Difference between revisions of "Galaxy"

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{{ImageCenter|GalaxyLogoBigger.png|Galaxy||http://getgalaxy.org/}}
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{{Tool data
__NOTITLE__
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|name=Galaxy
 
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|status=mature
{{ComponentBox|{{GalaxyResourcesBoxItem}}|{{ComponentBoxEventsHeader}}|{{GalaxyEventsBoxItem}}||<hr />{{WCGBoxItem}}<hr />{{ISMBBoxItem}}}}
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|dev=active
 
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|support=active
[http://usegalaxy.org Galaxy] is an open, web-based platform for ''accessible, reproducible, and transparent'' computational biomedical research.
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|type=Genome Visualization and Editing, Workflow Management, Tool Integration, Analysis
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|platform=web
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|about=[http://usegalaxy.org Galaxy] is an open, web-based platform for ''accessible, reproducible, and transparent'' computational biomedical research.
 
* ''Accessibility:'' Galaxy enables users without programming experience to easily specify parameters and run tools and workflows.
 
* ''Accessibility:'' Galaxy enables users without programming experience to easily specify parameters and run tools and workflows.
 
* ''Reproducibility:'' Galaxy captures all information necessary so that any user can repeat and understand a complete computational analysis.
 
* ''Reproducibility:'' Galaxy captures all information necessary so that any user can repeat and understand a complete computational analysis.
 
* ''Transparency:'' Galaxy enables users to share and publish analyses via the web and create Pages--interactive, web-based documents that describe a complete analysis.
 
* ''Transparency:'' Galaxy enables users to share and publish analyses via the web and create Pages--interactive, web-based documents that describe a complete analysis.
  
Galaxy is open source for all organizations. The [http://usegalaxy.org public Galaxy service] makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist that has access to the Internet. Local Galaxy servers can be set up by [http://getgalaxy.org downloading the Galaxy application] and customizing it to meet particular needs.
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Galaxy is open source for all organizations. The [http://usegalaxy.org public Galaxy server] makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist that has access to the Internet. Local Galaxy servers can be set up by [http://getgalaxy.org downloading the Galaxy application] and customizing it to meet particular needs.
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[[File:GCC2016Logo.png|left|250px|link=https://gcc2016.iu.edu/|2016 Galaxy Community Conference]]
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=== 2016 Galaxy Community Conference ===
  
== 2011 Galaxy Community Conference ==
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The [https://gcc2016.iu.edu/ 2016 Galaxy Community Conference (GCC2016)] will be held June 25-29, at [https://gcc2016.iu.edu/location/ Indiana University] in Bloomington, Indiana, United states, immediately before the [[Jun 2016 GMOD Meeting|June 2016 GMOD Meeting]], also in Bloomington.
  
{{ImageLeft|GCC2011Logo.png|2011 Galaxy Community Conference|300|http://galaxy.psu.edu/gcc2011/}}
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Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it.  The conference also includes [https://gcc2016.iu.edu/training two days of training] offering in-depth topic coverage across several concurrent sessions, and [https://gcc2016.iu.edu/hacks/ two days of hackathons].
The [http://galaxy.psu.edu/gcc2011/ 2011 Galaxy Community Conference] was held 25-26 May, at the Conference Centre De Werelt in Lunteren, The Netherlands. This year the conference was sponsored and hosted by the [http://www.nbic.nl/ Netherlands Bioinformatics Centre (NBIC)].  There were almost 150 registrations and the conference featured [http://galaxy.psu.edu/gcc2011/Programme.html two full days] of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization, and best practices for using Galaxy to further your research.
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==Demo & Screencasts ==
 
  
Try the [http://usegalaxy.org/ public Galaxy server].  You can create a login and save your work, or use it anonymously.  Short [http://main.g2.bx.psu.edu/screencast screencasts] on how to use Galaxy for several example tasks are also available.
 
