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

Détails

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Etat: Public
Version: de l'auteur
ID Serval
serval:BIB_9B75E0356BD8
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
Périodique
BMC Systems Biology
Auteur(s)
Chaouiya C., Bérenguier D., Keating S.M., Naldi A., van Iersel M.P., Rodriguez N., Dräger A., Büchel F., Cokelaer T., Kowal B., Wicks B., Gonçalves E., Dorier J., Page M., Monteiro P.T., von Kamp A., Xenarios I., de Jong H., Hucka M., Klamt S., Thieffry D., Le Novère N., Saez-Rodriguez J., Helikar T.
ISSN
1752-0509 (Electronic)
ISSN-L
1752-0509
Statut éditorial
Publié
Date de publication
2013
Volume
7
Pages
135
Langue
anglais
Résumé
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.
Pubmed
Web of science
Open Access
Oui
Création de la notice
07/02/2014 20:56
Dernière modification de la notice
20/08/2019 15:02
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