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• SOPs
  == Internal Documentation == ...provides an area to collect standard operating procedures for each of the WormBase centers.
  396 bytes (39 words) - 22:28, 16 August 2010
• Worm Base Internal Documentation
  == Internal Documentation == *[[WormBase Staff Resources]] -- ''A guide to the tools available for WormBase staff''
  235 bytes (25 words) - 21:24, 10 November 2010
• Balloon Tooltips
  ...p_Balloons GMOD Wiki] for full documentation of the popup balloons used in WormBase. [[Category:Developer documentation]]
  178 bytes (27 words) - 20:47, 10 August 2010
• Project-wide documentation
  This page contains documentation applicable to all WormBase sites. [[Category:Developer documentation]]
  434 bytes (49 words) - 16:49, 5 June 2013
• Using collapsible sections
  = The Wormbase::Toggle Library = [[Category:Developer documentation]]
  71 bytes (7 words) - 18:41, 17 August 2010
• WebDev 2014.06.03-Agenda and Minutes
  == Documentation == * Sibyl will update our documentation as she learns about the project
  1 KB (161 words) - 14:29, 3 June 2014
• Website::Configuration
  [[Category:Developer documentation]] [[Category:WormBase 2.0]]
  62 bytes (5 words) - 17:48, 5 August 2010
• Paper Pipeline
  [[Caltech documentation]] #[[Alliance - migrating WormBase papers to Alliance ABC]]
  1 KB (130 words) - 21:21, 15 March 2021
• Website:Configuration
  [[Category:Developer documentation]] [[Category:WormBase 2.0]]
  226 bytes (26 words) - 14:38, 19 June 2014
• WBConfCall 2022.07.21-Agenda and Minutes
  **small error in C. elegans variant tm4928 [https://github.com/WormBase/website/issues/8698 #8698] - Stavros has self-assigned * New Starter: Matej Vucak - WormBase ParaSite's new developer. He's based in Matt Berriman's group at the Univer
  2 KB (233 words) - 15:30, 21 July 2022
• CSHL documentation
  ...developing, maintaining, and hosting WormBase. This page contains links to documentation relating to those topics. Much of this documentation will be obsolete shortly. Please see [[Developer documentation]] for up-to-date documents.
  2 KB (293 words) - 22:32, 24 December 2010
• Data mining
  ...l|About the WormBase data model]] - ''how data is stored and structured at WormBase'' ...es tutorial]] -''Examples and descriptions of commonly accessed classes at WormBase''
  2 KB (264 words) - 01:36, 1 April 2022
• Sanger documentation
  The following information pertains to data that is made available by the WormBase Group from The Wellcome Sanger Institute. ...n on the Wormbase Live release [http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/ Click].
  640 bytes (97 words) - 22:32, 16 August 2010
• Establishing the SVN repository
  Here's how the WormBase subversion repository was established. sudo chgrp wormbase svn
  343 bytes (53 words) - 22:57, 13 August 2010
• Design Specs: Templates
  To build a templating system for the next generation of the WormBase website. [[Category:Developer documentation]]
  375 bytes (51 words) - 18:49, 11 August 2010
• Wiki objectives and usage guidelines
  == About the WormBase Wiki == This document describes the objectives and usage guidelines of the WormBase Wiki.
  4 KB (573 words) - 02:51, 24 September 2007
• Design Specs: CSS
  Define standardized scheme of the next generation WormBase website using CSS * wormbase.css
  488 bytes (68 words) - 18:48, 11 August 2010
• WBConfCall 2015.10.15-Agenda and Minutes
  ...gene names/assembly in the research community drifting away from those in WormBase ...ng published with Wormbase-style gene names that have not been approved by WormBase (e.g. WBPaper00048552)
  3 KB (415 words) - 18:05, 22 October 2015
• Main Page
  ...is elegans] and related nematodes. WormBase is developed by an [http://www.wormbase.org/about/staff#01--10 international consortium] of researchers and compute *November 2020 -- ''[https://wiki.wormbase.org/images/Elections_Subcommittee_Proposal_toWBvote.docx Election Subcommit
  5 KB (646 words) - 17:11, 25 November 2020
• WBConfCall 2022.07.07-Agenda and Minutes
  ...WormBase ParaSite's new release 17] with genome updates, [https://parasite.wormbase.org/Caenorhabditis_elegans_prjna13758/Transcript/AFDB?db=core;g=WBGene00004 Please include a url link to pre-existing documentation on this topic, if relevant.
