Galaxy
Galaxy is "an open, web-based platform for performing accessible, reproducible, and transparent genomic science."
Galaxy provides a way to generate scientific workflows including data integration, and analysis persistence. It could be considered as a publishing platform making computational biology accessible to research scientists that do not have computer programming skills. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system.
ABiMS provides http://webtools.sb-roscoff.fr, a Galaxy instance that hosts tools developped at the Station Biologique de Roscoff in collaboration with the plateform:
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Cyanorak Blast: Blast query sequences on Synechococcus and Prochlorococcus strains (blastn, blastp, blastx, tblastn, tblastx). [webpage]
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Hectar: Predict subcellular targeting for heterokont proteins.
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MicRhoDE workflow: places query sequences into MicRhoDE tree (type-1 rhodopsin phylogeny). [webpage]
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Renkan BLAST: blast query sequences to 18S and 28S radiolaria databases (blastn). [webpage]
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WiseScaffolder: genome scaffolding of pre-assembled contigs using mate-pair data. [webpage]
Since 2020, ABiMS contributes actively and promotes the French National Galaxy instance: https://usegalaxy.fr. This instance aims to gather several lab scale Galaxy instances.
⚠️ That's why we are closing at short terms several of our local instances. We encourage you to migrate as soon as possible on https://usegalaxy.fr
- http://galaxy.sb-roscoff.fr: the generalist Galaxy instance with different thematics
- http://galaxy4metab.sb-roscoff.fr: Galaxy instance for metabarcoding analyses (tools: FROGS, Obitools, Mothur, Qiime, PICRUSt)
ABiMS is also part of the project Workflow4Metabolomics which proposes a dedicated Galaxy instance to analyse LC-MS, GS-MS and NMR data.
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.
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.
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.