SBML qualitative models

A model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt & 4 others Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomas Helikar

Research output: Contribution to journalArticle

59 Citations (Scopus)

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.

Original languageEnglish (US)
Article number135
JournalBMC Systems Biology
Volume7
DOIs
StatePublished - Dec 10 2013

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Markup languages
Systems Biology
Language
Infrastructure
Interaction
Modeling
Software
Model
Biological Models
Software Tools
Libraries
Collaborative Work
Biological Networks
Interoperability
Open Source
Specification
Specifications

ASJC Scopus subject areas

  • Structural Biology
  • Modeling and Simulation
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

SBML qualitative models : A model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. / Chaouiya, Claudine; Bérenguier, Duncan; Keating, Sarah M.; Naldi, Aurélien; van Iersel, Martijn P.; Rodriguez, Nicolas; Dräger, Andreas; Büchel, Finja; Cokelaer, Thomas; Kowal, Bryan; Wicks, Benjamin; Gonçalves, Emanuel; Dorier, Julien; Page, Michel; Monteiro, Pedro T.; von Kamp, Axel; Xenarios, Ioannis; de Jong, Hidde; Hucka, Michael; Klamt, Steffen; Thieffry, Denis; Le Novère, Nicolas; Saez-Rodriguez, Julio; Helikar, Tomas.

In: BMC Systems Biology, Vol. 7, 135, 10.12.2013.

Research output: Contribution to journalArticle

Chaouiya, 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 2013, 'SBML qualitative models: A model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools', BMC Systems Biology, vol. 7, 135. https://doi.org/10.1186/1752-0509-7-135
Chaouiya, Claudine ; Bérenguier, Duncan ; Keating, Sarah M. ; Naldi, Aurélien ; van Iersel, Martijn P. ; Rodriguez, Nicolas ; Dräger, Andreas ; Büchel, Finja ; Cokelaer, Thomas ; Kowal, Bryan ; Wicks, Benjamin ; Gonçalves, Emanuel ; Dorier, Julien ; Page, Michel ; Monteiro, Pedro T. ; von Kamp, Axel ; Xenarios, Ioannis ; de Jong, Hidde ; Hucka, Michael ; Klamt, Steffen ; Thieffry, Denis ; Le Novère, Nicolas ; Saez-Rodriguez, Julio ; Helikar, Tomas. / SBML qualitative models : A model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. In: BMC Systems Biology. 2013 ; Vol. 7.
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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, Tomas

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