TY - JOUR AU - Zhukova, A. AU - Sherman, D. J. PY - 2014 DA - 2014// TI - Knowledge-based generalization of metabolic models JO - J Comput Biol VL - 21 UR - https://doi.org/10.1089/cmb.2013.0143 DO - 10.1089/cmb.2013.0143 ID - Zhukova2014 ER - TY - JOUR AU - Bederson, B. AU - Meyer, J. PY - 1998 DA - 1998// TI - Implementing a zooming User Interface: experience building Pad++ JO - Softw Prac Exp VL - 28 UR - https://doi.org/3.0.CO;2-V DO - 3.0.CO;2-V ID - Bederson1998 ER - TY - JOUR AU - Nivala, A. -. M. AU - Brewster, S. AU - Sarjakoski, T. L. PY - 2008 DA - 2008// TI - Usability Evaluation of Web Mapping Sites JO - Cartographic J VL - 45 UR - https://doi.org/10.1179/174327708X305120 DO - 10.1179/174327708X305120 ID - Nivala2008 ER - TY - CHAP AU - Roberts, J. C. ED - Dykes, J. ED - MacEachren, A. M. ED - Kraak, M. -. J. PY - 2005 DA - 2005// TI - Exploratory visualization with multiple linked views BT - Exploring Geovisualization PB - Elsevier CY - Pergamon ID - Roberts2005 ER - TY - CHAP AU - Laufer, L. AU - Halacsy, P. AU - Somlai-Fischer, A. PY - 2011 DA - 2011// TI - Prezi meeting: Collaboration in a zoomable canvas based environment BT - CHI ’11 Extended Abstracts on Human Factors in Computing Systems. CHI EA ’11 PB - ACM CY - New York, NY, USA ID - Laufer2011 ER - TY - JOUR AU - Pook, S. AU - Vaysseix, G. AU - Barillot, E. PY - 1998 DA - 1998// TI - Zomit: biological data visualization and browsing JO - Bioinformatics. VL - 14 UR - https://doi.org/10.1093/bioinformatics/14.9.807 DO - 10.1093/bioinformatics/14.9.807 ID - Pook1998 ER - TY - JOUR AU - Hu, Z. AU - Mellor, J. AU - Wu, J. AU - Kanehisa, M. AU - Stuart, J. M. AU - DeLisi, C. PY - 2007 DA - 2007// TI - Towards zoomable multidimensional maps of the cell JO - Nat Biotechnol. VL - 25 UR - https://doi.org/10.1038/nbt1304 DO - 10.1038/nbt1304 ID - Hu2007 ER - TY - JOUR AU - Orth, J. D. AU - Conrad, T. M. AU - Na, J. AU - Lerman, J. A. AU - Nam, H. AU - Feist, A. M. PY - 2011 DA - 2011// TI - A comprehensive genome-scale reconstruction of Escherichia coli metabolism–2011 JO - Mol Syst Biol. VL - 7 UR - https://doi.org/10.1038/msb.2011.65 DO - 10.1038/msb.2011.65 ID - Orth2011 ER - TY - JOUR AU - Aung, H. W. AU - Henry, S. A. AU - Walker, L. P. PY - 2013 DA - 2013// TI - Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism JO - Ind Biotechnol. VL - 9 UR - https://doi.org/10.1089/ind.2013.0013 DO - 10.1089/ind.2013.0013 ID - Aung2013 ER - TY - JOUR AU - Thiele, I. AU - Swainston, N. AU - Fleming, R. M. T. AU - Hoppe, A. AU - Sahoo, S. AU - Aurich, M. K. PY - 2013 DA - 2013// TI - A community-driven global reconstruction of human metabolism JO - Nat Biotechnol. VL - 31 UR - https://doi.org/10.1038/nbt.2488 DO - 10.1038/nbt.2488 ID - Thiele2013 ER - TY - JOUR AU - von Landesberger, T. AU - Kuijper, A. AU - Schreck, T. AU - Kohlhammer, J. AU - van Wijk, J. J. AU - Fekete, J. -. D. PY - 2011 DA - 2011// TI - Visual Analysis of Large Graphs: State-of-the-Art and Future Research Challenges JO - Comput Graph Forum. VL - 30 UR - https://doi.org/10.1111/j.1467-8659.2011.01898.x DO - 10.1111/j.1467-8659.2011.01898.x ID - von Landesberger2011 ER - TY - JOUR AU - Herman, I. AU - Melancon, G. AU - Marshall, M. S. PY - 2000 DA - 2000// TI - Graph visualization and navigation in information visualization: A survey JO - IEEE Trans Vis Comput Graph. VL - 6 UR - https://doi.org/10.1109/2945.841119 DO - 10.1109/2945.841119 ID - Herman2000 ER - TY - JOUR AU - Karp, P. D. AU - Paley, S. AU - Romero, P. PY - 2002 DA - 2002// TI - The Pathway Tools software JO - Bioinformatics. VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.suppl_1.S225 DO - 10.1093/bioinformatics/18.suppl_1.S225 ID - Karp2002 ER - TY - JOUR AU - Agren, R. AU - Liu, L. AU - Shoaie, S. AU - Vongsangnak, W. AU - Nookaew, I. AU - Nielsen, J. PY - 2013 DA - 2013// TI - The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum JO - PLoS Comput Biol. VL - 9 UR - https://doi.org/10.1371/journal.pcbi.1002980 DO - 10.1371/journal.pcbi.1002980 ID - Agren2013 ER - TY - JOUR AU - Wrzodek, C. AU - Büchel, F. AU - Ruff, M. AU - Dräger, A. AU - Zell, A. PY - 2013 DA - 2013// TI - Precise generation of systems biology models from KEGG pathways JO - BMC Syst Biol. VL - 7 UR - https://doi.org/10.1186/1752-0509-7-15 DO - 10.1186/1752-0509-7-15 ID - Wrzodek2013 ER - TY - JOUR AU - Pitkänen, E. AU - Jouhten, P. AU - Hou, J. AU - Syed, M. F. AU - Blomberg, P. AU - Kludas, J. PY - 2014 DA - 2014// TI - Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species JO - PLoS Comput Biol. VL - 10 UR - https://doi.org/10.1371/journal.pcbi.1003465 DO - 10.1371/journal.pcbi.1003465 ID - Pitkänen2014 ER - TY - JOUR AU - Swainston, N. AU - Smallbone, K. AU - Mendes, P. AU - Kell, D. AU - Paton, N. PY - 2011 DA - 2011// TI - The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks JO - J Integr Bioinformatics. VL - 8 ID - Swainston2011 ER - TY - JOUR AU - Hamilton, J. J. AU - Reed, J. L. PY - 2014 DA - 2014// TI - Software platforms to facilitate reconstructing genome-scale metabolic networks JO - Environ Microbiol. VL - 16 UR - https://doi.org/10.1111/1462-2920.12312 DO - 10.1111/1462-2920.12312 ID - Hamilton2014 ER - TY - JOUR AU - Li, C. AU - Donizelli, M. AU - Rodriguez, N. AU - Dharuri, H. AU - Endler, L. AU - Chelliah, V. PY - 2010 DA - 2010// TI - BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models JO - BMC Syst Biol. VL - 4 UR - https://doi.org/10.1186/1752-0509-4-92 DO - 10.1186/1752-0509-4-92 ID - Li2010 ER - TY - JOUR AU - Schellenberger, J. AU - Park, J. O. AU - Conrad, T. M. AU - Palsson, B. O. PY - 2010 DA - 2010// TI - BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions JO - BMC Bioinformatics. VL - 11 UR - https://doi.org/10.1186/1471-2105-11-213 DO - 10.1186/1471-2105-11-213 ID - Schellenberger2010 ER - TY - JOUR AU - Snoep, J. L. AU - Olivier, B. G. PY - 2003 DA - 2003// TI - JWS online cellular systems modelling and microbiology JO - Microbiology. VL - 149 UR - https://doi.org/10.1099/mic.0.C0124-0 DO - 10.1099/mic.0.C0124-0 ID - Snoep2003 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. AU - Sato, Y. AU - Furumichi, M. AU - Tanabe, M. PY - 2012 DA - 2012// TI - KEGG for integration and interpretation of large-scale molecular data sets JO - Nucleic Acids Res. VL - 40 UR - https://doi.org/10.1093/nar/gkr988 DO - 10.1093/nar/gkr988 ID - Kanehisa2012 ER - TY - JOUR AU - Milacic, M. AU - Haw, R. AU - Rothfels, K. AU - Wu, G. AU - Croft, D. AU - Hermjakob, H. PY - 2012 DA - 2012// TI - Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome JO - Cancers. VL - 4 UR - https://doi.org/10.3390/cancers4041180 DO - 10.3390/cancers4041180 ID - Milacic2012 ER - TY - JOUR AU - Croft, D. PY - 2013 DA - 2013// TI - Building models using Reactome pathways as templates JO - Methods