User contributions
From WormBaseWiki
Jump to navigationJump to search- 22:16, 16 April 2009 diff hist -1 WormBase Source Code
- 22:15, 16 April 2009 diff hist +178 WormBase Source Code
- 22:14, 16 April 2009 diff hist +320 WormBase Source Code
- 21:51, 16 April 2009 diff hist -1 WormBase Source Code →Reference: Migrating to Mercurial
- 21:51, 16 April 2009 diff hist +798 N WormBase Source Code New page: The WormBase source code is maintained using the distributed SCM system Mercurial. We use BitBucket.org as a convenient place to host the code and track issues: http://bitbucket.org/tha...
- 21:42, 16 April 2009 diff hist +16 Developer documentation →Source Code and Project Management
- 21:35, 16 April 2009 diff hist -34 Developer documentation →Source Code and Project Management
- 21:33, 16 April 2009 diff hist +4 Developer documentation →Source Code and Project Management
- 21:32, 16 April 2009 diff hist +53 Developer documentation →Source Code and Project Management
- 21:31, 16 April 2009 diff hist -122 Developer documentation →Getting started
- 21:30, 16 April 2009 diff hist +85 Developer documentation →Source Code and Project Management
- 13:45, 13 February 2009 diff hist +261 Release Schedule →Release Schedule & History
- 01:44, 22 January 2009 diff hist +1 Release Schedule →Release Schedule & History
- 01:44, 22 January 2009 diff hist +96 Release Schedule →Release Schedule & History
- 15:52, 12 January 2009 diff hist +261 Software Life Cycle: 1. Updating The Development Server
- 15:42, 12 January 2009 diff hist +231 Software Life Cycle: 1. Updating The Development Server →Create ePCR databases for available species
- 15:23, 12 January 2009 diff hist -32 Software Life Cycle: 1. Updating The Development Server →Compile ontology resources for the site
- 15:15, 12 January 2009 diff hist +595 Software Life Cycle: 1. Updating The Development Server
- 15:12, 12 January 2009 diff hist +105 Software Life Cycle: 1. Updating The Development Server
- 15:08, 12 January 2009 diff hist +64 Software Life Cycle: 1. Updating The Development Server →Development Server
- 15:07, 12 January 2009 diff hist +98 Software Life Cycle: 1. Updating The Development Server →Mirror ontology from Sanger
- 15:05, 12 January 2009 diff hist +118 Software Life Cycle: 1. Updating The Development Server →Mirror and unpack ACeDB from Sanger
- 15:04, 12 January 2009 diff hist +64 Software Life Cycle: 1. Updating The Development Server →Create necessary directories
- 15:03, 12 January 2009 diff hist +48 Software Life Cycle: 1. Updating The Development Server →Mirror ontology from Sanger
- 15:03, 12 January 2009 diff hist -76 Software Life Cycle: 1. Updating The Development Server →Mirror and unpack ACeDB from Sanger
- 15:01, 12 January 2009 diff hist +23 Software Life Cycle: 1. Updating The Development Server →Purge Disk Space
- 14:56, 8 January 2009 diff hist +105 Software Life Cycle: 1. Updating The Development Server →Development Server
- 14:54, 8 January 2009 diff hist +209 Software Life Cycle: 1. Updating The Development Server →Load genomic GFF DBs for available species
- 20:26, 6 January 2009 diff hist +242 Software Life Cycle: 1. Updating The Development Server
- 19:38, 6 January 2009 diff hist +47 Software Life Cycle: 1. Updating The Development Server
- 19:36, 6 January 2009 diff hist -1 Software Life Cycle: 1. Updating The Development Server →= Create necessary directories
- 19:36, 6 January 2009 diff hist +607 Software Life Cycle: 1. Updating The Development Server
- 19:21, 6 January 2009 diff hist +47 Software Life Cycle: 1. Updating The Development Server
- 19:20, 6 January 2009 diff hist +2,063 Software Life Cycle: 1. Updating The Development Server
- 18:49, 6 January 2009 diff hist +1,058 N Software Life Cycle: 1. Updating The Development Server New page: This is a quick description of how to update the development server with a new release of the database. == Development Server == The current development server is brie3: brie3.cshl.o...
