol Clifton NJ 2013, vol.1021, pp.127-146
DOI : 10.1007/978-1-62703-450-0_7

P. Shannon, A. Markiel, O. Ozier, N. Baliga, J. Wang et al., Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks, Genome Research, vol.13, issue.11, pp.2498-2504, 2003.
DOI : 10.1101/gr.1239303

R. Saito, M. Smoot, K. Ono, J. Ruscheinski, P. Wang et al., A travel guide to Cytoscape plugins, Nature Methods, vol.8, issue.11, pp.1069-1076, 2012.
DOI : 10.1038/nbt.1567

S. Pook, G. Vaysseix, and E. Barillot, Zomit: biological data visualization and browsing, Bioinformatics, vol.14, issue.9, pp.807-814, 1998.
DOI : 10.1093/bioinformatics/14.9.807

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/14/9/807

M. Latendresse and P. Karp, Web-Based Metabolic Network Visualization with a Zooming User Interface, BMC Bioinformatics, vol.12, issue.1, p.176, 2011.
DOI : 10.1186/1471-2105-12-176

Z. Hu, J. Mellor, J. Wu, M. Kanehisa, J. Stuart et al., Towards zoomable multidimensional maps of the cell, Nature Biotechnology, vol.30, issue.5, pp.547-554, 2007.
DOI : 10.1038/nbt1304

N. Juty, L. Novère, N. Laibe, and C. , Identifiers.org and MIRIAM Registry: community resources to provide persistent identification, Nucleic Acids Research, vol.40, issue.D1, pp.580-586, 2012.
DOI : 10.1093/nar/gkr1097