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- ==C. elegans as a model system to study disease and disease genes== ...g of new ones, based on the published literature, where elegans is used to model the biology of a disease and/or the orthologous elegans gene function is st5 KB (782 words) - 20:56, 8 January 2020
- The WS126 release of WormBase last month featured a complete genome with no gaps remaining in the genome == WormBase launches the 'WormBook' project ==4 KB (621 words) - 15:38, 24 September 2007
- ...nants worldwide also known as red stomach worm, wire worm or Barber's pole worm, is very common parasite and one the most pathogenic nematodes of ruminants ...ving model nematode ''Caenorhabditis elegans''. This makes it an important model of parasitic nematode biology that is commonly used for experimental studie3 KB (493 words) - 16:03, 15 December 2011
- == Adding worm disease models/data to the Monarch Initiative website== *http://monarchinitiative.org/ : connects phenotypes, diseases, models, and genes for translational research across species (People involved: Melissa Haendel5 KB (807 words) - 18:27, 4 September 2014
- https://github.com/WormBase/website/issues/5092 * Discussion on making available on WormBase the chapters we wrote for the WormBook.2 KB (369 words) - 16:38, 6 October 2016
- * File in /usr/local/wormbase/databases/{RELEASE}/orthology and automatically generated by orthology data * mark the elegans/worm genes with omim ortholgs, as caltech is unable to query into the proteins (done b4 KB (583 words) - 20:22, 29 July 2011
- New release of WormBase WS185, Wormpep185 and Wormrna185 Fri Nov 30 17:11:38 GMT 2007 vii) confirmed_genes.WS185.gz - DNA sequences of all genes confirmed by EST &/or cDNA6 KB (680 words) - 07:37, 11 January 2008
- ...cial wiki site for [http://www.wormbase.org WormBase], the database of the model organism [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditi WormBase is developed by an [http://www.wormbase.org/about/staff#01--10 international consortium] of researchers and compute4 KB (507 words) - 08:46, 8 October 2014
- New release of WormBase WS183, Wormpep183 and Wormrna183 Tue Oct 16 16:18:34 BST 2007 vii) confirmed_genes.WS183.gz - DNA sequences of all genes confirmed by EST &/or cDNA7 KB (800 words) - 10:01, 8 November 2007
- New release of WormBase WS186, Wormpep186 and Wormrna186 Fri Dec 21 08:57:59 GMT 2007 vii) confirmed_genes.WS186.gz - DNA sequences of all genes confirmed by EST &/or cDNA6 KB (683 words) - 05:51, 3 April 2008
- As the modENCODE DCC is overwhelmed with other work, she has proposed that WormBase make the data available to the public. Our position with providing primary data to users has always been that WormBase isn't a primary repository of data.5 KB (796 words) - 21:05, 10 March 2014
- [[WS241_Models.wrm | WS241 model details]] *These annotations need to be properly credited, so for the new GO annotation model we would like to create WBPerson objects for these groups and use Curator_c8 KB (1,246 words) - 15:52, 12 November 2013
- =WormBase Curated Data Types and Curation Methods= HMM - Hidden Markov Model9 KB (1,174 words) - 18:30, 29 August 2012
- ...current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/ ...e suggestion for the Alliance is to create a description based on a GO-CAM model6 KB (861 words) - 19:23, 5 November 2020
- * WB needs Genes from nameserver, which is on AWS, so need creds or AMI ? **** java -cp wb-names-export.jar clojure.main -m wormbase.names.export gene genes.csv7 KB (1,113 words) - 18:19, 6 April 2023
- ew release of WormBase WS184, Wormpep184 and Wormrna184 Thu Nov 8 12:09:34 GMT 2007 vii) confirmed_genes.WS184.gz - DNA sequences of all genes confirmed by EST &/or cDNA7 KB (831 words) - 07:36, 11 January 2008
- ==== Unified Interaction model - Chris & Kimberly ==== * PaulD: The model is OK but is the web capable of displaying it?5 KB (800 words) - 10:09, 17 February 2012
- *When mark a paper, separate into two different types of genes :stable vs unstable **Stable genes map to stable ID4 KB (612 words) - 17:13, 1 December 2011
- *WormBase - Bitbucket, GitHub (can commit code) *Is WormBase interested connecting to it?7 KB (1,117 words) - 16:39, 4 August 2011
- **How to get GO terms for a list of genes? International Worm Meeting6 KB (864 words) - 15:32, 6 June 2013
- **90 genes >= 10 publications **20,000 genes with RNAi data9 KB (1,302 words) - 16:38, 2 June 2011
- === Upstate NY Worm Meeting === === Midwest Worm Meeting ===11 KB (1,703 words) - 15:27, 5 April 2018
- * Todd working on a spell.wormbase.org site for doing worm SPELL analyses === Expression Pattern Model ===6 KB (906 words) - 15:34, 6 December 2018
