Konferensartikel

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

Ladda ner artikelhttp://dx.doi.org/10.3384/ecp09430016

Ingår i: 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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Publicerad: 2009-12-29

ISBN: 978-91-7393-513-5

ISSN: 1650-3686 (tryckt), 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.

Nyckelord

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

Referenser

[1] Larsdotter Nilsson; E. and Fritzson P.; (2003). BioChem - A Biological and Chemical Library for Modelica. Proceedings of the 3rd International Modelica Conference: 215-220.

[2] BioChem library. (Accessed 2009-08-18) http://www.mathcore.com/products/mathmodelica/libraries/biochem.php

[3] Systems Biology Markup Language (Accessed 2009-08-18) http://www.sbml.org

[4] The BioModels Database - A Database of Annotated Published Models. (Accessed 2009-08-18) http://www.ebi.ac.uk/biomodels-main/

[5] Systems Biology Workbench. (Accessed 2009-08-20) http://sbw.sourceforge.net/

[6] CellDesigner. (Accessed 2009-08-20) http://www.celldesigner.org/

[7] COPASI - Complex Pathway Simulator. (Accessed 2009-08-20) http://www.copasi.org

[8] libSBML. (Accessed 2009-08-18) http://sbml.org/Software/libSBML

[9] BioDyn. (Accessed 2009-08-18) http://cbbl.imim.es:8080/ByoDyn

[10] Gómez-Garrido; À. et al. (2008) ByoDyn: integrating computational methods for the analysis of biochemical models. P oster presented at the 4th Meeting of the Spanish Systems Biology Network (REBS).

[11] OpenModelica. (Accessed 2009-08-18) http://www.ida.liu.se/~pelab/modelica/OpenModelica.html

[12] Fritzson; P. et al. (2006) OpenModelica - A Free Open-Source Environment for System Modeling; Simulation; and Teaching. IEEE International Symposium on Computer-Aided Control Systems Design.

[13] Dalla Man C; Rizza R A and Cobelli C (2007). Meal simulation model of the glucose-insulin system; IEEE transactions on bio-medical engineering; Vol. 54; No. 10; pp. 1740-1749.

[14] Microsoft Silverlight. (Accessed 2009-08-18) http://silverlight.net

[15] Selivanov VA; et al.; (2008). The changes in the energy metabolism of human muscle induced by training. Journal of Theoretical Biology 252; 402-410. doi: 10.1016/j.jtbi.2007.09.039.

[16] The BioBridge portal. (Accessed 2009-08-18) http://www.biobridge.eu

[17] Sameith; K. et al.; (2008). Functional Modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage. Bioinformatics 24: 2602-2607.

[18] Losko; S. et al. (2006) Knowledge Networks of Biological and Medical Data: An Exhaustive and Flexible Solution to Model Life Science Domains. Lecture Notes in Computer Science 4075: 232-239.

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