SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

TitleSBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
Publication TypeJournal Article
Year of Publication2013
AuthorsChaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T
JournalBMC Syst Biol
Volume7
Pagination135
PubMed Date12/2013
ISSN1752-0509
KeywordsAnimals, Cells, Epidermal Growth Factor, Internet, Models, Biological, Programming Languages, Signal Transduction, Tumor Necrosis Factor-alpha
Abstract

BACKGROUND: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing.
RESULTS: We present the Systems Biology Markup Language (SBML) Qualitative Models Package ("qual"), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the collective effort to define the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyse qualitative models.
CONCLUSIONS: SBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks.

Alternate JournalBMC Syst Biol
PubMed ID24321545
PubMed Central IDPMC3892043
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