TY - JOUR
T1 - SBML qualitative models
T2 - A model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
AU - Chaouiya, Claudine
AU - Bérenguier, Duncan
AU - Keating, Sarah M.
AU - Naldi, Aurélien
AU - van Iersel, Martijn P.
AU - Rodriguez, Nicolas
AU - Dräger, Andreas
AU - Büchel, Finja
AU - Cokelaer, Thomas
AU - Kowal, Bryan
AU - Wicks, Benjamin
AU - Gonçalves, Emanuel
AU - Dorier, Julien
AU - Page, Michel
AU - Monteiro, Pedro T.
AU - von Kamp, Axel
AU - Xenarios, Ioannis
AU - de Jong, Hidde
AU - Hucka, Michael
AU - Klamt, Steffen
AU - Thieffry, Denis
AU - Le Novère, Nicolas
AU - Saez-Rodriguez, Julio
AU - Helikar, Tomáš
N1 - Copyright:
Copyright 2014 Elsevier B.V., All rights reserved.
PY - 2013/12/10
Y1 - 2013/12/10
N2 - 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.
AB - 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.
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U2 - 10.1186/1752-0509-7-135
DO - 10.1186/1752-0509-7-135
M3 - Article
C2 - 24321545
AN - SCOPUS:84889794047
VL - 7
JO - BMC Systems Biology
JF - BMC Systems Biology
SN - 1752-0509
M1 - 135
ER -