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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 project
    1 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 Univer
    2 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 svn
    343 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.css
    488 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 Subcommit
    5 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
  • back to [[Caltech documentation]]<br> ==WormBase's 48 hours to complete steps 7-9==
    395 bytes (55 words) - 21:11, 23 July 2013
  • [[An Overview of The WormBase Homepage]] GENERAL DOCUMENTATION
    2 KB (416 words) - 01:03, 22 July 2013
  • 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
  • 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
  • ...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 conve
    2 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/GFF3
    3 KB (334 words) - 23:13, 13 August 2010
  • == Update checklist for www.wormbase.org== | Checkout changes into brie3:/usr/local/wormbase-production
    1 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_online
    3 KB (422 words) - 23:12, 13 August 2010
  • 1. wormbase.com now available on domain marketplace * https://github.com/WormBase/website/issues/5790
    2 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.txt
    4 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 &gt; /usr/local/wormbase/logs/update.log
    2 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 m
    1 KB (176 words) - 18:47, 11 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
  • ...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
  • 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/website
    3 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
  • ...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
  • Optimizing performance of WormBase [[Category:Developer documentation]]
    1 KB (196 words) - 17:57, 16 August 2010
  • -rw-rw-rw- wormbase.conf ...(henceforth "the web application") and a series of external models in the WormBase::API namespace.
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  • == 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
  • [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
  • *Dumping process changes outlined [https://docs.google.com/a/wormbase.org/document/d/1nnuQY9OfV2VsBORj01ocoC985-5kOgxYCGOAZDeeKLQ/edit?pli=1 here ****Documentation
    6 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 display
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  • == About RSS feeds at WormBase == WormBase news feeds (using the RSS format) provide a convenient mechanism for stayin
    2 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 Sitemap
    4 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.pl
    2 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)
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  • 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.
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  • 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 use
    2 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-WS100.2003.05.13
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  • ...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.
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  • *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
  • **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.sh
    2 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.CONF
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  • * WormBase Social Hour? * WormBase list of data types to bring into the Alliance
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  • ** 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 s
    6 KB (911 words) - 17:13, 6 June 2019
  • "ftp://ftp.sanger.ac.uk/pub/wormbase/WS${WB_RELEASE} $ cd $HOME/mart-build/scripts/wormbase-mart
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  • ...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
  • WormBase staff can find this document in the "Documentation" directory and edit it there. = About Groups at WormBase =
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  • ...me effort; essentially only one person); already had most of the requested documentation ** Improved documentation of plans and workflows
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  • 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, b
    3 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/search
    3 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/
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  • 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</c
    3 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. Finally
    7 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/search
    3 KB (530 words) - 18:14, 17 August 2010
  • Return to [[Caltech documentation]] ==Form Documentation==
    11 KB (1,666 words) - 17:53, 19 June 2014
  • .../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 C
    3 KB (454 words) - 18:36, 10 July 2023
  • ** planning on remaining on wormbase as volunteer and handling intermine issues * Documentation - spreadsheet
    2 KB (240 words) - 16:14, 27 September 2013
  • | [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=up
    3 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/search
    4 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 data
    5 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/search
    4 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)
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  • * TH : wormbase infrastructre doc * Documentation
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  • | Is the wormbase pointer linked to the newly created acedb? | Is the Multi-Ontology Search Running? <br>URL: http://dev.wormbase.org/db/ontology/search
    4 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/search
    4 KB (723 words) - 18:21, 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/search
    4 KB (723 words) - 18:21, 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/search
    4 KB (725 words) - 18:20, 17 August 2010
  • ...created from multiple types of IDs at the same time (i.e. Uniprot name and WormBase protein IDs). In order to take full advantage of lists, it is recommended t ...d or changed, and other information can be entered, like a description for documentation, among other things. If you are logged in, the list will show in your ''My
    3 KB (453 words) - 19:49, 13 November 2018
  • == The C. briggsae genome in WormBase == ...genome (Stein et.al, PloS Biology, 2003) has been fully incorporated into WormBase. The C. briggsae genome can be viewed by itself or in synteny with the C. e
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  • Look at lib/WormBase/Web/Controller.pm. http://bitbucket.org/tharris/wormbase/src/tip/lib/WormBase/Web/Controller.pm
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  • | Is the wormbase pointer linked to the newly created acedb? | Is the Multi-Ontology Search Running? <br>URL: http://dev.wormbase.org/db/ontology/search
    4 KB (725 words) - 18:21, 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/search
    4 KB (610 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/search
    4 KB (735 words) - 18:22, 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/search
    4 KB (735 words) - 18:22, 17 August 2010
  • :http://wiki.wormbase.org/index.php/Website:Profiling * Documentation and boilerplate in place (all)
    2 KB (340 words) - 18:03, 20 July 2011
  • ...s of WormBase have been established for each developer at brie3:/usr/local/wormbase-devel. Developing and testing new code in a private installation ensures th ...ng production quality, feedback should also be solicited from wormbase-dev@wormbase.org.
