The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1

Claudine Chaouiya, Sarah M. Keating, Duncan Berenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel, Nicolas Le Novère, Tomáš Helikar

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Quantitative methods for modelling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modelling methods using information such as, for example, gene expression data coming from functional genomic experiments. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding qualitative models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Qualitative Models package for SBML Level 3 adds features so that qualitative models can be directly and explicitly encoded. The approach taken in this package is essentially based on the definition of regulatory or influence graphs. The SBML Qualitative Models package defines the structure and syntax necessary to describe qualitative models that associate discrete levels of activities with entity pools and the transitions between states that describe the processes involved. This is particularly suited to logical models (Boolean or multi-valued) and some classes of Petri net models can be encoded with the approach.

Original languageEnglish (US)
Number of pages1
JournalJournal of integrative bioinformatics
Volume12
Issue number2
DOIs
StatePublished - Jan 1 2015

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Systems Biology
Language
Gene Expression

ASJC Scopus subject areas

  • Medicine(all)

Cite this

The Systems Biology Markup Language (SBML) Level 3 Package : Qualitative Models, Version 1, Release 1. / Chaouiya, Claudine; Keating, Sarah M.; Berenguier, Duncan; Naldi, Aurélien; Thieffry, Denis; van Iersel, Martijn P.; Le Novère, Nicolas; Helikar, Tomáš.

In: Journal of integrative bioinformatics, Vol. 12, No. 2, 01.01.2015.

Research output: Contribution to journalArticle

Chaouiya, Claudine ; Keating, Sarah M. ; Berenguier, Duncan ; Naldi, Aurélien ; Thieffry, Denis ; van Iersel, Martijn P. ; Le Novère, Nicolas ; Helikar, Tomáš. / The Systems Biology Markup Language (SBML) Level 3 Package : Qualitative Models, Version 1, Release 1. In: Journal of integrative bioinformatics. 2015 ; Vol. 12, No. 2.
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