SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies
1
COS/BioQUANT, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
2
Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
3
Dept. of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Published
- Accepted
- Subject Areas
- Bioinformatics, Computational Biology, Mathematical Biology, Molecular Biology, Computational Science
- Keywords
- web service, virtual experiment, simulation study, reproducibility, modelling, SBML, CellML, model management
- Copyright
- © 2016 Bergmann et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2016. SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies. PeerJ Preprints 4:e2515v1 https://doi.org/10.7287/peerj.preprints.2515v1
Abstract
The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, a software that supports SED-ML Level 1 Version 2, including complex modifications and co-simulation of SBML and CellML models. This online application allows for creating, editing, simulating and validating SED-ML documents. It lowers the bar on working with SED-ML documents and helps users create valid simulation descriptions for models in CellML and SBML formats.
Availability and Implementation: sysbioapps.dyndns.org/SED-ML_Web_Tools.
Author Comment
This is a preprint submission of a manuscript that we want to publish in Oxford Journals Bioinformatics.