Is There A List Of Public Galaxy Servers?

Question

[Casey Bergman]

We've been looking into setting up a local Galaxy installation for our bioinformatics core facility and in the process of doing so I've stumbled across several Galaxy mirrors and instances that have been customized in various ways. Before we go re-inventing the wheel, I was wondering if there are any other known Galaxy servers out there that we could use to borrow design ideas or code from.

Here is the list I've put together thus far, others would be most welcome....

Main Galaxy Server: http://main.g2.bx.psu.edu/

Test Galaxy Server: http://test.g2.bx.psu.edu/

GeneNetwork Galaxy Mirror: http://galaxy.genenetwork.org:8080/

NBIC Galaxy Server: http://galaxy.nbic.nl/ (includes proteomics tools)

Galaxy/Rätsch Lab Server: http://galaxy.fml.mpg.de/ (includes machine learning based tools for sequence and tiling array data analysis)

Cistrome Galaxy Server: http://cistrome.org/ap/root (dry-lab workbench for integrative analysis of ChIP-chip/seq and gene expression data)

Genomic Hyper Browser Galaxy Server: http://hyperbrowser.uio.no/hb/ (statistical methodology and computing power to handle a variety of biological inquires on genomic datasets)

DBCLS Galaxy Server: http://preview.galaxy.dbcls.jp/ (includes text mining tools, DBCLS DBSearch Tools, semantic web tools)

EDIT 11 Aug 2011

Gene Ontology's Galaxy http://galaxy.berkeleybop.org:8080/ (GO, OBO, OWL processing)

EDIT 17 Nov 2011

JGI Galaxy https://galaxy.jgi-psf.org/ (Mirror site with reorganized tool layout and extensions for metagenomics, e.g. mothur)

[Mary]

Did you look through the slides from the developer's meetings? There have been at least a couple of them. There may be some sites you can harvest from there.

[Casey Bergman]

@Mary, not yet but very good suggestion.

[Tim]

The team behind the NBIC Galaxy instance you linked too are working on setting up a RPM repository for tools they have added to their instance.. For details see: https://wiki.nbic.nl/index.php/NBIC_%26_VIB_Bioinformatics_RPM_Repository

Answer 1

[Dave Clements]

Hello Casey et al.,

Thanks to this thread, there is now a public list of Galaxy servers:

http://wiki.g2.bx.psu.edu/Public%20Galaxy%20Servers

I'll announce this on the Galaxy mailing lists in the next week.

[Casey Bergman]

Many thanks for putting this together Dave.

Answer 2

[Pierre Lindenbaum]

I found that one using pubmed:

• http://host13.bioinfo3.ifom-ieo-campus.it:8080/

googling for "Galaxy team is a part of BX at Penn State."

• http://cancan.cshl.edu/publicgalaxy/
• http://www.genboree.org/galaxy/

[Casey Bergman]

+1, thanks for this Pierre, hadn't thought to look in pubmed yet. It looks like the IFOM-IEO server is tailored for chip analysis as well.

[Casey Bergman]

Looks like the Hannon lab installation is out of date, but still some useful things there as well.

[Casey Bergman]

Genboree site has lots of goodies, but most seem closed to Genboree project members.

[Chris Miller]

Genboree is run out of my old lab. IIRC, if you register for a genboree account, a lot of the site opens up to you. Their whole model is a account-based, hosted model where you can grant or revoke permissions on your data.

[ALchEmiXt]

@Casey. Looking for microarray tools in galaxy. Check out the http://galaxy.wur.nl instance. It also has the MUMmer suite and many conversion tools.

Answer 3

[Madelaine Gogol]

Here's the link to the talks from the Galaxy 2011 conference. Also see who has forked it on bitbucket, though of course a lot of these are private.

I'm assuming you know about the tool shed, which is the place to share tool wrappers, although it seems to be down right now. Here's the new version.

You could also try searching on the galaxy-dev mailing list (or ask there).

Answer 4

[tnabtaf]

Hello all,

The list of public servers, reconstructed from Google Cache. Descriptions are clipped to get under 5000 character posting limit

1. http://host13.bioinfo3.ifom-ieo-campus.it:8080/

   • Campus IFOM IEO
     Includes CARPET - Collection of Automated Routine Programs for Easy Tiling
     Campus IFOM-IEO

2. http://cistrome.org/ap/root

   • Cistrome Analysis Pipeline
     ChIP-chip/seq and gene expression data
     The Cistrome Analysis Pipeline has the standard Galaxy tools, plus 29 additional ChIP-chip and ChIP-seq specific tools. Requires login, anyone can create a login.
     Cistrome

3. http://preview.galaxy.dbcls.jp/

   • DBCLS Galaxy Adds text mining tools, DBCLS DBSearch Tools, semantic web tools
     Can be used without understanding Japanese
     Database Center for Life Science

4. Galaxy Main - Currently down

   • Biomedical research
     Strong on genomics; good central repository for shared Galaxy objects.
     Storage and computational quotas
     Galaxy Project

5. Galaxy Test - currently down

   • Beta version of Galaxy Main
     Not stable or persistent
     Storage and computational quotas
     Galaxy Project

