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| [[Category:Software]] [[Category:Working Groups]] | | [[Category:Software]] [[Category:Working Groups]] |
| 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.
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| [[Software and Utilities group summary]] | | For the legacy page, see [[Software_and_Utilities_(Archived)]] and [[Software and Utilities group summary]] |
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| * Timeline: [[SWUG_Timeline_2010-2011]]
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| * List of projects in progress: [[:Category:SWUG_Projects]]
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| * [[Software_Group_2010_Future_Plans]]
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| ==Meetings== | | ==Meetings== |
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| See [[:Category:SWUG-TCons]] for all new meetings | | See the GO calendar |
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| *[[SWUG:Meeting_at_Stanford_2011_06_23]]
| | Core meetings: |
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| *[[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 |
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| *[[SWUG:Meeting_2008_04_16]]
| | Also: |
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| *[[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 |
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| *[[SWUG:Meeting_2007_10_17]]
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| *[[SWUG:Meeting_2007_09_19]] - pre GOC meeting prep
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| *[[SWUG:Meeting_2007-08-22]]
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| * Visualisation meeting, 2007-08-16. No notes, demo only
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| *[[SWUG:Meeting_2007-08-08]]
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| *[[SWUG:Meeting_2007-07-25]]
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| *[[SWUG:Meeting_2007-06-27]]
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| *[[SWUG:Meeting_2007-05-30]]
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| *[[SWUG:Meeting_2007-04-18]]
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| *[[SWUG:Meeting_2007-04-04]]
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| * March 14 2007 -
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| * [[SWUG:Agenda_Template]]
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| '''Past Meetings:'''
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| *[[Database_Meeting_21_Nov_2006]]
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| '''Forthcoming meetings:'''
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| Schedule to be decided
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| *[[SWUG:Topics_for_future_meetings]]
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| == Reports ==
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| * [[SWUG:Report_200901]] | |
| * [[SWUG:Database_changes_2007]] | |
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| ==Mail List== | | ==Mail List== |
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| There is no public mailing list for this group.
| | * godev-internal on groups.io |
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| ==Resources== | | ==Resources== |
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| ===Documentation=== | | ===Documentation=== |
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| * http://gocwiki.geneontology.org/index.php/GO_FAQ#Software_and_tools
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| * http://wiki.geneontology.org/index.php/Example_Queries
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| * http://amigo.geneontology.org/dev
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| * http://www.geneontology.org/GO.database.shtml
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| * http://www.geneontology.org/GO.tools.software-libraries.shtml
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| ===Trackers=== | | ===Trackers=== |
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| * [http://sourceforge.net/tracker/?group_id=36855&atid=934137 GO database]
| | ===People=== |
| * [http://sourceforge.net/tracker/?group_id=36855&atid=747782 go-perl]
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| * [http://sourceforge.net/tracker/?group_id=36855&atid=494390 AmiGO Requests]
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| * [http://sourceforge.net/tracker/?group_id=36855&atid=908269 AmiGO bug reports]
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| * [http://sourceforge.net/tracker/?group_id=36855&atid=418260 Obo-edit requests]
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| * [http://sourceforge.net/tracker/?group_id=36855&atid=418257 Obo-edit bugs]
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| ===People===
| | The following people dedicate some portion of their time to the GO project |
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| * [[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) |
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| ===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) |
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| * [[SWUG:Quality_Control]] | | * Jim Balhoff RENCI (Noctua, Ontology Engineering) |
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| ==Wiki== | | ==Wiki== |
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| 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) |
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| ==Projects== | | ==Projects== |
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| ===Galaxy===
| | All projects are managed via GitHub projects. For a list of all, see the [https://github.com/orgs/geneontology/projects GO github projects page] |
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| [[Galaxy | Everything you need to know about GO Galaxy]] | |
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| ===OBO-Edit===
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| *[http://www.oboedit.org OBO-Edit public home page]
| | === GitHub Repos === |
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| *[[OBO-Edit]] wiki page | | * https://github.com/geneontology/noctua |
| | | * https://github.com/geneontology/amigo |
| *[http://wiki.geneontology.org/index.php/Category:OBO-Edit_working_group OBO-Edit working group] | | * https://github.com/biolink/ontobio/ |
| | * https://github.com/owlcollab/owltools |
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| ===AmiGO=== | | ===AmiGO=== |
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| ====General Interest====
| | * https://github.com/geneontology/amigo |
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| * [[AmiGO_Manual:_Overview]] | | * [[AmiGO_Manual:_Overview]] |
| * [[AmiGO_Manual:_Installation]] | | * [[AmiGO_Manual:_Installation]] |
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| * [http://sourceforge.net/tracker/?group_id=36855&atid=908269 AmiGO bug reports] | | * [http://sourceforge.net/tracker/?group_id=36855&atid=908269 AmiGO bug reports] |
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| ====Internal interest==== | | ===Noctua=== |
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| * [[:Category:AmiGO working group|AmiGO working group]]
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| * [[AmiGO_Big_Ideas]]
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| * [[SWUG:AmiGO_Architecture_Roadmap]]
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| * [[AmiGO]]
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| ===RefGenome===
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| * [[RG:_Software]]
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| ===TreeCurationTool===
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| Collaboration with PantherDB
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| * https://sourceforge.net/projects/pantherdb
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| ===GO database and go-perl===
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| Main page: http://www.geneontology.org/GO.database.shtml
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| * [[:Category:go-dev Code Org|go-dev Code Org]] : Thoughts on the organization of go-dev source.
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| * [[ GoDB loading ]] Proposal for refactoring go-full loads
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| * [[SWUG:Database]] - future database development
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| * [[ gp2protein report ]] This is a script run "peridically" to cross-check gp2protein files submitted by mods.
