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Software and Utilities (Archived) - Revision history
2024-03-29T09:27:29Z
Revision history for this page on the wiki
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https://wiki.geneontology.org/index.php?title=Software_and_Utilities_(Archived)&diff=74342&oldid=prev
Pascale: /* People */
2019-04-12T13:08:45Z
<p><span dir="auto"><span class="autocomment">People</span></span></p>
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Pascale
https://wiki.geneontology.org/index.php?title=Software_and_Utilities_(Archived)&diff=67863&oldid=prev
Cjm: Cjm moved page Software and Utilities Acrhived to Software and Utilities (Archived)
2018-03-10T19:37:52Z
<p>Cjm moved page <a href="/Software_and_Utilities_Acrhived" class="mw-redirect" title="Software and Utilities Acrhived">Software and Utilities Acrhived</a> to <a href="/Software_and_Utilities_(Archived)" title="Software and Utilities (Archived)">Software and Utilities (Archived)</a></p>
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Cjm
https://wiki.geneontology.org/index.php?title=Software_and_Utilities_(Archived)&diff=67859&oldid=prev
Cjm: Created page with "Category:Software The purpose of the <b>Software and Utilities</b> group (SWUG) is to support both the GOC and the user community with technical, software, bioinformatics..."
2018-03-10T00:29:49Z
<p>Created page with "<a href="/Category:Software" title="Category:Software">Category:Software</a> The purpose of the <b>Software and Utilities</b> group (SWUG) is to support both the GOC and the user community with technical, software, bioinformatics..."</p>
<p><b>New page</b></p><div>[[Category:Software]] <br />
The purpose of the <b>Software and Utilities</b> group (SWUG) is to support both the GOC and the user community with technical, software, bioinformatics and computer-science related matters. In addition, this group will help drive the GOC through the research and provision of new computational technologies and methodologies relating to ontologies and ontology-based data analysis. This group is responsible for creating, clarifying and extending the common model that underpins all of GO. Ontology development tools are necessary for the [[Ontology Development]] group to perform its function. In addition, the [[Annotation Outreach]] group and wider community need means of exploring and utilizing GO and existing annotations. This group complements all the other groups.<br />
<br />
[[Software and Utilities group summary]]<br />
<br />
* Timeline: [[SWUG_Timeline_2010-2011]]<br />
* List of projects in progress: [[:Category:SWUG_Projects]]<br />
* [[Software_Group_2010_Future_Plans]]<br />
<br />
==Meetings==<br />
<br />
See [[:Category:SWUG-TCons]] for all new meetings<br />
<br />
*[[SWUG:Meeting_at_Stanford_2011_06_23]]<br />
<br />
*[[SWUG:Meeting_2008_04_30]]<br />
<br />
*[[SWUG:Meeting_2008_04_16]]<br />
<br />
*[[SWUG:Meeting_2008_02_05]]<br />
<br />
*[[SWUG:Meeting_2007_12_12]]<br />
<br />
*[[SWUG:Meeting_2007_10_17]]<br />
<br />
*[[SWUG:Meeting_2007_09_19]] - pre GOC meeting prep<br />
<br />
*[[SWUG:Meeting_2007-08-22]]<br />
<br />
* Visualisation meeting, 2007-08-16. No notes, demo only<br />
<br />
*[[SWUG:Meeting_2007-08-08]]<br />
<br />
*[[SWUG:Meeting_2007-07-25]]<br />
<br />
*[[SWUG:Meeting_2007-06-27]]<br />
<br />
*[[SWUG:Meeting_2007-05-30]]<br />
<br />
*[[SWUG:Meeting_2007-04-18]]<br />
<br />
*[[SWUG:Meeting_2007-04-04]]<br />
<br />
* March 14 2007 - <br />
<br />
* [[SWUG:Agenda_Template]]<br />
<br />
'''Past Meetings:'''<br />
<br />
*[[Database_Meeting_21_Nov_2006]]<br />
<br />
'''Forthcoming meetings:'''<br />