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  • ==1. Take a look at the original page on dev.wormbase.org== * Look for common elements that already existing in WormBase::Model.pm. You can ignore these (although you still need to specify them i
    3 KB (404 words) - 21:07, 9 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/search
    4 KB (762 words) - 18:20, 17 August 2010
  • :http://wiki.wormbase.org/index.php/Website:Profiling ...y commited scripts; Todd will slot in to pipeline for WS227 (see Xapian in WormBase doc)
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  • ** wormbase.org accounts via the web-app * Test site for release 3 live: test.parasite.wormbase.org
    11 KB (1,714 words) - 11:04, 27 July 2015
  • ...rty library, please add the library to the /js directory tree, load it via wormbase.js and document its use here or on another wiki page (or at least provide a = wormbase.js =
    5 KB (743 words) - 23:43, 13 August 2010
  • = WormBase Coding Standards and Style Guide = =Documentation=
    6 KB (950 words) - 15:36, 19 June 2014
  • See [[WormBase Staff Resources]]. ===WormBase WebDev Team Members/Contacts===
    11 KB (1,786 words) - 14:31, 17 May 2016
  • Is there a link from WormBase to Alaska, and an announcement about its function? == WormBase resources for non-coding RNA ==
    3 KB (561 words) - 18:39, 6 February 2020
  • ...se obtained from computational analysis-'IEA annotations' are displayed by WormBase. Clicking on the reference links to the citation display page. ...etc. Clicking on the evidence code links to the Gene ontology consortium's documentation on evidence codes and their usuage.
    3 KB (502 words) - 18:28, 17 August 2010
  • ...ely with new libraries), I am now including required perl modules with the WormBase software. This includes modules for both different versions of Perl and dif ...directory is automatically mirrored into the staging directory (/usr/local/wormbase-production), and from there distributed to production nodes as necessary.
