Chaouiya2013 - EGF and TNFalpha mediated signalling pathway

Chaouiya2013 - EGF and TNFalpha mediated signalling pathway

This model is described in the article:

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

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.
BMC Syst Biol 2013; 7: 135
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.

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