User contributions
From WormBaseWiki
Jump to navigationJump to search- 15:56, 24 September 2007 diff hist 0 CSHL documentation →Development
- 15:55, 24 September 2007 diff hist +884 N Developer notes New page: == File paths == It's important to be consistent with where we place things on the filesystem since it makes it easier to find things, and easier to handle proxy redirects. Here are some ...
- 15:55, 24 September 2007 diff hist 0 CSHL documentation →Development
- 15:54, 24 September 2007 diff hist +3,039 N Formal development strategy New page: == Development Strategy == ==== 1. Step 1: Developing new features and databases ==== New features and databases should be developed on the WormBase development machine brie3 or a privat...
- 15:54, 24 September 2007 diff hist +87 CSHL documentation →Reimplementation
- 15:52, 24 September 2007 diff hist +166 CSHL documentation →Hardware platform
- 15:49, 24 September 2007 diff hist +1,319 N Optimizing site performance New page: Optimizing performance of WormBase 1. Here is a good guide from S. Beckman: [http://perl.apache.org/docs/1.0/guide/performance.html#Measuring_the_Memory_of_the_Process [1]] 2. Turn off K...
- 15:49, 24 September 2007 diff hist +253 CSHL documentation →Hardware platform
- 15:45, 24 September 2007 diff hist +11,966 N WormBase Infrastructure New page: == The WormBase Infrastructure == This document describes the WormBase infrastructure including hardware and software configuration. === Document conventions === Commands that require s...
- 15:45, 24 September 2007 diff hist +2,255 N Cronjobs New page: == Restart the blat server == Root privileges: yes<br /> Runs on: all nodes 0 4 * * * /usr/local/wormbase/util/admin/restart_blat.pl Checks whether the blat servers (gfServer) for C. e...
- 15:44, 24 September 2007 diff hist +139 N Balloon Tooltips New page: Please see the [http://www.gmod.org/wiki/index.php/Popup_Balloons GMOD Wiki] for full documentation of the popup balloons used in WormBase.
- 15:41, 24 September 2007 diff hist +3,350 N WormBook New page: http://www.wormbase.org/wiki/images/WormBook_1.png Current status [18 Jun 2007] 144 chapters 31 movies 704 images 397 Mb zip download Please also visit the '''[http://en.wi... current
- 15:40, 24 September 2007 diff hist +7,283 N WormBase Newsletter No. 2, February 2003 New page: == WormBase User's Survey == In preparation for our annual Advisory Board Meeting, we are conducting an on-line survey. Please access it from the WormBase home page. Your opinion in setti...
- 15:40, 24 September 2007 diff hist +10,144 N WormBase Newsletter No. 3, October 2003 New page: == WormBase Version Freeze == In the spring, several bioinformaticians requested freezes for WormBase releases so that they could both work with and refer to a specific version of the C. ... current
- 15:39, 24 September 2007 diff hist +6,055 N WormBase Newsletter No. 4, February 2004 New page: == The C. briggsae genome in WormBase == The C. briggsae draft genome (Stein et.al, PloS Biology, 2003) has been fully incorporated into WormBase. The C. briggsae genome can be viewed by ... current
- 15:39, 24 September 2007 diff hist +3,304 N WormBase Newsletter No. 5, May 2004 New page: == Using WormBase for bioinformatics == Version freezes: We would like to remind our users that WormBase offers version freezes. Every tenth release is available, so that bioinformatician... current
- 15:38, 24 September 2007 diff hist +4,102 N WormBase Newsletter No. 6, August 2004 New page: == The C. elegans genome is complete! == The WS126 release of WormBase last month featured a complete genome with no gaps remaining in the genome sequence. == WormBase launches the 'Worm... current
- 15:38, 24 September 2007 diff hist +2,604 N Talk:Former How To Build A WormBase Mirror New page: === Some things to maybe add but most probably are installed anyways: === * AceDB: You will need gdk/gtk+ maybe gtk2, X-Windows libraries/headers and readline to compile. * GTop: depends ...
- 15:37, 24 September 2007 diff hist +236 N Talk:Main Page New page: == Worm Community Forum == A Forum for announcements, informal information dissemination, and discussion for the Worm Community has been set up. Please use the [http://www.wormbase.org/fo... current
- 15:36, 24 September 2007 diff hist -10 Sanger documentation
- 15:35, 24 September 2007 diff hist +456 N Sanger documentation New page: The following information pertains to data that is made available by the WormBase Group from The Wellcome Sanger Institute. ---- ---- * Links. Here we all are! [http://www.sanger.ac.uk...
- 15:34, 24 September 2007 diff hist +971 N Reporting sequence for RNAi New page: In order to properly display the information gained from an RNAi experiment on the WormBase website, the curators need to be able to figure out the exact sequence used for interference by ...
- 15:34, 24 September 2007 diff hist +496 N RNAi curation New page: When an RNAi experiment is curated by WormBase, the experimental details are attached to the sequence of the interfering RNA, not directly to the gene name; therefore stating “we did...
- 15:32, 24 September 2007 diff hist +2,217 N UserGuide:Autocompletion New page: = Wormbase Suggest (AKA autocompletion) = As you type text into the query field on the wormbase home page, Wormbase Suggest does a fast, context-sensitive, asynchronous search on a simpli...
- 15:31, 24 September 2007 diff hist +1,047 N AceDB class-Interaction New page: '''Description:''' [description of class] <br /> This class holds 3 types of interaction data: 1) ''Genetic Interaction'' [description of type, source, dataset, specific storage charac...
- 15:31, 24 September 2007 diff hist +229 N AceDB class-Y2H New page: '''Description:''' [description of class] [description of data set] <br /> '''For each object within the class:''' - A bait and target are specified. [description of how fields are pop...
- 15:31, 24 September 2007 diff hist +24 AceDB classes
- 15:30, 24 September 2007 diff hist +16 AceDB classes
- 15:28, 24 September 2007 diff hist +678 N Nomenclature New page: [http://www.wormbase.org/wiki/index.php/UserGuide:Nomenclature|Genetic Nomenclature Guidelines for ''C. elegans'']] [http://www.wormbase.org/wiki/index.php/UserGuide:Nomenclature_nematode...
