User contributions
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Jump to navigationJump to search- 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'' ...