Difference between revisions of "Galaxy (biomedical software)"

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'''Galaxy''' is a  
'''Galaxy''' is free web-based, open-source collaboration software designed for "accessible, reproducible, and transparent computational biomedical research."<ref name="GalaxyWikiHome">{{cite web |url=http://wiki.g2.bx.psu.edu/FrontPage |title=Galaxy Wiki |publisher=The Pennsylvania State University |accessdate=29 September 2012}}</ref> Galaxy's key features include dataset management, history management, data visualization, workflow specification, and an extensible tool set.<ref name="GalaxyWikiLearn">{{cite web |url=http://wiki.g2.bx.psu.edu/Learn |title=Galaxy Wiki - Learn Galaxy |publisher=The Pennsylvania State University |accessdate=29 September 2012}}</ref> The program can be accessed either by one of several public servers or via an installation of a personal web instance.
 
It's worth noting Galaxy has no official version numbers. This is best explained by Greg Von Kuster of the Galaxy development team<ref name="GalaxyListVer">{{cite web |url=http://user.list.galaxyproject.org/How-to-determine-version-of-Galaxy-from-main-page-td4223309.html |title=How to determine version of Galaxy from main page |author=Von Kuster, Greg |publisher=The Pennsylvania State University |date=21 December 2011 |accessdate=29 September 2012}}</ref>:
 
<blockquote>Galaxy does not have versions as you'd find in commercial products.  There is a strict requirement that Galaxy provide reproducible behavior always, so any new feature introduced into Galaxy (or any enhancement to an existing feature) must not break any older feature that came before.  Because of this, you can always think of Galaxy as being "version 1" if it helps.
 
Galaxy does, however have different distributed "builds" or mercurial "changeset revision" numbers.</blockquote>


==Product history==
==Product history==


Galaxy was originally developed by Penn State's Anton Nekrutenko and Emory Univerity's James Taylor in 2005<ref name="GalaxyCloud" /><ref name="GalaxyGrant" />, citing "'a huge disconnect' between computer science development tools and algorithms on the one hand, and the researchers wanting to use them on the other."<ref name="GalaxyNGS">{{cite web |url=http://www.bio-itworld.com/issues/2011/galaxy-provides-life-support-for-NGS-exploration.html |title=Galaxy Provides Life Support for NGS Exploration |author=Davies, Kevin |publisher=Bio-IT World  |date=27 September 2011 |accessdate=29 September 2012}}</ref>
Galaxy was originally developed by Penn State's Anton Nekrutenko and Emory Univerity's James Taylor in 2005<ref name="GalaxyCloud" /><ref name="GalaxyGrant" />, citing "'a huge disconnect' between computer science development tools and algorithms on the one hand, and the researchers wanting to use them on the other."<ref name="GalaxyNGS">{{cite web |url=http://www.bio-itworld.com/issues/2011/galaxy-provides-life-support-for-NGS-exploration.html |title=Galaxy Provides Life Support for NGS Exploration |author=Davies, Kevin |publisher=Bio-IT World  |date=27 September 2011 |accessdate=29 September 2012}}</ref> As development continued on it over the years, Galaxy became increasingly popular; by January 2011 the Penn State-hosted main Galaxy instance handled more than 150,000 jobs and maintained more than seven [[Base pair|terabases]] of user data, usage roughly growing at a rate of 5-10% each month.<ref name="GalaxyNGS" />


==Features==
==Features==


Base features of Galaxy include<ref name="GalaxyMITPDF">{{cite web |url=http://jura.wi.mit.edu/bio/education/hot_topics/galaxy/Galaxy_June2012.pdf |format=PDF |title=Galaxy - Web based platform for bioinformatics analysis |publisher=Bioinformatics and Research Computing at MIT |pages=1–53 |date=21 June 2012 |accessdate=29 September 2012}}</ref>:


* data analysis
* dataset management
* workflow management
* data uploads and downloads
* data sharing
* data visualization
* filtering and sorting
* history
* FASTA manipulation
* sequence and alignment management
* quality control


==Hardware/software requirements==
==Hardware/software requirements==


Users wanting to use Main, the primary web instance, will simply need a web browser.
For users who wish to install their own instance, you will need:


* Python 2.5 or greater
* the ability to build Python eggs (Windows only)
* <code><nowiki>-dev</nowiki></code> packages for OpenSSL and Bzip2 (Linux only)
For more information, visit the "[http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy Get Galaxy]" page.


