Standards > model/format > bsg-s000148


ready Simulation Experiment Description Markup Language

Abbreviation:SED-ML


General Information
SED-ML is an XML-based format for encoding simulation setups, to ensure exchangeability and reproducibility of simulation experiments. It follows the requirements defined in the MIASE guidelines.


Record updated: Aug. 10, 2016, 10:01 a.m. by The BioSharing Team.





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Connectivity

Implementing Databases (4)
A repository of mathematical models of biological and biomedical systems
BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-linked to publicly available reference information.

WholeCellSimDB
WholeCellSimDB is a database of whole-cell model simulations designed to make it easy for researchers to explore and analyze whole-cell model predictions including predicted: - Metabolite concentrations, - DNA, RNA and protein expression, - DNA-bound protein positions, - DNA modification positions, and - Ribome positions.

Physiome Model Repository
The Physiome Model Repository (PMR) is the main online repository for the IUPS Physiome Project, providing version and access controlled repositories, called workspaces, for users to store their data. PMR also provides a mechanism to create persistent access to specific revisions of a workspace, termed exposures. Exposure plugins are available for specific types of data (e.g., CellML or FieldML documents) which enable customizable views of the data when browsing the repository via a web browser, or an application accessing the repository’s content via web services.

JWS Online
JWS Online is a Systems Biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models.

Implementing Policies

This record is not implemented by any policy.


Credit

Record Maintainer

Funding agency

Maintainer

Grant Number(s)

  • 031 6194 (BMBF)

  • BB/D019621/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)

  • DFG Research Training Group 1387/1 (Deutsche Forschungsgemeinschaft (DFG), Germany)

  • GM070923 (NIGMS NIH)

  • GM081070 (NIGMS NIH)

  • P41-RR013186 (National Institute of Health (NIH), USA)

  • U54-RR022232 (National Institute of Health (NIH), USA)


Publications

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

Waltemath D,Adams R,Bergmann FT,Hucka M,Kolpakov F,Miller AK,Moraru II,Nickerson D,Sahle S,Snoep JL,Le Novere N
BMC Syst Biol 2011

View Paper (PubMed) View Paper (DOI)

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

Bergmann FT,Cooper J,Le Novere N,Nickerson D,Waltemath D
J Integr Bioinform 2015

View Paper (PubMed) View Paper (DOI)