    5 KB (819 words) - 17:37, 16 August 2010
  • Dear Dr. Kishore, Harris, Cain, Raciti, van Auken and all Wormbase staff, Given your expertise at Wormbase, your perspective would be extremely valuable. I am therefore warmly inviti
    4 KB (657 words) - 17:19, 15 June 2023
  • It is easy to link to WormBase. You can link to HTML pages, text-only dumps, images, and XML pages. All objects in WormBase have a '''name''' and a '''class'''. The name is a unique identifier which
    6 KB (1,087 words) - 15:07, 19 June 2014
  • WormBase Virtual Machines are created for each release of the database. This proces To simplify the download and update process, WormBase virtual machines are split into modules. The primary virtual machine conta
    5 KB (752 words) - 23:33, 13 August 2010
  • '''THIS DOCUMENT IS NOW DEPRECATED. PLEASE REFER TO THE PROJECT DOCUMENTATION MAINTAINED ON GOOGLE DRIVE.''' https://docs.google.com/a/wormbase.org/document/d/1oPpj8d5gibUc-gpUZorl6ETT5baE6mp-v2bMedKauiA/edit#
    25 KB (3,632 words) - 03:11, 28 October 2013
  • ...e in order to reduce complexity and increase functionality. In the end the WormBase architecture should be significantly more robust, take less effort to maint To use Datomic/DynamoDB as a centralized database system for the WormBase project
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  • The 2016 edition of the WormBase Scientific Advisory Board meeting will take place at Caltech on 4/5 Feb 201 ...ology.ucsd.edu/research/faculty/adchisholm Andrew Chisholm], [http://blog.wormbase.org/2015/12/18/call-for-nominations-for-a-worm-board WormBoard]
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  • ...rimary front end caching server (web-web1.wormbase.org/fe.wormbase.org) at WormBase. This server runs the Squid Reverse Proxy server. = Checkout the wormbase-admin module =
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  • # to set up our local WormBase CPAN local: /usr/local/wormbase/minicpan
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  • The Ontology Annotator (OA) is a curation tool developed by WormBase for a variety of curation purposes including the curation of phenotypes, at List of WormBase OA configurations:
    20 KB (3,124 words) - 19:59, 19 February 2020
  • WormBase meeting announcement *Arun will prepare documentation
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  • WormMart is WormBase's implementation of the [http://www,biomart.org BioMart] data warehouse. In simple terms, WormMart is built by transforming WormBase's AceDB database into a BioMart schema MySQL database. Standard BioMart too
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  • Human disease relevance descriptions were introduced in late 2011, on the WormBase gene page, to serve both the worm researcher and the biomedical researcher '''Examples of automated descriptions based on OMIM orthology that existed in WormBase prior to 2012:
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  • We will need to create a tab-delimited gpi file with each WormBase release. These specifications are based, in part, on the documentation on the GOC's go-annotation github repository:
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  • The following documentation explains the use and backend for the Phenotype form found here: https://wormbase.org//submissions/phenotype.cgi
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  • ...ndex of available Ace classses; see the [https://spreadsheets.google.com/a/wormbase.org/ccc?key=tygSYCz49YW5hyCcYMHUZ1Q#gid=2 Google Doc] for migration status. |[[WormBase Model:2_point_data|2_point_data]]
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  • ** documentation on web * WormBase/website-mobile on github
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  • The following documentation explains the use and backend for the Allele-Phenotype form found here: ...le-Phenotype" option under the "Submit data" menu header at the top of the WormBase homepage:
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  • ===From WormBase documentation:===
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  • Part of the WormBase::API. Needs to be able to connect to multiple http://bitbucket.org/tharris/wormbase/src/tip/lib/WormBase/API/Role/Service.pm
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  • Mining WormBase with MySQL &amp; PostgreSQL ...ng genomic features. This is the access method of choice to use for mining WormBase for:
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  • ...for automated concise descriptions is available online: https://github.com/WormBase/automated_descriptions The requirements are outlined here: http://wiki.wormbase.org/index.php/Generation_of_automated_descriptions
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  • *WormBase booth with desks and poster space *How do we handle? Can we put description in WormBase?
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  • This document describes collaborative tools available to WormBase team members. It's strongly encouraged that all team members of WormBase request a '''wormbase.org''' account.
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  • WormBase frozen releases are hosted on the virtualized server: All WormBase-specific files are maintained in a shared directory.
