User contributions
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Jump to navigationJump to search- 22:50, 6 October 2007 diff hist +2 How to build a frozen release →Configuring VMXs as hosted frozen releases
- 20:31, 4 October 2007 diff hist +149 How to build a WormBase Virtual Machine →Building virtual disks for a new release
- 20:29, 4 October 2007 diff hist -443 How to build a WormBase Virtual Machine
- 20:24, 4 October 2007 diff hist -139 How to build a WormBase Virtual Machine
- 20:17, 4 October 2007 diff hist -369 How to build a WormBase Virtual Machine →Updating the software after distribution
- 19:34, 4 October 2007 diff hist +248 WormBase Infrastructure →Frozen release servers
- 14:12, 4 October 2007 diff hist +205 Mailing lists →Public Mailing Lists
- 14:10, 4 October 2007 diff hist 0 Virtual Machines
- 14:10, 4 October 2007 diff hist +6 Virtual Machines →Mailing List
- 14:09, 4 October 2007 diff hist +687 Virtual Machines
- 13:57, 4 October 2007 diff hist -1,561 Virtual Machines
- 11:50, 4 October 2007 diff hist +551 Managing Perl libraries across nodes
- 20:04, 3 October 2007 diff hist -1,527 How to build a frozen release
- 20:03, 3 October 2007 diff hist -1,800 How to build a WormBase Virtual Machine →Configuring VMXs as hosted frozen releases
- 20:00, 3 October 2007 diff hist -1,232 How to build a WormBase Virtual Machine
- 19:46, 3 October 2007 diff hist +602 How to build a WormBase Virtual Machine
- 19:25, 3 October 2007 diff hist +245 How to build a WormBase Virtual Machine →Building virtual disks for a new release
- 19:19, 3 October 2007 diff hist -25 How to build a WormBase Virtual Machine →Directory structure of the Virtual Machines
- 18:39, 3 October 2007 diff hist -112 Former How To Build A WormBase Mirror →Installing Perl modules
- 18:06, 3 October 2007 diff hist +294 How to build a WormBase Virtual Machine
- 18:04, 3 October 2007 diff hist -486 How to build a WormBase Virtual Machine →About the WormBase core virtual machines
- 18:03, 3 October 2007 diff hist -6 How to build a WormBase Virtual Machine →Base Virtual Machines
- 17:37, 3 October 2007 diff hist +107 CSHL documentation →Software platform
- 17:36, 3 October 2007 diff hist +349 How to build a WormBase Virtual Machine →Building virtual disks for a new release
- 16:55, 3 October 2007 diff hist +98 How to build a WormBase Virtual Machine →Directory structure of the Virtual Machines
- 16:49, 3 October 2007 diff hist +626 How to build a WormBase Virtual Machine
- 16:43, 3 October 2007 diff hist +29 How to build a WormBase Virtual Machine →Updating the software
- 16:42, 3 October 2007 diff hist +557 How to build a WormBase Virtual Machine →Virtual Machine exceptions
- 16:33, 3 October 2007 diff hist +70 How to build a WormBase Virtual Machine →Overview
- 15:26, 3 October 2007 diff hist -35 CSHL documentation →Reimplementation
- 15:26, 3 October 2007 diff hist +160 CSHL documentation →Software platform
- 15:24, 3 October 2007 diff hist -172 CSHL documentation →Administration
- 15:21, 3 October 2007 diff hist +1 CSHL documentation →Administration
- 15:20, 3 October 2007 diff hist +23 Base node configuration - CentOS5
- 15:18, 3 October 2007 diff hist +1,477 N Base node configuration - CentOS5 New page: Configuring a fresh install of Cent OS 5 for WormBase Install and configure Apache2, mod_perl,and php5 > yum install httpd httpd-devel > yum install mod_perl > yum install php php-gd php-...
- 15:15, 3 October 2007 diff hist -13 CSHL documentation
- 15:14, 3 October 2007 diff hist -2 CSHL documentation →Hardware platform
- 15:14, 3 October 2007 diff hist +58 CSHL documentation →Hardware platform
- 15:13, 3 October 2007 diff hist +303 Website:Monitoring services →What WormBase monitors
- 15:11, 3 October 2007 diff hist +73 Website:Monitoring services
- 15:09, 3 October 2007 diff hist +68 Website:Monitoring services →Configuring monit
- 15:08, 3 October 2007 diff hist +708 Website:Monitoring services
- 15:01, 3 October 2007 diff hist +782 N Website:Monitoring services New page: = Overview = Load-balancing and automatic failover mechanisms are essential components of a high-availability system. Equally important is efficient detection of failing services and ser...
