title: SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
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.
authors: Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal. chaouiya@igc.gulbenkian.pt.
authors: Claudine
authors: C
authors: Chaouiya
authors: Duncan
authors: D
authors: Bérenguier
authors: Sarah M
authors: SM
authors: Keating
authors: Aurélien
authors: A
authors: Naldi
authors: Martijn P
authors: MP
authors: van Iersel
authors: Nicolas
authors: N
authors: Rodriguez
authors: Andreas
authors: A
authors: Dräger
authors: Finja
authors: F
authors: Büchel
authors: Thomas
authors: T
authors: Cokelaer
authors: Bryan
authors: B
authors: Kowal
authors: Benjamin
authors: B
authors: Wicks
authors: Emanuel
authors: E
authors: Gonçalves
authors: Julien
authors: J
authors: Dorier
authors: Michel
authors: M
authors: Page
authors: Pedro T
authors: PT
authors: Monteiro
authors: Axel
authors: A
authors: von Kamp
authors: Ioannis
authors: I
authors: Xenarios
authors: Hidde
authors: H
authors: de Jong
authors: Michael
authors: M
authors: Hucka
authors: Steffen
authors: S
authors: Klamt
authors: Denis
authors: D
authors: Thieffry
authors: Nicolas
authors: N
authors: Le Novère
authors: Julio
authors: J
authors: Saez-Rodriguez
authors: Tomáš
authors: T
authors: Helikar
mesh_terms: D000818:Animals; D002477:Cells / Q000166:cytology / Q000378:metabolism; D004815:Epidermal Growth Factor / Q000378:metabolism; D020407:Internet; D008954:Models, Biological; D011381:Programming Languages; D015398:Signal Transduction; D014409:Tumor Necrosis Factor-alpha / Q000378:metabolism
chemical_list: D014409:Tumor Necrosis Factor-alpha; D004815:Epidermal Growth Factor