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  • WormBase GO progress report *Adopt aspects of the WormBase Ontology Annotator
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  • -rwxrwxr-x 1 todd wormbase 20053 Jul 6 14:06 cell.cgi -rwxrwxr-x 1 todd wormbase 3916 Jul 6 14:06 make_pedigree.cgi
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  • * Help documentation still needs to be written up ...urces/person/WBPerson363#02--10 Low complexity person], [http://juancarlos.wormbase.org/resources/person/WBPerson625#02--10 High complexity person]
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  • ** SAB wiki: http://wiki.wormbase.org/index.php/2016_Advisory_Board_Meeting#Organisation_of_SAB_talks * Will finish up, write documentation and make live
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  • ...gene-disease association file, on the FTP site:ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/ONTOLOGY/disease_association.WS245.wb, however this is incom ...archinitiative.org from WormBase? Possibly from the DO term page? there is documentation at http://monarchinitiative.org/page/services and http://monarchinitiative.
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  • ** https://names.wormbase.org/gene * API documentation :
    5 KB (759 words) - 15:02, 11 September 2019
  • * Curators should address concerns before he leaves (documentation, SVM stuff, etc.) * Yesterday we (FlyBase, ZFIN, and WormBase) presented paper curation status tracking
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  • ***Incorporating the [http://caltech.wormbase.org/virtualworm/ virtual worm] and [http://browser.openworm.org/ browser] **Supporting links to WormBase (in general)
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  • ''This document describes the fourth and final stage of the WormBase software release cycle, moving new databases and software into production. ...t mediate production release are maintained in the git [https://github.com/WormBase/website-admin website-admin] repository.
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  • *Double up SPELL queries with the main WormBase instance on the cloud to consolidate? *How to more fully incorporate SPELL into WormBase?
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  • * http://wiki.wormbase.org/index.php/2014_Advisory_Board_Meeting Paul will begin meeting with “ What is WormBase” and his talk will include an introduction to the following topics (not n
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  • Phenotype curation at WormBase entails the assignment of a phenotype term from the ''C. elegans'' Phenotyp ...cgi curation_status.cgi] and described in great detail on the [http://wiki.wormbase.org/index.php/Caltech_documentation#Curation_Progress Curation_progress] w
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  • '''Finish documentation of current paper type mappings (PubMed vs postgres vs Journal) for informin ...r changing the Paper models and Paper editor to allow for multiple types - WormBase'''
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  • * Wiki documentation at: http://wiki.wormbase.org/index.php/Contacting_the_Community#Community_Contact_.26_Curation_Track === Status of WormBase User Survey? ===
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  • ...just know what are problematic URLs; should all be handled by main URL www.wormbase.org ** https://github.com/WormBase/website/issues/6044
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  • ** Documentation error meant that crucial step at start of build was missed. * Redesign of the home page. Make it more WormBase compliant.
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  • The WormBase production environment consists of a series of partially redundant web and ...e root directory. It's configuration and init files are maintained in the wormbase-admin module.
    32 KB (4,370 words) - 20:48, 18 June 2014
  • ...uild a robust and scalable platform for hosting the next generation of the WormBase website. [http://bitbucket.org/tharris/wormbase/issues/?component=Rearch:scalability Reported Issiues (bitbucket.org)]
    7 KB (1,258 words) - 18:49, 11 August 2010
  • ...chines" (or VMX) are self-contained packages of everything you need to use WormBase locally ...ents. First, you will need the primary virtual machine, which contains the WormBase software, within a Linux operating system.
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  • WormMart is WormBase's implementation of the [http://www,biomart.org BioMart] data warehouse. [http://www.biomart.org/user-docs.pdf Official BioMart Documentation]
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  • * Todd working on a spell.wormbase.org site for doing worm SPELL analyses * New WormBase release linked to the new SPELL website (https://spell.wormbase.org)
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  • cd /usr/local/wormbase/build cd /usr/local/wormbase/services
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  • GBrowse is one of the central -- and most heavily used -- components of the WormBase site. To meet this demand, we use a number of dedicated servers using GBro 2. $app_root/$app/wormbase.env sets the GBROWSE_CONF and GBROWSE_HTDOCS environment variables.
