Difference between revisions of "Software and Utilities"

From GO Wiki
Jump to: navigation, search
(Meetings)
(People)
 
(18 intermediate revisions by 5 users not shown)
Line 1: Line 1:
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.
+
[[Category:Software]] [[Category:Working Groups]]
  
[[Software and Utilities group summary]]
+
For the legacy page, see [[Software_and_Utilities_(Archived)]] and [[Software and Utilities group summary]]
  
* Timeline: [[SWUG_Timeline_2010-2011]]
 
* List of projects in progress: [[:Category:SWUG_Projects]]
 
* [[Software_Group_2010_Future_Plans]]
 
  
 
==Meetings==
 
==Meetings==
  
See [[:Category:SWUG-TCons]] for all new meetings
+
See the GO calendar
  
*[[SWUG:Meeting_at_Stanford_2011_06_23]]
+
Core meetings:
  
*[[SWUG:Meeting_2008_04_30]]
+
* biweekly all-day thursday LBL hack days (anyone can zoom in)
 +
* biweekly Noctua calls
 +
* adhoc zooms between developers as needed
  
*[[SWUG:Meeting_2008_04_16]]
+
Also:
  
*[[SWUG:Meeting_2008_02_05]]
+
* updates on go-managers calls
 
+
* ontology engineering team join ontology calls
*[[SWUG:Meeting_2007_12_12]]
+
* most devs join annotation calls
 
 
*[[SWUG:Meeting_2007_10_17]]
 
 
 
*[[SWUG:Meeting_2007_09_19]] - pre GOC meeting prep
 
 
 
*[[SWUG:Meeting_2007-08-22]]
 
 
 
* Visualisation meeting, 2007-08-16. No notes, demo only
 
 
 
*[[SWUG:Meeting_2007-08-08]]
 
 
 
*[[SWUG:Meeting_2007-07-25]]
 
 
 
*[[SWUG:Meeting_2007-06-27]]
 
 
 
*[[SWUG:Meeting_2007-05-30]]
 
 
 
*[[SWUG:Meeting_2007-04-18]]
 
 
 
*[[SWUG:Meeting_2007-04-04]]
 
 
 
* March 14 2007 -
 
 
 
* [[SWUG:Agenda_Template]]
 
 
 
'''Past Meetings:'''
 
 
 
*[[Database_Meeting_21_Nov_2006]]
 
 
 
'''Forthcoming meetings:'''
 
 
 
Schedule to be decided
 
 
 
*[[SWUG:Topics_for_future_meetings]]
 
 
 
== Reports ==
 
 
 
* [[SWUG:Report_200901]]
 
* [[SWUG:Database_changes_2007]]
 
  
 
==Mail List==
 
==Mail List==
  
Send to mailing list:
+
* godev-internal on groups.io
 
 
*[mailto:software-group@geneontology.org software-group@geneontology.org]
 
 
 
To subscribe, email [mailto:software-group-request@geneontology.org software-group-request@geneontology.org] with 'subscribe' in the body of the email
 
  
 
==Resources==
 
==Resources==
Line 72: Line 28:
 
===Documentation===
 
===Documentation===
  
* http://gocwiki.geneontology.org/index.php/GO_FAQ#Software_and_tools
 
* http://wiki.geneontology.org/index.php/Example_Queries
 
* http://amigo.geneontology.org/dev
 
* http://www.geneontology.org/GO.database.shtml
 
* http://www.geneontology.org/GO.tools.software-libraries.shtml
 
  
 
===Trackers===
 
===Trackers===
  
* [http://sourceforge.net/tracker/?group_id=36855&atid=934137 GO database]
+
===People===
* [http://sourceforge.net/tracker/?group_id=36855&atid=747782 go-perl]
 
* [http://sourceforge.net/tracker/?group_id=36855&atid=494390 AmiGO Requests]
 
* [http://sourceforge.net/tracker/?group_id=36855&atid=908269 AmiGO bug reports]
 
* [http://sourceforge.net/tracker/?group_id=36855&atid=418260 Obo-edit requests]
 
* [http://sourceforge.net/tracker/?group_id=36855&atid=418257 Obo-edit bugs]
 
  
===People===
+
The following people dedicate some portion of their time to the GO project
  
* [[External_Database_Contact_Info]]
+
* Seth Carbon LBL (Manager, Noctua, AmiGO, Solr, Infrastructure)
 +
* Eric Douglass LBL (Triplestore, Ontology Engineering and Semantic Tools, Pipeline)
 +
* Nathan Dunn LBL (Tools, AGR integration)
 +
* Ben Good LBL (Noctua, Pathway integration)
 +
* Marcin Joachimiak LBL, (Bioinformatics)
 +
* HyeongSik Kim LBL (OWL, Solr)
 +
* Suzanna Lewis LBL (PI)
 +
* Chris Mungall LBL (Lead)
 +
* Deepak Unni LBL (BioLink API)
  
===Principles===
+
* Laurent-Phillippe Albou USC (LBL affiliate) (Bioinformatics, Networks)
 +
* Dustin Ebert USC (Pipeline, GO-CAMs)
 +
* Huaiyu Mi USC (Panther, PAINT Pipeline)
 +
* Tremayne Mushayahama USC (Noctua)
 +
* Anushya Muruganujan USC (Panther, PAINT, Enrichment)
  
* [[SWUG:Quality_Control]]
+
* Jim Balhoff RENCI (Noctua, Ontology Engineering)
  
