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| The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models |
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| Author(s): Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J |
| Source: BIOINFORMATICS Volume: 19 Issue: 4 Pages: 524-531 Published: MAR 1 2003 |
| Times Cited: 493 References: 24 |
| Abstract: Motivation: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. Results: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others.
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| Document Type: Article |
| Language: English |
| Reprint Address: Hucka, M (reprint author), CALTECH, MC 107-81, Pasadena, CA 91125 USA |
Addresses:
1. CALTECH, Pasadena, CA 91125 USA
2. ERATO, Kitano Symbiot Syst Project, Tokyo, Japan
3. Univ Hertfordshire, Hatfield AL10 9AB, Herts England
4. Syst Biol Inst, Tokyo, Japan
5. Univ Calif Berkeley, Berkeley, CA 94720 USA
6. NASA, JPL, Pasadena, CA USA
7. Univ Cambridge, Cambridge, England
8. CNRS, BIP, Marseille, France
9. Univ Auckland, Auckland 1, New Zealand
10. GlaxoSmithKline, Stevenage, Herts England
11. Max Planck Inst Complex Tech Syst, Magdeburg, Germany
12. Univ Stellenbosch, ZA-7600 Stellenbosch, South Africa
13. EML, Heidelberg, Germany
14. Univ Connecticut, Ctr Hlth, Farmington, CT USA
15. Virginia Bioinformat Inst, Blacksburg, VA USA
16. Keio Univ, Tokyo, Japan
17. Physiome Sci Inc, Princeton, NJ USA
18. Sony Comp Sci Labs Inc, Tokyo, Japan
19. LION Biosci AG, Heidelberg, Germany
20. Univ Calif Irvine, Sch Informat & Comp Sci, Irvine, CA USA |
| Publisher: OXFORD UNIV PRESS, GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND |
| Subject Category: Biochemical Research Methods; Biotechnology & Applied Microbiology; Computer Science, Interdisciplinary Applications; Mathematical & Computational Biology; Statistics & Probability |
| IDS Number: 652ZL |
| ISSN: 1367-4803 |
| DOI: 10.1093/bioinformatics/btg015 |
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