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- == 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
- == Internal Documentation == *[[WormBase Staff Resources]] -- ''A guide to the tools available for WormBase staff''235 bytes (25 words) - 21:24, 10 November 2010
- ...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
- This page contains documentation applicable to all WormBase sites. [[Category:Developer documentation]]434 bytes (49 words) - 16:49, 5 June 2013
- = The Wormbase::Toggle Library = [[Category:Developer documentation]]71 bytes (7 words) - 18:41, 17 August 2010
- == Documentation == * Sibyl will update our documentation as she learns about the project1 KB (161 words) - 14:29, 3 June 2014
- [[Category:Developer documentation]] [[Category:WormBase 2.0]]62 bytes (5 words) - 17:48, 5 August 2010
- [[Caltech documentation]] #[[Alliance - migrating WormBase papers to Alliance ABC]]1 KB (130 words) - 21:21, 15 March 2021
- [[Category:Developer documentation]] [[Category:WormBase 2.0]]226 bytes (26 words) - 14:38, 19 June 2014
- **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 Univer2 KB (233 words) - 15:30, 21 July 2022
- ...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
- ...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
- 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
- Here's how the WormBase subversion repository was established. sudo chgrp wormbase svn343 bytes (53 words) - 22:57, 13 August 2010
- 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
- == 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
- Define standardized scheme of the next generation WormBase website using CSS * wormbase.css488 bytes (68 words) - 18:48, 11 August 2010
- ...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
- ...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 Subcommit5 KB (646 words) - 17:11, 25 November 2020
- ...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
- [[An Overview of The WormBase Homepage]] GENERAL DOCUMENTATION2 KB (416 words) - 01:03, 22 July 2013
- back to [[Caltech documentation]]<br> ==WormBase's 48 hours to complete steps 7-9==395 bytes (55 words) - 21:11, 23 July 2013
- cd /usr/local/wormbase/trac/src ./configure -with-mta_user=nobody --with-trac_user=wormbase-help976 bytes (132 words) - 17:45, 17 August 2010
- 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 compute4 KB (507 words) - 08:46, 8 October 2014
- ...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
- ...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
- ...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 conve2 KB (271 words) - 14:09, 19 June 2014
- The WormBase ''C. briggsae'' GFF3 files can be downloaded from: ftp://ftp.wormbase.org/pub/wormbase/genomes/briggsae/genome_feature_tables/GFF33 KB (334 words) - 23:13, 13 August 2010
- == Update checklist for www.wormbase.org== | Checkout changes into brie3:/usr/local/wormbase-production1 KB (144 words) - 18:22, 17 August 2010
- 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
- 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
- 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
- ...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
- The code base: $WORMBASE/utils/gff3_validator/ http://dev.wormbase.org/db/validate_gff3/validate_gff3_online3 KB (422 words) - 23:12, 13 August 2010
- 1. wormbase.com now available on domain marketplace * https://github.com/WormBase/website/issues/57902 KB (378 words) - 16:32, 3 August 2017
- * 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.txt4 KB (583 words) - 20:22, 29 July 2011
- 0 4 * * * /usr/local/wormbase/util/admin/restart_blat.pl 1 1 * * * /usr/local/bin/wb_update_wormbase.pl > /usr/local/wormbase/logs/update.log2 KB (351 words) - 17:30, 19 June 2014
- 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
- Maintain and document configuration of the next generation WormBase website. ** current wormbase.conf (Config::General) file contains model info which can get complex and m1 KB (176 words) - 18:47, 11 August 2010
- ...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
- 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
- ''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
- 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
- 2. Find and follow the repo WormBase/website project: https://github.com/WormBase/website3 KB (528 words) - 09:52, 22 June 2012
- <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
- * 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
- 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
- (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
- [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 performance of WormBase [[Category:Developer documentation]]1 KB (196 words) - 17:57, 16 August 2010
- ...ist of the most prominent classes in use in the AceDB database employed by WormBase. To display the current model of any class, include the following text in your documentation:4 KB (568 words) - 11:06, 23 May 2011
