Journal
BMC SYSTEMS BIOLOGY
Volume 7, Issue -, Pages -Publisher
BMC
DOI: 10.1186/1752-0509-7-135
Keywords
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Categories
Funding
- European Union [ECFP7-KBBE-2011-5, 289434]
- Nebraska NASA Space Grant Consortium grant (Technology for collaborative biomedical research)
- National Institutes of Health [5R01DA030962]
- Fundacao para a Ciencia e a Tecnologia [PTDC/EIA-CCO/099229/2008, Pest-OE/EEI/LA0021]
- US National Institute of General Medical Sciences [GM070923]
- Marie Curie International Outgoing Fellowship [332020]
- Swiss Federal Government through the Federal Office of Education Science and Innovation (SERI)
- European Commission FP6 project ENFIN (Experimental Network for Functional INtegration) [LSHG-CT-2005-518254]
- Federal Ministry of Education and Research (BMBF, Germany) [0315756, 0315744]
- EMBL-EBI
- Fundação para a Ciência e a Tecnologia [PTDC/EIA-CCO/099229/2008] Funding Source: FCT
- Biotechnology and Biological Sciences Research Council [BB/J019305/1] Funding Source: researchfish
- BBSRC [BB/J019305/1] Funding Source: UKRI
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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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