A. Zhukova and D. J. Sherman, Knowledge-based generalization of metabolic models, J Comput Biol, vol.21, issue.7, pp.534-581, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00925881

B. Bederson and J. Meyer, Implementing a zooming User Interface: experience building Pad++, Softw Prac Exp, vol.28, issue.10, pp.1101-1136, 1998.

A. Nivala, S. Brewster, and T. L. Sarjakoski, Usability Evaluation of Web Mapping Sites, Cartographic J, vol.45, issue.2, pp.129-167, 2008.

J. C. Roberts, Exploratory visualization with multiple linked views, pp.159-80, 2005.

L. Laufer, P. Halacsy, and A. Somlai-fischer, Prezi meeting: Collaboration in a zoomable canvas based environment, CHI '11 Extended Abstracts on Human Factors in Computing Systems. CHI EA '11, pp.749-52, 2011.

S. Pook, G. Vaysseix, and E. Barillot, Zomit: biological data visualization and browsing, Bioinformatics, vol.14, issue.9, pp.807-821, 1998.

Z. Hu, J. Mellor, J. Wu, M. Kanehisa, J. M. Stuart et al., Towards zoomable multidimensional maps of the cell, Nat Biotechnol, vol.25, issue.5, pp.547-54, 2007.

J. D. Orth, T. M. Conrad, J. Na, J. A. Lerman, H. Nam et al., A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011, Mol Syst Biol, vol.7, issue.1, p.535, 2011.

H. W. Aung, S. A. Henry, and L. P. Walker, Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism, Ind Biotechnol, vol.9, issue.4, pp.215-243, 2013.

I. Thiele, N. Swainston, R. Fleming, A. Hoppe, S. Sahoo et al., A community-driven global reconstruction of human metabolism, Nat Biotechnol, vol.31, issue.5, pp.419-444, 2013.

T. Von-landesberger, A. Kuijper, T. Schreck, J. Kohlhammer, J. J. Van-wijk et al., Visual Analysis of Large Graphs: State-of-the-Art and Future Research Challenges, Comput Graph Forum, vol.30, issue.6, pp.1719-1768, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00712779

I. Herman, G. Melancon, and M. S. Marshall, Graph visualization and navigation in information visualization: A survey, IEEE Trans Vis Comput Graph, vol.6, issue.1, pp.24-43, 2000.

P. D. Karp, S. Paley, and P. Romero, The Pathway Tools software, Bioinformatics, vol.18, issue.1, pp.225-257, 2002.

R. Agren, L. Liu, S. Shoaie, W. Vongsangnak, I. Nookaew et al., The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum, PLoS Comput Biol, vol.9, issue.3, p.1002980, 2013.

C. Wrzodek, F. Büchel, M. Ruff, A. Dräger, and A. Zell, Precise generation of systems biology models from KEGG pathways, BMC Syst Biol, vol.7, p.15, 2013.

E. Pitkänen, P. Jouhten, J. Hou, M. F. Syed, P. Blomberg et al., Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species, PLoS Comput Biol, vol.10, issue.2, p.1003465, 2014.

N. Swainston, K. Smallbone, P. Mendes, D. Kell, and N. Paton, The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks, J Integr Bioinformatics, vol.8, issue.2, p.186, 2011.

J. J. Hamilton and J. L. Reed, Software platforms to facilitate reconstructing genome-scale metabolic networks, Environ Microbiol, vol.16, issue.1, pp.49-59, 2014.

C. Li, M. Donizelli, N. Rodriguez, H. Dharuri, L. Endler et al., BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models, BMC Syst Biol, vol.4, p.92, 2010.

J. Schellenberger, J. O. Park, T. M. Conrad, and B. O. Palsson, BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions, BMC Bioinformatics, vol.11, p.213, 2010.

J. L. Snoep and B. G. Olivier, JWS online cellular systems modelling and microbiology, Microbiology, vol.149, issue.11, pp.3045-3052, 2003.

M. Kanehisa, S. Goto, Y. Sato, M. Furumichi, and M. Tanabe, KEGG for integration and interpretation of large-scale molecular data sets, Nucleic Acids Res, vol.40, pp.109-123, 2012.

M. Milacic, R. Haw, K. Rothfels, G. Wu, D. Croft et al., Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome, Cancers, vol.4, issue.4, pp.1180-211, 2012.

