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  • NBC sign off documentation
    * 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 b
    4 KB (583 words) - 20:22, 29 July 2011
  • WormBase-Caltech Weekly Calls September 2021
    *microPublication author tracking for all species *stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/P
    2 KB (325 words) - 15:24, 7 October 2021
  • WBConfCall 2020.07.16-Agenda and Minutes
    * Protein aligner appears to be broken: https://github.com/WormBase/website/issues/7793 *Are/will HGNC genes be made available as objects in WB so that we can refer to them in differen
    3 KB (529 words) - 18:26, 16 July 2020
  • WBConfCall 2012.02.16-Agenda and Minutes
    ==== 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
  • WBConfCall 2020.06.18-Agenda and Minutes
    ===Testing data for WS278 model changes=== *All disease data files passed Caltech and Hinxton testing
    3 KB (490 words) - 17:22, 18 June 2020
  • December 15, 2010
    ;item 3 - Interaction Model (slides 4-5, attached .ppt in documents distributed section) #Chris and Gary will try to map WormBase interaction types to BioGRID interaction types and figure out what the diff
    3 KB (475 words) - 22:50, 17 December 2010
  • WormBase-Caltech Weekly Calls November 2011
    *When mark a paper, separate into two different types of genes :stable vs unstable **Stable genes map to stable ID
    4 KB (612 words) - 17:13, 1 December 2011
  • WormBase-Caltech Weekly Calls August 2011
    *How do we make sure all papers go through SVM pipeline? Physical Interaction model
    4 KB (650 words) - 17:08, 1 September 2011
  • WormBase-Caltech Weekly Calls May 2020
    * Open to all ...ed to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
    5 KB (701 words) - 15:38, 4 June 2020
  • BASIC PROTOCOL 2: PERFORMING A DATABASE SEARCH
    This protocol presents how to conduct a general search of WormBase ...king on the Home link at the top left of any WormBase Web page (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png).
    3 KB (545 words) - 19:56, 11 August 2010
  • WS146
    <pre>New release of WormBase WS146, Wormpep146 and Wormrna146 Thu Jul 28 14:01:21 BST 2005 vii) confirmed_genes.WS146.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (670 words) - 11:09, 21 December 2011
  • WBConfCall 2014.03.06-Agenda and Minutes
    As the modENCODE DCC is overwhelmed with other work, she has proposed that WormBase make the data available to the public. ...o the public could be as simple as just providing a directory where we let all of this sit, or something more complicated.
    5 KB (796 words) - 21:05, 10 March 2014
  • WBConfCall 2018.06.21-Agenda and Minutes
    * http://wiki.wormbase.org/index.php/2018_Advisory_Board_Meeting *?RO_term proposal sent to models@wormbase list
    4 KB (691 words) - 17:16, 21 June 2018
  • WormBase Model:Expr pattern
    [[WormBase Models]] == Model ==
    4 KB (497 words) - 22:42, 6 December 2010
  • WS175
    New release of WormBase WS175, Wormpep175 and Wormrna175 Fri May 4 16:29:43 BST 2007 vii) confirmed_genes.WS175.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    6 KB (680 words) - 10:54, 21 December 2011
  • WBConfCall 2012.12.06-Agenda and Minutes
    = Proposed Model changes = Link to the model changes proposed for WS236 [[WS236_Models.wrm]]
    5 KB (752 words) - 18:55, 6 December 2012
  • WBConfCall 2023.02.02-Agenda and Minutes
    ** Do we want standard Alliance gene pages for all genes from non-canonical species? ...ly be supported on Alliance pages for entities like genes from the related model organism clade/group?
    2 KB (348 words) - 17:52, 2 February 2023
  • WS188
    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
  • WS216
    New release of WormBase WS216, Wormpep216 and Wormrna216 Tue Jun 29 12:53:35 BST 2010 vii) confirmed_genes.WS216.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    7 KB (818 words) - 11:10, 21 December 2011
  • Haemonchus contortus
    ...ving model nematode ''Caenorhabditis elegans''. This makes it an important model of parasitic nematode biology that is commonly used for experimental studie The current assembly shown at WormBase is from August 2009 and provided by a collaboration of the Wellcome Trust S
    3 KB (493 words) - 16:03, 15 December 2011
  • WS204
    New release of WormBase WS204, Wormpep204 and Wormrna204 Fri Jun 26 20:17:06 BST 2009 vii) confirmed_genes.WS204.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (648 words) - 16:16, 21 December 2011
  • WS198
    <pre>New release of WormBase WS198, Wormpep198 and Wormrna198 Thu Dec 18 19:31:36 GMT 2008 vii) confirmed_genes.WS198.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    6 KB (692 words) - 16:51, 21 December 2011
  • WS213
    New release of WormBase WS213, Wormpep213 and Wormrna213 Tue Mar 23 16:36:18 GMT 2010 vii) confirmed_genes.WS213.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (764 words) - 16:45, 21 December 2011
  • WormBase Literature Curation Workflow
    =WormBase Curated Data Types and Curation Methods= HMM - Hidden Markov Model
    9 KB (1,174 words) - 18:30, 29 August 2012
  • WS199
    <pre>New release of WormBase WS199, Wormpep199 and Wormrna199 Tue Feb 3 12:09:54 GMT 2009 ...'s in the genome vii) confirmed_genes.WS199.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (661 words) - 16:51, 21 December 2011
  • WS205
    New release of WormBase WS205, Wormpep205 and Wormrna205 Wed Jul 22 10:29:27 BST 2009 vii) confirmed_genes.WS205.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (711 words) - 16:31, 21 December 2011
  • WS173