  4 KB (585 words) - 21:44, 7 July 2022
• UserGuide:General Description
  [[An Overview of The WormBase Homepage]] GENERAL DOCUMENTATION
  2 KB (416 words) - 01:03, 22 July 2013
• GSA linking pipeline
  back to [[Caltech documentation]]<br> ==WormBase's 48 hours to complete steps 7-9==
  395 bytes (55 words) - 21:11, 23 July 2013
• Trac installation notes
  cd /usr/local/wormbase/trac/src ./configure -with-mta_user=nobody --with-trac_user=wormbase-help
  976 bytes (132 words) - 17:45, 17 August 2010
• Main Page Temp
  This is the official wiki site for [http://www.wormbase.org WormBase], the database of the model organism [http://en.wikipedia.org/wiki/Caenorha WormBase is developed by an [http://www.wormbase.org/about/staff#01--10 international consortium] of researchers and compute
  4 KB (507 words) - 08:46, 8 October 2014
• User Guide 2010:TOC
  ...a of the model nematode ''Caenorhabditis elegans'' and related nematodes. WormBase is developed by an international consortium of researchers and computer sci *[[UserGuide:General_Description|Overview of WormBase]]
  4 KB (613 words) - 09:23, 30 June 2011
• WebDev 2016.02.23-Agenda and Minutes
  ...pollo people on handling subtracks, there is an example in the [http://dev.wormbase.org:10004/index.html?data=data%2Fc_elegans_simple&loc=I%3A9861261..9879060& #**Need to make sure that documentation reflects changes and is up to date.
  3 KB (478 words) - 15:41, 23 February 2016
• Website:WormBase::API
  ...is likely out of date. Consult WormBase::Model.pm for the most up-to-date documentation.''' Common elements are provided by WormBase::Model, superclass for all WormBase::Model::* classes. Should you come across any of these elements when conve
  2 KB (271 words) - 14:09, 19 June 2014
• GFF3 features (C. briggsae)
  The WormBase ''C. briggsae'' GFF3 files can be downloaded from: ftp://ftp.wormbase.org/pub/wormbase/genomes/briggsae/genome_feature_tables/GFF3
  3 KB (334 words) - 23:13, 13 August 2010
• Update checklist template
  == Update checklist for www.wormbase.org== | Checkout changes into brie3:/usr/local/wormbase-production
  1 KB (144 words) - 18:22, 17 August 2010
• Website:Testing And Profiling
  please go to [http://wiki.wormbase.org/index.php/Unit_Testing Unit Testing] ...apache is configured as described in the [[Website:Deployment|deployment]] documentation, listening on port 8000.
  2 KB (248 words) - 18:38, 18 June 2014
• CVS Access To WormBase
  You may browse the repository at http://brebiou.cshl.edu/viewcvs/wormbase-site. The WormBase source code is freely available via anonymous CVS.
