The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models

Bioinformatics

Volumn 19, Issue 4, 2003, Pages 524-531

  Hucka, M ^a,b   Finney, A ^a,b   Sauro, H M ^a,b   Bolouri, H ^a,b,c   Doyle, J C ^a   Kitano, H ^a,b,d,o,q   Arkin, A P ^e   Bornstein, B J ^f   Bray, D ^g   Cornish Bowden, A ^h   Cuellar, A A ⁱ   Dronov, S ^j   Gilles, E D ^k   Ginkel, M ^k   Gor, V ^f   Goryanin, I I ^j   Hedley, W J ⁱ   Hodgman, T C ^j   Hofmeyr, J H ^l   Hunter, P J ⁱ   Juty, N S ^j   Kasberger, J L ^e   Kremling, A ^k   Kummer, U ^t   Le Novere N ^g   Loew, L M ^m   Lucio, D ^m   Mendes, P ⁿ   Minch, E ^r   Mjolsness, E D ^s   Nakayama, Y ^o   Nelson, M R ^p   Nielsen, P F ⁱ   Sakurada, T ^o   Schaff, J C ^m   Shapiro, B E ^f   Shimizu, T S ^g   Spence, H D ^j   Stelling, J ^k   Takahashi, K ^o   Tomita, M ^o   Wagner, J ^m   Wang, J ^p   more..

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c UNIVERSITY OF HERTFORDSHIRE   (United Kingdom)

^d Systems Biology Institute   (Japan)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^g UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^h CNRS   (France)

ⁱ UNIVERSITY OF AUCKLAND   (New Zealand)

^j GLAXOSMITHKLINE   (United Kingdom)

^k MAX PLANCK INSTITUTE FOR DYNAMICS OF COMPLEX TECHNICAL SYSTEMS   (Germany)

^l STELLENBOSCH UNIVERSITY   (South Africa)

^m UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

ⁿ VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^o KEIO UNIVERSITY   (Japan)

^p Physiome Sciences   (United States)

^q SONY COMPUTER SCIENCE LABORATORIES INC   (Japan)

^r Axaron Bioscience AG   (Germany)

^s UNIVERSITY OF CALIFORNIA   (United States)

^t NONE

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOCHEMISTRY; BIOTECHNOLOGY; CELL FUNCTION; CELL METABOLISM; COMPUTER LANGUAGE; COMPUTER MODEL; COMPUTER PROGRAM; COMPUTER SYSTEM; GENE CONTROL; MEDICAL RESEARCH; MOLECULAR BIOLOGY; PRIORITY JOURNAL; SIGNAL TRANSDUCTION;

DATABASE MANAGEMENT SYSTEMS; DATABASES, FACTUAL; DOCUMENTATION; GENE EXPRESSION REGULATION; HYPERMEDIA; INFORMATION STORAGE AND RETRIEVAL; METABOLISM; MODELS, BIOLOGICAL; MODELS, CHEMICAL; PROGRAMMING LANGUAGES; SOFTWARE; SOFTWARE DESIGN; TERMINOLOGY; VOCABULARY, CONTROLLED;

EID: 0037342537     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg015     Document Type: Article

References (24)

1. Abbott,A. (1999) Alliance of US labs plans to build map of cell signaling pathways. Nature, 402, 219-220.
2. Achard,F., Vaysseix,G. and Barillot,E. (2001) XML, bioinformatics and data integration. Bioinformatics, 17, 115-125.
3. Arkin,A.P. (2001) Simulac & Deduce. Available via the World Wide Web at http://gobi.lbl.gov/~aparkin.
4. Biron,P.V. and Malhotra,A. (2000) XML Schema part 2: Datatypes, Available via the World Wide Web at http://www.w3.org/TR/xmlschema-2/.
5. Bray,T., Paoli,J. and Sperberg-McQueen,C.M. (1998) Extensible markup language (XML) 1.0, Available via the World Wide Web at http://www.w3.org/TR/1998/REC-xml-19980210.
6. Brown,C.T., Rust,A.G., Clarke,P.J.C., Pan,Z., Schilstra,M.J., De Buysshcher,T., Griffin,G., Wold,B.J., Cameron,R.A., Davidson,E.H. and Bolouri,H. (2002) New computational approaches for analysis of cis-regulatory networks. Developmental Biology, 246, 86-102.
7. Bureau International des Poids et Mesures (2000) The International System of Units (SI) supplement 2000. Available via the World Wide Web at http://www.bipm.fr/pdf/si-supplement2000.pdf.
8. Ginkel,M., Kremling,A., Tränkle,F., Gilles,E.D. and Zeitz,M. (2000) Application of the process modeling tool ProMoT to the modeling of metabolic networks. In Troch,I. and Breitenecker,F. (eds), Proc. of the 3rd MATHMOD.
9. Goryanin,I., Hodgman,T.C. and Selkov,E. (1999) Mathematical simulation and analysis of cellular metabolism and regulation. Bioinformatics, 15, 749-758.
10. Hedley,W.J., Nelson,M.R., Bullivant,D.P. and Nielson,P.F. (2001) A short introduction to CellML. Phil. Trans. Roy. Soc. London A, 359, 1073-1089.
11. Hucka,M., Finney,A., Sauro,H.M. and Bolouri,H. (2003) Systems Biology Markup Language (SBML) Level 1: Structures and facilities for basic model definitions, Available via the World Wide Web at http://www.sbml.org/.
12. Kitano,H. (2002) Systems biology: a brief overview. Science, 295, 1662-1664.
13. Mendes,P. (1997) Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci., 22, 361-363.
14. Morton-Firth,C.J. and Bray,D. (1998) Predicting temporal fluctuations in an intracellular signalling pathway. J. Theor. Biol., 192, 117-128.
15. Object Management Group (2002) UML Specification documents available via the World Wide Web at http://www.omg.org/uml/.
16. Sauro,H.M. (2000) Jarnac: a system for interactive metabolic analysis. In Hofmeyr,J.-H., Rohwer,J. and Snoep,J. (eds), Animating the Cellular Map. Stellenbosch Univ. Press.
17. Schaff,J., Slepchenko,B., Morgan,F., Wagner,J., Resasco,D., Shin,D., Choi,Y.S., Loew,L., Carson,J., Cowan,A. et al. (2001) Virtual Cell. Available via the World Wide Web at http://www.nrcam.uchc.edu.
18. Schuster,S., Fell,D.A. and Dandekar,T. (2000) A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol., 18, 326-332.
19. Shapiro,B.E. and Mjolsness,E.D. (2001) Developmental simulations with Cellerator. In Yi,T.-M., Hucka,M., Morohashi,M. and Kitano,H. (eds), Proceedings of the Second International Conference on Systems Biology (ICSB2001). Omnipress.
20. Skonnard,A. and Gudgin,M. (2001) Essential XML Quick Reference, Addison-Wesley.
21. Thompson,H.S., Beech,D., Maloney,M. and Mendelsohn,N. (2000) XML Schema part 1: Structures. Available via the World Wide Web at http://www.w3.org/TR/xmlschema-1/.
22. Tomita,M., Nakayama,Y., Naito,Y., Shimizu,T., Hashimoto,K., Takahashi,K., Matsuzaki,Y., Yugi,K., Miyoshi,F., Saito,Y. et al. (2001) E-Cell. Available via the World Wide Web at http://www.e-cell.org/.
23. Unicode Consortium, (1996) The Unicode Standard, Version 2.0. Addison-Wesley Developers Press.
24. C, (2000) W3C's math home page. Available via the World Wide Web at http://www.w3.org/Math/.