Difference between revisions of "Galaxy"

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[[File:GalaxyLogoBigger.png|center|400px|alt=Galaxy logo]]
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<div class="compBoxHdr">Status</div>
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*Mature release
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*active development
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*active support
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<div class="compBoxHdr">Resources</div>
 
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*[http://galaxyproject.org Home Page]
 
*[http://galaxyproject.org Home Page]
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==About Galaxy==
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[http://usegalaxy.org Galaxy] is an open, web-based platform for ''accessible, reproducible, and transparent'' computational biomedical research.
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* ''Accessibility:'' Galaxy enables users without programming experience to easily specify parameters and run tools and workflows.
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* ''Reproducibility:'' Galaxy captures all information necessary so that any user can repeat and understand a complete computational analysis.
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* ''Transparency:'' Galaxy enables users to share and publish analyses via the web and create Pages--interactive, web-based documents that describe a complete analysis.
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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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Visit the [http://galaxyproject.org Galaxy Project home page].
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=== 2013 Galaxy Community Conference ===
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[[File:GCC2013Logo.png|left|200px|link=http://wiki.galaxyproject.org/Events/GCC2013|2013 Galaxy Community Conference]]
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The [http://wiki.galaxyproject.org/Events/GCC2013 2013 Galaxy Community Conference (GCC2013)] will be held June 30 through July 2 at the University of Oslo in Oslo, Norway.  GCC2013 will feature a Tutorial Day followed by two days of presentations, discussions, lightning talks, breakouts, and keynotes 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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[http://wiki.galaxyproject.org/Events/GCC2012 GCC2012] was held in Chicago had over 200 attendees.  Slides and videos of all talks at [http://wiki.galaxyproject.org/Events/GCC2012 GCC2012] and [http://wiki.galaxyproject.org/Events/GCC2011 GCC2011] are available on the Galaxy wiki.
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==Downloads==
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Galaxy download and installation information is at [http://getgalaxy.org/ GetGalaxy.org].
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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.
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==Using Galaxy==
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Please visit the [http://wiki.galaxyproject.org/ Galaxy Wiki] for full documentation on all aspects of getting, installing, and using Galaxy.
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==Contacts and Mailing Lists==
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{| class="wikitable"
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|
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! Mailing List Link
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! Description
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! Archive(s)
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{{Template:MailingListsGalaxy}}
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==Publications, Tutorials, and Presentations==
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See [[:Category:Galaxy]].
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===Tutorials===
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The Galaxy project has a wealth of training materials, including the [[Galaxy Tutorial|GMOD Galaxy Tutorial]] plus a number of other items linked to from Galaxy's [http://wiki.galaxyproject.org/Learn Learning Hub]:
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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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===Publications on or mentioning Galaxy===
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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/order/to_read,desc, Galaxy CiteULike Group] for over 500 papers about, using, and referencing Galaxy.
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[[Category:Analysis]]
 
[[Category:Analysis]]

Revision as of 22:06, 1 March 2013


Galaxy logo
Status
  • Mature release
  • Development: active
  • Support: active
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.

2014 Galaxy Community Conference

2014 Galaxy Community Conference

The 2014 Galaxy Community Conference (GCC2013) will be held June 30 through July 2, at the Homewood Campus of Johns Hopkins University], in Baltimore, Maryland, United States.

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 will also includes a Training Day offering in-depth topic coverage, across several concurrent sessions.  See the GCC2013 web site for an idea of what happens at a Galaxy Community Conference. The GCC2013 site includes links to slides and videos for all accepted talks.

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. High volume. Nabble, Mailman
galaxy-proteomics General questions and discussion regarding proteomics in Galaxy. Low volume. Nabble, Mailman
galaxy-france Cette liste est destinée à l'information (et aux discussions) de la Communauté francaise Galaxy. (This list is for announcements to (and discussion within) the French Galaxy Community. Most list content is in French.) Faible volume / Low volume. Nabble
galaxy-commits Galaxy source control commit messages. Mailman

Galaxy in the wild

Public installations of Galaxy: Galaxy maintains a list of public Galaxy servers

Galaxy Development

Development team

The Galaxy Development Team are listed on the Galaxy wiki; in addition to the core developers, there are also extensive contributions from the Galaxy user community.


More on Galaxy

See Category:Galaxy




Raw tool data at Galaxy/tool data