==Videos, screenshots, and other media==
==Videos, screenshots, and other media==


Over 60 screencasts concerning how to use Galaxy are available via [http://wiki.g2.bx.psu.edu/Learn/Screencasts the Galaxy wiki].


For additional tutorials provided by other entities, check out the "[http://wiki.g2.bx.psu.edu/Learn#Other_Tutorials Learn]" section of the wiki. The "[https://main.g2.bx.psu.edu/galaxy101 Galaxy 101]" tutorial may also be of use.


==Entities using Galaxy==
==Entities using Galaxy==


Entities using Galaxy include<ref name="GalaxyMemb">{{cite web |url=http://wiki.g2.bx.psu.edu/Community/Members |title=Galaxy - Community/Members |publisher=The Pennsylvania State University |accessdate=29 September 2012}}</ref>:


Cistrome, Emory University, Netherlands Bioinformatics Centre, Penn State University


==Further reading==


* {{cite journal |journal=Genome Research |year=2005 |volume=15 |issue=10 |pages=1451–1455 |title=Galaxy: A platform for interactive large-scale genome analysis |author=Giardine, Belinda; Riemer, Cathy; Hardison, Ross C.; Burhans, Richard; Elnitski, Laura; Shah, Prachi; Zhang, Yi; Blankenberg, Daniel; Albert, Istvan; Taylor, James; Miller, Webb; Kent, W. James; Nekrutenko, Anton |url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240089/ |doi=10.1101/gr.4086505}}


==Further reading==
* {{cite journal |journal=Current Protocols in Molecular Biology |year=2010 |volume=Chapter 19 |issue=Unit 19.10.1–21 |title=Galaxy: a web-based genome analysis tool for experimentalists |author=Blankenberg, Daniel; Von Kuster, Gregory; Coraor, Nathaniel; Ananda, Guruprasad; Lazarus, Ross; Mangan, Mary; Nekrutenko, Anton; Taylor, James |url=http://onlinelibrary.wiley.com/doi/10.1002/0471142727.mb1910s89/abstract |doi=10.1002/0471142727.mb1910s89}}
 
* {{cite journal |journal=Genome Biology |year=2010 |volume=11 |issue=8 |pages=R86 |title=Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences |author=Goecks, Jeremey; Nekrutenko, Anton; Taylor, James; The Galaxy Team |url=http://genomebiology.com/2010/11/8/R86 |doi=10.1186/gb-2010-11-8-r86}}


* {{cite journal |journal=Genome Research |year=2005 |volume=15 |issue=10 |pages=1451–1455 |title=Galaxy: A platform for interactive large-scale genome analysis |author=Giardine, Belinda; Riemer, Cathy; Hardison, Ross C.; Burhans, Richard; Elnitski, Laura; Shah, Prachi; Zhang, Yi; Blankenberg, Daniel; Albert, Istvan; Taylor, James; Miller, Webb; Kent, W. James; Nekrutenko, Anton |url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240089/ |doi=10.1101/gr.4086505}}
* {{cite web |url=http://www.bio-itworld.com/issues/2011/galaxy-provides-life-support-for-NGS-exploration.html |title=Galaxy Provides Life Support for NGS Exploration |author=Davies, Kevin |publisher=Bio-IT World  |date=27 September 2011 |accessdate=29 September 2012}}


==External links==
==External links==


 
* [https://main.g2.bx.psu.edu/ Main public Galaxy server]
* [http://wiki.g2.bx.psu.edu/PublicGalaxyServers?action=show&redirect=Public+Galaxy+Servers List of other public Galaxy servers]
* [http://wiki.g2.bx.psu.edu/ Galaxy wiki]
* [http://wiki.g2.bx.psu.edu/Galaxy%20Project/Statistics Galaxy statistics]


==References==
==References==

Revision as of 22:57, 29 September 2012

Galaxy
150px‎
Developer(s) Galaxy development team
Initial release 2005 (2005)[1][2]
Written in Python
Operating system Unix-like
Type Laboratory informatics software
License(s) See wiki
Website galaxy.psu.edu

Galaxy is free web-based, open-source collaboration software designed for "accessible, reproducible, and transparent computational biomedical research."[3] Galaxy's key features include dataset management, history management, data visualization, workflow specification, and an extensible tool set.[4] The program can be accessed either by one of several public servers or via an installation of a personal web instance.