- 18:37, 6 January 2009 diff hist +136 Developer documentation
- 14:59, 17 December 2008 diff hist +141 Release Schedule
- 23:47, 9 December 2008 diff hist +347 N Administration:Installing WormBase New page: == Server == wormbase.res.oicr.on.ca The WormBase development server is at wormbase.res.oicr.on.ca. The machine is firewalled behind chickenwire. You will need to tunnel in order to co...
- 23:39, 9 December 2008 diff hist +150 Developer documentation
- 23:34, 9 December 2008 diff hist +26 Developer documentation
- 14:08, 17 November 2008 diff hist +38 Pristionchus pacificus
- 14:07, 17 November 2008 diff hist +67 Caenorhabditis remanei
- 14:07, 17 November 2008 diff hist +67 Caenorhabditis japonica
- 14:06, 17 November 2008 diff hist +67 Caenorhabditis briggsae
- 14:05, 17 November 2008 diff hist 0 Caenorhabditis brenneri
- 14:04, 17 November 2008 diff hist +67 Caenorhabditis brenneri
- 14:03, 17 November 2008 diff hist -19 Caenorhabditis elegans
- 14:03, 17 November 2008 diff hist +87 Caenorhabditis elegans
- 14:02, 17 November 2008 diff hist +243 N WormBase Identifiers New page: == Protein IDs == WP:.* -- ''Caenorhabditis elegans'' BP:.* -- ''Caenorhabditis briggae'' RP:.* -- ''Caenorhabditis remanei'' CN:.* -- ''Caenorhabditis brenneri'' JA:.* -- ''Caenorh... current
- 14:00, 17 November 2008 diff hist +78 Data mining
- 15:47, 6 November 2008 diff hist +245 Converting GFF2 to GFF3
- 18:50, 3 November 2008 diff hist +7 WormBase Infrastructure
- 13:42, 22 October 2008 diff hist +205 Release Schedule
- 17:41, 6 October 2008 diff hist +860 N Species available through WormBase (overview) New page: {| width="100%" cellspacing="1" cellpadding="1" border="1" |- | Species | Genome Browser | BLAST | BLAT | Gene Page | Sequence Page | Protein Page | Orthology |- |[[Brugia malayi|''Brugia ...
- 17:22, 6 October 2008 diff hist +14 Main Page
- 01:11, 24 September 2008 diff hist +5,204 Building WormMart
- 13:50, 21 September 2008 diff hist +87 Release Schedule
- 23:33, 17 September 2008 diff hist +7 Downloads
- 17:07, 8 September 2008 diff hist +1,150 Release notes
- 14:34, 16 August 2008 diff hist +89 Release Schedule
- 00:26, 19 July 2008 diff hist +92 Release Schedule
- 18:52, 10 July 2008 diff hist +936 N Trac installation notes New page: = Installing Email2Trac = Email2Trac is located at: https://subtrac.sara.nl/oss/email2trac/wiki/Email2tracInstallation Fetch the current source: cd /usr/local/wormbase/trac/src ft...