- -rw-rw-rw- wormbase.conf ...(henceforth "the web application") and a series of external models in the WormBase::API namespace.10 KB (1,357 words) - 14:03, 19 June 2014
- [ftp://ftp.sanger.ac.uk/pub2/wormbase/data/compara.tar.bz2 Compara tarball for WS163] (mysql dumps) .../software/compara/index.html Compara Page] (including how to install / API documentation)21 KB (2,963 words) - 18:18, 11 August 2010
- == Using WormBase for bioinformatics == .... elegans genome (eg., http://ws120.wormbase.org). If you need to refer to WormBase in a publication, please refer to one of the freeze versions.3 KB (514 words) - 15:39, 24 September 2007
- *Dumping process changes outlined [https://docs.google.com/a/wormbase.org/document/d/1nnuQY9OfV2VsBORj01ocoC985-5kOgxYCGOAZDeeKLQ/edit?pli=1 here ****Documentation6 KB (864 words) - 15:32, 6 June 2013
- 2. Find and follow the tharris/wormbase project: http://bitbucket.org/tharris/wormbase/4 KB (616 words) - 18:35, 17 August 2010
- $WORMBASE/cgi-perl/misc/paper: CGI script that contains the code segment $WORMBASE/cgi-perl/misc/geo_map_by_paper: CGI script that generates the display4 KB (711 words) - 23:25, 13 August 2010
- == About RSS feeds at WormBase == WormBase news feeds (using the RSS format) provide a convenient mechanism for stayin2 KB (390 words) - 08:28, 13 June 2012
- ! genenames at wormbase dot org Back to [[WormBase SVMs]]2 KB (241 words) - 17:46, 17 August 2010
- The following documentation refers to google's sitemapgen. This has been supplanted by Google Site Map To facilitate the indexing of WormBase content, a [https://www.google.com/webmasters/sitemaps/login Google Sitemap4 KB (553 words) - 17:31, 19 June 2014
- GFF data is provided to CSHL as part of the Wormbase build. The data is provided in GFF2 format and converted to GFF3 at the CSH Conversion script: $WORMBASE/util/import_export/wormbase_gff2togff3.pl2 KB (286 words) - 18:26, 11 August 2010
- The Wormbase BLAST/BLAT page can be accessed by the "Blast / Blat" link on the top navig $WORMBASE/cgi-perl/searches/blast_blat (CGI script)4 KB (506 words) - 20:45, 10 August 2010
- WormBase uses virtual machines to quickly and easily create frozen releases. scp brie6.cshl.org:/usr/local/vmx/wormbase-WS110.2003.10.01.tgz .2 KB (316 words) - 18:22, 11 August 2010
- There are two types of interaction objects in Wormbase: Interaction and YH. Interaction class holds a number of interaction types ...aims to provide a consolidated compact view of the interaction objects in Wormbase. It replaces the previous views.2 KB (328 words) - 23:39, 13 August 2010
- Configuring a fresh install of Cent OS 5 for WormBase [[Category:Developer documentation]]2 KB (225 words) - 20:53, 10 August 2010
- [[Caltech documentation]]<br> |WormBase re-evalutation||6/22-7/5: IWM||(?)2 KB (241 words) - 23:04, 13 August 2010
- Notes on installing Gbrowse in the WormBase environment. One barrier to packaging GBrowse with the rest of the wormbase code-base in CVS has been the architecture dependent paths that GBrowse use2 KB (339 words) - 23:10, 13 August 2010
- 6. Edit /usr/local/wormbase/conf/localdefs.pm and httpd.conf with the appropriate hostname tar czf wormbase-WS100.2003.05.13-server.tgz wormbase-WS100.2003.05.132 KB (282 words) - 23:34, 13 August 2010
- *WormBase posters will be assigned a session and poster board ***[https://github.com/WormBase/website/issues/1205 Genes]2 KB (295 words) - 16:39, 16 May 2013
- ...spec/models.wrm?root=ensembl&view=log as specified in the ?Paper model] in WormBase. ...daily to select those that should be included in the curation pipeline and WormBase bibliography.3 KB (403 words) - 16:02, 27 March 2019
- **See the [[User_Guide_for_Curators]] for documentation of how the form works from a users' perspective. **See the [[ccc.cgi documentation]] for more specific details about the code.5 KB (817 words) - 15:11, 18 February 2014
- '''WormBase::API Czar''' -- ''Oversee development of the external Model'' -- '''Norie'' * See the [[Website:Profiling|Profiling documentation]] for additional details and progress.2 KB (261 words) - 00:48, 24 December 2010
- * Citace upload deadline will be 6pm Monday, November 25th (added to WormBase calendar) * We will want to provide a public notice (likely via the WormBase blog) about what topic we have focused on for that release of the database/10 KB (1,664 words) - 17:02, 4 December 2013
- ...velopment environments help to avoid these conflicts. But with a site like WormBase that has large memory and hard disk requirements, maintaining a separate en http://bitbucket.org/tharris/wormbase-admin/src/tip/util/create_private_wormbase/create_private_wormbase.sh2 KB (381 words) - 18:42, 17 August 2010