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  • ** Type Micropublication: biology instead of Wormbase in the publisher field (as opposed as shown in the screenshot) *Received 12/12/2016, Accepted 01/27/2017. Available starting WormBase release WS259, Published Online 02/08/2017.
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  • *Should we take minutes of Caltech WormBase group meetings and send around? *WormBase-wide conference call twice per month
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  • *Does she want lab experience only, or would she want to do some WormBase work? *Itai wants to display his expression images in WormBase
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  • Archived RNAi documentation may be found [[RNAi/archive | here]] This is the ?RNAi data model as of WormBase Release WS251:
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  • [http://www.wormbase.org/wiki/index.php/First-pass_schedule%2C_instructions%2C_automation First- .../wiki/index.php/Caltech_documentation#SVMs_for_First_Pass_Curation Caltech documentation page].
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  • also see [http://wiki.wormbase.org/index.php/Mark_up_policy WB markup policy] =Linking entities in GENETICS/G3 articles to WormBase resource pages=
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  • * for the records- documentation on the import here: http://wiki.wormbase.org/index.php/TransgeneOme_import ...a is dynamic: people can add images and annotations; will be updated every WormBase release
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  • * Maybe they could curate for WormBase * Jae & Kimberly put in GitHub ticket to make retractions clear on WormBase site
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  • * Many authors want to share and make links to their database/website via WormBase * Publisher = WormBase? Caltech?
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  • ...e) the directions below may be slightly out-of-sync with how the principal WormBase architecture is built. ...2, the suggested minimum hardware requirements for a basic installation of WormBase are:''
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  • ...document describes how to install and configure the Intermine instance at WormBase. ...tyle="color: red">'''Previous build examples are available at: http://wiki.wormbase.org/index.php/Website:WormMine_Builds'''</span>
    25 KB (3,652 words) - 23:06, 25 December 2014
  • [[Caltech documentation]]<br> ...sitive for a data type, data are stored in the tfp table; see [http://wiki.wormbase.org/index.php/Textpresso Textpresso flagging pipelines]
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  • *We should make an announcement on the main WormBase page that WormMart will remain at WS220 and Intermine will replace it Documentation for Protein-2-GO tool
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  • ='''WormBase Gene Ontology Progress Report, December 2011'''= Developer, WormBase, Caltech, Pasadena, CA.
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  • ...plemented or accepted for the official GFF3 spec. It exists solely here on WormBase to get community input. http://www.wormbase.org/wiki/images/Gff3_spec_Figure2.png
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  • * Can someone send Paul the latest AFP form location and documentation ** Wen followed up with him: WormBase curator could attend and present on JBrowse, scientific writing, micropubli
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  • == WormBase Administration == ...t describes maintenance of the various hardware and software components of WormBase. This includes monitoring the health of the site, starting and stopping var
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  • http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?root=ensembl&view=log ...ng the format Exprnnnn where n is a number; these values correspond to the WormBase ID of the Expr_pattern object; individual entries are comma-separated.
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  • ...THIS PAGE IS NOW MAINTAINED AS PART OF THE WEBSITE PROPER AT: [http://www.wormbase.org/about/release_schedule release_schedule] == WormBase Release And Access Statistics ==
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  • WormBase is updated with each new build of the database released from Sanger. The li brie3&gt; cd /usr/local/wormbase-production
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  • ==Documentation== **Documenting elements of WormBase workflow to ease transition for new staff and keep track of changes made
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  • * WormBase uses EnsemblCompara and other methods (not aggregate method like DIOPT) * Orthology synchrony is a challenge; WormBase and FlyBase may need to pay special attention to orthology calls and discre
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  • The WormBase ''C. elegans'' GFF3 files can be downloaded from: ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/genome_feature_tables/GFF3
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  • PLEASE NOTE THAT AS OF 2009.09, THIS DOCUMENTATION IS DEPRECATED. Should you wish to install WormBase locally, please see:
    60 KB (9,496 words) - 23:06, 13 August 2010
  • ...ibing an interactor entity or condition that does not fall into a standard WormBase category WBProcess ?WBProcess XREF Interaction // WormBase biological process associated with the interaction
    59 KB (8,367 words) - 22:00, 14 December 2018
  • ...y </nowiki>''C. elegans'' gene in the published literature can be found in WormBase, by reference either to genes or to cell or tissue types. There are results ...elopers group actively invites suggestions for improvement from users, and WormBase's source code is freely available for local installation and improvement.