- 15:27, 24 September 2007 diff hist +1,072 N NGASP submit New page: == Submitting nGASP gene prediction files == Gene predictions must be submitted by anonymous ftp to ftp.wormbase.org (change directory to ''pub/wormbase/nGASP/incoming'') Pleas...
- 15:24, 24 September 2007 diff hist +6,708 N Suggested pre-release data checks New page: This page is for people to add checks that should be done to confirm data is correct prior to public release of the database from Sanger. Ideally, you should give a description, an acedb q...
- 15:23, 24 September 2007 diff hist +1 WormBaseWiki:About
- 15:22, 24 September 2007 diff hist +976 N WormBaseWiki:About New page: The WormBaseWiki is maintained by the WormBase Consortium and is hosted at the [http://www.cshl.edu Cold Spring Harbor Laboratory] in Cold Spring Harbor, NY, USA. ...
- 15:21, 24 September 2007 diff hist +1,003 N CVS Access To WormBase New page: == Browsing The CVS Server == You may browse the repository at http://brebiou.cshl.edu/viewcvs/wormbase-site. == Anonymous CVS Server == The WormBase source code is freely available via...
- 15:19, 24 September 2007 diff hist +1,166 N Strains New page: The ''Caenorhabditis'' Genetics Center (CGC) is supported by the National Institutes of Health - National Center for Research Resources. The CGC has been in operation since 1978, first at ...
- 15:18, 24 September 2007 diff hist +675 N Help desk schedule New page: The Help Desk officer is in charge of ensuring that emails to wormbase-help are responded to in a timely manner, preparing the agenda for the conference call, and acting as moderator durin...
- 15:15, 24 September 2007 diff hist +225 N Project-wide documentation New page: This page contains documentation applicable to all WormBase sites. * Conference call schedule * Help desk schedule * Wiki ** [[Wiki_objectives_and_usage_guideli...
- 15:14, 24 September 2007 diff hist +136 N User:Tharris New page: Todd Harris (harris@cshl.edu) http://www.wormbase.org/wiki/images/2003-aug-09.jpg Project Manager and Lead Developer, WormBase Website
- 15:12, 24 September 2007 diff hist +4,434 N UserGuide:Cell Search New page: == Cell Search == One of the much-cited advantages of C. elegans is that its cellular lineage and neuronal wiring are exactly known. WormBase provides several ways to search for specific ...
- 15:10, 24 September 2007 diff hist +1,102 N UserGuide:Expression profile Search New page: == Expr_profile Search == Expression Profile is a type of gene clustering analysis based on many sets of independent and sometimes unrelated microarray data (Kim et al. Science, 293: 2087...
- 15:09, 24 September 2007 diff hist +1,775 N UserGuide:Expression Search New page: == Expression Pattern Search == Given a cell, a Cell Group, or a Life Stage, you may wonder what kind of genes are expressed there. WormBase Expression Pattern Search provides you the too...
- 15:08, 24 September 2007 diff hist +1,563 N UserGuide:Advanced Search New page: This menu includes three kinds of search tools for advanced users to browse in WormBase for more specific results. CLASS BROWSER The top search panel is the Class Browser. It looks simil...
- 15:06, 24 September 2007 diff hist +19,516 N UserGuide:Definitions for Life Stages New page: == Definitions for Life Stages in WormBase == term: all stages goid: LS:0000002 definition: All C. elegans development stages, including embryo, larva and adult stage. definition_referenc...
- 15:05, 24 September 2007 diff hist +2,068 N UserGuide:Embryonic Stage/Time Correlation Table 2 New page: == Embryonic Stage/Time Correlation Table 2 == Standard Temperature: 20 degree C proliferating embryo (=early) 0-350min Until cleavage is over elongating embryo (=mid) 350-620min D...
- 15:04, 24 September 2007 diff hist +1,714 N UserGuide:Embryonic Cell/Time Correlation Table 1 New page: == Embryonic Cell/Time Correlation Table 1 == Standard Temperature: 20 degree C Embryonic Life_stage, Cell number, Time and Morphology correlation table (At 20 degree) Cell Number Tim...
- 15:00, 24 September 2007 diff hist +5,563 N UserGuide:Full Text Journals New page: Locate Full Text of articles on line Journals with PDF Online Journal URL PDF since (Year) PDF since (Vol/Issu) Annual Review of Genetics http://genet.AnnualReviews.org 1996 Vol.30 Arch...
- 14:59, 24 September 2007 diff hist -2 WormBase Newsletters current
- 14:58, 24 September 2007 diff hist 0 WormBase Newsletters
- 14:57, 24 September 2007 diff hist -24 WormBase Newsletters
- 14:55, 24 September 2007 diff hist +1,753 N WormBase Newsletters New page: == About the WormBase newsletter == The WormBase newsletter is published four times a year and distributed to members of the wormbase-announce mailing list. If you would like to automatic...
- 14:52, 24 September 2007 diff hist +990 User:Mh6
- 14:51, 24 September 2007 diff hist +1,925 N Presentations New page: === 25 June - 1 July 2007, 16th International C. elegans Meeting, UCLA === === 1-3 Nov 2005, Scientific Advisory Board Meeting, CSHL === '''<font color="black">Presentations</font>''' fr...
- 14:48, 24 September 2007 diff hist +8 Publications
- 14:46, 24 September 2007 diff hist +3,924 N Publications New page: '''This page lists papers and book chapters describing WormBase.''' '''WormBase: new content and better access'''<br /> Tamberlyn Bieri, Igor Antoshechkin, Carol Bastiani, Darin Blasiar, ...
- 14:42, 24 September 2007 diff hist +1 Experimental protocols
- 14:40, 24 September 2007 diff hist +1,033 N Experimental protocols New page: These are community-contributed protocols. (That means you!!) Please click on these links to start new WIKI pages and type in your protocols. We will organize them as needed. # [[Genetics...
