The simulation experiment description markup language (SED-ML): language specification for level 1 version 4
Open accessAbstract
Computational simulation experiments increasingly inform modern biological research, and bring with them the need to provide ways to annotate, archive, share and reproduce the experiments performed. These simulations increasingly require extensive collaboration among modelers, experimentalists, and engineers. The Minimum Information About a Simulation Experiment (MIASE) guidelines outline the information needed to share simulation experiments. SED-ML is a computer-readable format for the information outlined by MIASE, created as a community project and supported by many investigators and software tools. The first versions of SED-ML focused on deterministic and stochastic simulations of models. Level 1 Version 4 of SED-ML substantially expands these capabilities to cover additional types of models, model languages, parameter estimations, simulations and analyses of models, and analyses and visualizations of simulation results. To facilitate consistent practices across the community, Level 1 Version 4 also more clearly describes the use of SED-ML constructs, and includes numerous concrete validation rules. SED-ML is supported by a growing ecosystem of investigators, model languages, and software tools, including eight languages for constraint-based, kinetic, qualitative, rule-based, and spatial models, over 20 simulation tools, visual editors, model repositories, and validators. Additional information about SED-ML is available at https://sed-ml.org/.
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- Authors
- Smith, L. P., Bergmann, F. T., Garny, A., Helikar, T., Karr, J., Nickerson, D., Sauro, H., Waltemath, D., & König, M.
- Affiliations
- University of Washington (US)
- Heidelberg University (DE)
- University of Auckland (NZ)
- University of Nebraska–Lincoln (US)
- Icahn School of Medicine at Mount Sinai (US)
- Universität Greifswald (DE)
- Humboldt-Universität zu Berlin (DE)
- Corresponding author
- Smith, Lucian P.
- ORCID
- Venue
- Journal of Integrative Bioinformatics
- Publisher
- Walter de Gruyter GmbH
- Published
- 2021-09-01
- Volume
- 18
- Issue
- 3
- Pages
- 20210021-20210021
- ISSN
- 1432-4385 (ISSN-L)
- 1613-4516
- PMC
- PMC8560344
- OpenAlex
- W3201819843
- Cited by
- 17
- References
- 18
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 8 · 2023: 3 · 2022: 3 · 2021: 1
- FWCI
- 3.20
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Lincoln (University of Nebraska) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- edoc Publication server (Humboldt University of Berlin) (submittedVersion, cc-by)
- edoc Publication server (Humboldt University of Berlin) (cc-by)
- Funders
- National Science Foundation (P41GM109824, 2020-2022, 1933453)
- Deutsche Forschungsgemeinschaft (FOR 5151, 436883643)
- Bundesministerium für Bildung und Forschung (436883643, FOR 5151 QuaLiPerF, 031L0054)
- German Network for Bioinformatics Infrastructure
- National Institute of General Medical Sciences (P41GM109824, R01GM123032, R35GM119771, R35GM119770)
- Topics
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- SED-ML, reproducibility, parameter estimation, model analysis, simulation result visualization, language specification, validation rules, constraint-based modeling, kinetic model, rule-based models, spatial modeling, model language
- MeSH terms
- Language, Models, Biological, Programming Languages, Ecosystem, Systems Biology
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