Mol Biol. VL - 1021 UR - https://doi.org/10.1007/978-1-62703-450-0_14 DO - 10.1007/978-1-62703-450-0_14 ID - Croft2013 ER - TY - JOUR AU - Hucka, M. AU - Finney, A. AU - Sauro, H. M. AU - Bolouri, H. AU - Doyle, J. C. AU - Kitano, H. PY - 2003 DA - 2003// TI - The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models JO - Bioinformatics. VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg015 DO - 10.1093/bioinformatics/btg015 ID - Hucka2003 ER - TY - JOUR AU - van Iersel, M. P. AU - Villéger, A. C. AU - Czauderna, T. AU - Boyd, S. E. AU - Bergmann, F. T. AU - Luna, A. PY - 2012 DA - 2012// TI - Software support for SBGN maps: SBGN-ML and LibSBGN JO - Bioinformatics (Oxford, England). VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts270 DO - 10.1093/bioinformatics/bts270 ID - van Iersel2012 ER - TY - JOUR AU - Lloyd, C. M. AU - Halstead, M. D. B. AU - Nielsen, P. F. PY - 2004 DA - 2004// TI - CellML: its future, present and past JO - Progress Biophys Mol Biol. VL - 85 UR - https://doi.org/10.1016/j.pbiomolbio.2004.01.004 DO - 10.1016/j.pbiomolbio.2004.01.004 ID - Lloyd2004 ER - TY - JOUR AU - de Matos, P. AU - Alcántara, R. AU - Dekker, A. AU - Ennis, M. AU - Hastings, J. AU - Haug, K. PY - 2010 DA - 2010// TI - Chemical Entities of Biological Interest: an update JO - Nucleic Acids Res. VL - 38 UR - https://doi.org/10.1093/nar/gkp886 DO - 10.1093/nar/gkp886 ID - de Matos2010 ER - TY - JOUR PY - 2014 DA - 2014// TI - Activities at the Universal Protein Resource (UniProt) JO - Nucleic Acids Res. VL - 42 UR - https://doi.org/10.1093/nar/gkt1140 DO - 10.1093/nar/gkt1140 ID - ref29 ER - TY - JOUR AU - Thiele, I. AU - Palsson, B. O. PY - 2010 DA - 2010// TI - A protocol for generating a high-quality genome-scale metabolic reconstruction JO - Nat Protoc. VL - 5 UR - https://doi.org/10.1038/nprot.2009.203 DO - 10.1038/nprot.2009.203 ID - Thiele2010 ER - TY - JOUR AU - Thiele, I. AU - Vlassis, N. AU - Fleming, R. M. T. PY - 2014 DA - 2014// TI - fastGapFill: efficient gap filling in metabolic networks JO - Bioinformatics. VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu321 DO - 10.1093/bioinformatics/btu321 ID - Thiele2014 ER - TY - JOUR AU - Klamt, S. AU - Saez-Rodriguez, J. AU - Gilles, E. D. PY - 2007 DA - 2007// TI - Structural and functional analysis of cellular networks with CellNetAnalyzer JO - BMC Syst Biol. VL - 1 UR - https://doi.org/10.1186/1752-0509-1-2 DO - 10.1186/1752-0509-1-2 ID - Klamt2007 ER - TY - JOUR AU - Copeland, W. B. AU - Bartley, B. A. AU - Chandran, D. AU - Galdzicki, M. AU - Kim, K. H. AU - Sleight, S. C. PY - 2012 DA - 2012// TI - Computational tools for metabolic engineering JO - Metab Eng. VL - 14 UR - https://doi.org/10.1016/j.ymben.2012.03.001 DO - 10.1016/j.ymben.2012.03.001 ID - Copeland2012 ER - TY - JOUR AU - Schulz, M. AU - Uhlendorf, J. AU - Klipp, E. AU - Liebermeister, W. PY - 2006 DA - 2006// TI - SBMLmerge, a system for combining biochemical network models JO - Genome Inform Int Conf Genome Inform. VL - 17 ID - Schulz2006 ER - TY - JOUR AU - Krause, F. AU - Uhlendorf, J. AU - Lubitz, T. AU - Schulz, M. AU - Klipp, E. AU - Liebermeister, W. PY - 2010 DA - 2010// TI - Annotation and merging of SBML models with semanticSBML JO - Bioinformatics. VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp642 DO - 10.1093/bioinformatics/btp642 ID - Krause2010 ER - TY - JOUR AU - Umeton, R. AU - Nicosia, G. AU - Dewey, C. F. PY - 2012 DA - 2012// TI - OREMPdb: a semantic dictionary of computational pathway models JO - BMC Bioinformatics. VL - 13 Suppl 4 UR - https://doi.org/10.1186/1471-2105-13-S4-S6 DO - 10.1186/1471-2105-13-S4-S6 ID - Umeton2012 ER - TY - JOUR AU - Coskun, S. A. AU - Cicek, A. E. AU - Lai, N. AU - Dash, R. K. AU - Ozsoyoglu, Z. M. AU - Ozsoyoglu, G. PY - 2013 DA - 2013// TI - An online model composition tool for system biology models JO - BMC Syst Biol. VL - 7 UR - https://doi.org/10.1186/1752-0509-7-88 DO - 10.1186/1752-0509-7-88 ID - Coskun2013 ER - TY - JOUR AU - Funahashi, A. AU - Matsuoka, Y. AU - Jouraku, A. AU - Morohashi, M. AU - Kikuchi, N. AU - Kitano, H. PY - 2008 DA - 2008// TI - CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks JO - Proc IEEE. VL - 96 UR - https://doi.org/10.1109/JPROC.2008.925458 DO - 10.1109/JPROC.2008.925458 ID - Funahashi2008 ER - TY - JOUR AU - Rohn, H. AU - Junker, A. AU - Hartmann, A. AU - Grafahrend-Belau, E. AU - Treutler, H. AU - Klapperstück, M. PY - 2012 DA - 2012// TI - VANTED v2: a framework for systems biology applications JO - BMC Syst Biol. VL - 6 UR - https://doi.org/10.1186/1752-0509-6-139 DO - 10.1186/1752-0509-6-139 ID - Rohn2012 ER - TY - JOUR AU - Smoot, M. E. AU - Ono, K. AU - Ruscheinski, J. AU - Wang, P. -. L. AU - Ideker, T. PY - 2011 DA - 2011// TI - Cytoscape 2.8: new features for data integration and network visualization JO - Bioinformatics. VL - 27 UR - https://doi.org/10.1093/bioinformatics/btq675 DO - 10.1093/bioinformatics/btq675 ID - Smoot2011 ER - TY - JOUR AU - Fruchterman, T. M. J. AU - Reingold, E. M. PY - 1991 DA - 1991// TI - Graph drawing by force-directed placement JO - Softw Prac Exp. VL - 21 UR - https://doi.org/10.1002/spe.4380211102 DO - 10.1002/spe.4380211102 ID - Fruchterman1991 ER - TY - BOOK AU - Tamassia, R. PY - 2007 DA - 2007// TI - Handbook of graph drawing and visualization (discrete mathematics and its applications) PB - Hall/CRC CY - Boca Raton ID - Tamassia2007 ER - TY - STD TI - Jensen PA, Papin JA. MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data. Bioinformatics. 2014. doi:10.1093/bioinformatics/btt758. ID - ref43 ER - TY - JOUR AU - Barillot, E. AU - Guyon, F. AU - Cussat-Blanc, C. AU - Viara, E. AU - Vaysseix, G. PY - 1998 DA - 1998// TI - HuGeMap: a distributed and integrated Human Genome Map database JO - Nucleic Acids Res. VL - 26 UR - https://doi.org/10.1093/nar/26.1.106 DO - 10.1093/nar/26.1.106 ID - Barillot1998 ER - TY - JOUR AU - Jianu, R. AU - Laidlaw, D. H. PY - 2013 DA - 2013// TI - What Google Maps can do for biomedical data dissemination: examples and a design study JO - BMC Res Notes. VL - 6 UR - https://doi.org/10.1186/1756-0500-6-179 DO - 10.1186/1756-0500-6-179 ID - Jianu2013 ER - TY - JOUR AU - Yates, T. AU - Okoniewski, M. J. AU - Miller, C. J. PY - 2008 DA - 2008// TI - X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis JO - Nucleic Acids Res. VL - 36 ID - Yates2008 ER - TY - JOUR AU - Arakawa, K. AU - Tamaki, S. AU - Kono, N. AU - Kido, N. AU - Ikegami, K. AU - Ogawa, R. PY - 2009 DA - 2009// TI - Genome Projector: zoomable genome map with multiple views JO - BMC Bioinformatics. VL - 10 UR - https://doi.org/10.1186/1471-2105-10-31 DO - 10.1186/1471-2105-10-31 ID - Arakawa2009 ER - TY - JOUR AU - Gasteiger, E. AU - Gattiker, A. AU - Hoogland, C. AU - Ivanyi, I. AU - Appel, R. D. AU - Bairoch, A. PY - 2003 DA - 2003// TI - ExPASy: The proteomics server for in-depth protein knowledge and analysis JO - Nucleic Acids Res. VL - 31 UR - https://doi.org/10.1093/nar/gkg563 DO - 10.1093/nar/gkg563 ID - Gasteiger2003 ER - TY - JOUR AU - Kuperstein, I. AU - Cohen, D. P. AU - Pook, S. AU - Viara, E. AU - Calzone, L. AU - Barillot, E. PY - 2013 DA - 2013// TI - NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps JO - BMC Syst Biol. VL - 7 UR - https://doi.org/10.1186/1752-0509-7-100 DO - 10.1186/1752-0509-7-100 ID - Kuperstein2013 ER - TY - JOUR AU - Latendresse, M. AU - Karp, P. D. PY - 2011 DA - 2011// TI - Web-based metabolic network visualization with a zooming user interface JO - BMC Bioinformatics. VL - 12 UR - https://doi.org/10.1186/1471-2105-12-176 DO - 10.1186/1471-2105-12-176 ID - Latendresse2011 ER - TY - JOUR AU - Caspi, R. AU - Altman, T. AU - Dreher, K. AU - Fulcher, C. A. AU - Subhraveti, P. AU - Keseler, I. M. PY - 2012 DA - 2012// TI - The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases JO - Nucleic Acids Res. VL - 40 UR - https://doi.org/10.1093/nar/gkr1014 DO - 10.1093/nar/gkr1014 ID - Caspi2012 ER - TY - JOUR AU - Herrgård, M. J. AU - Swainston, N. AU - Dobson, P. AU - Dunn, W. B. AU - Arga, K. Y. AU - Arvas, M. PY - 2008 DA - 2008// TI - A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology JO - Nat Biotechnol. VL - 26 UR - https://doi.org/10.1038/nbt1492 DO - 10.1038/nbt1492 ID - Herrgård2008 ER - TY - BOOK AU - Metzler, D. E. AU - Metzler, C. M. PY - 2001 DA - 2001// TI - Biochemistry: The Chemical Reactions of Living Cells, 2nd Edition, 2nd edn. Biochemistry: The Chemical Reactions of Living Cells, vol. v. 1 PB - Academic Press CY - San Diego ID - Metzler2001 ER - TY - STD TI - Zhukova A, Sherman DJ. Knowledge-based metabolic model generalization library web page. http://metamogen.gforge.inria.fr. UR - http://metamogen.gforge.inria.fr ID - ref54 ER - TY - STD TI - Hucka M, Hoops S, Keating SM, Le Novère N, Sahle S, Wilkinson DJ. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. 2008. doi:10.1038/npre.2008.2715.1. ID - ref55 ER - TY - STD TI - Hucka M. SBML Level 3 Groups Proposal. 2012. http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Groups_Proposal_Updated_\%282012-06\%29. UR - http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Groups_Proposal_Updated_%282012-06%29 ID - ref56 ER - TY - JOUR AU - Büchel, F. AU - Rodriguez, N. AU - Swainston, N. AU - Wrzodek, C. AU - Czauderna, T. AU - Keller, R. PY - 2013 DA - 2013// TI - Path2Models: large-scale generation of computational models from biochemical pathway maps JO - BMC Syst Biol. VL - 7 UR - https://doi.org/10.1186/1752-0509-7-116 DO - 10.1186/1752-0509-7-116 ID - Büchel2013 ER - TY - STD TI - Diestel R. Graph Theory: Springer Graduate Text GTM 173: Reinhard Diestel; 2012, p. 451. http://identifiers.org/isbn/978-3-642-14278-9. UR - http://identifiers.org/isbn/978-3-642-14278-9 ID - ref58 ER - TY - CHAP AU - Auber, D. ED - Jünger, M. ED - Mutzel, P. ED - Farin, G. ED - Hege, H. -. C. ED - Hoffman, D. ED - Johnson, C. R. ED - Polthier, K. ED - Rumpf, M. PY - 2004 DA - 2004// TI - Tulip – A Huge Graph Visualization Framework BT - Graph Drawing Software. Mathematics and Visualization PB - Springer CY - Berlin Heidelberg ID - Auber2004 ER - TY - JOUR AU - Bornstein, B. J. AU - Keating, S. M. AU - Jouraku, A. AU - Hucka, M. PY - 