Supporting SBML as a Model Exchange Format in Software Applications

  • Sarah M. Keating
  • Nicolas Le Novère
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1021)

Abstract

This chapter describes the Systems Biology Markup Language (SBML) from its origins. It describes the rationale behind and importance of having a common language when it comes to representing models. This chapter mentions the development of SBML and outlines the structure of an SBML model. It provides a section on libSBML, a useful application programming interface (API) library for reading, writing, manipulating and validating content expressed in the SBML format. Finally the chapter also provides a description of the SBML Toolbox which provides a means of facilitating the import and export of SBML from both MATLAB and Octave (http://www.gnu.org/software/octave/) environments.

Key words

SBML Systems biology standards Reproducibility Exchange format Language 

References

  1. 1.
    Kell DB, Mendes P (2008) The markup is the model: reasoning about systems biology models in the Semantic. Web era. J Theor Biol 252:538–543PubMedCrossRefGoogle Scholar
  2. 2.
    Hedley W, Nelson MR, Bullivant DP, Nielsen PF (2001) A short introduction to CellML. Philos Transact A Math Phys Eng Sci 359(5):1073–1079CrossRefGoogle Scholar
  3. 3.
    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 Novère 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, SBML Forum (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4):524–31PubMedCrossRefGoogle Scholar
  4. 4.
    Bray T, Paoli J, Sperberg-McQueen CM, Maler E (2000) Extensible Markup Language (XML) 1.0 (second edition), W3C recommendation 6-October-2000. Available via the World Wide Web at http://www.w3.org/TR/1998/REC-xml-19980210.
  5. 5.
    Stromback L, Lambrix P (2005) Representations of molecular pathways: an evaluation of SBML, PSI ML and BioPAX. Bioinformatics 21(24):4401–4407PubMedCrossRefGoogle Scholar
  6. 6.
    Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M (2006) BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 34:D689–D691PubMedCrossRefGoogle Scholar
  7. 7.
    Goldbeter A (1991) A minimal cascase model for the mitotic oscillator involving cyclin and cdc2 kinase. Proc Natl Acad Sci U S A 88(20):9107–9111PubMedCrossRefGoogle Scholar
  8. 8.
    Curto R, Voit EO, Sorribas A, Cascante M (1998) Mathematical models of purine metabolism in man. Math Biosci 151(1):1–49PubMedCrossRefGoogle Scholar
  9. 9.
    ElowitzMB LS (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403(6767):335–338CrossRefGoogle Scholar
  10. 10.
    Hodgkin AL, Huxley AF (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117(5):500–544PubMedGoogle Scholar
  11. 11.
    Izhikevich EM (2004) Simple model of spiking neurons. IEEE Trans Neural Netw 14(6):1569–1573CrossRefGoogle Scholar
  12. 12.
    Tham LS, Wang L, Soo RA, Lee SC, Lee HS, Yong WP, Goh BC, Holford NH (2008) A pharmacodynamic model for the time course of tumor shrinkage by gemcitabine + carboplatin in non-small cell lung cancer patients. Clin Cancer Res 14:4213–4218PubMedCrossRefGoogle Scholar
  13. 13.
    Munz P, Hudea I, Imad J, Smith RJ (2009) When zombies attack!: Mathematical modelling of an outbreak of zombie infection. In: Tchuenche JM, Chiyaka C (eds) Infectious disease modelling research progress. Nova Science, New York, pp 133–150Google Scholar
  14. 14.
    Hucka M, Bergmann F, Hoops S, Keating SM, Sahle S, Wilkinson DJ (2009) The Systems Biology Markup Language (SBML) language specification for level 3 version 1 core. Available via the World Wide Web at http://www.sbml.org/Documents/Specifications.
  15. 15.
    Hucka M, Hoops S, Keating SM, Le Nov`ere N, Sahle S, Wilkinson DJ (2008) Systems Biology Markup Language (SBML) level 2: Structures and facilities for model definitions. Available via the World Wide Web at http://www.sbml.org/Documents/Specifications.
  16. 16.
    Hucka M, Finney A, Sauro HM, Bolouri H (2001) 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/Documents/Specifications.
  17. 17.
    Ausbrooks R, Buswell S, Carlisle D, Dalmas S, Devitt S, Diaz A, Froumentin M, Hunter R, Ion P, Kohlhase M,Miner R, Poppelier N, Smith B, Soiffer N, Sutor R, Watt S (2003) Mathematical Markup Language (MathML) version 2.0 (second edition). Available via the World Wide Web at http://www.w3.org/TR/MathML2/
  18. 18.
    Bornstein BJ, Keating SM, Jouraku A, Hucka M (2008) LibSBML: an API library for SBML. Bioinformatics 24(6):880–881PubMedCrossRefGoogle Scholar
  19. 19.
    Dräger A, Rodriguez N, Dumousseau M, Dörr A, Wrzodek C, Le Novère N, Zell A, Hucka M (2011) JSBML: a flexible Java library for working with SBML. Bioinformatics 27(15):2167–2168PubMedCrossRefGoogle Scholar
  20. 20.
    Keating SM, Bornstein BJ, Finney A, Hucka M (2006) SBMLToolbox: an SBML toolbox for MATLAB users. Bioinformatics 22(10):1275–1277PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Sarah M. Keating
    • 1
  • Nicolas Le Novère
    • 2
  1. 1.EMBL Outstation–European Bioinformatics InstituteCambridgeUK
  2. 2.Babraham InstituteCambridgeUK

Personalised recommendations