    New release of WormBase WS173, Wormpep173 and Wormrna173 Fri Mar 23 18:22:22 GMT 2007 vii) confirmed_genes.WS173.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    6 KB (639 words) - 10:55, 21 December 2011
  • WS187
    New release of WormBase WS187, Wormpep187 and Wormrna187 Fri Jan 25 20:22:16 GMT 2008 vii) confirmed_genes.WS187.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (647 words) - 16:43, 21 December 2011
  • WS171
    <nowiki>New release of WormBase WS171, Wormpep171 and Wormrna171 Thu Feb 8 15:28:27 GMT 2007 vii) confirmed_genes.WS171.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    6 KB (652 words) - 10:55, 21 December 2011
  • WormBase-Caltech Weekly Calls June 2015
    * Added remark that optional fields apply to "ALL OBSERVED PHENOTYPES" for an allele * I could not find an ontology that was ready built to adopt; few genetic model organisms, of those, FB has the most useful. Other mods use controlled voca
    6 KB (982 words) - 15:33, 2 July 2015
  • WBConfCall 2014.09.03-Agenda and Minutes
    *http://monarchinitiative.org/ : connects phenotypes, diseases, models, and genes for translational research across species (People involved: Melissa Haendel ...y enthusiastic response from Chris and Nicole about including worm disease model data
    5 KB (807 words) - 18:27, 4 September 2014
  • WS192
    <pre>New release of WormBase WS192, Wormpep192 and Wormrna192 Tue Jun 24 11:23:32 BST 2008 vii) confirmed_genes.WS192.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    6 KB (763 words) - 10:43, 21 December 2011
  • WS203
    New release of WormBase WS203, Wormpep203 and Wormrna203 Thu May 28 13:24:17 BST 2009 vii) confirmed_genes.WS203.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (662 words) - 16:50, 21 December 2011
  • WS163
    <pre>New release of WormBase WS163, Wormpep163 and Wormrna163 Thu Aug 17 10:49:02 BST 2006 WS163 was built by Paul Davis [paul.davis@wormbase.org]
    6 KB (645 words) - 10:57, 21 December 2011
  • WS191
    <pre>New release of WormBase WS191, Wormpep191 and Wormrna191 Mon Jun 2 09:50:52 BST 2008 vii) confirmed_genes.WS191.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    6 KB (756 words) - 16:53, 21 December 2011
  • WS196
    <pre>New release of WormBase WS196, Wormpep196 and Wormrna196 Fri Oct 31 16:00:42 GMT 2008 vii) confirmed_genes.WS196.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (748 words) - 16:41, 21 December 2011
  • WS208
    New release of WormBase WS208, Wormpep208 and Wormrna208 Tue Oct 27 13:31:22 GMT 2009 vii) confirmed_genes.WS208.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    5 KB (581 words) - 16:50, 21 December 2011
  • WS212
    <pre>New release of WormBase WS212, Wormpep212 and Wormrna212 Mon Mar 1 11:51:04 GMT 2010 vii) confirmed_genes.WS212.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    5 KB (582 words) - 11:16, 21 December 2011
  • WS158
    <pre>New release of WormBase WS158, Wormpep158 and Wormrna158 Thu May 4 13:10:59 BST 2006 WS158 was built by Paul Davis [paul.davis@wormbase.org]
    6 KB (673 words) - 11:07, 21 December 2011
  • WS209
    New release of WormBase WS209, Wormpep209 and Wormrna209 Fri Nov 27 11:57:36 GMT 2009 vii) confirmed_genes.WS209.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (687 words) - 16:50, 21 December 2011
  • WS197
    <pre>New release of WormBase WS197, Wormpep197 and Wormrna197 Wed Nov 26 19:40:37 GMT 2008 vii) confirmed_genes.WS197.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    6 KB (672 words) - 16:43, 21 December 2011
  • WS201
    New release of WormBase WS201, Wormpep201 and Wormrna201 Wed Mar 25 15:30:27 GMT 2009 vii) confirmed_genes.WS201.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (665 words) - 16:42, 21 December 2011
  • WS160
    New release of WormBase WS160, Wormpep160 and Wormrna160 Thu Jun 15 16:29:46 BST 2006 vii) confirmed_genes.WS160.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    6 KB (706 words) - 10:50, 21 December 2011
  • WormBase-Caltech Weekly Calls December 2014
    * Do we want to capture and distinguish all affiliations? ...reviously only with a text description are getting updated to fit the data model
    4 KB (633 words) - 19:09, 6 January 2015
  • WormBase-Caltech Weekly Calls February 2015
    * What implications does this have for the WormBase Ontology Browser? * We are establishing a pipeline to share all physical and genetic interactions with BioGRID
    8 KB (1,120 words) - 16:19, 5 March 2015
  • WormBase Models
    = 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
  • WormBase-Caltech Weekly Calls December 2011
    Interaction model WormBase meeting announcement
    6 KB (903 words) - 16:37, 5 January 2012
  • WS214
    New release of WormBase WS214, Wormpep214 and Wormrna214 Tue Apr 27 15:37:39 BST 2010 vii) confirmed_genes.WS214.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (709 words) - 16:49, 21 December 2011
  • WS182
    New release of WormBase WS182, Wormpep182 and Wormrna182 Thu Sep 27 11:59:39 BST 2007 vii) confirmed_genes.WS182.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (716 words) - 16:48, 21 December 2011
  • WS147
    <pre>New release of WormBase WS147, Wormpep147 and Wormrna147 Thu Aug 18 16:59:45 BST 2005 vii) confirmed_genes.WS147.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    7 KB (815 words) - 11:09, 21 December 2011
  • WS176
    new release of WormBase WS176, Wormpep176 and Wormrna176 Mon May 21 11:58:06 BST 2007 vii) confirmed_genes.WS176.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    7 KB (783 words) - 10:46, 21 December 2011
  • WBConfCall 2021.03.04-Agenda and Minutes
    * Chrome failing to download ftp data [https://github.com/WormBase/website/issues/8087 #8087] ** Harmonized Alliance model would be persistent and integrated.