- 14:36, 24 September 2007 diff hist +166 CSHL documentation
- 14:34, 24 September 2007 diff hist +3,192 N CSHL documentation New page: The WormBase Cold Spring Harbor team is in charge of developing, maintaining, and hosting WormBase. This page contains links to documentation relating to those topics. == Development == ...
- 14:29, 24 September 2007 diff hist +9,083 N GFF3 features (C. elegans) New page: This article describes features included in the C. elegans GFF3 files. For introduction information on the GFF3 files, please see GFF3 features article. The WormBase ''C...
- 14:26, 24 September 2007 diff hist +2,880 N GFF3 features (C. briggsae) New page: This article describes features included in the ''C. briggsae'' GFF3 files. For introduction information on the GFF3 files, please see [[GFF3_features GFF3 features] article. The WormBase...
- 14:23, 24 September 2007 diff hist +5,037 N Downloads New page: WormBase maintains a public FTP site where you can find many commonly requested files and datasets, the WormBase software and prepackaged databases: '''ftp://ftp.wormbase.org/pub/wormbase...
- 14:21, 24 September 2007 diff hist 0 Tools
- 14:20, 24 September 2007 diff hist +1 Tools
- 14:20, 24 September 2007 diff hist +982 N Tools New page: [http://elbrus.caltech.edu/cgi-bin/igor/motif_search/motif_search.cgi Motif Search] Search for DNA or protein motifs in ''C. elegans'' genome. [http://elbrus.caltech.edu/cgi-bin/igor/coex...
- 14:19, 24 September 2007 diff hist +2,248 N UserGuide:Gene Ontology New page: == Gene Ontology Search == Gene Ontology (GO) is a controlled vocabulary aimed at capturing three different aspects of a gene product in a living organism: its biological process or proce...
- 14:16, 24 September 2007 diff hist +3,264 N UserGuide:Gene Ontology Page New page: == Gene Ontology Page == The Gene Ontology (GO) project (www.geneontology.org) has a central goal of building a controlled vocabulary that captures three different aspects of a gene produ...
- 14:15, 24 September 2007 diff hist +3,174 N UserGuide:ePCR New page: == ePCR == The ePCR search page serves two functions: (1). Find coordinates in the genome that can theoretically produce a PCR product given a pair of primer sequences, and (2). Find the ...
- 14:14, 24 September 2007 diff hist +5 UserGuide:Display Tools
- 14:13, 24 September 2007 diff hist +1,548 N UserGuide:Display Tools New page: Various Displays of WormBase Data: Most result pages in WormBase contain a submenu below the main menu and WormBase logo. The submenu usually is for different kinds of display. There are ...
- 14:11, 24 September 2007 diff hist +6,652 N UserGuide:Gene Page New page: == Gene Summary Page == The Gene Summary page provides concise information on gene identification, genetic location, function, gene ontology, available alleles, cDNAs, protein similaritie...
- 14:09, 24 September 2007 diff hist +1 UserGuide:Genome Dumper
- 14:09, 24 September 2007 diff hist +2,440 N UserGuide:Genome Dumper New page: == Genome Dumper == WormBase provides large sets of genomic sequence data through its Genome Dumper. This can be useful for getting data sets like the complete set of 5' flanking regions ...
- 14:08, 24 September 2007 diff hist -12 UserGuide:How to Obtain Reagents
- 14:07, 24 September 2007 diff hist +2,922 N UserGuide:How to Obtain Reagents New page: * How do I request a strain? In the Strain page, there is tag called "Location", which means the location of the strain, usually, the location is at CGC, or a two-character name standing ...
- 14:06, 24 September 2007 diff hist +1,166 N UserGuide:Interval Search New page: Interval Search is a tool designed to retrieve all of the predicted genes and cosmids within a genetically defined region. This resource is extremely useful when a mutation has been mapped...
- 14:05, 24 September 2007 diff hist +4,952 N UserGuide:Life Stage System in WormBase New page: == Life Stages Used in WormBase == Version 1.03 05-24-02 This DAG file is created for Lifestage system used in WormBase. * $C. elegans Development DAG ; LS:0000001 o $a...
- 14:04, 24 September 2007 diff hist +1,439 N UserGuide:Microarray Page New page: Microarray Data: WormBase holds published microarray data performed using either Affymetrix chips or chips from the Stanford Microarray Database. These data can be accessed from the Gene ...
- 14:03, 24 September 2007 diff hist +3,858 N UserGuide:Neuron Search New page: This search page is (we hope) designed to be largely self-explanatory. There are some points about this page that may not be obvious, though: http://www.wormbase.org/wiki/images/I_neuron1...
- 12:06, 24 September 2007 diff hist +6,573 N UserGuide:Nomenclature nematode New page: = Genetic Nomenclature for Nematodes = == Curation and Supervision == An accepted system of gene nomenclature was established for the nematode ''Caenorhabditis elegans'' in the nineteen ...
- 11:47, 24 September 2007 diff hist +4,206 N UserGuide:Genetic Map New page: The Genetic Map is a very useful resource for forward genetic mapping. The WormBase Genetic Map inherited its look from ACeDB, however because of internet interface, many features have bee...
- 11:29, 24 September 2007 diff hist +25,318 N UserGuide:Nomenclature New page: = Genetic Nomenclature for ''Caenorhabditis elegans'' = Genetic nomenclature for ''Caenorhabditis elegans'' is supervised by [http://wormbase.org/ WormBase] in collaboration with the [htt...
- 11:24, 24 September 2007 diff hist +4,551 N UserGuide:RNAi Search New page: OVERVIEW: RNAi PHENOTYPE SEARCH The ability to inactivate C. elegans genes by RNAi has allowed mass screens for diverse phenotypes, induced by mass RNAi-knockout of most of the genes on a...
- 11:22, 24 September 2007 diff hist +3,072 N UserGuide:Sequence Page New page: A Sequence Report page provides those data for a given gene that are most pertinent to its genomic sequence rather than to its more general, classical biology. A schematic diagram is given...