- * What implications does this have for the WormBase Ontology Browser? * WormBase has imported all worm (C. elegans) physical (protein-protein) interactions from BioGRID8 KB (1,120 words) - 16:19, 5 March 2015
- New release of WormBase WS188, Wormpep188 and Wormrna188 Fri Feb 29 14:53:33 GMT 2008 WS188 was built by [Michael Han (michael.paulini@wormbase.org)]6 KB (769 words) - 11:01, 21 December 2011
- This protocol describes how to BLAST a sequence against the sequences in WormBase. Further discusion of the BLAST algorithm can be found in ''UNITS 3.3, 3.4, ...is the method of choice for searching the ''C. elegans'' genome with a non-worm protein or nucleic acid sequence.3 KB (401 words) - 20:02, 11 August 2010
- * Explaining job posting options via the forum in new Worm Breeder's Gazette article * Wen will make the model change proposal10 KB (1,464 words) - 17:09, 13 August 2015
- == OMIM links to/from WormBase == * Ranjana working on linking between WormBase and OMIM2 KB (384 words) - 20:25, 21 May 2015
- = The A - Z of WormBase Models = Document created from [http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?root=ensembl&view=markup&pathrev=WS218 WS218] models.16 KB (2,207 words) - 23:06, 9 January 2014
- * Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room * We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out8 KB (1,228 words) - 20:57, 14 July 2020
- 6 Oct 2010: The latest changes to the assembly are due to be added to WormBase in release WS221. ...this is done, we are happy to turn the ownership of the genome sequence to WormBase. - Paul Sternberg.3 KB (437 words) - 16:02, 15 December 2011
- '''Field 4 Experimental model for (dis_humandoid):''' <br/ > '''Field 11 Last Updated for Exp Model (dis_lastupdateexpmod):''' <br/ >14 KB (2,085 words) - 20:27, 7 July 2022
- *JD Wong started at WormBase this week; will focus on building WormBase instance of Intermine *Once in place, we can build pre-canned queries that we can embed in WormBase pages (maybe in response to help desk inquiries)7 KB (1,123 words) - 16:39, 6 December 2012
- **Virtual worm web page & FTP *Virtual worm access to data7 KB (1,074 words) - 17:19, 4 October 2012
- * Some genes have human orthology mentioned in automated descriptions, even though the o * WormBase uses EnsemblCompara and other methods (not aggregate method like DIOPT)12 KB (1,809 words) - 16:33, 1 March 2018
- WORM paper Interaction model6 KB (903 words) - 16:37, 5 January 2012
- *Up-to-date mapping to genes is not currently done AMIGO2 (Wormbase Ontology Browser)5 KB (850 words) - 15:32, 5 September 2013
- === Model changes === * SAB suggested continuing site visits for WormBase tutorials7 KB (1,062 words) - 14:41, 2 August 2018
- *Prioritize with genes with little to no known information *Focus on genes in other species9 KB (1,339 words) - 19:02, 31 January 2013
- * Valerio generated new files to ignore/filter-out problematic genes Title: WormBase 2019 - Data, Tools and Community Curation9 KB (1,364 words) - 15:39, 7 February 2019
- ...s are being dealt with or closed, except github ticket [https://github.com/WormBase/website/issues/8156| #8156] * https://github.com/WormBase/website/issues/8156 - - needs a reply from textpresso group -Valerio will t4 KB (709 words) - 13:27, 5 April 2021
- * After worm meeting, (June 27th) * Left over bandanas? paid ~$1 per bandana before. We have enough for WormBase staff8 KB (1,213 words) - 15:29, 6 July 2017
- * We will need to learn to model in Datomic to start building curation tools that run off of Datomic ...ill want to build a curation tool directly on top of Datomic; will need to model currently un-dumped fields in Datomic4 KB (571 words) - 16:48, 3 March 2016
- * Invited to give 25+5 minute talk at Worcester Area Worm Meeting on November 14th * Would be good to meet with individual labs and lab members to discuss WormBase11 KB (1,664 words) - 16:29, 7 December 2017
- * 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
- *Once exposed to worm community at International Meeting, can develop focus groups to enhance/imp Virtual Worm Site5 KB (752 words) - 17:07, 7 July 2011
- * Wen will create ticket to create wormbase.org URL * Working on mapping fosmids to latest release of WormBase8 KB (1,224 words) - 15:34, 21 July 2016
- ...a testing environment for curators/users. we'll have to rely on juancarlos.wormbase.org as cost/benefit analysis is unfavourable to consider other options. * Enter list of genes, get a list of anatomy terms6 KB (906 words) - 21:38, 30 September 2015
- * Weird genes ** Handful of genes in C.elegans that have contrived structures to accommodate an frameshift /5 KB (741 words) - 10:57, 21 August 2015
- * Some data sets, like tiling arrays, might conclude genes that are expressed in a cell/tissue * Genes that are detected at convincing levels (present call) in cell/tissue9 KB (1,490 words) - 15:35, 6 October 2016