    4 KB (743 words) - 12:22, 5 March 2021
  • WS206
    New release of WormBase WS206, Wormpep206 and Wormrna206 Fri Aug 28 13:06:57 BST 2009 vii) confirmed_genes.WS206.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    7 KB (796 words) - 16:46, 21 December 2011
  • WormBase-Caltech Weekly Calls May 2019
    === SObA for all ontologies === * SObA graph search for all ontologies
    6 KB (911 words) - 17:13, 6 June 2019
  • WS210
    New release of WormBase WS210, Wormpep210 and Wormrna210 Tue Dec 22 12:35:31 GMT 2009 vii) confirmed_genes.WS210.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (721 words) - 16:46, 21 December 2011
  • WS178
    New release of WormBase WS178, Wormpep178 and Wormrna178 Wed Jul 4 12:56:45 BST 2007 vii) confirmed_genes.WS178.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    7 KB (762 words) - 10:53, 21 December 2011
  • WS180
    New release of WormBase WS180, Wormpep180 and Wormrna180 Fri Aug 17 13:41:37 BST 2007 vii) confirmed_genes.WS180.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    7 KB (771 words) - 10:52, 21 December 2011
  • WS181
    New release of WormBase WS181, Wormpep181 and Wormrna181 Fri Sep 7 11:40:20 BST 2007 vii) confirmed_genes.WS181.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    8 KB (885 words) - 16:47, 21 December 2011
  • WS189
    New release of WormBase WS189, Wormpep189 and Wormrna189 Thu Apr 3 10:28:39 BST 2008 WS189 was built by [Paul Davis (paul.davis@wormbase.org)]
    6 KB (668 words) - 11:01, 21 December 2011
  • WS138
    <pre>New release of WormBase WS138, Wormpep138 and Wormrna138 Thu Jan 20 11:55:33 GMT 2005 vii) confirmed_genes.WS138.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (740 words) - 11:19, 21 December 2011
  • Specifications for a DAF for gene-disease data
    ...parate AGR orthology pipeline to link human genes and their orthologs from model organisms. !Project_name: WormBase (WB) Version WS258
    10 KB (1,599 words) - 18:53, 24 January 2019
  • WS154
    <pre>New release of WormBase WS154, Wormpep154 and Wormrna154 Fri Feb 10 12:46:08 GMT 2006 vii) confirmed_genes.WS154.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    7 KB (749 words) - 11:08, 21 December 2011
  • WS195
    ...&nbsp;&nbsp; 4401 (18.4%)&nbsp;&nbsp;&nbsp; No transcriptional evidence at all<br><br>Status of entries: Protein Accessions<br>--------------------------- ...open your database, e.g.<br>&nbsp;&nbsp;&nbsp; type 'xace /users/yourname/wormbase' at the command prompt.<br><br>5. See the acedb website for more informatio
    11 KB (1,614 words) - 16:52, 21 December 2011
  • WBConfCall 2015.09.17-Agenda and Minutes
    *Models will get flagged with a milestone when the model is approved and ready *WormBook.org can now be repurposed as an arm of WormBase, use for micro-publications, genome announcements/descriptions, granular re
    1 KB (219 words) - 17:03, 17 September 2015
  • WS193
    <pre>New release of WormBase WS193, Wormpep193 and Wormrna193 Fri Jul 25 22:12:15 BST 2008 vii) confirmed_genes.WS193.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    8 KB (944 words) - 16:52, 21 December 2011
  • WS289
    New release of WormBase WS288 WS288 was built by Stavros Diamantakis with the input from the WormBase Community and Team. Thank you!
    16 KB (1,733 words) - 21:55, 11 May 2023
  • WS179
    New release of WormBase WS179, Wormpep179 and Wormrna179 Mon Jul 30 12:21:01 BST 2007 vii) confirmed_genes.WS179.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    8 KB (843 words) - 10:53, 21 December 2011
  • WS172
    <nowiki>New release of WormBase WS172, Wormpep172 and Wormrna172 Fri Mar 2 16:35:57 GMT 2007 vii) confirmed_genes.WS172.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    7 KB (783 words) - 10:55, 21 December 2011
  • WS207
    New release of WormBase WS207, Wormpep207 and Wormrna207 Mon Sep 28 11:47:26 BST 2009 vii) confirmed_genes.WS207.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (675 words) - 16:42, 21 December 2011
  • Hinxton 2015.08- Meeting minutes
    ** Result was that all non-elegans species were build using old data ** Needed to re-start all T2 builds from scratch
    5 KB (741 words) - 10:57, 21 August 2015
  • WormBase-Caltech Weekly Calls February 2016
    * 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 Datomic
    4 KB (571 words) - 16:48, 3 March 2016
  • WormBase-Caltech Weekly Calls January 2019
    * Valerio generated new files to ignore/filter-out problematic genes Title: WormBase 2019 - Data, Tools and Community Curation
    9 KB (1,364 words) - 15:39, 7 February 2019
  • WBConfCall 2023.04.06-Agenda and Minutes
    * 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.csv
    7 KB (1,113 words) - 18:19, 6 April 2023
  • WS284
    New release of WormBase WS284 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES)
    17 KB (1,841 words) - 21:54, 11 May 2023
  • WS174
    vii) confirmed_genes.WS174.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA xiii) geneIDs.WS174.gz - list of all current gene identifiers with CGC &amp; molecular names (when known)
    8 KB (938 words) - 10:54, 21 December 2011
  • WS170
    New release of WormBase WS170, Wormpep170 and Wormrna170 Fri Jan 19 09:31:14 GMT 2007 vii) confirmed_genes.WS170.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    8 KB (820 words) - 10:51, 21 December 2011
  • WS200
    New release of WormBase WS200, Wormpep200 and Wormrna200 Tue Feb 24 12:51:18 GMT 2009 vii) confirmed_genes.WS200.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (722 words) - 16:43, 21 December 2011
  • WBConfCall 2021.04.01-Agenda and Minutes
    ...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 t
    4 KB (709 words) - 13:27, 5 April 2021
  • WormBase-Caltech Weekly Calls December 2017
    * There shouldn't be model changes (that affect Caltech) for this next upload * Wen can talk with Ranjana to incorporate (particularly for info-sparse genes)
    6 KB (921 words) - 16:52, 4 January 2018
  • WS135
    <pre>New release of WormBase WS135, Wormpep135 and Wormrna135 Thu Nov 11 13:32:31 GMT 2004 vii) confirmed_genes.WS135.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (689 words) - 11:19, 21 December 2011
  • WBConfCall 2014.01.23-Agenda and Minutes
    Sanger WormBase/ParaSite * New model/class: Rnaseq_library - Gary W.
    4 KB (617 words) - 17:14, 23 January 2014
  • WBConfCall 2013.11.07-Agenda and Minutes
    [[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_c
    8 KB (1,246 words) - 15:52, 12 November 2013
  • WS194
    <pre>New release of WormBase WS194, Wormpep194 and Wormrna194 Tue Sep 2 10:54:51 BST 2008 vii) confirmed_genes.WS194.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    8 KB (936 words) - 16:48, 21 December 2011
  • WormMine
    [http://intermine.wormbase.org/tools/wormmine/begin.do WormMine] [https://github.com/WormBase/intermine WormMine Github]
    15 KB (2,088 words) - 16:16, 15 October 2020
  • INTRODUCTION
    ...l traits such as gene expression patterns and neuronal connectivity. Also, WormBase contains sequence and gene structures of ''C. briggsae'' and ''C. remanei'' ...n of WormBase available in September, 2005 (WS147 release; BioPerl/Generic Model Organism Database software).
    2 KB (365 words) - 00:06, 1 December 2010
  • WormBase-Caltech Weekly Calls September 2016
    * 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/tissue
    9 KB (1,490 words) - 15:35, 6 October 2016
  • WS177
    New release of WormBase WS177, Wormpep177 and Wormrna177 Fri Jun 15 15:39:40 BST 2007 vii) confirmed_genes.WS177.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    9 KB (819 words) - 10:53, 21 December 2011
  • WormBase-Caltech Weekly Calls December 2012
    *Prioritize with genes with little to no known information *Focus on genes in other species
    9 KB (1,339 words) - 19:02, 31 January 2013
  • WS190
    <pre>New release of WormBase WS190, Wormpep190 and Wormrna190 Fri Apr 25 11:03:36 BST 2008 vii) confirmed_genes.WS190.gz - DNA sequences of all genes confirmed by EST &amp;/or cDNA
    8 KB (913 words) - 16:46, 21 December 2011
  • WS236 Models.wrm
    Model changes to ?Gene and ?Transposon I'd like to change tags in the ?Gene model and #Gene_history_action hash.
