Conference article

Creating a Bridge between Modelica and the Systems Biology Community

Jan Brugård
MathCore Engineering AB, Linköping, Sweden

Daniel Hedberg
MathCore Engineering AB, Linköping, Sweden

Marta Cascante
Departamento de Bioquímica y Biología Molecular, Universitat de Barcelona, Spain

Gunnar Cedersund
Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden \ Freiburg Institute for Advanced Studies, School of Life Sciences, Germany

Alex Gómez-Garrido
Grup de Recerca en Informàtica Biomèdica, Universitat Pompeu Fabra, Barcelona, Spain

Dieter Maier
Biomax Informatics AG, Martinsried, Germany

Elin Nyman
Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden

Vitaly Selivanov
Departamento de Bioquímica y Biología Molecular, Universitat de Barcelona, Spain

Peter Strålfors
Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden

Download articlehttp://dx.doi.org/10.3384/ecp09430016

Published in: Proceedings of the 7th International Modelica Conference; Como; Italy; 20-22 September 2009

Linköping Electronic Conference Proceedings 43:52, s. 473-479

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Published: 2009-12-29

ISBN: 978-91-7393-513-5

ISSN: 1650-3686 (print), 1650-3740 (online)

Abstract

The Systems Biology Markup Language (SBML) is the leading modelling language within systems biology. It is a computer-readable format for representing models of biochemical reaction networks in software. SBML has been evolving since 2000 thanks to an international community of software developers and users. At the same time the Modelica language has evolved as the leading object-oriented modelling language for convenient; componentoriented modelling of complex physical systems.

As a part of the EC-funded BioBridge project Math-Core has developed the Modelica library BioChem and the MathModelica Systems Biology toolbox. With the release of version 1.0 of the BioChem library and the MathModelica Systems Biology toolbox it will be possible to import and export from Modelica to SBML. The toolbox also allows to publish the Modelica models as interactive HTML pages; with biochemical and experimental enzyme characterizations derived from the BioBridge portal and BioXM knowledge management environment.

Keywords

Modelica tools; SBML; library; biological systems; cellular pathways; translator

References

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