Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)
Abstract
The creation of computational simulation experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such experiments. Efforts such as SBML or CellML standardize the formal representation of computational models in various areas of biology. The Simulation Experiment Description Markup Language (SED-ML) describes what procedures the models are subjected to, and the details of those procedures. These standards, together with further COMBINE standards, describe models sufficiently well for the reproduction of simulation studies among users and software tools. The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format that encodes, for a given simulation experiment, (i) which models to use; (ii) which modifications to apply to models before simulation; (iii) which simulation procedures to run on each model; (iv) how to post-process the data; and (v) how these results should be plotted and reported. SED-ML Level 1 Version 1 (L1V1) implemented support for the encoding of basic time course simulations. SED-ML L1V2 added support for more complex types of simulations, specifically repeated tasks and chained simulation procedures. SED-ML L1V3 extends L1V2 by means to describe which datasets and subsets thereof to use within a simulation experiment.
Additional Information
© 2018, Frank T. Bergmann et al., published by De Gruyter, Berlin/Boston. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. Received: 2017-12-31; Accepted: 2018-02-02; Published Online: 2018-03-19. The SED-ML specification is developed with the input of many people. The following individuals served as past SED-ML Editors and contributed to SED-ML specifications. Their efforts helped shape what SED-ML is today. Richard Adams (editor, 2011-2012); Frank Bergmann (editor, 2011-2014); Jonathan Cooper (editor, 2012-2015); Nicolas Le Novère (editorial advisor, 2011-2012, 2013); Andrew Miller (editor, 2011-2012); Ion Moraru (editor, 2014-2016); Sven Sahle (editor, 2014-2016); Herbert Sauro. Moreover, we would like to thank all the participants of the meetings where SED-ML has been discussed as well as the members of the SED-ML community.Attached Files
Published - Simulation_Experiment_Description_Markup_Language__SED-ML__Level_1_Version_3__L1V3_.pdf
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Additional details
- Eprint ID
- 85875
- Resolver ID
- CaltechAUTHORS:20180416-112214706
- Created
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2018-04-16Created from EPrint's datestamp field
- Updated
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2021-11-15Created from EPrint's last_modified field