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Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

Dagmar Waltemath1, Richard Adams2, Frank T Bergmann3, Michael Hucka3, Fedor Kolpakov4, Andrew K Miller5, Ion I Moraru6, David Nickerson5, Sven Sahle7, Jacky L Snoep1089 and Nicolas Le Novère11*

Author Affiliations

1 Department of Systems Biology & Bioinformatics, Institute of Computer Science, University of Rostock, D-18051 Rostock, Germany

2 Centre for Systems Biology Edinburgh, CHWaddington Building, University of Edinburgh, Edinburgh EH9 3JD, UK

3 California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA

4 Institute of Systems Biology Ltd., Detskiy proezd 15, Novosibirsk, 630090, Russia

5 Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand

6 Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT 06030, USA

7 BIOQUANT, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, Germany

8 Department of Biochemistry, Stellenbosch University, Privatebag X1, Matieland 7602, South Africa

9 Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, the University of Manchester, 131 Princess Street Manchester, M1 7DN, UK

10 Molecular Cell Physiology, VU University, Amsterdam, The Netherlands

11 EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK

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BMC Systems Biology 2011, 5:198  doi:10.1186/1752-0509-5-198

Published: 15 December 2011

Additional files

Additional file 1:

SED-ML examples file. Repressilator simulation described in SED-ML.

Format: XML Size: 8KB Download file

Open Data