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  • [[Caltech documentation]] <br> Archived Interaction documentation may be found [[Gene_Interaction/archive | here]]
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  • * In either case users need a good legend and/or documentation ** Starting with WormBase and MGI GO annotations into GO-CAM
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  • The WormBase development server at OICR is a virtual server with the following stats: All WormBase components are collected under a single directory: /usr/local/wormbase
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  • === WormBase Literature System Migration to Alliance === * Documentation for SOP
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  • [[Category:WormBase Documentation]]
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  • ''back to''' [[Caltech documentation]]<br> **process pages will dissect the chapters and link them to entities in WormBase,
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  • ...THIS PAGE IS NOW MAINTAINED AS PART OF THE WEBSITE PROPER AT: [http://www.wormbase.org/about/release_schedule release_schedule] | width="20%" | [ftp://ftp.sanger.ac.uk/pub/wormbase ftp.sanger.ac.uk]
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  • back to [[Caltech documentation]] ...the antibody string matching pipeline. See GitHub repo: https://github.com/WormBase/entity-extraction-antibody
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  • ****WormBase - Kimberly Van Auken, Ranjana Kishore (others?) *This documentation is written based on using the form on a Mac running OS X 10.6.8 and Firefox
    30 KB (4,868 words) - 14:50, 11 June 2013
  • ...This page includes a Topic paper filter to search for papers related to a WormBase Biological Topic. ...opic paper filtering drop down menu. The drop down menu provides a list of WormBase Biological Topics as read from the Topic Curation OA. If a topic is selecte
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  • back to [[Caltech documentation]] ..._curator and cns_curator||"If you do not have a WBPerson ID please contact WormBase to have one assigned."
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  • ...ww.wormbase.org/about/Frequently_asked_questions FAQ pages] on the new www.wormbase.org site. === How should I cite WormBase? ===
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  • ===WormBase Uploads=== ...produced weekly to the WormBase .ace file for upload: [[UniProtKB gpad to WormBase .ace]]
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  • This page contains archived (outdated/obsolete) RNAi documentation ...ing author; for a list of all labs' two-letter codes look here: http://www.wormbase.org/db/misc/laboratory?name=*;class=laboratory), date of publication (accep
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  • ...l traits such as gene expression patterns and neuronal connectivity. Also, WormBase contains sequence and gene structures of C. briggsae and C. remanei, two cl ...so far. All of the information in this chapter is based on the version of WormBase available in September, 2005 (WS147 release; BioPerl/Generic Model Organism
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  • [https://raw.githubusercontent.com/WormBase/wormbase-pipeline/master/wspec/models.wrm variation model]<br> *phenotype_ontology ftp://ftp.wormbase.org/pub/wormbase/releases/WS251/ONTOLOGY/phenotype_ontology.WS251.obo (correct for latest r
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  • ...iles are obtained from the EBI FTP site: ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/<release>/species 1. Best BlastP hits file: ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS246/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS246.best
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  • Karen Yook/WormBase-Caltech/@wbperson712 need to improve documentation and guidelines
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  • Karen Yook/WormBase-Caltech/@wbperson712 need to improve documentation and guidelines
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  • [[Caltech documentation]] <br> ||| ||Name||WormBase Molecule ID assigned in-house||mop_name||text||Name||WBMolID -added after t
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  • [[Caltech documentation]] <br> ...ta from the literature and individual laboratories and display them in the WormBase gene expression page.
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