- 11:20, 24 September 2007 diff hist +184 N UserGuide:Wormpep file descriptions New page: A description of the files contained in the wormpep data can be found on the [http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/current/wormpep.shtml Sanger Institute C.elegans site]
- 11:17, 24 September 2007 diff hist +762 N UserGuide:Person Page New page: SEARCH FOR PERSON INFO Wormbase stores information about people who work in the worm field. Users can access this from the Simple Search page by specifying the Object type "Person" and ty...
- 11:15, 24 September 2007 diff hist +1,250 N UserGuide:Marker/Strain Search New page: This page is designed to assist in the selection of SNPs and visible genetic markers for mapping experiments. The seach results will yield a list of loci and details on how to score the mu...
- 10:57, 24 September 2007 diff hist +1,697 N UserGuide:Batch Downloads New page: Batch information retrieval is very convenient for presentation of different types of data in the form of a table. There are two ways to do this. First, one can use a set of prefabricated ...
- 10:31, 24 September 2007 diff hist +115 N MediaWiki:Loginprompt New page: You must have cookies enabled to log in to {{SITENAME}}. <br> Not a member? Request an account. current
- 10:30, 24 September 2007 diff hist +2 MediaWiki:Nologinlink
- 10:28, 24 September 2007 diff hist -16 MediaWiki:Sidebar current
- 10:28, 24 September 2007 diff hist +4 MediaWiki:Sidebar
- 10:26, 24 September 2007 diff hist +12 MediaWiki:Sidebar
- 10:26, 24 September 2007 diff hist +47 MediaWiki:Sidebar
- 10:25, 24 September 2007 diff hist +1 MediaWiki:Gotaccount current
- 10:20, 24 September 2007 diff hist +68 N MediaWiki:Gotaccount New page: Create a new WormBaeWiki user account. Already have an account? $1.
- 10:19, 24 September 2007 diff hist 0 Request Account
- 10:18, 24 September 2007 diff hist +272 N Request Account New page: Due to ongoing problems with spam, write-access to the WormBase wiki is by request only. If you'd like to contribute to the Wiki, please email Todd Harris (harris@cshl.org). Please inclu...
- 10:16, 24 September 2007 diff hist +38 MediaWiki:Sidebar
- 10:11, 24 September 2007 diff hist +144 N MediaWiki:Sidebar New page: * navigation ** mainpage|mainpage ** User_Guide|User Guide ** FAQs|FAQs ** meetings|Meetings ** recentchanges-url|recentchanges ** helppage|help
- 09:53, 24 September 2007 diff hist -10 MediaWiki:Nologinlink
- 09:52, 24 September 2007 diff hist +28 N MediaWiki:Nologinlink New page: Create or request an account
- 03:30, 24 September 2007 diff hist -10 About the WormBase data model
- 03:30, 24 September 2007 diff hist +592 N About the WormBase data model New page: == Learning More about the '''<font color="black">Data</font>''' '''<font color="black">Model</font>''' == The '''<font color="black">data</font>''' '''<font color="black">model</font>'''...
- 03:28, 24 September 2007 diff hist +1,155 N Converting Coordinates between releases New page: = GFF coordinate conversion = A tool written in Perl for converting GFF files between the different releases of the C.elegans genome. The needed files are available [ftp://ftp.sanger.ac....
- 03:27, 24 September 2007 diff hist +5,809 N Linking To WormBase New page: It is easy to link to WormBase. You can link to HTML pages, text-only dumps, images, and XML pages. == Naming Conventions == All objects in WormBase have a '''name''' and a '''class'''. ...
- 03:25, 24 September 2007 diff hist +11,344 N Mining WormBase with Bio::DB::GFF New page: Mining WormBase with MySQL & PostgreSQL The BioPerl library provides a simple relational schema and database access layer for querying genomic features. This is the access method of c...
- 03:24, 24 September 2007 diff hist +676 N Mining AceDB/WormBase with AcePerl New page: WormBase can be queried from the command line using AcePerl. This allows you to write sophisticated Perl scripts to mine WormBase. For details, see the [http://stein.cshl.org/AcePerl/ AceP...
- 03:23, 24 September 2007 diff hist +1,304 N Data mining:WormMart:Example 1 new New page: === Example 1: List all synonyms for the following genes; bli-1, egl-43, lag-1 === * Start a new WormMart query: [http://dev.wormbase.org/biomart/martview [HERE]]. * Select the '''curren...
- 03:22, 24 September 2007 diff hist -2 Data mining:WormMart:Example 3 →Download the set of all RNAi experiments that resulted in an embryonic lethal (Emb) phenotype, and in which the target genes are classified as serine/threonine kinases.
- 03:21, 24 September 2007 diff hist -1 Data mining:WormMart:Example 3 →Download the set of all RNAi experiments that resulted in an embryonic lethal (Emb) phenotype, and in which the target genes are classified as serine/threonine kinases.
- 03:21, 24 September 2007 diff hist +1 Data mining:WormMart:Example 3 →Download the set of all RNAi experiments that resulted in an embryonic lethal (Emb) phenotype, and in which the target genes are classified as serine/threonine kinases.
- 03:20, 24 September 2007 diff hist +15,806 N Data mining:WormMart:Example 3 New page: === Download the set of all RNAi experiments that resulted in an embryonic lethal (Emb) phenotype, and in which the target genes are classified as serine/threonine kinases. === * Start a ...
- 03:19, 24 September 2007 diff hist +11,498 N Data mining:WormMart:Example 2 New page: === Example 2: From all genes in C.elegans that have an ortholog in C. briggsae, are located in chromosome III, have an observed larval lethal phenotype in an RNAi screen, and have annotat...