It's worth noting Galaxy has no official version numbers. This is best explained by Greg Von Kuster of the Galaxy development team[5]:

Galaxy does not have versions as you'd find in commercial products. There is a strict requirement that Galaxy provide reproducible behavior always, so any new feature introduced into Galaxy (or any enhancement to an existing feature) must not break any older feature that came before. Because of this, you can always think of Galaxy as being "version 1" if it helps. Galaxy does, however have different distributed "builds" or mercurial "changeset revision" numbers.

Product history

Galaxy was originally developed by Penn State's Anton Nekrutenko and Emory Univerity's James Taylor in 2005[1][2], citing "'a huge disconnect' between computer science development tools and algorithms on the one hand, and the researchers wanting to use them on the other."[6] As development continued on it over the years, Galaxy became increasingly popular; by January 2011 the Penn State-hosted main Galaxy instance handled more than 150,000 jobs and maintained more than seven terabases of user data, usage roughly growing at a rate of 5-10% each month.[6]

Features

Base features of Galaxy include[7]:

  • data analysis
  • dataset management
  • workflow management
  • data uploads and downloads
  • data sharing
  • data visualization
  • filtering and sorting
  • history
  • FASTA manipulation
  • sequence and alignment management
  • quality control

Hardware/software requirements

Users wanting to use Main, the primary web instance, will simply need a web browser.

For users who wish to install their own instance, you will need:

  • Python 2.5 or greater
  • the ability to build Python eggs (Windows only)
  • -dev packages for OpenSSL and Bzip2 (Linux only)

For more information, visit the "Get Galaxy" page.

Videos, screenshots, and other media

Over 60 screencasts concerning how to use Galaxy are available via the Galaxy wiki.

For additional tutorials provided by other entities, check out the "Learn" section of the wiki. The "Galaxy 101" tutorial may also be of use.

Entities using Galaxy

Entities using Galaxy include[8]:

Cistrome, Emory University, Netherlands Bioinformatics Centre, Penn State University

Further reading





External links

References

  1. ↑ 1.0 1.1 "Galaxy DNA-Analysis Software is Now Available "in the Cloud"". The Pennsylvania State University. 11 November 2011. http://science.psu.edu/news-and-events/2011-news/Nekrutenko11-2011. Retrieved 29 September 2012. 
  2. ↑ 2.0 2.1 "Penn State awarded grant to expand Galaxy biomedical analysis software". The Pennsylvania State University. 18 June 2012. http://live.psu.edu/story/60111. Retrieved 29 September 2012. 
  3. ↑ "Galaxy Wiki". The Pennsylvania State University. http://wiki.g2.bx.psu.edu/FrontPage. Retrieved 29 September 2012. 
  4. ↑ "Galaxy Wiki - Learn Galaxy". The Pennsylvania State University. http://wiki.g2.bx.psu.edu/Learn. Retrieved 29 September 2012. 
  5. ↑ Von Kuster, Greg (21 December 2011). "How to determine version of Galaxy from main page". The Pennsylvania State University. http://user.list.galaxyproject.org/How-to-determine-version-of-Galaxy-from-main-page-td4223309.html. Retrieved 29 September 2012. 
  6. ↑ 6.0 6.1 Davies, Kevin (27 September 2011). "Galaxy Provides Life Support for NGS Exploration". Bio-IT World. http://www.bio-itworld.com/issues/2011/galaxy-provides-life-support-for-NGS-exploration.html. Retrieved 29 September 2012. 
  7. ↑ "Galaxy - Web based platform for bioinformatics analysis" (PDF). Bioinformatics and Research Computing at MIT. 21 June 2012. pp. 1–53. http://jura.wi.mit.edu/bio/education/hot_topics/galaxy/Galaxy_June2012.pdf. Retrieved 29 September 2012. 
  8. ↑ "Galaxy - Community/Members". The Pennsylvania State University. http://wiki.g2.bx.psu.edu/Community/Members. Retrieved 29 September 2012. 
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