Search results
From WormBaseWiki
Jump to navigationJump to searchCreate the page "WormBase Model:View" on this wiki! See also the search results found.
- == 1. Model and View development (Norie, Adrian; 10 minutes) == ...orking on pictures, working on mapping, new file under Wormbase API called model map: Oligo, Sequence, Anatomy698 bytes (98 words) - 20:11, 23 March 2011
- [[WormBase Models]] == Model ==206 bytes (28 words) - 14:34, 4 October 2010
- [[WormBase Models]] == Model ==2 KB (208 words) - 14:36, 4 October 2010
- ...ist of the most prominent classes in use in the AceDB database employed by WormBase. To display the current model of any class, include the following text in your documentation:4 KB (568 words) - 11:06, 23 May 2011
- [[WormBase Models]] == Model ==1 KB (122 words) - 13:28, 4 October 2010
- Lets add a blank tool to WormBase, I shall call you "lineage" In <code>wormbase.conf</code>1 KB (203 words) - 18:46, 19 June 2014
- [[WormBase Models]] == Model ==2 KB (305 words) - 08:49, 5 October 2010
- A Backbone.js + jQuery Mobile app for accessing the Wormbase database through its RESTful API. wormbase-mobile5 KB (769 words) - 15:16, 19 June 2014
- '''NOTE: This document is likely out of date. Consult WormBase::Model.pm for the most up-to-date documentation.''' ...generically in the reimplementation. This maximizes code reuse and makes model and template writing easier and faster.2 KB (271 words) - 14:09, 19 June 2014
- '''Configuration Czar''' -- ''View and application configuration'' -- '''Norie''' '''WormBase::API Czar''' -- ''Oversee development of the external Model'' -- '''Norie'''2 KB (261 words) - 00:48, 24 December 2010
- WormBase staff can find this document in the "Documentation" directory and edit it t = About Groups at WormBase =5 KB (757 words) - 01:45, 2 June 2014
- ...menu includes three kinds of search tools for advanced users to browse in WormBase for more specific results. ...lasses in the Class Browser about the data structure of WormBase, such as "Model".2 KB (273 words) - 18:24, 17 August 2010
- 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, ...e.org/wiki/index.php/Image:Fig_1_8_01.png). This will lead to http://blast.wormbase.org/db/searches/blat. This is the method of choice for searching the ''C. e3 KB (401 words) - 20:02, 11 August 2010
- -rw-rw-rw- wormbase.conf ...(henceforth "the web application") and a series of external models in the WormBase::API namespace.10 KB (1,357 words) - 14:03, 19 June 2014
- AMIGO2 (Wormbase Ontology Browser) ...ken AMIGO2 infrastructure to make an ontology browser for integration into WormBase5 KB (850 words) - 15:32, 5 September 2013
- https://spreadsheets.google.com/a/wormbase.org/spreadsheet/ccc?key=0Aj0AS0c7xC1VdGZSQnlvdTBlbUpPRWJVYlE4Tk9WRlE&hl=en_ * Model development support for flat file queries (Norie)2 KB (310 words) - 00:50, 14 July 2011
- ...e jbrowse track selection with a plugin, between a simple vs detailed/full view--needs a proxy update to work fully. ** temporarily deployed at http://dev.wormbase.org:9004/, Kimberly shared with GO group for feedback2 KB (280 words) - 14:45, 12 April 2016
- :http://wiki.wormbase.org/index.php/Website:Profiling * Model development support for flat file queries (Norie)2 KB (340 words) - 18:03, 20 July 2011
- ...reviously only with a text description are getting updated to fit the data model ...should be pushed from #Interactor_info into Interactor tag of ?Interaction model4 KB (633 words) - 19:09, 6 January 2015
- ...le/archive here] for an archive of outdated/obsolete information about the WormBase gene association file. To view the (now deprecated) GAF 2.0 format specification, visit:12 KB (1,718 words) - 17:45, 5 February 2021
- * ?Construct model === ?Construct model ===8 KB (1,218 words) - 17:46, 2 April 2014
- This page contains information pertinent to employees of WormBase. ...VPuB__KmNs5tErO6VXDY/pub New Employee Orientation] -- ''Getting started at WormBase, for employees at any location. Read this first.''12 KB (1,638 words) - 18:25, 18 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
- :http://wiki.wormbase.org/index.php/Website:Profiling '''* COMPLETE Model development support for flat file queries (Norie)'''3 KB (440 words) - 20:32, 27 July 2011
- *We should be able to start configuring for WormBase at that point *Gary will propose appropriate model changes (e.g. Add "silencer" and "enhancer" to method for GBrowse display)7 KB (1,059 words) - 15:37, 1 August 2013
- ** Should have a guide for users [http://www.wormbase.org/about/Frequently_asked_questions#f--10 Here] * User needs WormBase official response.3 KB (423 words) - 16:35, 7 September 2017
- === Construct model/annotation === ...d to add "Construct" under list of "Detection methods" in the ?Interaction model4 KB (622 words) - 16:47, 6 August 2014
- * Who from WormBase will go? * Working out how inferred annotations propagate from Noctua/LEGO model to GAF9 KB (1,377 words) - 16:44, 2 February 2017
- model? It seems pretty redundant with the Paper information and I'm not to WormBase?"4 KB (599 words) - 00:25, 4 May 2012
- ...a of the model nematode ''Caenorhabditis elegans'' and related nematodes. WormBase is developed by an international consortium of researchers and computer sci *[[UserGuide:General_Description|Overview of WormBase]]4 KB (613 words) - 09:23, 30 June 2011
- Curators checked their model proposals in this file: ...k/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?revision=1.396&root=ensembl&view=markup pre-WS241]]6 KB (909 words) - 21:56, 21 November 2013
- *?Human_disease model vs tag in ?Gene model? *Similar discussion to ?Process model discussion5 KB (847 words) - 17:49, 1 March 2012
- * We will need to learn to model in Datomic to start building curation tools that run off of Datomic ...has access to Colonnade & trAceView (table maker tool and web interface to view Datomic data like in ACEDB)4 KB (571 words) - 16:48, 3 March 2016