    8 KB (1,073 words) - 15:31, 14 December 2012
  • WormBase Model:CDS
    [[WormBase Models]] == Model ==
    4 KB (410 words) - 17:08, 17 August 2010
  • WormBase-Caltech Weekly Calls December 2013
    * There are papers in the WormBase collection that are used as paper evidence for some concise descriptions * These papers are lumped in with all the other papers, come up as false positives in flagging pipelines
    6 KB (823 words) - 19:38, 2 January 2014
  • WormBase-Caltech Weekly Calls September 2015
    ...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 terms
    6 KB (906 words) - 21:38, 30 September 2015
  • Old pipeline for disease data
    Note: All disease_relevant descriptions have been removed from the concise descriptio ...one GO term. If a gene needs to be attached to a unrelated disease, enter all data on a new line, by hitting 'New' in the OA.
    14 KB (2,085 words) - 20:27, 7 July 2022
  • WS211
    <pre>New release of WormBase WS211, Wormpep211 and Wormrna211 Fri Jan 29 13:26:05 GMT 2010 vii) confirmed_genes.WS211.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (766 words) - 16:38, 21 December 2011
  • WormBase-Caltech Weekly Calls July 2011
    Root Passwords for all machines *All code in production use in BitBucket or equivalent
    7 KB (1,117 words) - 16:39, 4 August 2011
  • WS142
    <pre>New release of WormBase WS142, Wormpep142 and Wormrna142 Fri Apr 15 18:22:51 BST 2005 vii) confirmed_genes.WS142.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    7 KB (720 words) - 11:09, 21 December 2011
  • WormBase-Caltech Weekly Calls August 2013
    *Up-to-date mapping to genes is not currently done AMIGO2 (Wormbase Ontology Browser)
    5 KB (850 words) - 15:32, 5 September 2013
  • WS217
    New release of WormBase WS217, Wormpep217 and Wormrna217 Wed Jul 28 09:25:17 BST 2010 vii) confirmed_genes.WS217.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    8 KB (915 words) - 11:10, 21 December 2011
  • WBConfCall 2012.04.19-Agenda and Minutes
    == 1. Model changes (Hinxton) == 1a) Variation model sign off
    7 KB (1,182 words) - 13:50, 20 April 2012
  • WormBase-Caltech Weekly Calls February 2011
    *Should we take minutes of Caltech WormBase group meetings and send around? *WormBase-wide conference call twice per month
    8 KB (1,282 words) - 17:08, 7 July 2011
  • WormBase-Caltech Weekly Calls March 2014
    * ?Construct model * miRNA analyses have used completely different platforms than protein-coding genes, so requires a different dataset for each
    8 KB (1,218 words) - 17:46, 2 April 2014
  • Coding standards
    = WormBase Coding Standards and Style Guide = foreach my $gene (@genes) {
    6 KB (950 words) - 15:36, 19 June 2014
  • WormBase-Caltech Weekly Calls January 2014
    ...Karen, others are welcome. Visit the construct model requests [http://wiki.wormbase.org/index.php/WormBase_Model:Construct here] ...arned enough Catalyst to create a workable ontology browser on the caltech wormbase sandbox.
    10 KB (1,583 words) - 18:16, 5 February 2014
  • Feature WishList
    ''This is a running list of proposed features at WormBase'' ...ase) as well as those looking to the system to help understand orthologous genes implicated in disease.
    6 KB (842 words) - 17:01, 21 October 2011
  • WS169
    <pre>New release of WormBase WS169, Wormpep169 and Wormrna169 Fri Dec 22 15:09:52 GMT 2006 vii) confirmed_genes.WS169.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    8 KB (787 words) - 10:56, 21 December 2011
  • WormBase-Caltech Weekly Calls May 2011
    **90 genes >= 10 publications **20,000 genes with RNAi data
    9 KB (1,302 words) - 16:38, 2 June 2011
  • WS228
    New release of WormBase WS228 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:
    14 KB (1,572 words) - 10:37, 11 November 2011
  • WS131
    <pre>New release of WormBase WS131, Wormpep131 and Wormrna131 Tue Sep 7 15:06:49 BST 2004 vii) confirmed_genes.WS131.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (669 words) - 11:18, 21 December 2011
  • WS107
    <pre>New release of WormBase WS107, Wormpep107 and Wormrna107 Fri Aug 8 13:44:00 BST 2003 vii) confirmed_genes.WS107.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (659 words) - 11:17, 21 December 2011
  • WormBase-Caltech Weekly Calls October 2016
    * First draft up on WormBase development site ...ion) and lower level (individual gene product function)? There may be, but all of this information is valuable
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  • WS227
    New release of WormBase WS227 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:
    15 KB (1,738 words) - 11:20, 21 December 2011
  • WormBase-Caltech Weekly Calls January 2012
    *Patch sent in; all OK *?Human_disease model vs tag in ?Gene model?
    5 KB (847 words) - 17:49, 1 March 2012
  • WS225
    New release of WormBase WS225, Wormpep225 and Wormrna225 Tue Apr 5 11:57:03 BST 2011 genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data
    16 KB (1,674 words) - 11:38, 20 April 2011
  • WormBase-Caltech Weekly Calls July 2015
    * Sending out e-mails to all labs/PIs reminding about new data forms * Gary Williams only using high quality data, taking care of all curation (including meta data)
    10 KB (1,464 words) - 17:09, 13 August 2015
  • WS202
    New release of WormBase WS202, Wormpep202 and Wormrna202 Tue Apr 28 16:02:08 BST 2009 vii) confirmed_genes.WS202.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (770 words) - 11:06, 21 December 2011
  • WS221
    New release of WormBase WS221, Wormpep221 and Wormrna221 Tue Nov 23 12:32:16 GMT 2010 genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data
    17 KB (1,758 words) - 16:47, 21 December 2011
  • WBConfCall 2015.05.21-Agenda and Minutes
    == OMIM links to/from WormBase == * Ranjana working on linking between WormBase and OMIM
    2 KB (384 words) - 20:25, 21 May 2015
  • WS223
    New release of WormBase WS223, Wormpep223 and Wormrna223 Mon Jan 24 12:12:08 GMT 2011 genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data
    15 KB (1,610 words) - 11:20, 21 December 2011
  • WS222
    New release of WormBase WS222, Wormpep222 and Wormrna222 Mon Dec 20 12:07:08 GMT 2010 WS222 was built by Michael Paulini (michael.paulini@wormbase.org)
    15 KB (1,647 words) - 10:06, 22 December 2010
  • WS127
    <pre>New release of WormBase WS127, Wormpep127 and Wormrna127 Tue Jul 6 13:12:51 BST 2004 vii) confirmed_genes.WS127.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    7 KB (872 words) - 11:18, 21 December 2011
  • WBConfCall 2016.10.06-Agenda and Minutes
    https://github.com/WormBase/website/issues/5092 * Discussion on making available on WormBase the chapters we wrote for the WormBook.
