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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

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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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 structue 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.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Chaouiya, Claudine ; Keating, Sarah M. ; Berenguier, Duncan ; Naldi, Aurélien ; Thieffry, Denis ; van Iersel, Martijn P. ; Le Novère, Nicolas ; Helikar, Tomáš  (2015)  SBML Level 3 package: Qualitative Models, Version 1, Release 1. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 12(2): Special Issue: Standards in Systems Biology, 2015

Online-Journal: http://journal.imbio.de
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2015/5374



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