- 03:17, 24 September 2007 diff hist -4 Data mining:WormMart:Example 1 →Example 1: List all synonyms for the following genes; bli-1, egl-43, lag-1
- 03:16, 24 September 2007 diff hist +8,427 N Data mining:WormMart:Example 1 New page: === Example 1: List all synonyms for the following genes; bli-1, egl-43, lag-1 === * Start a new WormMart query: [http://www.wormbase.org/biomart/martview [HERE]]. * On the '''START''' p...
- 03:15, 24 September 2007 diff hist 0 Data mining:WormMart
- 03:15, 24 September 2007 diff hist +1,633 N Data mining:WormMart New page: == Introduction == WormMart (http://www.wormbase.org/BioMart/martview) provides easy and interactive access to data en masse. In particular, WormMart enables users to retrieve sequences a...
- 03:13, 24 September 2007 diff hist +805 N Data mining:AQL tutorial New page: AQL search [http://www.wormbase.org/db/searches/aql_query [1]] is strictly dependent on current database models: one must consult the models to construct a successful query. '''Documentat...
- 03:10, 24 September 2007 diff hist +5,299 N GFF2 features New page: This page describes genomic annotations found in WormBase's GFF2 genome feature tables. {| cellspacing="4" | ALLELE:. | 14814 |- | cDNA_match:BLAT_mRNA_BEST | 24512 |- | cDNA_match:BLAT_m...
- 03:09, 24 September 2007 diff hist +1,744 N AceDB classes tutorial New page: The following table lists common WormBase classes. {| border="1" |- class="datatitle" ! Object ! Name ! Class ! Notes |- class="databody" ! A Predicted Gene | A cosmid dot name, such as F...
- 03:01, 24 September 2007 diff hist +358 N SOPs New page: == Internal Documentation == This page provides an area to collect standard operating procedures for each of the WormBase centers. * [[Project-wide_documentation|Project-wide documentati...
- 02:52, 24 September 2007 diff hist +2 Main Page
- 02:51, 24 September 2007 diff hist +4,000 N Wiki objectives and usage guidelines New page: == About the WormBase Wiki == This document describes the objectives and usage guidelines of the WormBase Wiki. Wikis are community-driven, collaborative websites. Users may freely post ... current
- 02:50, 24 September 2007 diff hist +2 Main Page
- 02:45, 24 September 2007 diff hist +1,968 N AceDB classes New page: This is a list 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...
- 02:31, 24 September 2007 diff hist +1,169 N Data mining New page: == Data Model == # About the WormBase data model - ''how data is stored and structured at WormBase'' # AceDB classes - ''A comprehensiv...
- 02:28, 24 September 2007 diff hist +1,866 N RSS news feeds New page: == About RSS feeds at WormBase == WormBase news feeds (using the RSS format) provide a convenient mechanism for staying up-to-date with new datasets, features, and system status. Browsers...
- 02:26, 24 September 2007 diff hist +2,123 N Mailing lists New page: == Public Mailing Lists == WormBase maintains four public/semi-public mailing lists: '''wormbase-announce@wormbase.org''' Announcements of general interest to the community, including a...
- 02:25, 24 September 2007 diff hist +62,608 N Former How To Build A WormBase Mirror New page: = Hardware requirements = WormBase runs on a Unix or Linux system (with the caveat that Mac OS X is, essentially, a Unix system). A relatively fast system with generous memory is strongly...
- 02:19, 24 September 2007 diff hist +12,620 N Virtual Machines New page: = Overview = "Virtual Machines" (or VMX) are self-contained packages of everything you need to use WormBase locally. To keep downloads small, we've split virtual machines into two compone...
- 02:16, 24 September 2007 diff hist +1,796 N Local installation of WormBase New page: Imagine being able to run WormBase on your own local computer, unencumbered from server load at www.wormbase.org, network latency, or even the need for a network connection. Run BLAST sear...
- 02:05, 24 September 2007 diff hist +48 N Gene Prediction New page: This page has been moved. Please see: NGASP current
- 01:00, 24 September 2007 diff hist +40 Main Page →Community Resources
- 00:59, 24 September 2007 diff hist +3,761 N Job Openings New page: '''Please place job postings on the Worm Community Forum at ''' http://www.wormbase.org/forums/ Note: you need to register again at the Forum. ---- ''' Old submissions ''' ---- 11. ...
- 00:45, 24 September 2007 diff hist +1,721 N Citing WormBase New page: Please cite WormBase as follows: WormBase web site, http://www.wormbase.org, release WSXX, date XXX. Use the current WS release number and release date in your citation. This informatio...
- 00:40, 24 September 2007 diff hist +2 FAQs →TEMPLATE
- 00:39, 24 September 2007 diff hist +8,128 N FAQs New page: __NOTOC__ '''Contents:''' #top - 0-9 A B C D E F G H I J K L M N O [[...
- 00:31, 24 September 2007 diff hist +23 Main Page →Using WormBase
- 00:29, 24 September 2007 diff hist +56 Glossary of terms
- 00:28, 24 September 2007 diff hist +56 Glossary of terms
- 00:27, 24 September 2007 diff hist +13 Glossary of terms
- 00:25, 24 September 2007 diff hist -96 Glossary of terms
- 00:22, 24 September 2007 diff hist +8,107 N Glossary of terms New page: '''Contents:''' [#top Top] - [#0.E2.80.939 0–9] [#A A] [#B B] [#C C] [#D D] [#E E] [#F F] [#G G] [#H H] [#I I] [#J J] [#K K] [#L L] [#M M] [#N N] [#O O] [#P P] [#Q Q] [#R R] [#S S] [...
- 22:12, 23 September 2007 diff hist +7,619 N UserGuide:Blast Search New page: OVERVIEW: http://www.wormbase.org/wiki/images/I_blast1.jpg BLAST is a method for searching either protein or DNA databases with either a protein or a DNA query sequence. Positive matches ...
- 22:08, 23 September 2007 diff hist +5,791 N UserGuide:Browse Genome New page: Browse Genome OVERVIEW You have a sequence that you want to work on -- a predicted gene, a cDNA, an STS marker -- or a sequence about which you have some descriptive traits. You want to e...