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  • WBConfCall 2013.10.17-Agenda and Minutes
    * sequences for proteins and genomic features for all species except C.sp 5 and C.sp.11 ...gff3, transcripts from gff3 has been expanded to represent all species in wormbase (besides any of the "sp" species)
    2 KB (361 words) - 16:32, 17 October 2013
  • WS234
    New release of WormBase WS234 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:
    15 KB (1,653 words) - 10:13, 18 January 2013
  • WS231
    New release of WormBase WS231 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:
    16 KB (1,820 words) - 14:15, 13 September 2012
  • WS224
    New release of WormBase WS224, Wormpep224 and Wormrna224 Fri Mar 4 14:58:13 GMT 2011 genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data
    15 KB (1,583 words) - 11:13, 21 December 2011
  • WormBase-Caltech Weekly Calls November 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
  • WS218
    New release of WormBase WS218, Wormpep218 and Wormrna218 Tue Aug 24 genomes DIR - contains a sub dir for each WormBase species with
    15 KB (1,756 words) - 11:21, 21 December 2011
  • WormBase-Caltech Weekly Calls June 2014
    === WormBase Ontology Browser (WOBr) for WS244 release === * Final data model may still need refinement?
    6 KB (801 words) - 17:29, 2 July 2014
  • WormBase-Caltech Weekly Calls June 2017
    * Left over bandanas? paid ~$1 per bandana before. We have enough for WormBase staff ...ng on ?Phenotype_assay (?Phenotype_experiment/?Phenotype_annotation) class model
    8 KB (1,213 words) - 15:29, 6 July 2017
  • WS122
    <pre>New release of WormBase WS122, Wormpep122 and Wormrna122 March 26th 2004 vii) confirmed_genes.WS122.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (721 words) - 11:18, 21 December 2011
  • WormBase-Caltech Weekly Calls May 2017
    * GO-CAM (Gene Ontology - Causal Activity Model(ing)) ...rds, tool could pull up all relevant annotations to help start with GO CAM model building
    8 KB (1,229 words) - 15:31, 1 June 2017
  • WBConfCall 2016.01.07-Agenda and Minutes
    http://wiki.wormbase.org/index.php/2016_Advisory_Board_Meeting#Organisation_of_SAB_talks ==2. WormBase exhibit at the GSA meeting Dev., Cell Bio and Gene Expression Meeting==
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  • WormBase Model:Clone
    [[WormBase Models]] == Model ==
    10 KB (1,176 words) - 22:24, 18 March 2014
  • WBConfCall 2011.11.17-Agenda and Minutes
    <pre> Dear All, * WormBook mirror: will move from wormbase.sanger.ac.uk to
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  • WormBase-Caltech Weekly Calls August 2012
    ***Benefit of curating phenotypes in other species? Particularly useful for genes not in C. elegans, for example ****Cell functions, 10 or 100 highest/preferentially expressed genes, cell connections, cell signals
    12 KB (1,878 words) - 15:55, 6 September 2012
  • WS235
    New release of WormBase WS235 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:
    15 KB (1,708 words) - 10:14, 18 January 2013
  • WS220
    New release of WormBase WS220, Wormpep220 and Wormrna220 Mon Oct 25 13:22:36 BST 2010 genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data
    16 KB (1,762 words) - 11:10, 21 December 2011
  • WormBase-Caltech Weekly Calls July 2013
    *Getting real-time updates of gene list for genes in OA *Would be good to track all accounts on Spica (and any other machine)
    7 KB (1,059 words) - 15:37, 1 August 2013
  • WormBase-Caltech Weekly Calls October 2013
    === WormBase Ontology Browser (WOBr) === *Currently movie files are all from three large scale movie datasets, so names are currently unique
    13 KB (1,983 words) - 16:40, 7 November 2013
  • WormBase-Caltech Weekly Calls December 2015
    * Curators will likely need to work with a models "master" to make model changes * http://juancarlos.wormbase.org , look at a gene page, open Phenotype Graph widget
    5 KB (776 words) - 16:50, 7 January 2016
  • WormBase-Caltech Weekly Calls February 2012
    EPIC data into WormBase *Need to modify model and display for data
    7 KB (1,070 words) - 17:47, 1 March 2012
  • WS232
    New release of WormBase WS232 WS232 was built by Michael Paulini [michael.paulini@wormbase.org]
    15 KB (1,729 words) - 14:15, 13 September 2012
  • WS219
    New release of WormBase WS219, Wormpep219 and Wormrna219 Tue Oct 5 16:04:14 BST 2010 WS219 was built by [Michael Paulini (michael.paulini@wormbase.org)]
    15 KB (1,622 words) - 11:11, 21 December 2011
  • WormBase Paper Categorization
    * Topics commonly studied in C. elegans due to its advantages as a model system **Essential genes
    10 KB (1,279 words) - 18:20, 18 October 2013
  • WormBase-Caltech Weekly Calls February 2013
    *Can we collect all gene models, for example, without any bias and display any info we have? *SPELL construction has changed; all data sets exist as separate flat files
    8 KB (1,161 words) - 16:34, 7 March 2013
  • WormBase-Caltech Weekly Calls April 2012
    **Reasonably satisfied with coverage of human disease genes **Performs similar to WormBase
    7 KB (1,158 words) - 17:20, 3 May 2012
  • WormBase Model:Gene cluster
    [[WormBase Models]] == Model ==
    15 KB (1,645 words) - 18:54, 23 January 2014
  • WS112
    <pre>New release of WormBase WS112, Wormpep112 and Wormrna112 Fri Oct 17 18:38:57 BST 2003 vii) confirmed_genes.WS112.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (735 words) - 11:17, 21 December 2011
  • WormBase-Caltech Weekly Calls February 2018
    * 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
  • WormBase-Caltech Weekly Calls March 2015
    === GO data model change === * Worm pick holders (pencil grips) with WormBase logos; can they be printed on?