- 14:48, 3 October 2007 diff hist 0 CSHL documentation →Administration
- 14:48, 3 October 2007 diff hist -12 CSHL documentation →Administration
- 14:46, 3 October 2007 diff hist +4 CSHL documentation →Monitoring
- 14:45, 3 October 2007 diff hist +33 CSHL documentation →Monitoring
- 12:01, 3 October 2007 diff hist +124 How to build a WormBase Virtual Machine →About the WormBase core virtual machines
- 20:48, 2 October 2007 diff hist +69 Managing Perl libraries across nodes
- 20:05, 2 October 2007 diff hist -19 Managing Perl libraries across nodes →Initial module list
- 20:04, 2 October 2007 diff hist -1,261 Former How To Build A WormBase Mirror →Installing Apache and mod_perl
- 19:41, 2 October 2007 diff hist -110 Managing Perl libraries across nodes →Configure CPAN
- 19:36, 2 October 2007 diff hist +166 Managing Perl libraries across nodes →Configure CPAN
- 19:27, 2 October 2007 diff hist -249 Managing Perl libraries across nodes →Preparing Nodes
- 19:24, 2 October 2007 diff hist +1,048 How to build a WormBase Virtual Machine
- 19:15, 2 October 2007 diff hist -41 Managing Perl libraries across nodes →Install AcePerl
- 19:14, 2 October 2007 diff hist -1 Managing Perl libraries across nodes →Intiial module list
- 19:14, 2 October 2007 diff hist -415 Managing Perl libraries across nodes →Rebuild Apache and mod_perl
- 19:13, 2 October 2007 diff hist +42 Managing Perl libraries across nodes →Adjust @INC
- 19:11, 2 October 2007 diff hist -827 Managing Perl libraries across nodes
- 19:08, 2 October 2007 diff hist +50 Managing Perl libraries across nodes →Configure CPAN
- 18:23, 2 October 2007 diff hist +84 How to build a WormBase Virtual Machine →Overview
- 18:08, 2 October 2007 diff hist +1,534 How to build a WormBase Virtual Machine
- 18:02, 2 October 2007 diff hist -174 Former How To Build A WormBase Mirror →User and group accounts
- 18:44, 1 October 2007 diff hist -15,946 FAQs
- 18:44, 1 October 2007 diff hist +63,782 FAQs
- 09:30, 25 September 2007 diff hist -14 MediaWiki:Nologinlink current
- 09:30, 25 September 2007 diff hist +36 MediaWiki:Nologinlink
- 17:32, 24 September 2007 diff hist +97 N 2002 - West Coast Worm Meeting New page: August 10-13, 2002 UCSD, San Diego, California, USA http://www.biology.ucsd.edu/west_C_elegans/
- 17:31, 24 September 2007 diff hist +150 N 2002 - The 3rd Japanese C. elegans Meeting New page: August 6-8, 2002 Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan Organizer: Shin Takagi http://www.cbi.or.jp/~sano/wormjp/jwm2002/index.html
- 17:31, 24 September 2007 diff hist +132 N 2002 - Midwest Worm Meeting New page: June 28-30, 2002 Washington University in St. Louis Organizer: Kerry Kornfeld http://molecool.wustl.edu/kornfeldlab/mwwm2002.html
- 17:30, 24 September 2007 diff hist +1 Meetings →Past meetings
- 17:30, 24 September 2007 diff hist 0 Meetings →Past meetings
- 17:30, 24 September 2007 diff hist +53 N 2002 - East Coast Worm Meeting New page: June 14-16, 2002 http://elegans.swmed.edu/ECWM/2002/
- 17:29, 24 September 2007 diff hist +190 N 2003 - 14th International Worm Meeting New page: June 29 - July 3, 2003 University of California at Los Angeles Organizers: Geraldine Seydoux, Stuart Kim, Alex van der Bliek http://genetics.faseb.org/genetics/Celegans/2003abs/index.ht...
- 17:28, 24 September 2007 diff hist +113 N 2004 - East Coast Worm Meeting New page: June 11-13, 2004 Yale University Co-chairs: Frank Slack and Valerie Reinke http://www.yale.edu/slack/ECWM.html
- 17:27, 24 September 2007 diff hist +290 N 2004 - European Worm Meeting New page: May 22-25, 2004 Casino Kursaal, Interlaken, Switzerland Head organizer: Fritz Müller Co-organizers: Paolo Bazzicalupo, Jean-Louis Bessereau, Anton Gartner, Pierre Gönczy, Gert ...
- 17:27, 24 September 2007 diff hist +198 N 2004 - Midwest Worm Meeting New page: June 11-13, 2004 University of Kansas, Lawrence Organizing Committee: Matthew Buechner, Mike Herman, Erik Lundquist, Lisa Timmons, Kathy Suprenant [http://people.ku.edu/~buechner Meetin...