2008 DA - 2008// TI - LibSBML: an API library for SBML JO - Bioinformatics. VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn051 DO - 10.1093/bioinformatics/btn051 ID - Bornstein2008 ER - TY - BOOK AU - Unwin, A. AU - Theus, M. AU - Hofmann, H. PY - 2006 DA - 2006// TI - Graphics of large datasets: visualizing a million PB - Springer CY - New York ID - Unwin2006 ER - TY - JOUR AU - Gabow, H. N. PY - 2000 DA - 2000// TI - Path-based depth-first search for strong and biconnected components JO - Inf Process Lett. VL - 74 UR - https://doi.org/10.1016/S0020-0190(00)00051-X DO - 10.1016/S0020-0190(00)00051-X ID - Gabow2000 ER - TY - STD TI - Hachul S, Jünger M. Large-graph layout with the fast multipole multilevel method. Technical report, Universität zu Köln, Institut für Informatik, Köln. 2005. http://e-archive.informatik.uni-koeln.de/509/. UR - http://e-archive.informatik.uni-koeln.de/509/ ID - ref63 ER - TY - JOUR AU - Sugiyama, K. AU - Tagawa, S. AU - Toda, M. PY - 1981 DA - 1981// TI - Methods for Visual Understanding of Hierarchical System Structures JO - IEEE Trans Syst Man Cybernet. VL - 11 UR - https://doi.org/10.1109/TSMC.1981.4308636 DO - 10.1109/TSMC.1981.4308636 ID - Sugiyama1981 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. PY - 2000 DA - 2000// TI - Gene Ontology: tool for the unification of biology JO - Nat Genet. VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - STD TI - Gauges R, Rost U, Sahle S, Wengler K, Bergmann FT. SBML Level 3 Layout Package Version 1 Release 1. 2013. http://identifiers.org/combine.specifications/sbml.level-3.version-1.layout.version-1.release-1 Accessed 23/10/14. UR - http://identifiers.org/combine.specifications/sbml.level-3.version-1.layout.version-1.release-1 ID - ref66 ER - TY - STD TI - Agafonkin V. Leaflet - a JavaScript library for mobile-friendly maps. http://leafletjs.com/. UR - http://leafletjs.com/ ID - ref67 ER - TY - STD TI - Butler H, Daly M, Doyle A, Gillies S, Schaub T, Schmidt C. GeoJSON Specification. http://geojson.org/geojson-spec.html. UR - http://geojson.org/geojson-spec.html ID - ref68 ER - TY - JOUR AU - Le Novère, N. AU - Hucka, M. AU - Mi, H. AU - Moodie, S. AU - Schreiber, F. AU - Sorokin, A. PY - 2009 DA - 2009// TI - The Systems Biology Graphical Notation JO - Nat Biotechnol. VL - 27 UR - https://doi.org/10.1038/nbt.1558 DO - 10.1038/nbt.1558 ID - Le Novère2009 ER - TY - STD TI - NCBI. NCBI Gene. http://www.ncbi.nlm.nih.gov/gene. ID - ref70 ER - TY - STD TI - Zhukova A, Sherman DJ. Mimoza web page. http://mimoza.bordeaux.inria.fr. UR - http://mimoza.bordeaux.inria.fr ID - ref71 ER - TY - STD TI - Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, 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. 1407.4992. ID - ref72 ER - TY - JOUR AU - Blankenberg, D. AU - Von Kuster, G. AU - Coraor, N. AU - Ananda, G. AU - Lazarus, R. AU - Mangan, M. PY - 2010 DA - 2010// TI - Galaxy: a web-based genome analysis tool for experimentalists JO - Current Protoc Mol Biol. VL - 19 ID - Blankenberg2010 ER - TY - STD TI - Böhringer K-F, Paulisch FN. Using constraints to achieve stability in automatic graph layout algorithms. In: Proceedings of the chi — conference on human factors in computing systems. ACM: 1990. p. 43–51. http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.35.7000. UR - http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.35.7000 ID - ref74 ER -