    7 KB (1,058 words) - 15:32, 2 April 2015
  • WS230
    New release of WormBase WS230 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:
    17 KB (1,950 words) - 09:37, 7 February 2012
  • WormBase-Caltech Weekly Calls April 2017
    * All checkboxes can be checked by default * WS259 adding more info (almost all meta data) on variations, laboratory and strains, RNAi phenotypes (hopefull
    7 KB (1,010 words) - 17:08, 4 May 2017
  • WormBase-Caltech Weekly Calls July 2018
    ...may want to give people the option to "opt-out" either for a paper or for all emails or both === Model changes ===
    7 KB (1,062 words) - 14:41, 2 August 2018
  • WormBase-Caltech Weekly Calls November 2017
    * Would be good to meet with individual labs and lab members to discuss WormBase * Someone looking for promoter sequences of pan-neuronal genes; neuronal marker
    11 KB (1,664 words) - 16:29, 7 December 2017
  • WormBase-Caltech Weekly Calls March 2013
    *Prepopulation: Display all (key?) experimental info on gene from WormBase, some Textpresso info like "ABC-1 encodes..." ***Model changes
    7 KB (1,047 words) - 15:34, 4 April 2013
  • WS117
    <pre>New release of WormBase WS117, Wormpep117 and Wormrna117 Tue Jan 20 10:22:06 GMT 2004 vii) confirmed_genes.WS117.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    6 KB (695 words) - 11:17, 21 December 2011
  • WormBase-Caltech Weekly Calls August 2014
    * Collecting model/pathway diagrams from papers and reviews: should we make ?Picture objects f ...remains an ad hoc approach; different topics are harder or easier to find all papers for
    6 KB (974 words) - 17:28, 3 September 2014
  • WS233
    New release of WormBase WS233 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:
    17 KB (2,002 words) - 14:17, 13 September 2012
  • WormBase-Caltech Weekly Calls March 2018
    ** Should we add a single column listing interacting genes with types in parentheses ** Want to indicate, for a query gene, genes for which multiple interaction types have been observed
    11 KB (1,703 words) - 15:27, 5 April 2018
  • WS226
    New release of WormBase WS226 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:
    21 KB (2,346 words) - 11:15, 21 December 2011
  • WormBase-Caltech Weekly Calls April 2011
    Transgene Model *Kimberly working on Physical Interaction model
    7 KB (1,103 words) - 18:28, 5 May 2011
  • WormBase-Caltech Weekly Calls November 2012
    *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
  • WormBase-Caltech Weekly Calls June 2020
    * Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room * Form is used all week, and hold on to it until asked to be submitted
    8 KB (1,228 words) - 20:57, 14 July 2020
  • Progress Report 2011
    ='''WormBase Gene Ontology Progress Report, December 2011'''= Developer, WormBase, Caltech, Pasadena, CA.
    13 KB (1,830 words) - 16:40, 13 December 2012
  • WormBase Model:Sequence
    [[WormBase Models]] == Model ==
    12 KB (1,258 words) - 09:29, 5 October 2010
  • WBConfCall 2018.07.19-Agenda and Minutes
    ...inding site (for example, a schematic of promoter etc. on the current gene model). * GO process terms for all C. elegans genes (currently only 9,000 proteins have process; fill in those without data wit
    11 KB (1,649 words) - 16:10, 19 July 2018
  • WormBase-Caltech Weekly Calls September 2013
    *Wen found that many authors don't publish lists of clustered genes *What would WormBase look like without any manually curated data?
    8 KB (1,225 words) - 16:33, 3 October 2013
  • WormBase-Caltech Weekly Calls July 2020
    ...heterogeneous natures. That means there may be no single solution to solve all those problems. ...gle public name is assigned to multiple WBgene ID, Wen has a list of these genes
    9 KB (1,369 words) - 22:47, 5 August 2020
  • WormBase-Caltech Weekly Calls January 2015
    * 150,000 new alleles, Mary Ann done just all bar 12 of them in time for WS247 Main outline [https://docs.google.com/a/wormbase.org/document/d/1l6pExlCMI88pi_-djk8jt7IzNsMDV-nIEY9Z1gBNh-A/edit here]- not
    10 KB (1,453 words) - 18:52, 4 February 2015
  • WormBase-Caltech Weekly Calls January 2013
    *Has overview widget with all relevant entities *We should make an announcement on the main WormBase page that WormMart will remain at WS220 and Intermine will replace it
    10 KB (1,553 words) - 18:04, 7 February 2013
  • WormBase-Caltech Weekly Calls April 2019
    * Make modification to ACEDB model? ...ence is held at Université de Montréal on June 2-5, 2019 and will focus on Model systems in cancer research (https://www.fourwav.es/view/1174/info/). The C.
    11 KB (1,676 words) - 15:28, 2 May 2019
  • Hinxton 2015.07- Meeting minutes
    ** Plan to update all tier2 species for WS250 ** Some species (e.g. P. pac) have few/no gene model changes, but could do with being brought up to latest models and have newes
    11 KB (1,714 words) - 11:04, 27 July 2015
  • WS229
    New release of WormBase WS229 species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files:
    17 KB (1,988 words) - 11:15, 21 December 2011
  • WBConfCall 2018.03.01-Agenda and Minutes
    == WormBase SAB Meeting Date == * [https://github.com/WormBase/website/issues/6213 SNPs in specific genomic regions in Hawaiian C. elegans
    4 KB (574 words) - 01:54, 2 March 2018
  • Gene Interaction/archive
    ...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
    50 KB (5,228 words) - 15:10, 21 July 2017
  • 20141022 - Phenotype2GO Pipeline
    ...arize how the Phenotype2GO-based GO annotations will be handled for future WormBase builds and GO uploads. *All papers will be included in the pipeline (see below for some details on this
    7 KB (1,164 words) - 17:54, 19 February 2015
  • WormBase-Caltech Weekly Calls June 2012
    *Wen needs all .ace files ready to test the midbuild **Chris will add all model changes proposed for WS233
    6 KB (983 words) - 18:02, 12 July 2012
  • WormBase-Caltech Weekly Calls April 2021
    All changes proposed above were approved by the group * Changes requested here: https://github.com/WormBase/website/issues/7900
    11 KB (1,782 words) - 17:55, 13 May 2021
  • WBConfCall 2013.06.20-Agenda and Minutes
    ** [https://github.com/WormBase/website/issues/1438 #1438 Track errors on RNA seq GBrowse view] ** [https://github.com/WormBase/website/issues/1091 #1091 OP50 sequence data deposition]
    8 KB (1,291 words) - 21:09, 23 June 2013
  • WormBase-Caltech Weekly Calls June 2011
    *Wrapped up support for all classes (display, etc.) *Make link on WormBase homepage
    5 KB (752 words) - 17:07, 7 July 2011
  • WormBase-Caltech Weekly Calls August 2018
    * Can use outreach@wormbase.org for consistency * May use the PMID in the subject line so e-mails will not be all in the same thread
    9 KB (1,366 words) - 15:19, 6 September 2018
  • WormBase-Caltech Weekly Calls May 2018
    * Wen had to debug; SPELL has limit of how many genes can be processed per data set (46,340) * Wen trying to accommodate, deleting some genes from data set that had no expression (kludge)
    14 KB (2,226 words) - 15:31, 7 June 2018
  • WBConfCall 2014.09.18-Agenda and Minutes
    * 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
    5 KB (763 words) - 00:51, 19 September 2014
  • WormBase-Caltech Weekly Calls May 2014
    === WormBase Ontology Browser (WOBr) === * http://juancarlos.wormbase.org/tools/ontology_browser
    8 KB (1,234 words) - 12:36, 4 June 2014
  • SOP for generating GO files for citace and GO consortium uploads
    ***Good genes for spot checks: **go_annotation.ace (from OA - orphan genes and ncRNA annotations - this file gets dumped third and last)
    23 KB (3,744 words) - 15:12, 23 December 2022
  • WormBase-Caltech Weekly Calls March 2017
    * Karen will need to become part time at WormBase (needs to be more than half time on SBIR) * Want clear, granular evidence for each assertion in a model, but need to accommodate probabilistic statements
    10 KB (1,527 words) - 15:32, 6 April 2017
  • Topic pages
    **process pages will dissect the chapters and link them to entities in WormBase, ===Genes===
    20 KB (3,088 words) - 19:17, 13 August 2020
  • WormBase-Caltech Weekly Calls March 2011
    *Paper .ACE file: Would include bibliographic info, journals, authors, genes associated from abstract or added manually ...l formal release; weird things about diff; new reference associations with genes; a lot of duplications?
