SED-ML web tools: generate, modify and export standard-compliant simulation studies

Frank T Bergmann; David Nickerson; Dagmar Waltemath; Martin Scharm

doi:10.1093/bioinformatics/btw812

SED-ML web tools: generate, modify and export standard-compliant simulation studies

Bioinformatics. 2017 Apr 15;33(8):1253-1254. doi: 10.1093/bioinformatics/btw812.

Authors

Frank T Bergmann¹, David Nickerson², Dagmar Waltemath³, Martin Scharm³

Affiliations

¹ COS/BioQUANT, Heidelberg University, Heidelberg, Germany.
² Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand.
³ Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.

Abstract

Summary: 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, an online application for creating, editing, simulating and validating SED-ML documents. The Web Tools implement all current SED-ML specifications and, thus, support complex modifications and co-simulation of models in SBML and CellML formats. Ultimately, the Web Tools lower the bar on working with SED-ML documents and help users create valid simulation descriptions.

Availability and implementation: http://sysbioapps.dyndns.org/SED-ML_Web_Tools/ .

Contact: fbergman@caltech.edu .

MeSH terms

Computer Simulation*
Internet
Programming Languages
Software*

Grants and funding

R01 GM081070/GM/NIGMS NIH HHS/United States