Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit
- Published
- Accepted
- Subject Areas
- Computational Biology, Computational Science
- Keywords
- database, combine archive, reproducibility, virtual experiments, simulation studies
- Copyright
- © 2015 Scharm 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
- 2015. Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit. PeerJ PrePrints 3:e792v1 https://doi.org/10.7287/peerj.preprints.792v1
Abstract
The COMBINE archive is a digital container format for files related to a virtual experiment in computational biology. It eases the management of numerous files related to a simulation study, fosters collaboration, and ultimately enables the exchange of reproducible research results. The CombineArchive Toolkit is a software for creating, exploring, modifying, and sharing COMBINE archives. Open model repositories such as BioModels Database are a valuable resource of models and associated simulation descriptions. However, so far no tool exists to export COMBINE archives for a given simulation study from such databases. Here we demonstrate how the CombineArchiveToolkit can be used to extract reproducible simulation studies from model repositories. We use the example of Masymos, a graph database with a sophisticated link concept to connect model-related files on the storage layer.
Author Comment
This article is submitted for the Workshop on Data Management for Life Sciences (DMforLS) 2015 at BTW 2015, Hamburg, Germany.