 
==Wiki==
 
==Wiki==
  
 
All software-and-utilities pages on the wiki should go in the wikispace SWUG (SoftWare Utilities Group)
 
All software-and-utilities pages on the wiki should go in the wikispace SWUG (SoftWare Utilities Group)
 +
  
 
==Projects==
 
==Projects==
  
===OBO-Edit===
+
All projects are managed via GitHub projects. For a list of all, see the [https://github.com/orgs/geneontology/projects GO github projects page]
 
 
*[http://www.oboedit.org OBO-Edit public home page]
 
  
*[[OBO-Edit]] wiki page
+
=== GitHub Repos ===
  
*[http://wiki.geneontology.org/index.php/Category:OBO-Edit_working_group OBO-Edit working group]
+
* https://github.com/geneontology/noctua
 +
* https://github.com/geneontology/amigo
 +
* https://github.com/biolink/ontobio/
 +
* https://github.com/owlcollab/owltools
  
 
===AmiGO===
 
===AmiGO===
  
====General Interest====
+
* https://github.com/geneontology/amigo
 
 
 
* [[AmiGO_Manual:_Overview]]
 
* [[AmiGO_Manual:_Overview]]
 
* [[AmiGO_Manual:_Installation]]
 
* [[AmiGO_Manual:_Installation]]
Line 118: Line 77:
 
* [http://sourceforge.net/tracker/?group_id=36855&atid=908269 AmiGO bug reports]
 
* [http://sourceforge.net/tracker/?group_id=36855&atid=908269 AmiGO bug reports]
  
====Internal interest====
+
===Noctua===
 
 
* [[:Category:AmiGO working group|AmiGO working group]]
 
* [[AmiGO_Big_Ideas]]
 
* [[SWUG:AmiGO_Architecture_Roadmap]]
 
* [[AmiGO]]
 
 
 
===RefGenome===
 
 
 
* [[RG:_Software]]
 
 
 
===TreeCurationTool===
 
 
 
Collaboration with PantherDB
 
 
 
* https://sourceforge.net/projects/pantherdb
 
 
 
 
 
 
 
===GO database and go-perl===
 
 
 
Main page: http://www.geneontology.org/GO.database.shtml
 
 
 
 
 
* [[:Category:go-dev Code Org|go-dev Code Org]] : Thoughts on the organization of go-dev source.
 
 
 
* [[ GoDB loading ]] Proposal for refactoring go-full loads
 
 
 
* [[SWUG:Database]] - future database development
 
 
 
 
 
* [[ gp2protein report ]] This is a script run "peridically" to cross-check gp2protein files submitted by mods.
 
 
 
===SO===
 
 
 
Main page: http://www.sequenceontology.org
 
 
 
====MiSO====
 
CVS http://song.cvs.sourceforge.net/song/software/scripts/miSO
 
 
 
browser http://song.sf.net/SO_view/index.html
 
 
 
====Cross-products in SO====
 
 
 
SO contains cross-product definitions of many composite terms. See
 
[[SO Cross Products]] for the methodology.
 
 
 
===Obol===
 
 
 
http://www.berkeleybop.org/obol
 
 
 
===Reference Genome Software Prototype===
 
 
 
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 )
 
 
 
To access the prototype: http://rails-dev.bioinformatics.northwestern.edu:24000
 
  
[[Category:Software]]
+
* [[Noctua]] Curator docs
 +
* https://github.com/geneontology/noctua
 +
* [https://docs.google.com/document/d/1w3mkF1RQIzwROOCMTkqjYaOn8ZbdsW52t-xA4DKt0vg/edit#heading=h.du3v9zif59jp Noctua Technical Stack]

Latest revision as of 12:57, 10 March 2018


For the legacy page, see Software_and_Utilities_(Archived) and Software and Utilities group summary


Meetings

See the GO calendar

Core meetings:

  • biweekly all-day thursday LBL hack days (anyone can zoom in)
  • biweekly Noctua calls
  • adhoc zooms between developers as needed

Also:

  • updates on go-managers calls
  • ontology engineering team join ontology calls
  • most devs join annotation calls

Mail List

  • godev-internal on groups.io

Resources

Documentation

Trackers

People

The following people dedicate some portion of their time to the GO project

  • Seth Carbon LBL (Manager, Noctua, AmiGO, Solr, Infrastructure)
  • Eric Douglass LBL (Triplestore, Ontology Engineering and Semantic Tools, Pipeline)
  • Nathan Dunn LBL (Tools, AGR integration)
  • Ben Good LBL (Noctua, Pathway integration)
  • Marcin Joachimiak LBL, (Bioinformatics)
  • HyeongSik Kim LBL (OWL, Solr)
  • Suzanna Lewis LBL (PI)
  • Chris Mungall LBL (Lead)
  • Deepak Unni LBL (BioLink API)
  • Laurent-Phillippe Albou USC (LBL affiliate) (Bioinformatics, Networks)
  • Dustin Ebert USC (Pipeline, GO-CAMs)
  • Huaiyu Mi USC (Panther, PAINT Pipeline)
  • Tremayne Mushayahama USC (Noctua)
  • Anushya Muruganujan USC (Panther, PAINT, Enrichment)
  • Jim Balhoff RENCI (Noctua, Ontology Engineering)

Wiki

All software-and-utilities pages on the wiki should go in the wikispace SWUG (SoftWare Utilities Group)


Projects

All projects are managed via GitHub projects. For a list of all, see the GO github projects page

GitHub Repos

AmiGO

Noctua