- 17:36, 10 July 2008 diff hist +290 Developer documentation
- 22:09, 27 June 2008 diff hist +81 N Caenorhabditis elegans New page: == About == == Phylogeny == == Assemblies == == Downloads == == References ==
- 22:08, 27 June 2008 diff hist -16 Main Page
- 22:07, 27 June 2008 diff hist +197 Main Page
- 22:03, 27 June 2008 diff hist +42 Main Page
- 22:01, 27 June 2008 diff hist -104 Downloads
- 17:51, 21 June 2008 diff hist -758 Release Schedule
- 17:49, 21 June 2008 diff hist +142 Release Schedule
- 17:01, 20 June 2008 diff hist +328 BLAST/BLAT Page
- 14:38, 20 June 2008 diff hist -109 WormBase Infrastructure
- 13:36, 11 June 2008 diff hist +230 Updating WormBase
- 13:06, 2 June 2008 diff hist +75 Main Page
- 13:05, 2 June 2008 diff hist +51 Main Page
- 13:03, 2 June 2008 diff hist -77 Main Page
- 13:02, 2 June 2008 diff hist +4 Related web resources
- 13:02, 2 June 2008 diff hist -11 Main Page
- 13:01, 2 June 2008 diff hist -192 Main Page
- 13:00, 2 June 2008 diff hist +89 Main Page
- 12:59, 2 June 2008 diff hist -21 Main Page
- 12:58, 2 June 2008 diff hist -421 About elegans
- 12:57, 2 June 2008 diff hist +46 Strains
- 12:56, 2 June 2008 diff hist -126 About elegans
- 12:56, 2 June 2008 diff hist +95 Main Page
- 12:44, 2 June 2008 diff hist +183 WormBaseWiki:Copyrights
- 21:43, 1 June 2008 diff hist +55 Main Page
- 21:42, 1 June 2008 diff hist +75 Software for nematode research
- 21:41, 1 June 2008 diff hist -109 Related web resources
- 21:38, 1 June 2008 diff hist +677 N Related web resources New page: ==Partner projects == *[ == Genome Sequencing Centers == *[http://www.sanger.ac.uk/Projects/C_elegans/ Wellcome Trust Sanger Institute C. elegans Site] *[http://genome.wustl.edu/genome....
- 21:35, 1 June 2008 diff hist +59 Main Page
- 21:29, 1 June 2008 diff hist +22 Mirror sites and frozen releases
- 21:29, 1 June 2008 diff hist -218 Mirror sites and frozen releases
- 21:27, 1 June 2008 diff hist +1,176 N Mirror sites and frozen releases New page: __TOC__ ===Main Site=== [http://www.wormbase.org/ www.wormbase.org] - ''Cold Spring Harbor Laboratory, NY USA'' ===Development server=== [http://dev.wormbase.org/ www.wormbase.org] - ''...
- 21:23, 1 June 2008 diff hist +50 Main Page
- 21:11, 1 June 2008 diff hist +3 Site Map
- 21:11, 1 June 2008 diff hist +6 Site Map
- 21:10, 1 June 2008 diff hist +15 Site Map
- 21:10, 1 June 2008 diff hist +1 Site Map
- 21:07, 1 June 2008 diff hist +2,475 N Site Map New page: ==Release Notes== *[http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/current/wormpep_changes.shtml New/Changed Genes] *[http://www.wormbase.org/wiki/index.php/Release_notes release note...
- 20:56, 1 June 2008 diff hist +14 m Main Page
- 19:10, 1 June 2008 diff hist +37 Software for nematode research
- 19:03, 1 June 2008 diff hist +506 N Software for nematode research New page: == Software Tools used by WormBase == *[http://stein.cshl.org/AcePerl/ AcePerl] *[http://www.gmod.org Generic Model Organism Database Project (GMOD)] *[http://www.bioperl.org BioPerl] ...
- 18:59, 1 June 2008 diff hist +36 Main Page
- 18:57, 1 June 2008 diff hist +761 N Key publications New page: *[http://www.wormbook.org WormBook] - ''Comprehensive online reference for C. elegans'' *[http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=ce2.TOC ''C. elegans'' II boo...
- 18:52, 1 June 2008 diff hist +22 Main Page
- 18:52, 1 June 2008 diff hist +87 Main Page
- 18:46, 1 June 2008 diff hist +1 Reagents
- 18:45, 1 June 2008 diff hist -39 Reagents
- 18:45, 1 June 2008 diff hist +55 Reagents
- 18:44, 1 June 2008 diff hist -83 Reagents
- 18:34, 1 June 2008 diff hist +1,922 N Reagents New page: Reagents for C. elegans research == Clones == * [http://www.its.caltech.edu/~wormbase/userguide/OtherResource/ObtainingReagents.html#elegans_genomic C. elegans genomic clones] * C. brigg...