- * Testing at juancarlos.wormbase.org (from there go to Tools > Ontology Browser) ** Add a Reactome display to WormBase?10 KB (1,474 words) - 15:54, 30 April 2014
- EPIC data into WormBase *Need to modify model and display for data7 KB (1,070 words) - 17:47, 1 March 2012
- <pre>New release of WormBase WS154, Wormpep154 and Wormrna154 Fri Feb 10 12:46:08 GMT 2006 http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE7 KB (749 words) - 11:08, 21 December 2011
- == 1. Model changes (Hinxton) == 1a) Variation model sign off7 KB (1,182 words) - 13:50, 20 April 2012
- New release of WormBase WS181, Wormpep181 and Wormrna181 Fri Sep 7 11:40:20 BST 2007 http://www.wormbase.org/wiki/index.php/Release_notes8 KB (885 words) - 16:47, 21 December 2011
- **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 WormBase29 KB (4,254 words) - 20:25, 27 April 2012
- ...eral discussion on DOI handling for micropublications and using the ?Paper model * Micropublications were displayed on ?Expr_pattern pages on WormBase/WormBook10 KB (1,475 words) - 16:57, 5 November 2015
- * We should remove underscores from "is_model_of" and translate to "is a model of" ...rmaster, working on developing the disease association file (DAF) from the WormBase build7 KB (1,073 words) - 16:26, 2 March 2017
- ...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
- **Groups will switch to using common data model that works for all and common ontology/ontologies in the near future. ** Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex5 KB (880 words) - 15:40, 3 September 2020
- **Performs similar to WormBase **Todd has made progress with getting Intermine for WormBase7 KB (1,158 words) - 17:20, 3 May 2012
- ***Integrated interaction model, genetic interaction ontology ***Need to update Gene expression model to accommodate Epic dataset (John Murray), 3D movies (Bill Mohler), and sin12 KB (1,878 words) - 15:55, 6 September 2012
- ...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
- ** model change to put topics in hierarchical structure. http://www.wormbase.org/tools/wormmine/template.do?name=Anatomy_LS_Genes&scope=all10 KB (1,485 words) - 18:08, 5 March 2014
- * Need to change "Tissue Enrichment Analysis" link title under WormBase Tools menu * There's a question about how we now handle model changes going forward7 KB (1,010 words) - 17:08, 4 May 2017
- === Model changes === ...leaf nodes with more granular information? Already available in unweighted view7 KB (1,062 words) - 14:41, 2 August 2018
- *WormBase - Bitbucket, GitHub (can commit code) *Is WormBase interested connecting to it?7 KB (1,117 words) - 16:39, 4 August 2011
- * 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 instead9 KB (1,377 words) - 16:36, 4 March 2021
- This page describes the development model used by the web development team at WormBase using git as our version control system. This includes our branching strate ...an in the main WormBase repository, or on a developer's fork. [http://wiki.wormbase.org/index.php/Development_workflow_-_webdev#Branch_stratgey Read more on ou9 KB (1,476 words) - 20:00, 11 August 2014
- * First draft up on WormBase development site === Expr_pattern model change ===8 KB (1,289 words) - 18:11, 10 November 2016
- *We should make an announcement on the main WormBase page that WormMart will remain at WS220 and Intermine will replace it *Mark Blaxter offered to donate his Brugia database into WormBase10 KB (1,553 words) - 18:04, 7 February 2013
- *Annotation matrix to view along with tree WormBase GO progress report9 KB (1,339 words) - 19:02, 31 January 2013
- *What would WormBase look like without any manually curated data? *Interaction model changed to update genetic interaction terms8 KB (1,225 words) - 16:33, 3 October 2013
- ...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. * Awaiting model approval to move ahead6 KB (906 words) - 21:38, 30 September 2015
- <http://www.wormbase.org/db/gene/gene?name=mpk-1;class=Gene><br> <http://www.wormbase.org/db/gene/gene?name=F43C1.1;class=Gene><br>14 KB (2,365 words) - 21:14, 23 July 2013
- ** 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 ** MP to create summary of gene model changes for each species11 KB (1,714 words) - 11:04, 27 July 2015
- ...hub.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
- 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
- ...just know what are problematic URLs; should all be handled by main URL www.wormbase.org === Disease model annotation class display ===11 KB (1,703 words) - 15:27, 5 April 2018
- * 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
- 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
- **process pages will dissect the chapters and link them to entities in WormBase, * Gene interaction networks (N-browse view?)20 KB (3,088 words) - 19:17, 13 August 2020
- ...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
- ...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
- Karen Yook/wormbase- Caltech/@wbperson712 ...compar- isons. To further reduce redundancy within UniProt, a gene-centric view of complete proteomes will be implemented. This will bring together canonic29 KB (4,082 words) - 19:15, 11 April 2014
- ...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
- ...orm IDs as an additional line in the gp2protein file; hopefully with a new model, they will be handled appropriately. ...'' - convert all UniProtKB IDs to WBGene IDs to allow for more streamlined view of C. elegans annotations in AmiGO and easier use of annotations in enrichm23 KB (3,744 words) - 15:12, 23 December 2022
- ==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
- ...u don't use it, is it in the emails you send out or in the submit forms in WormBase ? -- J answer Please keep form, must be the one linking to old papers asso http://www.wormbase.org/db/misc/person?name=WBPerson1823;class=Person119 KB (18,888 words) - 00:05, 2 May 2014