<br />
Schedule to be decided<br />
<br />
*[[SWUG:Topics_for_future_meetings]]<br />
<br />
== Reports ==<br />
<br />
* [[SWUG:Report_200901]]<br />
* [[SWUG:Database_changes_2007]]<br />
<br />
==Mail List==<br />
<br />
There is no public mailing list for this group.<br />
<br />
==Resources==<br />
<br />
===Documentation===<br />
<br />
* http://gocwiki.geneontology.org/index.php/GO_FAQ#Software_and_tools<br />
* http://wiki.geneontology.org/index.php/Example_Queries<br />
* http://amigo.geneontology.org/dev<br />
* http://www.geneontology.org/GO.database.shtml<br />
* http://www.geneontology.org/GO.tools.software-libraries.shtml<br />
<br />
===Trackers===<br />
<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=934137 GO database]<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=747782 go-perl]<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=494390 AmiGO Requests]<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=908269 AmiGO bug reports]<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=418260 Obo-edit requests]<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=418257 Obo-edit bugs]<br />
<br />
===People===<br />
<br />
* [[External_Database_Contact_Info]]<br />
<br />
===Principles===<br />
<br />
* [[SWUG:Quality_Control]]<br />
<br />
==Wiki==<br />
<br />
All software-and-utilities pages on the wiki should go in the wikispace SWUG (SoftWare Utilities Group)<br />
<br />
==Projects==<br />
<br />
===Galaxy===<br />
<br />
[[Galaxy | Everything you need to know about GO Galaxy]]<br />
<br />
===OBO-Edit===<br />
<br />
*[http://www.oboedit.org OBO-Edit public home page]<br />
<br />
*[[OBO-Edit]] wiki page<br />
<br />
*[http://wiki.geneontology.org/index.php/Category:OBO-Edit_working_group OBO-Edit working group]<br />
<br />
===AmiGO===<br />
<br />
====General Interest====<br />
<br />
* [[AmiGO_Manual:_Overview]]<br />
* [[AmiGO_Manual:_Installation]]<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=494390 AmiGO Requests]<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=908269 AmiGO bug reports]<br />
<br />
====Internal interest====<br />
<br />
* [[:Category:AmiGO working group|AmiGO working group]]<br />
* [[AmiGO_Big_Ideas]]<br />
* [[SWUG:AmiGO_Architecture_Roadmap]]<br />
* [[AmiGO]]<br />
<br />
===RefGenome===<br />
<br />
* [[RG:_Software]]<br />
<br />
===TreeCurationTool===<br />
<br />
Collaboration with PantherDB<br />
<br />
* https://sourceforge.net/projects/pantherdb<br />
<br />
<br />
<br />
===SO===<br />
<br />
Main page: http://www.sequenceontology.org<br />
<br />
====MiSO====<br />
CVS http://song.cvs.sourceforge.net/song/software/scripts/miSO<br />
<br />
browser http://song.sf.net/SO_view/index.html<br />
<br />
====Cross-products in SO====<br />
<br />
SO contains cross-product definitions of many composite terms. See <br />
[[SO Cross Products]] for the methodology.<br />
<br />
===Obol===<br />
<br />
http://www.berkeleybop.org/obol<br />
<br />
===Reference Genome Software Prototype===<br />
<br />
Sohel Merchant has created a prototype as support for the Reference Genome Annotation Project. Currently the project data is managed by means of a google spreadsheet that is difficult to use. The new database and interface will allow the administrator to enter new target genes and for the model organism curators to call their orthologs and to track curation progress of each gene. (For more on the Reference Genome Annotation Project: http://gocwiki.geneontology.org/index.php/Reference_Genome_Annotation_Project )<br />
<br />
To access the prototype: http://rails-dev.bioinformatics.northwestern.edu:24000</div>
Cjm