- 22:04, 23 September 2007 diff hist +2,278 N UserGuide:Simple Search New page: A simple search allows users to search WormBase for keywords contained in the database objects. The search can be broad (Anything) or can be restricted by searching for: 1) a particular ob...
- 21:57, 23 September 2007 diff hist +81 UserGuide:Release Notes
- 21:54, 23 September 2007 diff hist +1,216 N UserGuide:Release Notes New page: How can users find out what is new in each WormBase release? Actually all the information is in the notes for each new WS release, which can be directly accessed from the WormBase homepage...
- 21:52, 23 September 2007 diff hist +2,835 N UserGuide:General Description New page: An Overview of The WormBase Homepage GENERAL DOCUMENTATION CAVEAT: ALWAYS UNDER CONSTRUCTION At this writing, Wormbase is very much a dynamic, ongoing project. A good consequence of...
- 21:50, 23 September 2007 diff hist -511 User Guide
- 21:44, 23 September 2007 diff hist +2,793 N User Guide New page: GENERAL DOCUMENTATION CAVEAT: ALWAYS UNDER CONSTRUCTION At this writing, Wormbase is very much a dynamic, ongoing project. A good consequence of this is that new features and options are...
- 21:41, 23 September 2007 diff hist -1,693 WormBaseComparativeGenomicsTools
- 21:40, 23 September 2007 diff hist +6,147 N WormBaseComparativeGenomicsTools New page: * [#Genomic_Alignments <span class="tocnumber">1</span> <span class="toctext">Genomic Alignments</span>] ** [#Methods <span class="tocnumber">1.1</span> <span class="toctext">Methods</span...
- 21:39, 23 September 2007 diff hist 0 Other nematodes
- 21:39, 23 September 2007 diff hist +1,470 N Other nematodes New page: * '''Wikionchus''', a wiki for the Diplogastrid ''Pristionchus pacificus''<nowiki>: </nowiki>[http://www.pristionchus.org/wikionchus/index.php/Main_Page [1]] * '''WormBook section - [http:...
- 21:36, 23 September 2007 diff hist +7,777 N WS179 New page: = Release Notes = <nowiki> New release of WormBase WS179, Wormpep179 and Wormrna179 Mon Jul 30 12:21:01 BST 2007 WS179 was built by [Paul] ========================================...
- 21:36, 23 September 2007 diff hist +6,834 N WS178 New page: == Release Notes == <nowiki> New release of WormBase WS178, Wormpep178 and Wormrna178 Wed Jul 4 12:56:45 BST 2007 WS178 was built by Gary Williams ===============================...
- 21:35, 23 September 2007 diff hist +8,846 N WS177 New page: == Release Notes == <nowiki> New release of WormBase WS177, Wormpep177 and Wormrna177 Fri Jun 15 15:39:40 BST 2007 WS177 was built by Michael Han =================================...
- 21:34, 23 September 2007 diff hist +1 WS176
- 21:34, 23 September 2007 diff hist -1 WS176
- 21:33, 23 September 2007 diff hist +1 WS176
- 21:33, 23 September 2007 diff hist +7,646 N WS176 New page: <nowiki> new release of WormBase WS176, Wormpep176 and Wormrna176 Mon May 21 11:58:06 BST 2007 WS176 was built by Mary Ann Tuli =====================================================...
- 21:32, 23 September 2007 diff hist +6,435 N WS175 New page: <nowiki> New release of WormBase WS175, Wormpep175 and Wormrna175 Fri May 4 16:29:43 BST 2007 WS175 was built by [Anthony] ========================================================...
- 21:31, 23 September 2007 diff hist +8,126 N WS174 New page: = Release Notes = <nowiki> WS174 was built by Gary Williams ====================================================================== This directory includes: i) database.WS174.*.ta...
- 21:31, 23 September 2007 diff hist +6,176 N WS173 New page: = Release Notes = <nowiki> New release of WormBase WS173, Wormpep173 and Wormrna173 Fri Mar 23 18:22:22 GMT 2007 WS173 was built by Michael Han ===================================...
- 21:30, 23 September 2007 diff hist +6,910 N WS172 New page: <nowiki>New release of WormBase WS172, Wormpep172 and Wormrna172 Fri Mar 2 16:35:57 GMT 2007 WS172 was built by Mary Ann, with a little help from her friends ======================...
- 21:30, 23 September 2007 diff hist +6,090 N WS171 New page: <nowiki>New release of WormBase WS171, Wormpep171 and Wormrna171 Thu Feb 8 15:28:27 GMT 2007 WS171 was built by Anthony ============================================================...
- 21:29, 23 September 2007 diff hist +7,694 N WS170 New page: = Release Notes = <nowiki> New release of WormBase WS170, Wormpep170 and Wormrna170 Fri Jan 19 09:31:14 GMT 2007 WS170 was built by Paul Davis ====================================...
- 21:28, 23 September 2007 diff hist +7,163 N WS180 New page: <nowiki> New release of WormBase WS180, Wormpep180 and Wormrna180 Fri Aug 17 13:41:37 BST 2007 WS180 was built by Anthony ==========================================================...
- 21:28, 23 September 2007 diff hist +8,579 N WS181 New page: <nowiki> New release of WormBase WS181, Wormpep181 and Wormrna181 Fri Sep 7 11:40:20 BST 2007 WS181 was built by Gary Williams ====================================================...
- 21:26, 23 September 2007 diff hist +5 Nematode resequencing and diversity →Solexa Resequencing of two Wild C. elegans Isolates
- 21:26, 23 September 2007 diff hist -993 Nematode resequencing and diversity
- 21:25, 23 September 2007 diff hist +5,609 N Nematode resequencing and diversity New page: This is a community page for registering information about future and pending nematode (re)sequencing projects. Please describe briefly the species, population or isolate you will be (re)s...
