Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)
Open accessAbstract
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.
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- Authors
- Bergmann, F. T., Cooper, J., König, M., Moraru, I., Nickerson, D., Le Novère, N., Olivier, B. G., Sahle, S., Smith, L., & Waltemath, D.
- Affiliations
- California Institute of Technology (US)
- University of Oxford (GB)
- Humboldt-Universität zu Berlin (DE)
- University of Connecticut (US)
- University of Auckland (NZ)
- Babraham Institute Cambridge, Cambridgeshire, UK
- Heidelberg University (DE)
- University of Washington (US)
- University of Rostock (DE)
- Corresponding author
- König, Matthias
- ORCID
- Venue
- Journal of Integrative Bioinformatics
- Publisher
- Walter de Gruyter GmbH
- Published
- 2018-03-19
- Volume
- 15
- Issue
- 1
- Pages
- 262-262
- ISSN
- 1432-4385 (ISSN-L)
- 1613-4516
- PMC
- PMC6167040
- OpenAlex
- W2187364252
- Cited by
- 37
- References
- 17
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 1 · 2023: 2 · 2022: 1 · 2021: 3 · 2020: 6 · 2019: 5 · 2018: 4 · 2017: 1 · 2016: 5 · 2015: 2 · 2014: 3 · 2013: 1
- FWCI
- 6.39
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics (publishedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- VU Research Portal (publishedVersion, other-oa)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- edoc Publication server (Humboldt University of Berlin) (submittedVersion, cc-by-nc-nd)
- UCL Discovery (University College London) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- edoc Publication server (Humboldt University of Berlin)
- PUB – Publications at Bielefeld University (Bielefeld University)
- Topics
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Keywords
- SED-ML, computational model, model annotation, model reuse, model modification, simulation procedure, data post-processing, data subsets, reproducibility, SBML, CellML, XML markup
- MeSH terms
- Documentation, Models, Biological, Programming Languages, Information Storage and Retrieval, Guidelines as Topic, Internationality, Systems Biology, Biological Ontologies, Datasets as Topic
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