The JWS online simulation database

Martin Peters; Johann J Eicher; David D van Niekerk; Dagmar Waltemath; Jacky L Snoep

doi:10.1093/bioinformatics/btw831

The JWS online simulation database

Bioinformatics. 2017 May 15;33(10):1589-1590. doi: 10.1093/bioinformatics/btw831.

Authors

Martin Peters¹, Johann J Eicher², David D van Niekerk², Dagmar Waltemath¹, Jacky L Snoep^{2

3

4}

Affiliations

¹ Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.
² Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa.
³ MIB, CEAS, University of Manchester, UK.
⁴ Molecular Cell Physiology, VU University, Amsterdam, The Netherlands.

PMID: 28130238
DOI: 10.1093/bioinformatics/btw831

Abstract

Summary: JWS Online is a web-based platform for construction, simulation and exchange of models in standard formats. We have extended the platform with a database for curated simulation experiments that can be accessed directly via a URL, allowing one-click reproduction of published results. Users can modify the simulation experiments and export them in standard formats. The Simulation database thus lowers the bar on exploring computational models, helps users create valid simulation descriptions and improves the reproducibility of published simulation experiments.

Availability and implementation: The Simulation Database is available on line at https://jjj.bio.vu.nl/models/experiments/ .

Contact: jls@sun.ac.za .

MeSH terms

Computational Biology / methods*
Computer Simulation*
Databases, Factual*
Models, Biological
Reproducibility of Results