BioModels Database logo

BioModels Database

spacer

BIOMD0000000562 - Chaouiya2013 - EGF and TNFalpha mediated signalling pathway

 

This model makes use of one SBML L3 package (namely: qual). The infrastructure of BioModels currently provides only limited support for models with SBML packages. As a consequence, some features are not available for these models (for example, this affects the content displayed in the various tabs and the conversion of the model to other formats).
For more information regarding SBML packages, please refer to the SBML Level 3 packages page.
 |   |   |  Send feedback
Reference Publication
Publication ID: 24321545
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.
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC Syst Biol 2013; 7: 135
Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal. chaouiya@igc.gulbenkian.pt. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK saezrodriguez@ebi.ac.uk; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; thelikar2@unl.edu  [more]
Model
Original Model: BIOMD0000000562.origin
Submitter: Thomas Cokelaer
Submission ID: MODEL1411240000
Submission Date: 24 Nov 2014 14:20:43 UTC
Last Modification Date: 21 Jan 2015 11:01:30 UTC
Creation Date: 12 Dec 2014 17:21:20 UTC
Encoders:  Vijayalakshmi Chelliah
   Thomas Cokelaer
set #1
bqbiol:hasTaxon Taxonomy Homo sapiens
set #2
bqbiol:hasProperty Mathematical Modelling Ontology logical model
set #3
bqbiol:hasPart Gene Ontology tumor necrosis factor-mediated signaling pathway
Gene Ontology epidermal growth factor receptor signaling pathway
Notes
Chaouiya2013 - EGF and TNFalpha mediated signalling pathway

This model is described in the article:

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.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Model
Publication ID: 24321545 Submission Date: 24 Nov 2014 14:20:43 UTC Last Modification Date: 21 Jan 2015 11:01:30 UTC Creation Date: 12 Dec 2014 17:21:20 UTC
Mathematical expressions
Physical entities
Compartments Species
main      
Reactions (0)
   Spatial dimensions: NaN  Compartment size: NaN
Representative curation result(s)
Representative curation result(s) of BIOMD0000000562

Curator's comment: (updated: 12 Dec 2014 17:21:06 GMT)

Figure 4A and 4B of the reference publication has been reproduced using CellNOptR.
The script to obtain the figure is available as a python notebook that can be downloaded from below.

Additional file(s)
spacer
spacer