Search results
From WormBaseWiki
Jump to navigationJump to searchCreate the page "WormBase Documentation" on this wiki! See also the search results found.
- | 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
- Mining WormBase with MySQL & 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
- ...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_descriptions15 KB (2,321 words) - 17:36, 18 August 2017
- *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
- 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 GO progress report *Adopt aspects of the WormBase Ontology Annotator9 KB (1,339 words) - 19:02, 31 January 2013
- 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
- * 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
- -rwxrwxr-x 1 todd wormbase 20053 Jul 6 14:06 cell.cgi -rwxrwxr-x 1 todd wormbase 3916 Jul 6 14:06 make_pedigree.cgi16 KB (1,576 words) - 17:44, 16 August 2010
- ** SAB wiki: http://wiki.wormbase.org/index.php/2016_Advisory_Board_Meeting#Organisation_of_SAB_talks * Will finish up, write documentation and make live4 KB (640 words) - 19:07, 11 February 2016
- ...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
- ** 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 tracking5 KB (715 words) - 15:49, 4 August 2016
- ***Incorporating the [http://caltech.wormbase.org/virtualworm/ virtual worm] and [http://browser.openworm.org/ browser] **Supporting links to WormBase (in general)12 KB (1,878 words) - 15:55, 6 September 2012
- ''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.8 KB (1,229 words) - 16:17, 30 December 2013
- *Double up SPELL queries with the main WormBase instance on the cloud to consolidate? *How to more fully incorporate SPELL into WormBase?6 KB (971 words) - 16:24, 6 October 2011
- * 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 n5 KB (763 words) - 00:51, 19 September 2014
- 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] w7 KB (1,148 words) - 23:02, 23 October 2014
- '''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'''7 KB (1,103 words) - 18:08, 16 August 2010
- * Wiki documentation at: http://wiki.wormbase.org/index.php/Contacting_the_Community#Community_Contact_.26_Curation_Track === Status of WormBase User Survey? ===6 KB (926 words) - 16:49, 3 December 2015
- ...just know what are problematic URLs; should all be handled by main URL www.wormbase.org ** https://github.com/WormBase/website/issues/604411 KB (1,703 words) - 15:27, 5 April 2018
- ** Documentation error meant that crucial step at start of build was missed. * Redesign of the home page. Make it more WormBase compliant.5 KB (741 words) - 10:57, 21 August 2015
- 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.11 KB (1,664 words) - 18:43, 17 August 2010
- WormMart is WormBase's implementation of the [http://www,biomart.org BioMart] data warehouse. [http://www.biomart.org/user-docs.pdf Official BioMart Documentation]8 KB (1,307 words) - 14:39, 4 November 2010
- * 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)6 KB (906 words) - 15:34, 6 December 2018
- cd /usr/local/wormbase/build cd /usr/local/wormbase/services14 KB (1,410 words) - 19:29, 1 August 2013
- 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.20 KB (2,916 words) - 15:25, 4 August 2016
- ** 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 02/08/2017.9 KB (1,391 words) - 19:47, 19 April 2023
- *Should we take minutes of Caltech WormBase group meetings and send around? *WormBase-wide conference call twice per month8 KB (1,282 words) - 17:08, 7 July 2011
- *Does she want lab experience only, or would she want to do some WormBase work? *Itai wants to display his expression images in WormBase6 KB (983 words) - 18:02, 12 July 2012
- Archived RNAi documentation may be found [[RNAi/archive | here]] This is the ?RNAi data model as of WormBase Release WS251:29 KB (4,152 words) - 20:29, 30 July 2019
- [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].12 KB (1,832 words) - 18:43, 11 August 2010
- also see [http://wiki.wormbase.org/index.php/Mark_up_policy WB markup policy] =Linking entities in GENETICS/G3 articles to WormBase resource pages=14 KB (2,324 words) - 19:51, 9 January 2015
- * 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 release9 KB (1,490 words) - 15:35, 6 October 2016
- * Maybe they could curate for WormBase * Jae & Kimberly put in GitHub ticket to make retractions clear on WormBase site7 KB (1,020 words) - 15:33, 7 May 2020
- * Many authors want to share and make links to their database/website via WormBase * Publisher = WormBase? Caltech?10 KB (1,464 words) - 17:09, 13 August 2015
- ...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:''26 KB (3,522 words) - 19:10, 18 June 2014
- ...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]15 KB (2,589 words) - 16:42, 11 January 2018
- *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 tool10 KB (1,553 words) - 18:04, 7 February 2013
- ='''WormBase Gene Ontology Progress Report, December 2011'''= Developer, WormBase, Caltech, Pasadena, CA.13 KB (1,830 words) - 16:40, 13 December 2012
- ...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.png13 KB (1,951 words) - 23:14, 13 August 2010
- * 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, micropubli11 KB (1,676 words) - 15:28, 2 May 2019
- == 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 var16 KB (2,589 words) - 20:19, 29 March 2012
- 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.47 KB (6,852 words) - 04:27, 8 December 2020
- ...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 ==29 KB (3,687 words) - 11:01, 10 May 2013
- WormBase is updated with each new build of the database released from Sanger. The li brie3> cd /usr/local/wormbase-production34 KB (5,450 words) - 18:24, 17 August 2010
- ==Documentation== **Documenting elements of WormBase workflow to ease transition for new staff and keep track of changes made29 KB (4,254 words) - 20:25, 27 April 2012
- * 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 discre12 KB (1,809 words) - 16:33, 1 March 2018
- The WormBase ''C. elegans'' GFF3 files can be downloaded from: ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/genome_feature_tables/GFF319 KB (1,985 words) - 23:13, 13 August 2010
- 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 interaction59 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.30 KB (4,765 words) - 20:03, 11 August 2010
- [[Caltech documentation]] <br> Archived Interaction documentation may be found [[Gene_Interaction/archive | here]]53 KB (6,521 words) - 20:51, 7 March 2019
- * In either case users need a good legend and/or documentation ** Starting with WormBase and MGI GO annotations into GO-CAM13 KB (2,025 words) - 16:28, 7 November 2019
- 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/wormbase28 KB (3,957 words) - 19:55, 5 May 2022
- === WormBase Literature System Migration to Alliance === * Documentation for SOP36 KB (4,994 words) - 17:27, 14 February 2024
- [[Category:WormBase Documentation]]42 KB (5,348 words) - 16:49, 15 April 2024
- ''back to''' [[Caltech documentation]]<br> **process pages will dissect the chapters and link them to entities in WormBase,20 KB (3,088 words) - 19:17, 13 August 2020
