User contributions
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Jump to navigationJump to search- 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.