- 21:24, 23 September 2007 diff hist +78 BASIC PROTOCOL 10: MINING GENE DATA WITH WORMMART
- 21:23, 23 September 2007 diff hist +26 BASIC PROTOCOL 9: FINDING SEQUENCE SIMILARITIES WITH BLAST
- 21:23, 23 September 2007 diff hist +52 BASIC PROTOCOL 8: VIEWING THE C. BRIGGSAE GENOME AND ITS SYNTENY WITH C. ELEGANS
- 21:22, 23 September 2007 diff hist +104 BASIC PROTOCOL 7: USING THE GENOME BROWSER
- 21:21, 23 September 2007 diff hist +52 BASIC PROTOCOL 6: SEARCHING FOR GENE PRODUCTS WITH PARTICULAR SEQUENCE MOTIFS
- 21:20, 23 September 2007 diff hist +26 BASIC PROTOCOL 5: FINDING PROTEIN FEATURES
- 21:20, 23 September 2007 diff hist +26 BASIC PROTOCOL 4: EXAMINING A MOLECULAR SEQUENCE IN C. ELEGANS
- 21:19, 23 September 2007 diff hist +52 BASIC PROTOCOL 3: EXAMINING A GENE IN C. ELEGANS
- 21:19, 23 September 2007 diff hist +26 BASIC PROTOCOL 2: PERFORMING A DATABASE SEARCH
- 21:16, 23 September 2007 diff hist +26 BASIC PROTOCOL 1: NAVIGATING THE WormBase HOME PAGE
- 21:06, 23 September 2007 diff hist -8 BASIC PROTOCOL 1: NAVIGATING THE WormBase HOME PAGE
- 21:05, 23 September 2007 diff hist +8 BASIC PROTOCOL 1: NAVIGATING THE WormBase HOME PAGE
- 20:53, 23 September 2007 diff hist +3,312 N INTERNET RESOURCES New page: http://wormbase.org ''The main Web site for WormBase. It is meant to be slightly less bleeding-edge than the development site, but to be maximally stable.'' http://dev.wormbase.org ''Th...
- 20:52, 23 September 2007 diff hist +18,971 N FIGURE(S) New page: '''(http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png) The front Web page of WormBase, showing a general database search for''zyg-1'' and the Web Site Directory'''. This page giv...
- 20:51, 23 September 2007 diff hist -26 KEY REFERENCES
- 20:51, 23 September 2007 diff hist +1,329 N KEY REFERENCES New page: Brenner, 1974. See above. ''The beginning of modern C. elegans research, this article remains vividly readable and gives a clear introduction to the goals and tactics of worm genetics.'' ...
- 20:49, 23 September 2007 diff hist +31,128 N COMMENTARY New page: '''Background Information''' WormBase contains information about the genomic sequence of ''C. elegans'', its genes and their products, and its higher-level traits such as gene expression ...
- 20:47, 23 September 2007 diff hist +3,940 N ALTERNATE PROTOCOL 1: INSTALLING AND RUNNING WormBase LOCALLY New page: All of the protocols above assume that a user will work with one of the main WormBase servers, with his or her own computer operating merely as a client. However, for people who want to us...
- 20:45, 23 September 2007 diff hist +1,623 N BASIC PROTOCOL 12: EXAMINING THE GENOMIC CONTENT OF A CLASSICAL GENETIC INTERVAL New page: Within a defined physical or genetic interval, what gene markers and SNPs are available for mapping a newly identified mutation? WormBase provides a page specifically for this problem. Ne...
- 20:44, 23 September 2007 diff hist +4,343 N BASIC PROTOCOL 11: DOWNLOADING A BATCH OF SEQUENCES New page: In analyses of the ''C. elegans'' genome, it can be useful to have such things as the complete set of 5¢ flanking regions for all known or predicted genes in ''C. elegans''. One way Wor...
- 20:42, 23 September 2007 diff hist +3,307 N BASIC PROTOCOL 10: MINING GENE DATA WITH WORMMART New page: Web pages for a single Gene, Sequence, or Protein only allow relatively small amounts of data to be analyzed at a time; yet the rise of functional genomics has made it useful and necessary...
- 20:41, 23 September 2007 diff hist +2,499 N BASIC PROTOCOL 9: FINDING SEQUENCE SIMILARITIES WITH BLAST New page: 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, & 3.11''. '''''Necessary ...
- 20:40, 23 September 2007 diff hist +4,347 N BASIC PROTOCOL 8: VIEWING THE C. BRIGGSAE GENOME AND ITS SYNTENY WITH C. ELEGANS New page: At least six species in the ''Caenorhabditis'' genus have morphology and genetics close enough to ''C. elegans'' that they can be classed as its siblings (Cho et al., 2004; Kiontke et al.,...
- 20:39, 23 September 2007 diff hist 0 Searching WormBase for Information About C. elegans (Wiley) →UNIT 1.8 Searching WormBase for Information About Caenorhabditis elegans
- 20:37, 23 September 2007 diff hist +7,277 N BASIC PROTOCOL 7: USING THE GENOME BROWSER New page: All the sections of WormBase described so far consist mainly of written text. However, organisms have a text of their own, the genomic DNA sequence, within which important biological featu...
- 20:35, 23 September 2007 diff hist +1,702 N BASIC PROTOCOL 6: SEARCHING FOR GENE PRODUCTS WITH PARTICULAR SEQUENCE MOTIFS New page: One way to identify all ''C. elegans'' proteins sharing a given PFAM or InterPro motif is to check that motif's WormBase entry. One advantage of such searches is that hypertext links are g...
- 20:34, 23 September 2007 diff hist +3,030 N BASIC PROTOCOL 5: FINDING PROTEIN FEATURES New page: WormBase has, in addition to Gene and Sequence pages, Protein records that give the known or predicted details of a gene's protein product(s). '''''Necessary Resources''''' ''Hardware'' ...
- 20:32, 23 September 2007 diff hist +2,067 N BASIC PROTOCOL 4: EXAMINING A MOLECULAR SEQUENCE IN C. ELEGANS New page: WormBase has Sequence Pages as well as Gene Pages. Sequence Pages are focused on details of the nucleotide and predicted protein-coding sequences of genes. '''''Necessary Resources''''' ...
