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  • Update Matrix WS212
    | 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
  • Update Matrix WS210
    | 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
  • Lists
    ...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
  • Update Matrix WS213
    | 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
  • Design Specs: Application Request Flow
    Look at lib/WormBase/Web/Controller.pm. http://bitbucket.org/tharris/wormbase/src/tip/lib/WormBase/Web/Controller.pm
    3 KB (575 words) - 18:47, 11 August 2010
  • WormBase Newsletter No. 4, February 2004
    == 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
    6 KB (914 words) - 15:39, 24 September 2007
  • Update Matrix WS206
    | 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
  • Update Matrix WS215
    | 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
  • Update Matrix WS217
    | 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
  • WebDev 2011.07.20-Agenda and Minutes
    :http://wiki.wormbase.org/index.php/Website:Profiling * Documentation and boilerplate in place (all)
    2 KB (340 words) - 18:03, 20 July 2011
  • Formal development strategy
    ...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
  • HOWTO migrate a CGI
    ==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
  • Update Matrix WS207
    | 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
  • Hinxton 2015.07- Meeting minutes
    ** 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
  • WebDev 2011.07.27-Agenda and Minutes
    :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
  • Javascript libraries
    ...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
  • Coding standards
    = WormBase Coding Standards and Style Guide = =Documentation=
    6 KB (950 words) - 15:36, 19 June 2014
  • Co-op Documentation
    See [[WormBase Staff Resources]]. ===WormBase WebDev Team Members/Contacts===
    11 KB (1,786 words) - 14:31, 17 May 2016
  • WBConfCall 2020.02.06-Agenda and Minutes
    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
  • UserGuide:Gene Ontology Page
    ...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
  • Managing Perl libraries across nodes
    ...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
  • WBConfCall 2023.06.15-Agenda and Minutes
    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
  • Linking To WormBase
    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
  • How to build a WormBase Virtual Machine
    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
  • Software Life Cycle: 1. Updating The Development Server
    '''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
  • WormCloud:Overview
    ...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
    5 KB (842 words) - 19:41, 17 February 2016
  • 2016 Advisory Board Meeting
    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
  • Building Squid
    ...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
  • Ontology Annotator
    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
  • Managing Perl Libraries
    # to set up our local WormBase CPAN local: /usr/local/wormbase/minicpan
    6 KB (868 words) - 18:47, 13 April 2015
  • WormBase-Caltech Weekly Calls December 2011
    WormBase meeting announcement *Arun will prepare documentation
    6 KB (903 words) - 16:37, 5 January 2012
  • Building WormMart
    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
    6 KB (786 words) - 19:13, 18 June 2014
  • Disease and Drugs
    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
  • Specifications for WB gpi file
    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
  • Contributing Phenotype Connections
    The following documentation explains the use and backend for the Phenotype form found here: https://wormbase.org//submissions/phenotype.cgi
    26 KB (4,016 words) - 21:32, 8 April 2020
  • AceOjbect Redesign Page
    ...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
  • WebDev 2013.06.03-Agenda and Minutes
    ** documentation on web * WormBase/website-mobile on github
    3 KB (420 words) - 15:52, 7 June 2013
  • Contributing Allele Phenotype Connections
    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
  • TAIR
    ===From WormBase documentation:===
    14 KB (2,091 words) - 16:28, 9 December 2010
  • Design Specs: Database Connectivity
    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
    6 KB (980 words) - 18:48, 11 August 2010
  • Mining WormBase with Bio::DB::GFF
    Mining WormBase with MySQL &amp; PostgreSQL ...ng genomic features. This is the access method of choice to use for mining WormBase for:
    11 KB (1,663 words) - 17:45, 16 August 2010
  • Documentation for workflow and scripts
    ...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
    15 KB (2,321 words) - 17:36, 18 August 2017
  • WormBase-Caltech Weekly Calls April 2013
    *WormBase booth with desks and poster space *How do we handle? Can we put description in WormBase?
    4 KB (651 words) - 16:11, 2 May 2013
  • WormBase Staff Resources
    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.
    7 KB (1,036 words) - 14:30, 14 January 2016
  • WormBase-Caltech Weekly Calls December 2012
    WormBase GO progress report *Adopt aspects of the WormBase Ontology Annotator
    9 KB (1,339 words) - 19:02, 31 January 2013
  • Building Frozen Releases
    WormBase frozen releases are hosted on the virtualized server: All WormBase-specific files are maintained in a shared directory.
    8 KB (1,087 words) - 17:35, 19 June 2014
  • WormBase-Caltech Weekly Calls November 2016
    * 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]
    5 KB (831 words) - 16:49, 1 December 2016
  • Migration
    -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
    16 KB (1,576 words) - 17:44, 16 August 2010
  • WormBase-Caltech Weekly Calls January 2016
    ** SAB wiki: http://wiki.wormbase.org/index.php/2016_Advisory_Board_Meeting#Organisation_of_SAB_talks * Will finish up, write documentation and make live
    4 KB (640 words) - 19:07, 11 February 2016
  • WBConfCall 2014.09.03-Agenda and Minutes
    ...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.
    5 KB (807 words) - 18:27, 4 September 2014

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