Software and Utilities
The purpose of the Software and Utilities 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.
Software and Utilities group summary
- Timeline: SWUG_Timeline_2010-2011
- List of projects in progress: Category:SWUG_Projects
- Software_Group_2010_Future_Plans
Meetings
See Category:SWUG-TCons for all new meetings
- SWUG:Meeting_2007_09_19 - pre GOC meeting prep
- Visualisation meeting, 2007-08-16. No notes, demo only
- March 14 2007 -
Past Meetings:
Forthcoming meetings:
Schedule to be decided
Reports
Mail List
There is no public mailing list for this group.
Resources
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
People
Principles
Wiki
All software-and-utilities pages on the wiki should go in the wikispace SWUG (SoftWare Utilities Group)
Projects
Galaxy
Everything you need to know about GO Galaxy
OBO-Edit
- OBO-Edit wiki page
AmiGO
General Interest
Internal interest
RefGenome
TreeCurationTool
Collaboration with PantherDB
GO database and go-perl
Main page: http://www.geneontology.org/GO.database.shtml
- 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.
GO production server cron jobs
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