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Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)

Bergmann, Frank T. and Cooper, Jonathan and König, Matthias and Moraru, Ion and Nickerson, David and Le Novère, Nicolas and Olivier, Brett G. and Sahle, Sven and Smith, Lucian and Waltemath, Dagmar (2018) Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). Journal of Integrative Bioinformatics, 15 (1). Art. No. 20170086. ISSN 1613-4516. https://resolver.caltech.edu/CaltechAUTHORS:20180416-112214706

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1515/jib-2017-0086DOIArticle
https://www.degruyter.com/view/j/jib.ahead-of-print/jib-2017-0086/jib-2017-0086.xmlPublisherArticle
ORCID:
AuthorORCID
Bergmann, Frank T.0000-0001-5553-4702
Cooper, Jonathan0000-0001-6009-3542
König, Matthias0000-0003-1725-179X
Nickerson, David0000-0003-4667-9779
Le Novère, Nicolas0000-0002-6309-7327
Olivier, Brett G.0000-0002-5293-5321
Smith, Lucian0000-0001-7002-6386
Waltemath, Dagmar0000-0002-5886-5563
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.
Subject Keywords:Simulation experiment; computational modeling; reproducibility
Issue or Number:1
Record Number:CaltechAUTHORS:20180416-112214706
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20180416-112214706
Official Citation:Bergmann, F., Cooper, J., König, M., et al. (2018). Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). Journal of Integrative Bioinformatics, 0(0), pp. -. Retrieved 16 Apr. 2018, from doi:10.1515/jib-2017-0086
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:85875
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:16 Apr 2018 20:37
Last Modified:03 Oct 2019 19:36

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