D. Croft, Building models using Reactome pathways as templates, Methods Mol Biol, vol.1021, pp.273-83, 2013.

M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. 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.524-555, 2003.

M. P. Van-iersel, A. C. Villéger, T. Czauderna, S. E. Boyd, F. T. Bergmann et al., Software support for SBGN maps: SBGN-ML and LibSBGN, Bioinformatics, vol.28, issue.15, pp.2016-2037, 2012.

C. M. Lloyd, M. Halstead, and P. F. Nielsen, CellML: its future, present and past, Progress Biophys Mol Biol, vol.85, pp.433-50, 2004.

P. De-matos, R. Alcántara, A. Dekker, M. Ennis, J. Hastings et al., Chemical Entities of Biological Interest: an update, Nucleic Acids Res, vol.38, issue.1, pp.249-54, 2010.

, Activities at the Universal Protein Resource (UniProt), The UniProt Consortium, vol.42, pp.191-199, 2014.

I. Thiele and B. O. Palsson, A protocol for generating a high-quality genome-scale metabolic reconstruction, Nat Protoc, vol.5, issue.1, pp.93-121, 2010.

I. Thiele, N. Vlassis, and R. Fleming, fastGapFill: efficient gap filling in metabolic networks, Bioinformatics, vol.30, issue.17, pp.2529-2560, 2014.

S. Klamt, J. Saez-rodriguez, and E. D. Gilles, Structural and functional analysis of cellular networks with CellNetAnalyzer, BMC Syst Biol, vol.1, issue.2, 2007.

W. B. Copeland, B. A. Bartley, D. Chandran, M. Galdzicki, K. H. Kim et al., Computational tools for metabolic engineering, Metab Eng, vol.14, issue.3, pp.270-80, 2012.

M. Schulz, J. Uhlendorf, E. Klipp, and W. Liebermeister, SBMLmerge, a system for combining biochemical network models, Genome Inform Int Conf Genome Inform, vol.17, issue.1, pp.62-71, 2006.

F. Krause, J. Uhlendorf, T. Lubitz, M. Schulz, E. Klipp et al., Annotation and merging of SBML models with semanticSBML, Bioinformatics, vol.26, issue.3, pp.421-423, 2010.

R. Umeton, G. Nicosia, and C. F. Dewey, OREMPdb: a semantic dictionary of computational pathway models, BMC Bioinformatics, vol.13, 2012.

S. A. Coskun, A. E. Cicek, N. Lai, R. K. Dash, Z. M. Ozsoyoglu et al., An online model composition tool for system biology models, BMC Syst Biol, vol.7, p.88, 2013.

A. Funahashi, Y. Matsuoka, A. Jouraku, M. Morohashi, N. Kikuchi et al., CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks, Proc IEEE, vol.96, issue.8, pp.1254-65, 2008.

H. Rohn, A. Junker, A. Hartmann, E. Grafahrend-belau, H. Treutler et al., VANTED v2: a framework for systems biology applications, BMC Syst Biol, vol.6, issue.1, p.139, 2012.

M. E. Smoot, K. Ono, J. Ruscheinski, P. Wang, and T. Ideker, Cytoscape 2.8: new features for data integration and network visualization, Bioinformatics, vol.27, issue.3, pp.431-433, 2011.

T. Fruchterman and E. M. Reingold, Graph drawing by force-directed placement, Softw Prac Exp, vol.21, issue.11, pp.1129-64, 1991.

R. Tamassia, Handbook of graph drawing and visualization (discrete mathematics and its applications), 2007.

P. A. Jensen and J. A. Papin, MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data, Bioinformatics, 2014.

E. Barillot, F. Guyon, C. Cussat-blanc, E. Viara, and G. Vaysseix, HuGeMap: a distributed and integrated Human Genome Map database, Nucleic Acids Res, vol.26, issue.1, pp.106-113, 1998.

R. Jianu and D. H. Laidlaw, What Google Maps can do for biomedical data dissemination: examples and a design study, BMC Res Notes, vol.6, issue.1, p.179, 2013.

T. Yates, M. J. Okoniewski, and C. J. Miller, X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis, Nucleic Acids Res, vol.36, pp.780-786, 2008.

K. Arakawa, S. Tamaki, N. Kono, N. Kido, K. Ikegami et al., Genome Projector: zoomable genome map with multiple views, BMC Bioinformatics, vol.10, issue.1, p.31, 2009.

