Journal Article

Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI

Thomas Sütterlin, Christoph Kolb, Hartmut Dickhaus, Dirk Jäger and Niels Grabe

in Bioinformatics

Volume 29, issue 2, pages 223-229
Published in print January 2013 | ISSN: 1367-4803
Published online November 2012 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/bts659
Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI

More Like This

Show all results sharing this subject:

  • Bioinformatics and Computational Biology

GO

Show Summary Details

Preview

Motivation: Biological reality can in silico only be comprehensively represented in multi-scaled models. To this end, cell behavioural models addressing the multi-cellular level have to be semantically linked with mechanistic molecular models. These requirements have to be met by flexible software workflows solving the issues of different time scales, inter-model variable referencing and flexible sub-model embedding.

Results: We developed a novel software workflow (EPISIM) for the semantic integration of Systems Biology Markup Language (SBML)-based quantitative models in multi-scaled tissue models and simulations. This workflow allows to import and access SBML-based models. SBML model species, reactions and parameters are semantically integrated in cell behavioural models (CBM) represented by graphical process diagrams. By this, cellular states like proliferation and differentiation can be flexibly linked to gene-regulatory or biochemical reaction networks. For a multi-scale agent-based tissue simulation executable code is automatically generated where different time scales of imported SBML models and CBM have been mapped. We demonstrate the capabilities of the novel software workflow by integrating Tyson’s cell cycle model in our model of human epidermal tissue homeostasis. Finally, we show the semantic interplay of the different biological scales during tissue simulation.

Availability: The EPISIM platform is available as binary executables for Windows, Linux and Mac OS X at http://www.tiga.uni-hd.de. Supplementary data are available at http://www.tiga.uni-hd.de/supplements/SemSBMLIntegration.html.

Contact: niels.grabe@bioquant.uni-heidelberg.de

Journal Article.  5114 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

Full text: subscription required

How to subscribe Recommend to my Librarian

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.