VRML metabolic network visualizer

Computers in Biology and Medicine

Volumn 33, Issue 2, 2003, Pages 169-182

  Rojdestvenski, Igor ^a  

^a UMEÅ UNIVERSITY   (Sweden)

Author keywords

Biochemical; Database; Metabolic pathway; Visualization; VRML

Indexed keywords

COMPUTER SOFTWARE; INTERNET; METABOLISM;

METABOLIC NETWORK VISUALIZERS;

THREE DIMENSIONAL COMPUTER GRAPHICS;

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER LANGUAGE; COMPUTER PROGRAM; DATA BASE; ENGINEERING; INFORMATION PROCESSING; INTERNET; METABOLISM; MODEL; PRIORITY JOURNAL; THREE DIMENSIONAL IMAGING; VIRTUAL REALITY;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATA COLLECTION; DATABASES, FACTUAL; METABOLISM; MODELS, BIOLOGICAL; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 0037357156     PISSN: 00104825     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0010-4825(02)00062-8     Document Type: Article

References (26)

1. Boguski M.S. The turning point in genome research. Trends Biochem. Sci. 20:1995;295.
2. Chen C. Information Visualisation and Virtual Environments. 1999;Springer, London.
3. Waterworth J. Earnshaw R., Vince J. 3D on the Internet: Information, Images and Interaction. 1996a;97 Academic Press, New York.
4. Waterworth J. A pattern of islands: exploring public information space in a private vehicle. Brusilovsky P., Kommers P., Streitz N. Multimedia, Hypermedia and Virtual Reality, Lecture Notes in Computer Science. 1996b;Springer, Berlin.
5. Waterworth J. Creativity and sensation. the case for 'Synaesthetic Media' Leonardo. 30:1997;327.
6. D. Modjeska, Parallel worlds: spatial and textual representations of information structure, in: Workshop on Personalised and Social Navigation in Information Space, Swedish Institute of Computer Science, Stockholm, 1998.
7. I. Rojdestvenski, D. Modjeska, F. Pettersson, M. Rojdestvenskaia, P. Gustafsson, Sequence world: a genetics database in virtual reality, in: E. Banissi, M. Bannatyne, C. Chen (Eds.), Proceedings of the Information Visualization 2000 Conference (IV2000), London, UK, 2000, pp. 513-517.
8. Kanehisa M. Toward pathway engineering. a new database of genetic and molecular pathways Sci. Technol. Japan. 59:1996;34-38.
9. Kanehisa M. KEGG: from genes to biochemical pathways. Letovsky S. Bioinformatics: Databases and Systems. 1999;63-76 Kluwer Academic Publishers, Dordrecht.
10. Takai-Igarashi T., Kaminuma T. A pathway finding system for the cell signaling networks database. In Silico Biology. 1:1999;129-146.
11. Tsukamoto Y., Takiguchi K., Satou K., Furuichi E., Takagi T., Kuhara S. Application of a deductive database system for topological and similar three dimensional structures in protein. CABIOS. 13:1997;183.
12. Becker M.Y., Rojas I. A graph layout algorithm for drawing metabolic pathways. Bioinformatics. 17(5):2001;461-467.
13. A.J. Robinson, T.P. Flores, Novel techniques for visualizing biological information, ISMB'97, http://industry.ebi.ac.uk/~alan/Papers/ISMB97/.
14. Rojdestvenski I., Cottam M. Mapping of statistical physics to information theory with application to biological systems. J. Theor. Biol. 202:2000b;43-54.
15. Rojdestvenski I., Cottam M. Diagrammatic approach to calculation of the fluctuation correlation matrix in a metabolic system. BioSystems. 56:2000c;63-73.
16. Coombs J.H., Renear A.H., DeRose S.J. Markup systems and the future of scholarly text processing. Commun. Assoc. Comput. Mach. 30/11:1987;933-947. ISSN: 0001-0782.
17. H. Bolouri, A. Finney, M. Hucka, H. Sauro, J. Doyle, H. Kitano, The ERATO Systems Biology Workbench: an integrated environment for multiscale & multi-theoretic simulations of molecular biology, The First International Conference on Systems Biology (ICSB), Japan, November 14-16, 2000.
18. M. Hucka, A. Finney, H. Sauro, H. Bolouri, Systems Biology Markup Language (SBML) Level 1: Structures and Facilities for Basic Model Definitions, SBML Level 1, Version 1 (Final), 2 March 2001, http://www.cds.caltech.edu/erato.
19. Kolpakov F.A., Ananko E.A., Kolesov G.B., Kolchanov N.A. GeneNet. a gene network database and its automated visualization Bioinformatics. 14:1998;529-537.
20. Heldt H.-W. Plant Biochemistry and Molecular Biology. 1997;Oxford University Press, Oxford.
21. C. Keskin, V. Vogelmann, Effective visualization of hierarchical graphs with the cityscape metaphor, Workshop on New Paradigms in Information Visualization and Manipulation, 1997, pp. 52-57.
22. D. Modjeska, View vs. Overview: Hierarchical Data Visualization in Desktop Virtual Reality, Proceedings of NordiCHI 2000, STIMDI, Stockholm, Sweden, 2000a.
23. D. Modjeska, Hierarchical data visualization in desktop virtual reality, Ph.D. Thesis, University of Toronto, 2000b.
24. Mendes P. Biochemistry by numbers. simulation of biochemical pathways with Gepasi 3 Trends Biochem. Sci. 22:1997;361-363.
25. Delgado J., Liao J.C. Control of metabolic pathways by time-scale separation. BioSystems. 36:1995;55-70.
26. Cornish-Bowden A. Fundamentals of Enzyme Kinetics. 1995;Portland Press, London.