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BY 4.0 license Open Access Published by De Gruyter October 5, 2021

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4

  • Lucian P. Smith ORCID logo EMAIL logo , Frank T. Bergmann , Alan Garny , Tomáš Helikar , Jonathan Karr , David Nickerson ORCID logo , Herbert Sauro , Dagmar Waltemath ORCID logo and Matthias König ORCID logo

Abstract

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/.


Corresponding author: Lucian P. Smith, University of Washington, Seattle, USA, E-mail: . To contact the current SED-ML editors, E-mail:

  1. Author contribution: All authors have accepted responsibility for the entire content of this manuscript and approved its submission.

  2. Research funding: LS, HS, DN, and JK were supported by the National Institute for Biomedical Imaging and Bioengineering award P41GM109824. LS, HS also supported by the National Institute of General Medical Sciences and National Science Foundation awards R01GM123032 and 1933453, respectively. JK also supported by National Institute of General Medical Sciences, grant R35GM119771. FTB was supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network de.NBI (grant number 031L0104A). TH was supported by the National Institute of Health grant number R35GM119770. MK was supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (grant number 031L0054) and by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 QuaLiPerF by grant number 436883643.

  3. Conflict of interest statement: Authors state no conflict of interest.

Received: 2021-08-07
Accepted: 2021-08-26
Published Online: 2021-10-05

© 2021 Lucian P. Smith et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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