Simulation Experiment Description Markup Language
Abbreviation: SED-ML
Homepage http://sed-ml.org/
Countries that developed this resource Worldwide
Created in 2008
Taxonomic range
Knowledge Domains
Subjects
How to cite this record FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: Jan. 8, 2019, 1:27 p.m.; Last accessed: Nov 29 2020 10:34 p.m.
Record updated: March 15, 2018, 10:21 a.m. by The FAIRsharing Team.
| help | http://sed-ml.sourceforge.net/documents. ... |
| Mailing List | None |
| online documentation | http://sed-ml.sourceforge.net/documents/ ... |
| online documentation | http://sed-ml.org/documents/sed-ml-L1V1. ... |
Additional Information
| Contact | SED-ML Editors |
| CellDesigner | http://celldesigner.org/ | 4.4.1 |
| SED-ML Script Editor | http://libsedml.sourceforge.net/libSedML/SedMLScript.html | |
| SED-ML Web Tools | http://sysbioapps.dyndns.org/SED-ML_Web_Tools | |
| SED-ED | http://sourceforge.net/projects/jlibsedml/files | 2.2.3 |
| SBW Simulation Tool | https://sourceforge.net/p/sbwsimtool/wiki/Home/ | |
| clibsedml | http://sourceforge.net/projects/clibsedml/ | |
| jlibsedml | http://sourceforge.net/projects/jlibsedml/ | |
| libSedML | http://libsedml.sf.net/ | |
| Systems Biology Simulation Core Library | http://sourceforge.net/projects/simulation-core/ |
Conditions of Use
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
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
Reporting Guidelines
Terminology Artifacts
Models and Formats
Identifier Schemas
No identifier schema standards defined
Metrics
No metrics standards defined
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.
BioSimulators
BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects.
BioSimulations
BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g., COPASI, libRoadRunner/tellurium, NFSim, VCell). BioSimulations aims to help researchers discover published models that might be useful for their research and quickly try them via a simple web-based interface.
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This record is not implemented by any policy.
Record Maintainer
This record is maintained by dwaltemath ORCID
Funds
Biotechnology and Biological Sciences Research Council (BBSRC), UK (Government body)
Bundesministerium fur Bildung und Forschung (BMBF), Germany (Government body)
Deutsche Forschungsgemeinschaft (DFG) (Government body)
Marie Skodowska-Curie actions, Europe (Government body)
Maurice Wilkins Center for Molecular Biodiscovery, Auckland, New Zealand (Government body)
U.S. National Library of Medicine (Government body)
National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA (Government body)
Maintains
COmputational Modeling in BIology NEtwork (COMBINE) (Consortium)
SED-ML editors (Consortium)
Grant Number(s)
031 6194 (Bundesministerium fur Bildung und Forschung (BMBF), Germany)
BB/D019621/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
DFG Research Training Group 1387/1 (Deutsche Forschungsgemeinschaft (DFG))
GM070923 (National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA)
GM081070 (National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA)
P41-RR013186 (U.S. National Library of Medicine)
U54-RR022232 (U.S. National Library of Medicine)
