Wrangling Galaxy's reference data

Daniel James Blankenberg, James E. Johnson, James Taylor, Anton Nekrutenko

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Summary: The Galaxy platform has developed into a fully featured collaborative workbench, with goals of inherently capturing provenance to enable reproducible data analysis, and of making it straightforward to run one's own server. However, many Galaxy platform tools rely on the presence of reference data, such as alignment indexes, to function efficiently. Until now, the building of this cache of data for Galaxy has been an error-prone manual process lacking reproducibility and provenance. The Galaxy Data Manager framework is an enhancement that changes the management of Galaxy's built-in data cache from a manual procedure to an automated graphical user interface (GUI) driven process, which contains the same openness, reproducibility and provenance that is afforded to Galaxy's analysis tools. Data Manager tools allow the Galaxy administrator to download, create and install additional datasets for any type of reference data in real time.

Original languageEnglish (US)
Pages (from-to)1917-1919
Number of pages3
JournalBioinformatics
Volume30
Issue number13
DOIs
StatePublished - Jul 1 2014

Fingerprint

Galaxies
Provenance
Reproducibility
Cache
Managers
Graphical User Interface
Graphical user interfaces
Administrative Personnel
Data analysis
Alignment
Servers
Server
Enhancement

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Blankenberg, D. J., Johnson, J. E., Taylor, J., & Nekrutenko, A. (2014). Wrangling Galaxy's reference data. Bioinformatics, 30(13), 1917-1919. https://doi.org/10.1093/bioinformatics/btu119
Blankenberg, Daniel James ; Johnson, James E. ; Taylor, James ; Nekrutenko, Anton. / Wrangling Galaxy's reference data. In: Bioinformatics. 2014 ; Vol. 30, No. 13. pp. 1917-1919.
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Blankenberg, DJ, Johnson, JE, Taylor, J & Nekrutenko, A 2014, 'Wrangling Galaxy's reference data', Bioinformatics, vol. 30, no. 13, pp. 1917-1919. https://doi.org/10.1093/bioinformatics/btu119

Wrangling Galaxy's reference data. / Blankenberg, Daniel James; Johnson, James E.; Taylor, James; Nekrutenko, Anton.

In: Bioinformatics, Vol. 30, No. 13, 01.07.2014, p. 1917-1919.

Research output: Contribution to journalArticle

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Blankenberg DJ, Johnson JE, Taylor J, Nekrutenko A. Wrangling Galaxy's reference data. Bioinformatics. 2014 Jul 1;30(13):1917-1919. https://doi.org/10.1093/bioinformatics/btu119