BioModels Database: A Repository of Mathematical Models of Biological Processes

  • Vijayalakshmi Chelliah
  • Camille Laibe
  • Nicolas Le Novère
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1021)

Abstract

BioModels Database is a public online resource that allows storing and sharing of published, peer-reviewed quantitative, dynamic models of biological processes. The model components and behaviour are thoroughly checked to correspond the original publication and manually curated to ensure reliability. Furthermore, the model elements are annotated with terms from controlled vocabularies as well as linked to relevant external data resources. This greatly helps in model interpretation and reuse. Models are stored in SBML format, accepted in SBML and CellML formats, and are available for download in various other common formats such as BioPAX, Octave, SciLab, VCML, XPP and PDF, in addition to SBML. The reaction network diagram of the models is also available in several formats. BioModels Database features a search engine, which provides simple and more advanced searches. Features such as online simulation and creation of smaller models (submodels) from the selected model elements of a larger one are provided. BioModels Database can be accessed both via a web interface and programmatically via web services. New models are available in BioModels Database at regular releases, about every 4 months.

Key words

Controlled vocabularies, model interpretation SBML CellML Reaction network diagram 

References

  1. 1.
    Le Novère N, Bornstein B, Broicher A (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
  2. 2.
    Li C, Donizelli M, Rodriguez N et al (2010) BioModels Database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 4:92PubMedCrossRefGoogle Scholar
  3. 3.
    Le Novère N (2006) Model storage, exchange and integration. BMC Neurosci 7(Suppl 1):S11PubMedCrossRefGoogle Scholar
  4. 4.
    Snoep JL, Olivier BG (2002) Java Web Simulation (JWS); a web based database of kinetic models. Mol Biol Rep 29:259–263PubMedCrossRefGoogle Scholar
  5. 5.
    Lloyd CM, Halstead MDB, Nielsen PF (2004) CellML: its future, present and past. Prog Biophys Mol Biol 85:433–450PubMedCrossRefGoogle Scholar
  6. 6.
    Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29PubMedCrossRefGoogle Scholar
  7. 7.
    Hucka M, Finney A, Sauro HM (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19:524–531PubMedCrossRefGoogle Scholar
  8. 8.
    Le Novère N, Finney A, Hucka et al (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 23:1509–1515PubMedCrossRefGoogle Scholar
  9. 9.
    Hoops S, Sahle S, Gauges (2006) COPASI–a COmplex PAthway SImulator. Bioinformatics 22:3067–3074PubMedCrossRefGoogle Scholar
  10. 10.
    Mendes P, Hoops S, Sahle S (2009) Computational modeling of biochemical networks using COPASI. Methods Mol Biol 500(17–59):2009Google Scholar
  11. 11.
    Machné R, Finney A, Müller S (2006) The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics 22(1406–1407):2006Google Scholar
  12. 12.
    Bergmann FT, Sauro HM (2006) SBW—a modular framework for systems biology. pp. 37–1645.Google Scholar
  13. 13.
    Orth JD, Thiele I, Palsson BØ (2010) What is flux balance analysis? Nat Biotechnol 28:245–248PubMedCrossRefGoogle Scholar
  14. 14.
    Juty N, Le Novère N, Laibe C (2012) Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res 40:D580–D586PubMedCrossRefGoogle Scholar
  15. 15.
    Laibe C, Novère NL (2007) MIRIAM Resources: tools to generate and resolve robust cross-references in systems biology. BMC Syst Biol 1:58PubMedCrossRefGoogle Scholar
  16. 16.
    Demir E, Cary MP, Paley S et al (2010) The BioPAX community standard for pathway data sharing. Nat Biotechnol 28:935–942PubMedCrossRefGoogle Scholar
  17. 17.
    Moraru II, Schaff JC, Slepchenko BM (2008) Virtual cell modelling and simulation software environment. IET Syst Biol 2:352–362PubMedCrossRefGoogle Scholar
  18. 18.
    Ermentrout, B. (2002) Simulating, analyzing, and animating dynamical systems: a guide to XPPAUT for researchers and studentsGoogle Scholar
  19. 19.
    Dräger A, Planatscher H, Motsou W et al (2009) SBML2L(A)T(E)X: conversion of SBML files into human-readable reports. Bioinformatics 25:1455–1456PubMedCrossRefGoogle Scholar
  20. 20.
    Le Novère N, Hucka M, Mi H, Moodie S et al (2009) The systems biology graphical notation. Nat Biotechnol 27:735–741PubMedCrossRefGoogle Scholar
  21. 21.
    Li C, Courtot M, Le Novère N, Laibe C (2010) BioModels.net web services, a free and integrated toolkit for computational modelling software. Brief Bioinform 11:270–277PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Vijayalakshmi Chelliah
    • 1
  • Camille Laibe
    • 1
  • Nicolas Le Novère
    • 2
  1. 1.EMBL Outstation–European Bioinformatics InstituteCambridgeUK
  2. 2.Babraham InstituteCambridgeUK

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