- 17:26, 24 September 2007 diff hist +156 N 2004 - East Asia C. elegans Meeting New page: June 28 - July 1, 2004 Awaji Island, Japan Head Organizer: Hitoshi Sawa<br />Co-organizers: Asako Sugimoto, Junho Lee http://www.wormjp.umin.jp/EAWM.html
- 17:26, 24 September 2007 diff hist +224 N 2004 - West Coast Worm Meeting New page: August 21 - 24, 2004 University of California, Santa Barbara Organizer: Joel Rothman Program Committee: Morris Maduro, Dave Pilgrim, Bill Schafer [http://www.lifesci.ucsb.edu/mcdb/labs...
- 17:25, 24 September 2007 diff hist +186 N 2005 - 15th International Worm Meeting New page: June 25-29, 2005 University of California at Los Angeles Co-organizers: Monica Driscoll, Tim Schedl. Local organizer: Alex van der Bliek http://www.genetics-gsa.org/genetics/Celegans/
- 17:23, 24 September 2007 diff hist +320 N 2006 - GSA Model Organisms Meeting New page: The Genetics Society of America is having their first meeting focusing on model organisms: Genetic Analysis: Model Organisms to Human Biology, January 5-7, 2006. The Abstract deadline is N...
- 17:22, 24 September 2007 diff hist +552 N 2006 - European Worm Meeting New page: The European Worm Meeting will take place between the 29th of April and the 3rd of May 2006, at the town of Hersonissos on the island of Crete, Greece. The web site for the European Worm M...
- 17:12, 24 September 2007 diff hist +2,171 N 2006 - EMBO Caenorhabditis Evolution Workshop New page: EMBO WORKSHOP ON THE STUDY OF EVOLUTIONARY BIOLOGY WITH CAENORHABDITIS ELEGANS AND CLOSELY RELATED SPECIES 24-26 MAY 2006, INSTITUTO GULBENKIAN DE CIæNCIA, OEIRAS, PORTUGAL FIRST CALL ...
- 17:11, 24 September 2007 diff hist +2,244 N 2006 - Development and Evolution New page: == C. elegans Topic Meeting #1: Development & Evolution == We invite you to attend the 1st C.elegans Topic Meeting on Development and Evolution. The meeting will be held June 22 ‚Ä...
- 17:11, 24 September 2007 diff hist -35 Meetings →Past meetings
- 17:10, 24 September 2007 diff hist +186 N 2006 - Neuronal Development, Synaptic Function, and Behavior New page: Registration and information for the summer topic meeting #2 on "Neuronal Development, Synaptic Function, & Behavior" is [http://www.union.wisc.edu/CeNeuro/index.html now available].
- 17:09, 24 September 2007 diff hist +3,577 N Meetings New page: == Upcoming meetings == ''' From now on please post, or at least cross-post all new meeting announcements on the Worm Community Forum at ''' http://www.wormbase.org/forums/ Note: you ne...
- 16:47, 24 September 2007 diff hist +1,359 N Development notes WS163 New page: = Items to be announced = New GBrowse features # Pictar predictions # MiRanda predictions # TEC-RED tags = Development priorities = '''Molecular_change hash''' -- bumped to WS164 ([[Us...
- 16:46, 24 September 2007 diff hist +1,549 N Development notes WS164 New page: = Items to be announced = links to WormBook new phenotype ontology SNP tracks spli ncRNAz Compara Proteomics data = Development priorities = '''Proteomics datasets''' The proteomi...
- 16:46, 24 September 2007 diff hist +1,085 N Development notes WS165 New page: == Announcements == == Model Changes == ''Support for Cloned_by and the Laboratory_evidence tags has been added'' ([[User:Tharris Tharris] 10:40, 20 October 2006 (EDT)) http://cvsweb.sa...
- 16:46, 24 September 2007 diff hist +287 N Development notes WS166 New page: == To announce == == Model changes == Related_phenotypes . Dead . Alternate_phenotype  ?Phenotype for Carol to allow tracking of Phenotypes that have been merged or become obsolet...
- 16:46, 24 September 2007 diff hist +488 N Development notes WS167 New page: Slight change for Wen's addition of MovieURL to ?Expr_pattern ?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern ... Picture ?Picture XREF Expr_pattern ...
- 16:45, 24 September 2007 diff hist +335 N Development notes WS170 New page: == C. briggsae == Briggsae GFF database based on CB3 assembly (SM) Archiving legacy CB25 database == New Blast page == Public demo during WS170 life cycle (PC) == New database director...