  
==Requirements==
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|open source=Yes
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|licence=[http://opensource.org/licenses/AFL-3.0 Academic Free License 3.0]
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|input=Roadmaps,Sequences,ab1,affybatch,afg,axt,bam,bcf,bed,bedgraph,bigbed,bigwig,bowtie_base_index,bowtie_color_index,chrint,cisml,csfasta,csv,eland,elandmulti,encodepeak,eset,fasta,fastq,fastqcssanger,fastqillumina,fastqsanger,fastqsolexa,fli,fped,fphe,fqtoc,gatk_dbsnp,gatk_interval,gatk_recal,gatk_report,gatk_tranche,gd_indivs,gd_ped,gd_sap,gd_snp,[[GFF]],[[GFF3]],gtf,interval,lav,ldindep,len,linecount,lped,maf,malist,memexml,nex,nhx,pbed,phyloxml,picard_interval_list,pileup,pphe,qual454,qualillumina,qualsolexa,qualsolid,sam,scf,sff,snpmatrix,snptest,tabular,taxonomy,twobit,txt,vcf,velvet,wig,xml
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|output=zillions!
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|language=Python, XML
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|audience=public,private
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|release date=2005
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|use template=Yes
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|logo=GalaxyLogoBigger.png
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|screenshot=[[File:Galaxy screenshot-1.png|thumb|none|300px|Galaxy 'Upload file' tool]] [[File:Galaxy screenshot-2.png|thumb|none|300px|Galaxy 'Table Browser' tool]] [[File:Galaxy screenshot-3.png|thumb|none|300px|Editing the attributes of a data set in Galaxy]]
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|mail={{MailingListsFor|Galaxy}}
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|papers=See [http://wiki.galaxyproject.org/CitingGalaxy Citing Galaxy] for a core list of 25+ papers on Galaxy, and the [http://www.citeulike.org/group/16008/ Galaxy CiteULike group] for a fuller list of papers mentioning or using Galaxy.
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|tutorials=;[[Galaxy Tutorial]]
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:As taught at the [[2013 GMOD Summer School]]
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;[http://wiki.galaxyproject.org/Learn Galaxy Learning Hub]:
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:A wealth of training materials, including:
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:*[http://wiki.galaxyproject.org/Learn#Galaxy_101 Galaxy 101]
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:*[http://wiki.galaxyproject.org/Learn/Screencasts Screencasts]
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:*[http://wiki.galaxyproject.org/Learn#Shared_Pages.2C_Histories_.26_Workflows Shared Pages, Histories & Workflows]
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:*[http://wiki.galaxyproject.org/Learn#Other_Tutorials Other Tutorials]
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:*[http://wiki.galaxyproject.org/Learn#Datasets Working With Datasets]
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:*[http://wiki.galaxyproject.org/Learn and more!]
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; [http://bit.ly/gxyRNASEX RNA-Seq Example]
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: An introduction to NGS processing (specifically RNA-Seq) with [[Galaxy]].
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; [http://www.openhelix.com/cgi/tutorialInfo.cgi?id=82 OpenHelix Galaxy User Tutorial]
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: A Flash based tutorial on using Galaxy.  Provided by [http://www.openhelix.com OpenHelix].  Tutorial includes slides, handouts and exercises.  Requires subscription.
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|getting started preamble=Galaxy aims to be a zero configuration entirely self-contained system that provides a lightweight webserver, an embedded database and a multi-threaded job manager. All tools (and their parameters) can be specified via simple XML based configuration files.
  
