Bioinformatics Vol. 19 no. 4 2003
Pages 524-531
© 2003 Oxford University Press
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
1 Control and Dynamical Systems, MC 107-81,
California Institute of Technology, Pasadena, CA 91125, USA
2 ERATO Kitano Symbiotic Systems Project, Tokyo, Japan
3 University of Hertfordshire, Hertfordshire, UK
4 The Systems Biology Institute, Tokyo, Japan
5 University of California, Berkeley, CA, USA
6 NASA JPL, Pasadena, CA, USA
7 University of Cambridge, Cambridge, UK
8 CNRS-BIP, Marseille, France
9 University of Auckland, Auckland, New Zealand
10 GlaxoSmithKline, Stevenage, UK
11 Max-Planck-Institute for Complex Technical Systems, Magdeburg, Germany
12 University of Stellenbosch, Stellenbosch, South Africa
13 EML, Heidelberg, Germany
14 University of Connecticut Health Center, Farmington, CT, USA
15 Virginia Bioinformatics Institute,
Blacksburg, VA, USA
16 Keio University, Tokyo, Japan
17 Physiome Sciences Inc., Princeton, NJ,
USA
18 Sony Computer Science Laboratories,
Inc., Tokyo, Japan
19 LION bioscience AG, Heidelberg, Germany
20 School of Information and Computer
Science, University of California, Irvine, CA, USA
Received on May 17, 2002
; revised on October 15, 2002
; accepted on October 25, 2002
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.
Availability: The specification of SBML Level 1 is freely available from http://www.sbml.org/
Contact: sysbio-team{at}caltech.edu
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  R. Breitling, D. Gilbert, M. Heiner, and R. Orton A structured approach for the engineering of biochemical network models, illustrated for signalling pathways Brief Bioinform, September 1, 2008; 9(5): 404 - 421. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A.M. Willemsen, G.A. Jansen, J.C. Komen, S. van Hooff, H.R. Waterham, P.M.T. Brites, R.J.A. Wanders, and A.H.C. van Kampen Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways Bioinformatics, August 15, 2008; 24(16): i21 - i27. [Abstract] [PDF]
|
|
|
|
|
|
J. Saez-Rodriguez, S. Gayer, M. Ginkel, and E. D. Gilles Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules Bioinformatics, August 15, 2008; 24(16): i213 - i219. [Abstract] [PDF]
|
|
|
|
|
|
A. Weidemann, S. Richter, M. Stein, S. Sahle, R. Gauges, R. Gabdoulline, I. Surovtsova, N. Semmelrock, B. Besson, I. Rojas, et al. SYCAMORE--a systems biology computational analysis and modeling research environment Bioinformatics, June 15, 2008; 24(12): 1463 - 1464. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. P. Nickerson, A. Corrias, and M. L. Buist Reference descriptions of cellular electrophysiology models Bioinformatics, April 15, 2008; 24(8): 1112 - 1114. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. J. Bornstein, S. M. Keating, A. Jouraku, and M. Hucka LibSBML: an API Library for SBML Bioinformatics, March 15, 2008; 24(6): 880 - 881. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. W. Evans, C. S. Gillespie, and D. J. Wilkinson The SBML discrete stochastic models test suite Bioinformatics, January 15, 2008; 24(2): 285 - 286. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Li, T. Oinn, S. Soiland, and D. B. Kell Automated manipulation of systems biology models using libSBML within Taverna workflows Bioinformatics, January 15, 2008; 24(2): 287 - 289. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Grafahrend-Belau, S. Weise, D. Koschutzki, U. Scholz, B. H. Junker, and F. Schreiber MetaCrop: a detailed database of crop plant metabolism Nucleic Acids Res., January 11, 2008; 36(suppl_1): D954 - D958. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Alfieri, I. Merelli, E. Mosca, and L. Milanesi The cell cycle DB: a systems biology approach to cell cycle analysis Nucleic Acids Res., January 11, 2008; 36(suppl_1): D641 - D645. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Romano Automation of in-silico data analysis processes through workflow management systems Brief Bioinform, January 1, 2008; 9(1): 57 - 68. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Long and M. Roth Synthetic microarray data generation with RANGE and NEMO Bioinformatics, January 1, 2008; 24(1): 132 - 134. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. GONG and Z. ZHANG CellFrame: A Data Structure for Abstraction of Cell Biology Experiments and Construction of Perturbation Networks Ann. N.Y. Acad. Sci., December 1, 2007; 1115(1): 249 - 266. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. N. GUTENKUNST, F. P. CASEY, J. J. WATERFALL, C. R. MYERS, and J. P. SETHNA Extracting Falsifiable Predictions from Sloppy Models Ann. N.Y. Acad. Sci., December 1, 2007; 1115(1): 203 - 211. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Kurata, K. Inoue, K. Maeda, K. Masaki, Y. Shimokawa, and Q. Zhao Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis Nucleic Acids Res., November 29, 2007; 35(20): e134 - e134. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Wierling, R. Herwig, and H. Lehrach Resources, standards and tools for systems biology Brief Funct Genomic Proteomic, October 17, 2007; (2007) elm027v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Suderman and M. Hallett Tools for visually exploring biological networks Bioinformatics, October 15, 2007; 23(20): 2651 - 2659. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. D. Burgoon Clearing the Standards Landscape: the Semantics of Terminology and their Impact on Toxicogenomics Toxicol. Sci., October 1, 2007; 99(2): 403 - 412. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Vera, C. Sun, Y. Oertel, and O. Wolkenhauer PLMaddon: a power-law module for the MatlabTM SBToolbox Bioinformatics, October 1, 2007; 23(19): 2638 - 2640. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. S. Srinivasan, N. H. Shah, J. A. Flannick, E. Abeliuk, A. F. Novak, and S. Batzoglou Current progress in network research: toward reference networks for key model organisms Brief Bioinform, September 1, 2007; 8(5): 318 - 332. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Rodrigo, J. Carrera, and A. Jaramillo Genetdes: automatic design of transcriptional networks Bioinformatics, July 15, 2007; 23(14): 1857 - 1858. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Khatri, C. Voichita, K. Kattan, N. Ansari, A. Khatri, C. Georgescu, A. L. Tarca, and S. Draghici Onto-Tools: new additions and improvements in 2006 Nucleic Acids Res., July 13, 2007; 35(suppl_2): W206 - W211. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Schmidt, G. Drews, J. Vera, and O. Wolkenhauer SBML export interface for the systems biology toolbox for MATLAB Bioinformatics, May 15, 2007; 23(10): 1297 - 1298. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. C. Duarte, S. A. Becker, N. Jamshidi, I. Thiele, M. L. Mo, T. D. Vo, R. Srivas, and B. O. Palsson Global reconstruction of the human metabolic network based on genomic and bibliomic data PNAS, February 6, 2007; 104(6): 1777 - 1782. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Kolpakov, V. Poroikov, R. Sharipov, Y. Kondrakhin, A. Zakharov, A. Lagunin, L. Milanesi, and A. Kel CYCLONET--an integrated database on cell cycle regulation and carcinogenesis Nucleic Acids Res., January 12, 2007; 35(suppl_1): D550 - D556. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Mi, N. Guo, A. Kejariwal, and P. D. Thomas PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways Nucleic Acids Res., January 12, 2007; 35(suppl_1): D247 - D252. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. C. Mak, M. Daly, B. Gruebel, and T. Ideker CellCircuits: a database of protein network models Nucleic Acids Res., January 12, 2007; 35(suppl_1): D538 - D545. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. D. Vo and B. O. Palsson Building the power house: recent advances in mitochondrial studies through proteomics and systems biology Am J Physiol Cell Physiol, January 1, 2007; 292(1): C164 - C177. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus, M. Singhal, L. Xu, P. Mendes, and U. Kummer COPASI--a COmplex PAthway SImulator Bioinformatics, December 15, 2006; 22(24): 3067 - 3074. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Eccher and C. Priami Design and implementation of a tool for translating SBML into the biochemical stochastic {pi}-calculus Bioinformatics, December 15, 2006; 22(24): 3075 - 3081. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Stromback, V. Jakoniene, H. Tan, and P. Lambrix Representing, storing and accessing molecular interaction data: a review of models and tools Brief Bioinform, December 1, 2006; 7(4): 331 - 338. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Gilbert, H. Fuss, X. Gu, R. Orton, S. Robinson, V. Vyshemirsky, M. J. Kurth, C. S. Downes, and W. Dubitzky Computational methodologies for modelling, analysis and simulation of signalling networks Brief Bioinform, December 1, 2006; 7(4): 339 - 353. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Sanford, M. L.K. Yip, C. White, and J. Parkinson Cell++--simulating biochemical pathways Bioinformatics, December 1, 2006; 22(23): 2918 - 2925. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Deckard, F. T. Bergmann, and H. M. Sauro Supporting the SBML layout extension Bioinformatics, December 1, 2006; 22(23): 2966 - 2967. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Hyland, J. W. Pinney, G. A. McConkey, and D. R. Westhead metaSHARK: a WWW platform for interactive exploration of metabolic networks. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W725 - W728. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. S. Dasika, A. Burgard, and C. D. Maranas A Computational Framework for the Topological Analysis and Targeted Disruption of Signal Transduction Networks Biophys. J., July 1, 2006; 91(1): 382 - 398. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. L. Castle, O. Fiehn, R. Kaddurah-Daouk, and J. C. Lindon Metabolomics Standards Workshop and the development of international standards for reporting metabolomics experimental results Brief Bioinform, June 1, 2006; 7(2): 159 - 165. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Machne, A. Finney, S. Muller, J. Lu, S. Widder, and C. Flamm The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks Bioinformatics, June 1, 2006; 22(11): 1406 - 1407. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D.-Y. Lee, C. Yun, A. Cho, B. K. Hou, S. Park, and S. Y. Lee WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks Bioinformatics, May 1, 2006; 22(9): 1150 - 1151. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Schilstra, L. Li, J. Matthews, A. Finney, M. Hucka, and N. Le Novere CellML2SBML: conversion of CellML into SBML Bioinformatics, April 15, 2006; 22(8): 1018 - 1020. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. S. Gillespie, D. J. Wilkinson, C. J. Proctor, D. P. Shanley, R. J. Boys, and T. B. L. Kirkwood Tools for the SBML Community Bioinformatics, March 1, 2006; 22(5): 628 - 629. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. R. Boverhof and T. R. Zacharewski Toxicogenomics in Risk Assessment: Applications and Needs Toxicol. Sci., February 1, 2006; 89(2): 352 - 360. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. Dogrusoz, E. Z. Erson, E. Giral, E. Demir, O. Babur, A. Cetintas, and R. Colak PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization Bioinformatics, February 1, 2006; 22(3): 374 - 375. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. R. Vallabhajosyula, V. Chickarmane, and H. M. Sauro Conservation analysis of large biochemical networks Bioinformatics, February 1, 2006; 22(3): 346 - 353. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. D. Bader, M. P. Cary, and C. Sander Pathguide: a Pathway Resource List Nucleic Acids Res., January 1, 2006; 34(suppl_1): D504 - D506. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Le Novere, B. Bornstein, A. Broicher, M. Courtot, M. Donizelli, H. Dharuri, L. Li, H. Sauro, M. Schilstra, B. Shapiro, et al. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems Nucleic Acids Res., January 1, 2006; 34(suppl_1): D689 - D691. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Stromback and P. Lambrix Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX Bioinformatics, December 15, 2005; 21(24): 4401 - 4407. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Teusink, F. H. J. van Enckevort, C. Francke, A. Wiersma, A. Wegkamp, E. J. Smid, and R. J. Siezen In Silico Reconstruction of the Metabolic Pathways of Lactobacillus plantarum: Comparing Predictions of Nutrient Requirements with Those from Growth Experiments Appl. Envir. Microbiol., November 1, 2005; 71(11): 7253 - 7262. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Hunter and P. Nielsen A Strategy for Integrative Computational Physiology Physiology, October 1, 2005; 20(5): 316 - 325. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Yun, D.-Y. Lee, J. Jeong, S. Lee, and S. Y. Lee MFAML: a standard data structure for representing and exchanging metabolic flux models Bioinformatics, August 1, 2005; 21(15): 3329 - 3330. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Hu, J. Mellor, J. Wu, T. Yamada, D. Holloway, and C. DeLisi VisANT: data-integrating visual framework for biological networks and modules Nucleic Acids Res., July 1, 2005; 33(suppl_2): W352 - W357. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Mlecnik, M. Scheideler, H. Hackl, J. Hartler, F. Sanchez-Cabo, and Z. Trajanoski PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways Nucleic Acids Res., July 1, 2005; 33(suppl_2): W633 - W637. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Hattne, D. Fange, and J. Elf Stochastic reaction-diffusion simulation with MesoRD Bioinformatics, June 15, 2005; 21(12): 2923 - 2924. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. I. Moraru and L. M. Loew Intracellular Signaling: Spatial and Temporal Control Physiology, June 1, 2005; 20(3): 169 - 179. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|