  1 KB (150 words) - 23:05, 10 August 2010
• Data mining:AQL tutorial
  AQL search [http://www.wormbase.org/db/searches/aql_query [1]] is strictly dependent on current database mo '''Documentation at AceDB web site''' [http://www.acedb.org/Software/whelp/AQL/ [2]]
  834 bytes (137 words) - 15:09, 16 June 2011
• Importing PFAM Images
  ...eved when available and displayed in a baloon tip for these domains on the Wormbase gene page. Code: $WORMBASE/util/import_export/compile_pfam_images/
  1 KB (187 words) - 23:36, 13 August 2010
• GFF3 Validation
  The code base: $WORMBASE/utils/gff3_validator/ http://dev.wormbase.org/db/validate_gff3/validate_gff3_online
  3 KB (422 words) - 23:12, 13 August 2010
• WBConfCall 2017-08-03-Agenda and Minutes
  1. wormbase.com now available on domain marketplace * https://github.com/WormBase/website/issues/5790
  2 KB (378 words) - 16:32, 3 August 2017
• NBC sign off documentation
  * File in /usr/local/wormbase/databases/{RELEASE}/orthology and automatically generated by orthology data ...h the associations available from the orthology data compile -- /usr/local/wormbase/databases/{RELEASE}/orthology/go_id2omim_ids.txt
  4 KB (583 words) - 20:22, 29 July 2011
• Cronjobs
  0 4 * * * /usr/local/wormbase/util/admin/restart_blat.pl 1 1 * * * /usr/local/bin/wb_update_wormbase.pl &gt; /usr/local/wormbase/logs/update.log
  2 KB (351 words) - 17:30, 19 June 2014
• Developer documentation
  This page contains information pertinent to employees of WormBase. = Navigating and Editing the Developer Documentation =
  12 KB (1,638 words) - 18:25, 18 June 2014
• Design Specs: Application Configuration
  Maintain and document configuration of the next generation WormBase website. ** current wormbase.conf (Config::General) file contains model info which can get complex and m
  1 KB (176 words) - 18:47, 11 August 2010
• Session management
  ...ult user and IP tables as defined by CGI::Session::Auth::DBI. Note that at WormBase, we will probably not use authentication via IP. [[Category:Developer documentation]]
  955 bytes (120 words) - 22:36, 16 August 2010
• How to make a new Textpresso category
  WormBase has a [http://textpresso-dev.caltech.edu/cgi-bin/azurebrd/sentence_word_cat 4. Need textpresso-dev to be back up to accurately finish the documentation.
  3 KB (408 words) - 23:34, 13 August 2010
• Site statistics
  ''Access statistics are available to WormBase developers only'' Running total: [http://www.wormbase.org/stats/total/ all] | [http://www.wormbase.org/stats/total-nogoogle/ no spiders]
  7 KB (1,005 words) - 17:33, 19 June 2014
• Importing Protein Structure Data Images
  The structure data imported to Wormbase (see [[Importing Protein Structure Data]]) contains a large number of recor Code: $WORMBASE/util/import_export/compile_3d_images/
  2 KB (265 words) - 23:37, 13 August 2010
• Using github
  2. Find and follow the repo WormBase/website project: https://github.com/WormBase/website
  3 KB (528 words) - 09:52, 22 June 2012
• WBConfCall 2012.09.20-Agenda and Minutes
  <nowiki>#465</nowiki> https://github.com/WormBase/website/issues/465 I blasted (blastp) a protein seq against C. angaria and * We should store all code in a WormBase repository.
  1,013 bytes (152 words) - 16:35, 20 September 2012
• WormBase-Caltech Weekly Calls December 2015
  * http://juancarlos.wormbase.org , look at a gene page, open Phenotype Graph widget === Uberon linking to WormBase anatomy ontology ===
  5 KB (776 words) - 16:50, 7 January 2016
• Log file management and analysis
  todd> zcat /home/todd/projects/wormbase/log_archive/with_hosts/access_log.2008.gz | \ ...visitors -A -T --prefix http://www.wormbase.org --prefix http://wormbase.org - \
  2 KB (226 words) - 17:31, 19 June 2014
• Developer notes
  (These are now all object attributes supplied by WormBase::API::Role::Object. Please see the docs therein for their use). 1. Be certain to add the appropriate configuration to wormbase.conf (eg "fields remarks") to make the data accessible in your template.
  3 KB (485 words) - 15:37, 19 June 2014
• WBConfCall 2012.08.16-Agenda and Minutes
  [https://github.com/WormBase/website/issues/241 issue 241] "Nucl. Aligner Tool bug." [https://github.com/WormBase/website/issues/360 issue 360] "user-reported browser issues"
  2 KB (294 words) - 16:14, 16 August 2012
• Optimizing site performance
  Optimizing performance of WormBase [[Category:Developer documentation]]
  1 KB (196 words) - 17:57, 16 August 2010

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