- 20:31, 23 September 2007 diff hist +5,440 N BASIC PROTOCOL 3: EXAMINING A GENE IN C. ELEGANS New page: '''''Necessary Resources''''' ''Hardware'' A standard computer with a reasonably fast connection to the Internet (cable modem, DSL, or Ethernet recommended) ''Software'' Web brows...
- 20:29, 23 September 2007 diff hist +3,324 N BASIC PROTOCOL 2: PERFORMING A DATABASE SEARCH New page: This protocol presents how to conduct a general search of WormBase '''''Necessary Resources''''' ''Hardware'' A standard computer with a reasonably fast connection to the Internet (...
- 20:26, 23 September 2007 diff hist +2,770 N BASIC PROTOCOL 1: NAVIGATING THE WormBase HOME PAGE New page: '''''Necessary Resources''''' ''Hardware'' A standard computer with a reasonably fast connection to the Internet (cable modem, DSL, or Ethernet recommended) ''Software'' Web br...
- 20:16, 23 September 2007 diff hist +2,391 N INTRODUCTION New page: WormBase is the major public biological database for the nematode ''Caenorhabditis elegans'' (Chen et al., 2005). It is meant to be useful to any biologist who wants to use ''C. elegans'',...
- 20:15, 23 September 2007 diff hist +1,859 N Searching WormBase for Information About C. elegans (Wiley) New page: == UNIT 1.8 Searching WormBase for Information About Caenorhabditis elegans == INTRODUCTION [[BASIC_PROTOCOL_1:_NAVIGATING_THE_WormBase_HOME_PAGE|BASIC PROTOCOL 1: NAVIGATING THE Wor...
- 20:10, 23 September 2007 diff hist +920 Release notes →Statistics by release
- 20:05, 23 September 2007 diff hist -200 Release notes →Statistics by release
- 19:57, 23 September 2007 diff hist -399 Release notes →Statistics by release
- 19:48, 23 September 2007 diff hist +25,548 Release notes
- 19:48, 23 September 2007 diff hist +1,077 N Release notes New page: == WormBase Release And Access Statistics == Access statistics are only available to WormBase curators and developers. == Statistics by year == {| cellpadding="10" ! colspan="7" | Inclu...
- 19:18, 23 September 2007 diff hist +2 NGASP Results →'''NGASP Gene prediction competition'''
- 19:17, 23 September 2007 diff hist +9,866 N NGASP Results New page: == '''NGASP Gene prediction competition''' == The nGASP project parallels recent computational prediction initiatives including CASP, GASP, and EGASP. Participation is open to all academi...
- 19:14, 23 September 2007 diff hist -2 NGASP →Data
- 19:13, 23 September 2007 diff hist -23 Gene finders
- 19:12, 23 September 2007 diff hist +5,826 N Gene finders New page: Here is a list of some gene-finders. This is only intended as a preliminary and incomplete list of gene-finders, and we hope very much that many other authors of gene-finders will particip...
- 19:09, 23 September 2007 diff hist +21,159 N ComparaTutorial New page: =Places= [ftp://ftp.sanger.ac.uk/pub2/wormbase/data/compara.tar.bz2 Compara tarball for WS163] (mysql dumps) [http://www.ensembl.org/info/software/compara/index.html Compara Page] (includ...
- 18:50, 23 September 2007 diff hist +2,959 N Discussion New page: Additional community feedback & discussion for the nGASP project: #Consider also evaluating pipeline on a small genomic region of ''C. briggsae''. Species-specific differences e.g. he...
- 18:43, 23 September 2007 diff hist +389 N Resources New page: Here are some details of resources created for the nGASP project, as well as who made them: *wiki: - Tristan *''C. elegans'' sample regions: FASTA format from WS160 - Avril *protein align...
- 18:41, 23 September 2007 diff hist -30 NGASP →nGASP rules
- 18:39, 23 September 2007 diff hist +2 Test and training regions →How the nGASP test and training regions were chosen
- 18:39, 23 September 2007 diff hist +2,104 N Test and training regions New page: =How the nGASP test and training regions were chosen= Here is information about how we chose the test and training regions for the nGASP project. These regions were chosen by dividing the...
- 18:36, 23 September 2007 diff hist +6,183 N WS160 New page: <pre> New release of WormBase WS160, Wormpep160 and Wormrna160 Thu Jun 15 16:29:46 BST 2006 WS160 was built by Ant and Michael ===========================================================...
- 18:34, 23 September 2007 diff hist +21,510 N NGASP New page: This is the website for '''nGASP''', the nematode genome annotation assessment project. It outlines the methodology and resources to be used for evaluating various gene predictors on the ...
- 17:33, 23 September 2007 diff hist +676 N Guidelines for Users on Submitting/Reporting Data to WormBase New page: ==Rationale== In an attempt to facilitate the deposition of information into WormBase, we have created this section on the WormBase Wiki. We want to make researchers aware of the informa...
- 17:30, 23 September 2007 diff hist +560 N WormBaseWiki:Copyrights New page: WormBase is copyright © 1999-2006 California Institute of Technology, Cold Spring Harbor Laboratory, Washington University at St. Louis, and The Wellcome Trust Sanger Institute. Permissio...
- 17:28, 23 September 2007 diff hist +1,777 N Acceptable use policy New page: Drafted: 08 January 2005 ==Data access policy== As a web-based resource, WormBase (http://www.wormbase.org) is designed for users interacting with the resource on a page-by-page basis. U...
- 17:25, 23 September 2007 diff hist +1,078 N About elegans New page: ==Laboratory, Strain, and Allele Designations== The Caenorhabditis Elegans Centre (CGC) at http://www.cbs.umn.edu/CGC/CGChomepage.htm assigns specific identifying designations to each lab...
- 17:15, 23 September 2007 diff hist +7 Main Page
- 17:14, 23 September 2007 diff hist +1,946 Main Page restored the main page. Ugh, this is not going to be fun at all. Not one bit.