User contributions
From WormBaseWiki
Jump to navigationJump to search- 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...