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- 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
- | 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
- | 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 (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 ''My3 KB (453 words) - 19:49, 13 November 2018
- | 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 (725 words) - 18:21, 17 August 2010
- Look at lib/WormBase/Web/Controller.pm. http://bitbucket.org/tharris/wormbase/src/tip/lib/WormBase/Web/Controller.pm3 KB (575 words) - 18:47, 11 August 2010
- == 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. e6 KB (914 words) - 15:39, 24 September 2007
- | 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 (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/search4 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/search4 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.4 KB (600 words) - 14:55, 10 June 2014
- ==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 i3 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/search4 KB (762 words) - 18:20, 17 August 2010
- ** wormbase.org accounts via the web-app * Test site for release 3 live: test.parasite.wormbase.org11 KB (1,714 words) - 11:04, 27 July 2015
- :http://wiki.wormbase.org/index.php/Website:Profiling ...y commited scripts; Todd will slot in to pipeline for WS227 (see Xapian in WormBase doc)3 KB (440 words) - 20:32, 27 July 2011
- ...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 inviti4 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 which6 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 conta5 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 project5 KB (842 words) - 19:41, 17 February 2016
- 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]8 KB (1,130 words) - 13:27, 4 February 2016
- ...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 =20 KB (2,994 words) - 16:05, 23 August 2010
- 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
- # to set up our local WormBase CPAN local: /usr/local/wormbase/minicpan6 KB (868 words) - 18:47, 13 April 2015
- WormBase meeting announcement *Arun will prepare documentation6 KB (903 words) - 16:37, 5 January 2012
- 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 too6 KB (786 words) - 19:13, 18 June 2014
- 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 2012:5 KB (782 words) - 20:56, 8 January 2020
- 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:5 KB (720 words) - 20:46, 10 October 2016
- The following documentation explains the use and backend for the Phenotype form found here: https://wormbase.org//submissions/phenotype.cgi26 KB (4,016 words) - 21:32, 8 April 2020
- ...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]]12 KB (1,559 words) - 18:14, 15 June 2011
- ** documentation on web * WormBase/website-mobile on github3 KB (420 words) - 15:52, 7 June 2013
- 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:15 KB (2,325 words) - 23:32, 21 December 2015
- ===From WormBase documentation:===14 KB (2,091 words) - 16:28, 9 December 2010
- 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.pm6 KB (980 words) - 18:48, 11 August 2010