    13 KB (2,097 words) - 22:48, 7 April 2011
  • WormBase-Caltech Weekly Calls February 2021
    * Any more comments about the Wiki page and the proposal? https://wiki.wormbase.org/index.php/WormBase_gene_association_file * Will change ?Expr_pattern model to possibly remove ?Author reference and add in a ?Person reference instead
    9 KB (1,377 words) - 16:36, 4 March 2021
  • WormBase-Caltech Weekly Calls January 2018
    * Diseases are annotated to genes, alleles, and strains within WB * Eppendorf tube openers with WormBase logo?
    12 KB (1,930 words) - 17:12, 1 February 2018
  • WormBase-Caltech Weekly Calls June 2018
    * Issue for WBPaper00048704: https://wormbase.org/resources/paper/WBPaper00048704#0--10 * First author is "Li, C" as in PubMed (correct name) in WormBase as "Chun, L"
    8 KB (1,189 words) - 14:10, 5 July 2018
  • WormBase-Caltech Weekly Calls August 2017
    ** Maybe best, once new ?Phenotype_experiment model is in place, to just refer to perturbed gene === WormBase grant ===
    6 KB (912 words) - 01:40, 15 September 2017
  • Antibody
    ==Antibody Model== ...the antibody string matching pipeline. See GitHub repo: https://github.com/WormBase/entity-extraction-antibody
    21 KB (2,888 words) - 19:58, 9 April 2021
  • WormBase-Caltech Weekly Calls September 2012
    **Browse genes/proteins by class/GO annotation **We could extend the WormBase web app to interact with SPELL data
    7 KB (1,074 words) - 17:19, 4 October 2012
  • WormBase-Caltech Weekly Calls June 2016
    * Wen will create ticket to create wormbase.org URL * Chris identified all objects from various OAs that had the same initial import timestamp, Wen de
    8 KB (1,224 words) - 15:34, 21 July 2016
  • WormBase-Caltech Weekly Calls April 2014
    * Testing at juancarlos.wormbase.org (from there go to Tools > Ontology Browser) * Problems with handling inferred expression of genes in cells
    10 KB (1,474 words) - 15:54, 30 April 2014
  • Transgenes
    We curate all integrated (Is, In, Si, Ti), and select extrachromosomal (Ex) transgenes. ==Model Changes==
    29 KB (4,575 words) - 16:23, 3 March 2022
  • Tasks in Progress
    **Documenting elements of WormBase workflow to ease transition for new staff and keep track of changes made **Added information and links for getting started with WormBase
    29 KB (4,254 words) - 20:25, 27 April 2012
  • WormBase-Caltech Weekly Calls January 2021
    ...gen 2020 data over christmas, and I have repackaged the full release data (all 100k cells with annotations, but prior to the soupX processing) in an h5ad * Since they are thinking about simple things that can be offered in wormbase, I will also briefly talk about this dashboard that i made for a UCLA group
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  • WS215
    <pre>New release of WormBase WS215, Wormpep215 and Wormrna215 Thu May 27 18:15:29 BST 2010 vii) confirmed_genes.WS215.gz - DNA sequences of all genes confirmed by EST &/or cDNA
    19 KB (1,735 words) - 11:07, 21 December 2011
  • WBConfCall 2014.07.03-Agenda and Minutes
    === Resurrection of the second all-hands conference call? === ...ce we went to a once-a-month schedule. Proposal then: reinstate the second all-hands conference call. Topic-based calls for smaller groups can be arranged
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  • Gene Interaction
    ...ed ?Physical_interaction model has also been consolidated into this larger model. Note that #Interaction_info and #Interaction_type have been deprecated. WBProcess ?WBProcess XREF Interaction // WormBase biological process associated with the interaction
    53 KB (6,521 words) - 20:51, 7 March 2019
  • WormBase-Caltech Weekly Calls 2022
    [[WormBase-Caltech_Weekly_Calls_January_2022|January]] [[WormBase-Caltech_Weekly_Calls_February_2022|February]]
    10 KB (1,547 words) - 21:31, 2 January 2024
  • Software Life Cycle: 1. Updating The Development Server
    https://docs.google.com/a/wormbase.org/document/d/1oPpj8d5gibUc-gpUZorl6ETT5baE6mp-v2bMedKauiA/edit# This document describes the process of staging a new release of WormBase on the development server.
