Difference between revisions of "Galaxy"
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| − | === | + | === 2016 Galaxy Community Conference === |
| − | [[File: | + | [[File:GCC2016Logo.png|left|250px|link=https://gcc2016.iu.edu/|2016 Galaxy Community Conference]] |
| − | The [ | + | 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. |
| − | 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 | + | 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]. |
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| + | [[Category:Analysis]] | ||
| + | [[Category:Comparative Genomics]] | ||
| + | [[Category:GMOD Components]] | ||
| + | [[Category:Annotation]] | ||
| + | [[Category:Galaxy]] | ||
Revision as of 18:47, 26 February 2016
Status
- Mature release
- Development: active
- Support: active
Licence
Resources
Contents
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
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 ]https://gcc2016.iu.edu/training two days of training]] offering in-depth topic coverage across several concurrent sessions, and two days of hackathons.
Visit the Galaxy website.
Screenshots
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
- General Galaxy info
- User documentation
- Source code documentation
- Search the whole universe of Galaxy docs
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 platform | web + |
| Has URL | http://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 description | Galaxy is an open, … Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.
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[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 ]https://gcc2016.iu.edu/training 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 status | active + |
| Has input format | 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 + and xml + |
| Has licence | Academic Free License 3.0 + |
| Has logo | GalaxyLogoBigger.png + |
| Has output format | zillions! + |
| Has software maturity status | mature + |
| Has support status | active + |
| Has title | Galaxy 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 topic | Galaxy + |
| Is open source | Yes + |
| Link type | download +, source code +, documentation +, website +, social media +, other +, public server +, demo server + and wild URL + |
| Release date | 2005 + |
| Tool functionality or classification | Genome Visualization and Editing +, Workflow Management +, Tool Integration + and Analysis + |
| Written in language | Python + 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 + |