E. Gasteiger, A. Gattiker, C. Hoogland, I. Ivanyi, R. D. Appel et al., ExPASy: The proteomics server for in-depth protein knowledge and analysis, Nucleic Acids Res, vol.31, issue.13, pp.3784-3792, 2003.

I. Kuperstein, D. P. Cohen, S. Pook, E. Viara, L. Calzone et al., NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps, BMC Syst Biol, vol.7, issue.1, p.100, 2013.
URL : https://hal.archives-ouvertes.fr/inserm-00872428

M. Latendresse and P. D. Karp, Web-based metabolic network visualization with a zooming user interface, BMC Bioinformatics, vol.12, issue.1, p.176, 2011.

R. Caspi, T. Altman, K. Dreher, C. A. Fulcher, P. Subhraveti et al., The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases, Nucleic Acids Res, vol.40, pp.742-53, 2012.

M. J. Herrgård, N. Swainston, P. Dobson, W. B. Dunn, K. Y. Arga et al., A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology, Nat Biotechnol, vol.26, issue.10, pp.1155-60, 2008.

D. E. Metzler and C. M. Metzler, Biochemistry: The Chemical Reactions of Living Cells, vol.1, p.937, 2001.

A. Zhukova and D. J. Sherman, Knowledge-based metabolic model generalization library web page

M. Hucka, S. Hoops, S. M. Keating, L. Novère, N. Sahle et al., Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions, 2008.

M. Hucka, SBML Level 3 Groups Proposal, 2012.

F. Büchel, N. Rodriguez, N. Swainston, C. Wrzodek, T. Czauderna et al., Path2Models: large-scale generation of computational models from biochemical pathway maps, BMC Syst Biol, vol.7, issue.1, p.116, 2013.

R. G. Diestel and . Theory, Springer Graduate Text GTM 173: Reinhard Diestel, p.451, 2012.

D. Auber, P. Mutzel, G. Farin, H. Hege, D. Hoffman et al., Tulip -A Huge Graph Visualization Framework In: Jünger M, pp.105-131, 2004.

B. J. Bornstein, S. M. Keating, A. Jouraku, and M. Hucka, LibSBML: an API library for SBML, Bioinformatics, vol.24, issue.6, pp.880-881, 2008.

A. Unwin, M. Theus, and H. Hofmann, Graphics of large datasets: visualizing a million, 2006.

H. N. Gabow, Path-based depth-first search for strong and biconnected components, Inf Process Lett, vol.74, issue.3-4, pp.107-121, 2000.

S. Hachul and M. Jünger, Large-graph layout with the fast multipole multilevel method, 2005.

K. Sugiyama, S. Tagawa, and M. Toda, Methods for Visual Understanding of Hierarchical System Structures, IEEE Trans Syst Man Cybernet, vol.11, issue.2, pp.109-134, 1981.

M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler et al., Gene Ontology: tool for the unification of biology, Nat Genet, vol.25, issue.1, pp.25-34, 2000.

R. Gauges, U. Rost, S. Sahle, K. Wengler, and F. T. Bergmann, SBML Level 3 Layout Package Version 1 Release, 2013.

V. Agafonkin, Leaflet -a JavaScript library for mobile-friendly maps

H. Butler, M. Daly, A. Doyle, S. Gillies, T. Schaub et al., GeoJSON Specification

L. Novère, N. Hucka, M. Mi, H. Moodie, S. Schreiber et al., The Systems Biology Graphical Notation, Nat Biotechnol, vol.27, issue.8, pp.735-776, 2009.

N. Gene,

A. Zhukova and D. J. Sherman,

F. T. Bergmann, R. Adams, S. Moodie, J. Cooper, M. Glont et al., One file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project, 2014.

D. Blankenberg, V. Kuster, G. Coraor, N. Ananda, G. Lazarus et al., Galaxy: a web-based genome analysis tool for experimentalists, Current Protoc Mol Biol, vol.19, pp.19-10121, 2010.

K. Böhringer and F. N. Paulisch, Submit your next manuscript to BioMed Central and take full advantage of: ? Convenient online submission ? Thorough peer review ? No space constraints or color figure charges ? Immediate publication on acceptance ? Inclusion in PubMed, CAS, Scopus and Google Scholar ? Research which is freely available for redistribution, Proceedings of the chiconference on human factors in computing systems, pp.43-51, 1990.