- This method does not lift-over the data to the current version of WormBase. This data will be mapped to WS190. This a temporary fix while we wait fo ** -> wb-dev : /usr/local/wormbase/gbrowse_current/conf/FOLDER_SPECIFIED_IN_WORM.CONF2 KB (370 words) - 22:56, 10 August 2010
- ** Raymond: thinking of putting blurb on a separate documentation page * Can we track who is using this tool (and others)? SObA is hosted by WormBase so we'd have to ask Todd (Google analytics); SimpleMine is Caltech hosted s6 KB (911 words) - 17:13, 6 June 2019
- * WormBase Social Hour? * WormBase list of data types to bring into the Alliance3 KB (408 words) - 17:27, 17 December 2020
- "ftp://ftp.sanger.ac.uk/pub/wormbase/WS${WB_RELEASE} $ cd $HOME/mart-build/scripts/wormbase-mart2 KB (289 words) - 18:24, 17 August 2010
- ...Wormbase proteins (Wormpep) and they are displayed in the context of the Wormbase gene page. $WORMBASE/util/import_export/compile_3d_data/3 KB (408 words) - 23:36, 13 August 2010
- ...me effort; essentially only one person); already had most of the requested documentation ** Improved documentation of plans and workflows5 KB (611 words) - 17:09, 18 April 2019
- WormBase staff can find this document in the "Documentation" directory and edit it there. = About Groups at WormBase =5 KB (757 words) - 01:45, 2 June 2014
- 6. Documentation I'd like to be able to generate the REST interface documentation automatically. we can do this easily with good POD.9 KB (1,048 words) - 14:59, 15 February 2011
- http://wormbase.org ''The main Web site for WormBase. It is meant to be slightly less bleeding-edge than the development site, b3 KB (514 words) - 23:35, 13 August 2010
- | Is the wormbase pointer linked to the newly created acedb? | Is the Multi-Ontology Search Running? <br>URL: http://dev.wormbase.org/db/ontology/search3 KB (489 words) - 18:14, 17 August 2010
- ** temporarily deployed at http://dev.wormbase.org:9004/, Kimberly shared with GO group for feedback * Worked with Todd to get intermine accessible at http://intermine.wormbase.org/2 KB (280 words) - 14:45, 12 April 2016
- These parameters should be set in the my.cnf file (/etc/my.cnf on WormBase servers). <br> <code>brie3</code> (the primary WormBase development machine) acts as the master server, with <code>server-id = 1</c3 KB (417 words) - 17:50, 16 August 2010
- ...ges of individual datasets. This are shipped as virtual disks for use with WormBase virtual machines. [[Category:Developer documentation]]2 KB (261 words) - 18:27, 11 August 2010
- ...o at Kris Gunsalus' group at NYU. This tool is used by Wormbase to display Wormbase interaction data. ...d installer at this time and is installed manually. After it is installed, Wormbase interaction data needs to be dumped from AceDB and loaded to MySQL. Finally7 KB (1,133 words) - 17:52, 16 August 2010
- | Is the wormbase pointer linked to the newly created acedb? | Is the Multi-Ontology Search Running? <br>URL: http://dev.wormbase.org/db/ontology/search3 KB (530 words) - 18:14, 17 August 2010
- Return to [[Caltech documentation]] ==Form Documentation==11 KB (1,666 words) - 17:53, 19 June 2014
- ** planning on remaining on wormbase as volunteer and handling intermine issues * Documentation - spreadsheet2 KB (240 words) - 16:14, 27 September 2013
- .../github.com/WormBase/website/issues/9268 New widget/section on how to cite WormBase] * [https://github.com/WormBase/website/issues/9266 Issue with ASNS-1 (started at Hixton, then bounced to C3 KB (454 words) - 18:36, 10 July 2023
- | [https://github.com/WormBase/website/issues?direction=desc&labels=&milestone=10&page=1&sort=updated&stat | [https://github.com/WormBase/website/issues/assigned/tharris?direction=desc&labels=&milestone=10&sort=up3 KB (451 words) - 20:13, 21 May 2013
- | Is the wormbase pointer linked to the newly created acedb? | Is the Multi-Ontology Search Running? <br>URL: http://dev.wormbase.org/db/ontology/search4 KB (717 words) - 18:20, 17 August 2010
- Back to [[Caltech documentation]] [http://www.wormbase.org/wiki/index.php/Texpresso/Author/Curator_interim_form What type of data5 KB (746 words) - 18:57, 10 August 2010
- | Is the wormbase pointer linked to the newly created acedb? | Is the Multi-Ontology Search Running? <br>URL: http://dev.wormbase.org/db/ontology/search4 KB (719 words) - 18:21, 17 August 2010
- https://spreadsheets.google.com/a/wormbase.org/spreadsheet/ccc?key=0Aj0AS0c7xC1VdGZSQnlvdTBlbUpPRWJVYlE4Tk9WRlE&hl=en_ * Documentation and boilerplate in place (all)2 KB (310 words) - 00:50, 14 July 2011
- * TH : wormbase infrastructre doc * Documentation2 KB (280 words) - 19:14, 10 August 2010
- | Is the wormbase pointer linked to the newly created acedb? | Is the Multi-Ontology Search Running? <br>URL: http://dev.wormbase.org/db/ontology/search4 KB (738 words) - 18:20, 17 August 2010
- | Is the wormbase pointer linked to the newly created acedb? | Is the Multi-Ontology Search Running? <br>URL: http://dev.wormbase.org/db/ontology/search4 KB (723 words) - 18:21, 17 August 2010