    25 KB (3,632 words) - 03:11, 28 October 2013
  • WormBase-Caltech Weekly Calls April 2015
    ** Michael Paulini is adding Species information for the WBGene IDs in the genes.ace file ** For list of files, see: ftp://ftp.sanger.ac.uk/pub/consortia/wormbase/STAFF/mh6/nightly_geneace/
    8 KB (1,147 words) - 15:33, 7 May 2015
  • WormBase-Caltech Weekly Calls October 2015
    ...eral discussion on DOI handling for micropublications and using the ?Paper model * Micropublications were displayed on ?Expr_pattern pages on WormBase/WormBook
    10 KB (1,475 words) - 16:57, 5 November 2015
  • Gene Regulation
    == Interaction Model as of WS231 == ...ed ?Physical_interaction model has also been consolidated into this larger model. Note that #Interaction_info and #Interaction_type have been deprecated.
    59 KB (8,367 words) - 22:00, 14 December 2018
  • WBConfCall 2020.03.05-Agenda and Minutes
    * [https://github.com/WormBase/website/issues/7581 CGC bad WB link URL]; can this be closed? .../WormBase/website/issues/7579 Maureen Barr's question about protein coding genes with known function]; can this be closed?
    5 KB (857 words) - 14:36, 9 March 2020
  • Paper Tables in Postgres
    ...WormBase starting curating paper data, as PubMed currently does not curate all author affiliations for papers. ...has been checked out we assume that it has/will be curated completely for all aspects of RNAi.
    25 KB (3,238 words) - 16:42, 8 November 2019
  • WormBase-Caltech Weekly Calls April 2020
    * 14 volunteers so far, all have been assigned a WBPerson ID ...a good tool for quick communication among team members; would be good for all curators to join Slack to enable efficient communication
    7 KB (1,020 words) - 15:33, 7 May 2020
  • FAQs
    ...ww.wormbase.org/about/Frequently_asked_questions FAQ pages] on the new www.wormbase.org site. === How should I cite WormBase? ===
    67 KB (10,954 words) - 09:22, 19 February 2013
  • WormBase-Caltech Weekly Calls January 2017
    * Who from WormBase will go? * Whether all WB staff go depends on whether we have an all hands meeting before/after
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  • UserGuide:Reivsed Nomenclature
    .../p><h2>Genomes, assemblies, clones and contigs</h2><p>Reference genomes in WormBase are given version names, for example <i>C. elegans</i> has the version name ...<b>AscSuum_1.0</b> and <b>ASU_2.0</b></p><p>The genomes of most species in WormBase are incompletely assembled, being left as various sizes of contig. Only <i>
    56 KB (9,520 words) - 11:51, 21 October 2015
  • UserGuide:Revised Nomenclature
    .../p><h2>Genomes, assemblies, clones and contigs</h2><p>Reference genomes in WormBase are given version names, for example <i>C. elegans</i> has the version name ...<b>AscSuum_1.0</b> and <b>ASU_2.0</b></p><p>The genomes of most species in WormBase are incompletely assembled, being left as various sizes of contig. Only <i>
    56 KB (9,514 words) - 09:48, 23 October 2015
  • RNAi/archive
    ...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 An important point here is that RNAi target genes for an RNAi experiment are not submitted directly using the name of the tar
    47 KB (7,989 words) - 23:40, 1 September 2015
  • WormBase-Caltech Weekly Calls 2023
    * Trained a small GPT model with C. elegans literature. Reporting some results. ** Current data model at the ABC has negated as a Boolean (true/false).
    36 KB (4,994 words) - 17:27, 14 February 2024
  • VariationConciseDescriptions
    ...ercontent.com/WormBase/wormbase-pipeline/master/wspec/models.wrm variation model]<br> ...[[Generation_of_automated_descriptions | automated concise descriptions of genes]]. <br>
    36 KB (5,076 words) - 01:38, 2 March 2016
  • Gene Expression micropublications
    ...ity scientific findings directly to a well established central repository (WormBase). Data will be publically shared and could be mined alongside data curated ...localization experiments (e.g. ISH, smFISH, immunohistochemistry). If the model will prove to be successful, we will scale it up to include submission of o
    21 KB (3,194 words) - 02:08, 17 May 2018
  • Gene Ontology
    ===WormBase Uploads=== ...produced weekly to the WormBase .ace file for upload: [[UniProtKB gpad to WormBase .ace]]
    30 KB (3,904 words) - 18:45, 13 May 2020
  • WormBase-Caltech Weekly Calls November 2013
    * 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
  • RNAi
    ...directly resulting from the RNAi in question. Hopefully these issues will all be addressed below. == RNAi Data Model ==
    29 KB (4,152 words) - 20:29, 30 July 2019
  • COMMENTARY
    ...03). Finally, there are an increasing number of functional annotations for genes, provided both in free text and as Gene Ontology terms (Harris et al., 2004 ...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
  • ISB2014 Session4 Microbial Informatics
    link to all ISB2014 notes: Karen Yook/wormbase- Caltech/@wbperson712
    29 KB (4,082 words) - 19:15, 11 April 2014
  • Concise Descriptions
    http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?root=ensembl&view=log Before dumping the papers file, double-check the 'Find Dead Genes' list on the paper editor and make any necessary updates.
    47 KB (6,852 words) - 04:27, 8 December 2020
  • Working Group:Sequence Features
    ** See github ticket 2867 https://github.com/WormBase/website/issues/2867#issuecomment-48041365 ** add a sequence feature table in sequence widget to display all features related to the gene
    23 KB (3,248 words) - 12:58, 22 September 2014
  • Pictures
    ==Picture Data Model== ...ta from the literature and individual laboratories and display them in the WormBase gene expression page.
    120 KB (19,719 words) - 16:44, 20 October 2023
  • Expression Pattern
    Current model (WS280) ...CDS ?CDS XREF Expr_pattern // for coding genes
    104 KB (15,303 words) - 19:39, 11 May 2023
  • Searching WormBase for Information About C. elegans (Wiley)
    ...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 ...n of WormBase available in September, 2005 (WS147 release; BioPerl/Generic Model Organism Database software).
    103 KB (16,375 words) - 23:39, 30 November 2010
  • WS244 Models.wrm
    == Model changes for WS244 == * This cycle we see 5 model changes in 4 classes:
    235 KB (23,325 words) - 10:33, 3 July 2014
  • Molecule
    ...(from [http://www.nlm.nih.gov/cgi/mesh/2009/MB_cgi?mode=&index=24714&field=all&HM=&II=&PA=&form=&input= nlm.nih.gov] and [http://en.wikipedia.org/wiki/Sm ==Model==
    50 KB (6,966 words) - 19:15, 13 August 2020
  • FP curator comments for St.Louis and Sanger structure correction data type
    [[http://www.wormbase.org/wiki/index.php?title=How_to_FirstPass&action=submit back]] | 4381||Sequence correction K08A8.1 St. Louis, see fig.2; Wormbase shows eight exons, paper shows five. ||48:45.7
    40 KB (4,083 words) - 23:02, 13 August 2010
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