Info

Galaxy

Data intensive biomedical biology for everyone.

Information on Galaxy training

 

TraIT is currently collaborating with the Dutch Galaxy community to setup a nationwide infrastructure for demonstrations and trainings of Galaxy, as well as the deployment of bespoke Galaxy environments. More information will follow soon.

 

Galaxy is an open, web-based platform for data intensive biomedical research. You can perform, reproduce, and share complete analyses. The system is developed and supported by the Galaxy team lead by the Nekrutenko lab at Penn State University and the Taylor lab at Johns Hopkins University, along with contributions from the community.

The Galaxy platform can be used to upload your data and analyse them with various tools and workflows (in combination with reference data when available). Generated output files can then be downloaded for further downstream analysis or visualised within Galaxy itself.

You can do further analysis and visualization on the output data or download this data for use outside Galaxy. Tools are available in several categories (like NGS, proteomics, statistics, and general purpose). Several pipelines have been created specifically for CTMM projects and are (being made) available as Galaxy workflows, for example the RNA-Seq EdgeR pipeline or the QDNAseq Copynumber Aberration Tool.

Using Galaxy further has the following advantages:

  • tools are easier to use via the web interface in Galaxy compared to the underlying command-line interface;

  • automatic information is generated about the analysis runs: useful for provenance and reproducibility.

Please cite Galaxy (1, 2, 3) and TraIT specific pipelines (4, 5, 6).

 

For further questions regarding the Galaxy platform, including requests for usage, please contact the TraIT ServiceDesk at servicedesk@ctmm-trait.nl.

 

References:

  1. Goecks, J, Nekrutenko, A, Taylor, J and The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010 Aug 25;11(8):R86.

  2. Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. "Galaxy: a web-based genome analysis tool for experimentalists". Current Protocols in Molecular Biology. 2010 Jan; Chapter 19:Unit 19.10.1-21.

  3. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. "Galaxy: a platform for interactive large-scale genome analysis." Genome Research. 2005 Oct; 15(10):1451-5.

  4. Hiltemann S, Hoogstrate Y, der Spek Pv, Jenster G, Stubbs A. "iReport : a generalised Galaxy solution for integrated experimental reporting." Gigascience. 2014

  5. Hiltemann S, McClellan EA, van Nijnatten J, Horsman S, Palli I, Teles Alves I, Hartjes T, Trapman J, van der Spek P, Jenster G, Stubbs A. "iFUSE: integrated fusion gene explorer." Bioinformatics. 2013 Jul 1;29(13):1700-1.

  6. Hiltemann S, Mei H, de Hollander M, Palli I, van der Spek P, Jenster G, Stubbs A. "CGtag : complete genomics toolkit and annotation in a cloud-based Galaxy." Gigascience. 2014 Jan 24;3(1):1.