6. http://galaxy.genenetwork.org/

   • GeneNetwork Galaxy Mirror
     Mirrors Galaxy Main
     University of Tennessee Center for Integrative and Translational Genomics

7. http://www.genboree.org/galaxy/

   • Genboree
     Has several Genboree specific additions.
     Bioinformatics Research Laboratory at Baylor College of Medicine

8. http://hyperbrowser.uio.no/hb/

   • Genomic Hyperborwser
     "statistical methodology and computing power to handle a variety of biological inquires on genomic datasets"
     Norwegian Functional Genomics Program

9. http://galaxy.berkeleybop.org:8080/

   • Gene Ontololgy (GO)
     The Gene Ontology's Galaxy installation.
     A Galaxy install tailored for manipulating ontologies. Includes OBO, OWL, Pellet and other annotation manipulation tools.
     Gene Ontology Project

10. http://recode.ucc.ie:8080/

    • GWIPS-viz
      Tools for the analysis of protein synthesis. The server is at the stage of early development. At present it includes tools for motif searches and visualization. University College Cork

11. http://cancan.cshl.edu/publicgalaxy/

    • Hannon Lab
      Offers several tools published by the Hannon Laboratory for cross-tabulation, column normalization, as well as several Unix Tools
      Hannon Lab

12. http://huttenhower.sph.harvard.edu/lefse/

    • Huttenhower Lab
      "metagenomic and functional genomic analyses, intended for research and academic use"
      Implements "LDA Effect Size (LEfSe) (Segata et. al 2011) Huttenhower Lab

13. http://urgi.versailles.inra.fr/galaxy

    • INRA-URGI
      Offers S-MART conversion and MAPHiTS tools.
      "Mapping Analysis Pipeline for High-Throughput Sequences" (MAPHiTS). INRA URGI

14. http://mgtaxa.jcvi.org/

    • MGTAXA
      Prediction of metagenomic taxonomy
      Provides a flexible interface to the tools the MGTAXA team have developed for the prediction of metagenomic taxonomy.
      JCVI

15. http://nebula.curie.fr/

    • Nebula
      "allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data."
      "Nebula is a web service provided by Institut Curie."
      Institut Curie

16. http://galaxy.nmcdsp.org/

    • Netherlands Metabolomics Centre
      Metabolomics
      Include MTSiP package Netherlands Metabolimics Centre

17. http://galaxy.tuebingen.mpg.de/

    • Oqtans
      Customized Galaxy, extended with machine learning based tools for sequence and tiling array data analysis.
      Machine Learning in Biology (MLB) Group at the Friedrich Miescher Laboratory of the Max Planck Society

18. http://regulatorygenomics.upf.edu/galaxy

    • Regulatory Genomics Galaxy
      Regulatory genomics, including the Pyicos package. Chip/clip/rna seq data analysis.
      "This Galaxy instance is on a TESTING phase and contains experimental software. Use at your own risk" A paper and the source are also available.
      Regulatory Genomics Group @ Pompeu Fabra University

19. http://galaxy.nbic.nl/

    • Sombrero
      NBIC's development Galaxy server
      Beware that your data may vanish without notice
      Netherlands Bioinformatics Centre (NBIC)

20. http://discovery.hsci.harvard.edu/galaxy

    • Stem Cell Discovery Engine (SCDE)
      Database of curated cancer stem cell experiments coupled to Galaxy.
      Includes tools for stem cell gene list comparisons.
      Hide Lab @ Harvard School of Public Health, Harvard Stem Cell Institute.

21. http://symd.nci.nih.gov/

    • SymD
      "SymD is a tool for detecting internally symmetric protein structures."
      US National Cancer Institute (NCI)

22. http://galaxy.wur.nl/

    • Wageningen University Galaxy
      Includes microarray tools, the MUMmer suite, and many conversion tools.
      Part of the Plant Research International ChIP-seq Analysis Tool (PRI-CAT)
      Requires login, anyone can create a login.
      Wageningen University

Answer 5

[tnabtaf]

This is a partial list and hasn't been updated much since the list was put on the wiki (which is now down). I'll crawl through my email archives and post other servers here in the next hour.

Dave C

Answer 6

[tnabtaf]

Hello all,

The Google Cache of the Public Galaxy Servers page is at http://webcache.googleusercontent.com/search?q=cache:j6LZRFrtqR0J:wiki.g2.bx.psu.edu/PublicGalaxyServers

I'll try and post that complete list here, in case that cache goes away.

In the meantime, here's a list generated from my email archive. Some of this may be redundant with entries above:

• http://preview.galaxy.dbcls.jp
• http://recode.ucc.ie:8080/ - motif searches and visualization http://galaxy.nmcdsp.org/ - metabolomics
• http://nebula.curie.fr/ - A WEB-SERVER FOR ADVANCED CHIP-SEQ DATA ANALYSIS
• http://mgtaxa.jcvi.org/ - metagenomic classification
• http://discovery.hsci.harvard.edu/galaxy - Stem cell discovery engine
• http://cistrome.org/ap/root - ChIP-* Analysis
• http://symd.nci.nih.gov/ - Protein symmetry detection

Hope this helps,

Dave C.