* Python version '''2.4''' or higher
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Full documentation on all aspects of getting, installing, and using Galaxy is available from the [https://wiki.galaxyproject.org/ Galaxy Wiki].
* '''Mac OS X''' currently requires Universal "Fat" Python 2.4 (the Python 2.4 build officially supported by Apple) from http://macpython.org/ ([http://pythonmac.org/packages/py24-fat/index.html direct link])
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|doc=*[http://wiki.galaxyproject.org/ General Galaxy info]
* Galaxy runs fine in most Posix environments. It is not currently supported on Windows platforms, but necessary Python eggs can be built by those desiring to host it on Windows.
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*[http://wiki.galaxyproject.org/Learn User documentation]
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*[http://docs.galaxyproject.org/ Source code documentation]
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*[http://galaxyproject.org/search/ Search the whole universe of Galaxy docs]
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|survey link=Galaxy
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|contact email=[mailto:clements@galaxyproject.org Dave Clements] or [mailto:outreach@galaxyproject.org Galaxy Outreach]
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|dev status=
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}}
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<!-- extra links:
 +
<div class="compBoxHdr">Resources</div>
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*[http://galaxyproject.org Home Page]
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*[http://usegalaxy.org Public Server]
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*[http://wiki.galaxyproject.org/ Galaxy Wiki]
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*[http://getgalaxy.org Download / Cloud]
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*[[Galaxy Tutorial]]
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*[http://galaxyproject.org/search Search]
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*[http://wiki.galaxyproject.org/Community/GalaxyAdmins/SurveyResults 2012 Survey]
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<hr />
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{{GalaxyEventsBoxItem}}
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-->
  
==Documentation==
 
  
* Most Galaxy documentation is in the [http://wiki.g2.bx.psu.edu/ Galaxy Wiki].
 
* [http://www.genome.org/cgi/content/abstract/15/10/1451 Galaxy: A platform for interactive large-scale genome analysis], by Belinda Giardine, Cathy Riemer, Ross C. Hardison, Richard Burhans, Laura Elnitski, Prachi Shah, Yi Zhang, [[User:DanB|Daniel Blankenberg]], Istvan Albert, [[User:JamesTaylor|James Taylor]], Webb Miller, W. James Kent and Anton Nekrutenko, Genome Res. 15:1451-1455, 2005
 
  
== Mailing Lists ==
 
  
{{MailingListsFor|Galaxy}}
 
  
==Downloads==
 
  
Galaxy aims to be a zero configuration entirely self-contained system that provides a lightweight webserver, an embedded database and a multi-threaded job manager. All tools (and their parameters) can be specified via simple XML based configuration files. Galaxy download and installation information is located [http://g2.trac.bx.psu.edu/wiki/HowToInstall here].
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{{SemanticLink
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|linkurl=http://getgalaxy.org
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|linktype=download
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}}
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{{SemanticLink
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|linkurl=https://github.com/galaxyproject/galaxy/
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|linktype=source code
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}}
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{{SemanticLink
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|linkurl=https://docs.galaxyproject.org
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|linktitle=Galaxy source code documentation
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|linktype=documentation
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}}
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{{SemanticLink
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|linkurl=http://galaxyproject.org/
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|linktype=website
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}}
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{{SemanticLink
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|linkurl=http://wiki.galaxyproject.org/
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|linktype=documentation
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}}
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{{SemanticLink
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|linkurl=https://twitter.com/galaxyproject
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|linktype=social media
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}}
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{{SemanticLink
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|linkurl=http://www.citeulike.org/group/16008/
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|linktitle=Galaxy bibliography on Cite-U-Like
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|linktype=other
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}}
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{{SemanticLink
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|linkurl=http://www.mendeley.com/groups/1710745/
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|linktitle=Galaxy bibliography on Mendeley
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|linktype=other
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}}
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{{SemanticLink
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|linkurl=https://trello.com/board/galaxy-development-inbox/50686d0302dfa79d13d90c45
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|linktitle=Galaxy Trello board
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|linktype=other
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}}
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{{SemanticLink
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|linkurl=http://usegalaxy.org/
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|linktype=public server
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|linkdesc=A fully-fledged, fully-supported instance
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}}
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{{SemanticLink
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|linkurl=https://test.g2.bx.psu.edu/
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|linktype=demo server
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|linkdesc=Test instance
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}}
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{{SemanticLink
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|linkurl=http://wiki.galaxyproject.org/PublicGalaxyServers
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|linktitle=List of public Galaxy servers
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|linktype=wild URL
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}}
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{{SemanticLink
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|linkurl=https://galaxyproject.github.io
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|linktitle=List of Galaxy Produced Softawre
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|linktype=documentation
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}}
  