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| ===GO production server cron jobs===
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| *GO Production Servers AmiGO2
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| <pre>
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| For AmiGO 2: loading server = golr, user = golr
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| *Daily GOlr update
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| 5 0 * * * /tools/admin/scripts/load-golr
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| For AmiGO 2: web server = amigo2a & amigo2b, user = golr
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| * no cronjobs
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| </pre>
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| *GO Production Servers AmiGO1
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| <pre>
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| For AmiGO 1: (golite & goterm) loading server = claret, user = mysql
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| *Perform GO loads
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| 5 0 * * * /db0/home/mysql/bin/load-go-data-wrapper goterm > /dev/null 2>&1
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| 30 1 * * 6 /db0/home/mysql/bin/load-go-data-wrapper-bulk golite > /dev/null 2>&1
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| *Download uniprot files for GO loading when a new release is available
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| 5 12 * * 6 /db0/home/mysql/bin/get_uniprot_files.pl
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| *Perform mysqldump
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| 35 11 * * * /db0/home/mysql/bin/mysqlDumpBackupLinuxCompress.pl goterm go
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| 5 01 * * 1 /db0/home/mysql/bin/mysqlDumpBackupLinuxCompress.pl golite go
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| *Copy GO loads into ftp area
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| *bumped 10 hours forward as dumpowl is sloooow
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| * needs manual manipulation depending on how long the load takes.
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| 00 12 * * * /db0/home/mysql/bin/copy-go-to-ftp term
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| 35 01 * * 2 /db0/home/mysql/bin/copy-go-to-ftp lite
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| </pre>
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| <pre>
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| For AmiGO 1: (gofull) loading server = oro-new, user = mysql
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| * Perform GO load
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| 45 1 1 * * /db0/home/mysql/bin/load-go-data-wrapper-bulk gofull > /dev/null 2>&1
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| *Copy GO loads into ftp area
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| (has to be manually run after gofull run finishes)
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| #45 1 7 * * /db0/home/mysql/bin/copy-go-to-ftp full
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| 40 06 08 07 * /db0/home/mysql/bin/copy-go-to-ftp full
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| *Perform mysqldump
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| 45 1 20 * * /db0/home/mysql/bin/mysqlDumpBackupLinuxCompress.pl gofull go
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| </pre>
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| <pre>
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| For AmiGO 1: web server = goweb1, user = mysql
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| *Kill runaway MySQL GO queries
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| 0-59/5 * * * * /db0/home/mysql/bin/kill-wild-mysqld.pl
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| *Monitor load and if high print all running processes
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| 0-59/12 * * * * /db0/home/mysql/bin/monitor-load.pl
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| *Refesh cache after golite load
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| 00 12 * * 1 /share/goweb/www-data/html/go-dev/amigo/refresh.pl
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| *clean up cache and sessions
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| 1 * * * * /share/goweb/www-data/bin/refresh-wrapper.sh
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| </pre>
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| <pre>
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| For AmiGO 1: web server = goweb2, user = mysql
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| *Kill runaway MySQL GO queries
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| 0,5,10,15,20,25,30,35,40,45,50,55 * * * * /db0/home/mysql/bin/kill-wild-mysqld.pl
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| * Monitor load and if high print all running processes
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| 0-59/5 * * * * /db0/home/mysql/bin/monitor-load.pl
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| *Refesh cache after golite load
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| 00 12 * * 1 /share/goweb/www-data/html/go-dev/amigo/refresh.pl
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| *clean up cache and sessions
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| 1 * * * * /share/goweb/www-data/bin/refresh-wrapper.sh
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| </pre>
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| * GO scripts by Mike (from Stuart’s email)
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| <pre>
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| For GAF processing scripts server=meatloaf user=gocvs
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| *GO Processing
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| 20 3 1 * * /share/go/bin/monthly-save.script
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| *for GO home page
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| *process gene-association files and output included HTML files
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| 0 2,6,12,14,18,23 * * * /share/go/bin/namespace-counts.pl
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| *copy repository to ftp space
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| 10,40 * * * * /share/go/bin/copy_repository.go >> /share/go/logs/copy_repository.go.log 2>&1
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| *Gene Association Filtering Script
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| 45 19 * * * /share/go/bin/filter-gene-association-wrapper.pl
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| *Counts for Annotation Table
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| 45 21 * * * /share/go/bin/GO-HTML-counts.pl
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| *added per Cherry GOCVS sandbox
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| 10 2 * * * /share/ftp/go/software/utilities/sf-ontology-tracker-digest.pl >> /share/go/logs/sourceforce-trackers.log 2>&1
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| 20 2 * * * /share/ftp/go/software/utilities/sf-annotation-tracker-digest.pl >> /share/go/logs/sourceforce-trackers.log 2>&1
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| </pre>
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| * There are other jobs run as root, but those are mostly things like backups and fixing file ownerships at the filesystem level.
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| ===SO===
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| Main page: http://www.sequenceontology.org
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| ====MiSO====
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| CVS http://song.cvs.sourceforge.net/song/software/scripts/miSO
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| browser http://song.sf.net/SO_view/index.html
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| ====Cross-products in SO====
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| SO contains cross-product definitions of many composite terms. See
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| [[SO Cross Products]] for the methodology.
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| ===Obol===
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| http://www.berkeleybop.org/obol
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| ===Reference Genome Software Prototype===
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| 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 )
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| To access the prototype: http://rails-dev.bioinformatics.northwestern.edu:24000
| | * [[Noctua]] Curator docs |
| | * https://github.com/geneontology/noctua |
| | * [https://docs.google.com/document/d/1w3mkF1RQIzwROOCMTkqjYaOn8ZbdsW52t-xA4DKt0vg/edit#heading=h.du3v9zif59jp Noctua Technical Stack] |