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
- GO Production Servers AmiGO2
For AmiGO 2: loading server = golr, user = golr *Daily GOlr update 5 0 * * * /tools/admin/scripts/load-golr For AmiGO 2: web server = amigo2a & amigo2b, user = golr * no cronjobs
- GO Production Servers AmiGO1
For AmiGO 1: (golite & goterm) loading server = claret, user = mysql *Perform GO loads 5 0 * * * /db0/home/mysql/bin/load-go-data-wrapper goterm > /dev/null 2>&1 30 1 * * 6 /db0/home/mysql/bin/load-go-data-wrapper-bulk golite > /dev/null 2>&1 *Download uniprot files for GO loading when a new release is available 5 12 * * 6 /db0/home/mysql/bin/get_uniprot_files.pl *Perform mysqldump 35 11 * * * /db0/home/mysql/bin/mysqlDumpBackupLinuxCompress.pl goterm go 5 01 * * 1 /db0/home/mysql/bin/mysqlDumpBackupLinuxCompress.pl golite go *Copy GO loads into ftp area *bumped 10 hours forward as dumpowl is sloooow * needs manual manipulation depending on how long the load takes. 00 12 * * * /db0/home/mysql/bin/copy-go-to-ftp term 35 01 * * 2 /db0/home/mysql/bin/copy-go-to-ftp lite
For AmiGO 1: (gofull) loading server = oro-new, user = mysql * Perform GO load 45 1 1 * * /db0/home/mysql/bin/load-go-data-wrapper-bulk gofull > /dev/null 2>&1 *Copy GO loads into ftp area (has to be manually run after gofull run finishes) #45 1 7 * * /db0/home/mysql/bin/copy-go-to-ftp full 40 06 08 07 * /db0/home/mysql/bin/copy-go-to-ftp full *Perform mysqldump 45 1 20 * * /db0/home/mysql/bin/mysqlDumpBackupLinuxCompress.pl gofull go
For AmiGO 1: web server = goweb1, user = mysql *Kill runaway MySQL GO queries 0-59/5 * * * * /db0/home/mysql/bin/kill-wild-mysqld.pl *Monitor load and if high print all running processes 0-59/12 * * * * /db0/home/mysql/bin/monitor-load.pl *Refesh cache after golite load 00 12 * * 1 /share/goweb/www-data/html/go-dev/amigo/refresh.pl *clean up cache and sessions 1 * * * * /share/goweb/www-data/bin/refresh-wrapper.sh
For AmiGO 1: web server = goweb2, user = mysql *Kill runaway MySQL GO queries 0,5,10,15,20,25,30,35,40,45,50,55 * * * * /db0/home/mysql/bin/kill-wild-mysqld.pl * Monitor load and if high print all running processes 0-59/5 * * * * /db0/home/mysql/bin/monitor-load.pl *Refesh cache after golite load 00 12 * * 1 /share/goweb/www-data/html/go-dev/amigo/refresh.pl *clean up cache and sessions 1 * * * * /share/goweb/www-data/bin/refresh-wrapper.sh
- GO scripts by Mike (from Stuart’s email)
For GAF processing scripts server=meatloaf user=gocvs *GO Processing 20 3 1 * * /share/go/bin/monthly-save.script *for GO home page *process gene-association files and output included HTML files 0 2,6,12,14,18,23 * * * /share/go/bin/namespace-counts.pl *copy repository to ftp space 10,40 * * * * /share/go/bin/copy_repository.go >> /share/go/logs/copy_repository.go.log 2>&1 *Gene Association Filtering Script 45 19 * * * /share/go/bin/filter-gene-association-wrapper.pl *Counts for Annotation Table 45 21 * * * /share/go/bin/GO-HTML-counts.pl *added per Cherry GOCVS sandbox 10 2 * * * /share/ftp/go/software/utilities/sf-ontology-tracker-digest.pl >> /share/go/logs/sourceforce-trackers.log 2>&1 20 2 * * * /share/ftp/go/software/utilities/sf-annotation-tracker-digest.pl >> /share/go/logs/sourceforce-trackers.log 2>&1
- There are other jobs run as root, but those are mostly things like backups and fixing file ownerships at the filesystem level.
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