 
[[Category:Analysis]]
 
[[Category:Analysis]]

Revision as of 18:55, 26 February 2016

Galaxy logo
Status
  • Mature release
  • Development: active
  • Support: active
Licence
{{{PAGENAME}}} is open source

Academic Free License 3.0

Resources


About Galaxy

Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.

  • Accessibility: Galaxy enables users without programming experience to easily specify parameters and run tools and workflows.
  • Reproducibility: Galaxy captures all information necessary so that any user can repeat and understand a complete computational analysis.
  • Transparency: Galaxy enables users to share and publish analyses via the web and create Pages--interactive, web-based documents that describe a complete analysis.

Galaxy is open source for all organizations. The public Galaxy server makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist that has access to the Internet. Local Galaxy servers can be set up by downloading the Galaxy application and customizing it to meet particular needs.


2016 Galaxy Community Conference

2016 Galaxy Community Conference

The 2016 Galaxy Community Conference (GCC2016) will be held June 25-29, at Indiana University in Bloomington, Indiana, United states, immediately before the June 2016 GMOD Meeting, also in Bloomington.

Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it.  The conference also includes two days of training offering in-depth topic coverage across several concurrent sessions, and two days of hackathons.


Visit the Galaxy website.

Screenshots

Galaxy 'Upload file' tool
Galaxy 'Table Browser' tool
Editing the attributes of a data set in Galaxy

Downloads

Using Galaxy

Galaxy aims to be a zero configuration entirely self-contained system that provides a lightweight webserver, an embedded database and a multi-threaded job manager. All tools (and their parameters) can be specified via simple XML based configuration files.

Full documentation on all aspects of getting, installing, and using Galaxy is available from the Galaxy Wiki.


Documentation

Publications, Tutorials, and Presentations

Publications on or mentioning Galaxy

See Citing Galaxy for a core list of 25+ papers on Galaxy, and the Galaxy CiteULike group for a fuller list of papers mentioning or using Galaxy.

Tutorials

Galaxy Tutorial
As taught at the 2013 GMOD Summer School
Galaxy Learning Hub
A wealth of training materials, including:
RNA-Seq Example
An introduction to NGS processing (specifically RNA-Seq) with Galaxy.
OpenHelix Galaxy User Tutorial
A Flash based tutorial on using Galaxy. Provided by OpenHelix. Tutorial includes slides, handouts and exercises. Requires subscription.


Contacts and Mailing Lists

Mailing List Link Description Archive(s)
Galaxy
(Search everything)
galaxy-announce Announcements of interest to the Galaxy community. Low volume and moderated. Nabble, Mailman
Galaxy Help General questions and discussion about using Galaxy. Also used for announcements relevant to the Galaxy user community. This is not a mailing list, but an online forum, based on the popular Discourse platform. High volume.
galaxy-dev Discussion and questions regarding local installations and development of Galaxy. Medium volume. Nabble, Mailman

Galaxy in the wild

Public installations of Galaxy:



More on Galaxy

See Category:Galaxy


Facts about "Galaxy"RDF feed
Available on platformweb +
Has URLhttp://getgalaxy.org +, https://github.com/galaxyproject/galaxy/ +, https://docs.galaxyproject.org +, http://galaxyproject.org/ +, http://wiki.galaxyproject.org/ +, https://twitter.com/galaxyproject +, http://www.citeulike.org/group/16008/ +, http://www.mendeley.com/groups/1710745/ +, https://trello.com/board/galaxy-development-inbox/50686d0302dfa79d13d90c45 +, http://usegalaxy.org/ +, https://test.g2.bx.psu.edu/ +, http://wiki.galaxyproject.org/PublicGalaxyServers + and https://galaxyproject.github.io +
Has descriptionGalaxy is an open, Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.
  • Accessibility: Galaxy enables users without programming experience to easily specify parameters and run tools and workflows.
  • Reproducibility: Galaxy captures all information necessary so that any user can repeat and understand a complete computational analysis.
  • Transparency: Galaxy enables users to share and publish analyses via the web and create Pages--interactive, web-based documents that describe a complete analysis.

