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The CombineArchive Toolkit - facilitating the transfer of research results

, , , , ,
  Dept. of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
DOI
10.7287/peerj.preprints.514v1
Published
Accepted
Subject Areas
Computational Biology, Computational Science
Keywords
COMBINE Archive, Collaborative Research, Reproducible Results
Copyright
© 2014 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
Scharm M, Wendland F, Peters M, Wolfien M, Theile T, Waltemath D. 2014. The CombineArchive Toolkit - facilitating the transfer of research results. PeerJ PrePrints 2:e514v1

Abstract

Sharing in silico experiments is essential for the advance of research in computational biology. Consequently, the COMBINE archive was designed as a digital container format. It eases the management of numerous files, fosters collaboration, and ultimately enables the exchange of reproducible research results. However, manual handling of COMBINE archives is tedious and error prone. We therefore developed the CombineArchive Toolkit. It supports scientists in promoting and publishing their work by means of creating, exploring, modifying, and sharing archives.

Author Comment

We developed the CombineArchive Toolkit. It consists of a core library, a desktop application, and a web based interface. Taken together, our tools support researchers in creating and exploring COMBINE archives.

Additional Information

Competing Interests

Authors declare no competing interests.

Author Contributions

Martin Scharm conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Florian Wendland performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Martin Peters performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Markus Wolfien performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Tom Theile performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Dagmar Waltemath conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Funding

MS, MP, MW, and DW are funded by the German Federal Ministry of Education and Research (e:Bio program SEMS, FKZ 031 6194). TT is funded by the German Research Foundation (Training Group 1505/2 Welisa). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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