- 16:45, 24 September 2007 diff hist +182 N Development notes WS171 New page: Select development tasks during WS171 Reconcile the update procedure. It's broken at several stages. Modularize? Test and move the new database filesystem structure into production
- 16:45, 24 September 2007 diff hist +819 N Development notes WS173 New page: == RESOLVED == From Mary Ann Tuli: 1) Here is advance notice that I added a new Database in WS173 Database : "NemaGENETAG_Consortium" Name "NemaGENETAG_Consortium" Description "Nema...
- 16:44, 24 September 2007 diff hist +75 CSHL documentation
- 16:35, 24 September 2007 diff hist +1,697 N Creating Virtual Disks New page: Data modules are self-contained packages of individual datasets. This are shipped as virtual disks for use with WormBase virtual machines. Users can mix-and-match data modules. And since ...
- 16:32, 24 September 2007 diff hist +87 CSHL documentation →Virtual Machines / Freezes
- 16:31, 24 September 2007 diff hist +1 Site statistics
- 16:31, 24 September 2007 diff hist +1,934 N Site statistics New page: == Web server access statistics == See the [[Release_notes|release notes page] for per-release, per year, and year-to-date access statistics. == Google == [https://www.google.com/webmas...
- 16:28, 24 September 2007 diff hist +1,982 N Configuring a server to host virtual machines New page: WormBase uses virtual machines to quickly and easily create frozen releases. This document describes how to set up a server to host these virtual machines. == Format the server == The a...
- 16:28, 24 September 2007 diff hist +3,551 N How to build a WormBase Virtual Machine New page: === Establishing the Virtual Machine === === Installing the OS === === Preparing the system for a WormBase installation === === Installing the WormBase core files === === Preparing a V...
- 16:09, 24 September 2007 diff hist +2,183 N Using CGI-Toggle New page: == NAME == CGI::Toggle -- Utility methods for collapsible sections == SYNOPSIS == use CGI ':standard'; use CGI::Toggle print header(), start_html('Toggle Test'), h1("Toggle Test"), tog...
- 16:08, 24 September 2007 diff hist +1 General administration →Author
- 16:07, 24 September 2007 diff hist +17,984 N General administration New page: == WormBase Administration == This document describes maintenance of the various hardware and software components of WormBase. This includes monitoring the health of the site, starting an...
- 16:06, 24 September 2007 diff hist +6,209 N Managing Perl libraries across nodes New page: Standardizing modules across nodes ---- In order to standardize modules across nodes (and avoid the headache of having to update each node separately with new libraries), I am now includ...
- 16:06, 24 September 2007 diff hist -73 CSHL documentation →General Admin
- 16:05, 24 September 2007 diff hist +2,149 N Managing servers hosting virtual machines New page: There are two options for managing servers hosting virtual machines, the VMWare Server console, and a web interface to the console. == The Console Application == The console application ...
- 16:05, 24 September 2007 diff hist +19 CSHL documentation →Virtual Machines / Freezes
- 16:04, 24 September 2007 diff hist +3,363 N How to build a frozen release New page: = Launch the base virtual machine = I've created base virtual machines for Fedora Core 4 and Fedora Core 5 that are pre-configured for a WormBase installation. This includes: * suitable ...
- 16:03, 24 September 2007 diff hist +2,101 N Creating a Google Sitemap New page: == Synopsis == To facilitate the indexing of WormBase content, a [https://www.google.com/webmasters/sitemaps/login Google Sitemap] file must be created. Google uses this file to index dyn...
- 16:02, 24 September 2007 diff hist +34,908 N Updating WormBase New page: == Document conventions == Commands that require super-user privileges are prefaced with "sudo" or a "$" prompt. If the system is configured correctly, you should not need to be a root us...
- 16:01, 24 September 2007 diff hist +90 N Coding standards New page: = File and Directory Names = = Code Formatting = == Indentation == == Variable names ==
- 16:00, 24 September 2007 diff hist +22 CSHL documentation →Software platform
- 15:59, 24 September 2007 diff hist -101 CSHL documentation →Development
- 15:58, 24 September 2007 diff hist +916 N Session management New page: == Session / User database == Session and user management uses a single database (wormbase_users). It is comprised of the following tables: The default sessions table (as defined by CGI:...
- 15:58, 24 September 2007 diff hist +33 N Using collapsible sections New page: = The Wormbase::Toggle Library =
- 15:57, 24 September 2007 diff hist +3,221 N Using private development sites New page: == Overview == Although we maintain a primary checked out version of the source on brie3, it's confusing and dangerous to have multiple people editing the same checked out source. Testing...
- 15:57, 24 September 2007 diff hist +4,714 N Javascript libraries New page: = Suggested Development Guidelines = If implementing a new DHTML feature, please try to make use of a library that is already in use at the site. If you add a new feature that relies on a...
- 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...