Galaxy is open source for all organizations. The public Galaxy server makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist that has access to the Internet. Local Galaxy servers can be set up by downloading the Galaxy application and customizing it to meet particular needs.


2016 Galaxy Community Conference

2016 Galaxy Community Conference[edit]

The 2016 Galaxy Community Conference (GCC2016) will be held June 25-29, at Indiana University in Bloomington, Indiana, United states, immediately before the June 2016 GMOD Meeting, also in Bloomington.

Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it.  The conference also includes two days of training offering in-depth topic coverage across several concurrent sessions, and two days of hackathons.
016.iu.edu/hacks/ two days of hackathons]. +, A fully-fledged, fully-supported instance + and Test instance +
Has development statusactive +
Has input formatRoadmaps +, Sequences +, ab1 +, affybatch +, afg +, axt +, bam +, bcf +, bed +, bedgraph +, bigbed +, bigwig +, bowtie_base_index +, bowtie_color_index +, chrint +, cisml +, csfasta +, csv +, eland +, elandmulti +, encodepeak +, eset +, fasta +, fastq +, fastqcssanger +, fastqillumina +, fastqsanger +, fastqsolexa +, fli +, fped +, fphe +, fqtoc +, gatk_dbsnp +, gatk_interval +, gatk_recal +, gatk_report +, gatk_tranche +, gd_indivs +, gd_ped +, gd_sap +, gd_snp +, GFF +, GFF3 +, gtf +, interval +, lav +, ldindep +, len +, linecount +, lped +, maf +, malist +, memexml +, nex +, nhx +, pbed +, phyloxml +, picard_interval_list +, pileup +, pphe +, qual454 +, qualillumina +, qualsolexa +, qualsolid +, sam +, scf +, sff +, snpmatrix +, snptest +, tabular +, taxonomy +, twobit +, txt +, vcf +, velvet +, wig + and xml +
Has licenceAcademic Free License 3.0 +
Has logoGalaxyLogoBigger.png +
Has output formatzillions! +
Has software maturity statusmature +
Has support statusactive +
Has titleGalaxy source code documentation +, Galaxy bibliography on Cite-U-Like +, Galaxy bibliography on Mendeley +, Galaxy Trello board +, List of public Galaxy servers + and List of Galaxy Produced Softawre +
Has topicGalaxy +
Is open sourceYes +
Link typedownload +, source code +, documentation +, website +, social media +, other +, public server +, demo server + and wild URL +
Release date2005 +
Tool functionality or classificationGenome Visualization and Editing +, Workflow Management +, Tool Integration + and Analysis +
Written in languagePython + and XML +
Has subobjectThis property is a special property in this wiki.Galaxy#http://getgalaxy.org +, Galaxy#https://github.com/galaxyproject/galaxy/ +, Galaxy#https://docs.galaxyproject.org +, Galaxy#http://galaxyproject.org/ +, Galaxy#http://wiki.galaxyproject.org/ +, Galaxy#https://twitter.com/galaxyproject +, Galaxy#http://www.citeulike.org/group/16008/ +, Galaxy#http://www.mendeley.com/groups/1710745/ +, Galaxy#https://trello.com/board/galaxy-development-inbox/50686d0302dfa79d13d90c45 +, Galaxy#http://usegalaxy.org/ +, Galaxy#https://test.g2.bx.psu.edu/ +, Galaxy#http://wiki.galaxyproject.org/PublicGalaxyServers + and Galaxy#https://galaxyproject.github.io +