- 18:31, 1 June 2008 diff hist -73 Main Page
- 18:29, 1 June 2008 diff hist +71 Main Page
- 15:50, 22 May 2008 diff hist 0 2008-SAB Meeting
- 15:28, 22 May 2008 diff hist -10 2008-SAB Meeting
- 15:25, 22 May 2008 diff hist -74 2008-SAB Meeting
- 15:24, 22 May 2008 diff hist 0 N File:12-2008-SAB-Rogers2.ppt current
- 15:23, 22 May 2008 diff hist 0 N File:9-2008-SAB-Williams.ppt current
- 15:22, 22 May 2008 diff hist 0 N File:10-2008-SAB-Davis.ppt current
- 15:17, 22 May 2008 diff hist 0 N File:2-2008-SAB-Harris.ppt current
- 15:07, 22 May 2008 diff hist +1 2008-SAB Meeting
- 15:07, 22 May 2008 diff hist -35 2008-SAB Meeting
- 15:06, 22 May 2008 diff hist 0 N File:11-2008-SAB-Blasiar.ppt current
- 14:33, 22 May 2008 diff hist +30 N 2008-SAB-Meeting Scientific 2008-SAB-Meeting Scientific moved to 2008-SAB Meeting: forked page name current
- 14:33, 22 May 2008 diff hist 0 m 2008-SAB Meeting 2008-SAB-Meeting Scientific moved to 2008-SAB Meeting: forked page name
- 13:38, 22 May 2008 diff hist +209 2008-SAB Meeting
- 13:30, 22 May 2008 diff hist 0 N File:6-2008-SAB-DeLaCruz.ppt current
- 13:28, 22 May 2008 diff hist +64 2008-SAB Meeting
- 13:15, 22 May 2008 diff hist 0 N File:5-2008-SAB-Han.ppt current
- 13:13, 22 May 2008 diff hist 0 N File:3-2008-SAB-McKay.ppt current
- 13:12, 22 May 2008 diff hist -30 2008-SAB Meeting
- 13:09, 22 May 2008 diff hist 0 N File:4-2008-SAB-Rogers.ppt current
- 13:09, 22 May 2008 diff hist +134 2008-SAB Meeting
- 13:05, 22 May 2008 diff hist +324 2008-SAB Meeting
- 11:06, 22 May 2008 diff hist +1,540 N 2008-SAB Meeting New page: __TOC__ =2008 Scientific Advisory Board Meeting= WormBase Advisory Board Meeting Wellcome Trust Sanger Institute 21-23 May 2008 ==Wednesday 21st May – Pre-meeting (WormBase staff only...
- 14:54, 21 May 2008 diff hist +180 N-Browse Installation & Interaction Data
- 20:38, 17 May 2008 diff hist +49 MySQL database replication
- 20:29, 17 May 2008 diff hist +1,788 MySQL database replication
- 19:16, 17 May 2008 diff hist +144 WormBase Infrastructure
- 19:06, 17 May 2008 diff hist +50 WormBase Infrastructure
- 19:04, 17 May 2008 diff hist +244 WormBase Infrastructure
- 19:00, 17 May 2008 diff hist +357 MySQL database replication
- 18:52, 17 May 2008 diff hist +136 MySQL database replication
- 18:50, 17 May 2008 diff hist +652 N MySQL database replication New page: = Description = We use mysql replication to mirror mysql databases from a single master mysqld server to a series of slave servers on back end nodes. This process is asynchronous and asym...
- 18:44, 17 May 2008 diff hist +1 Developer documentation
- 18:44, 17 May 2008 diff hist +228 Developer documentation
- 10:05, 3 May 2008 diff hist +46 Release Schedule
- 12:04, 22 April 2008 diff hist -81 Release Schedule
- 12:03, 22 April 2008 diff hist +1,127 Release Schedule
- 10:03, 18 April 2008 diff hist 0 N File:Iplant.png current
- 11:13, 16 April 2008 diff hist -63 Main Page
- 11:13, 16 April 2008 diff hist +640 Main Page
- 16:23, 8 April 2008 diff hist +41 Release Schedule →Release History
- 14:26, 23 March 2008 diff hist +88 Developer documentation →Getting started
- 14:10, 23 March 2008 diff hist +78 Developer documentation
- 14:07, 22 March 2008 diff hist +25 WS188 update checklist →Update checklist for www.wormbase.org current
- 14:01, 22 March 2008 diff hist +5 WS188 update checklist →Update checklist for www.wormbase.org
- 12:22, 22 March 2008 diff hist +73 Developer documentation →Administration
- 12:18, 22 March 2008 diff hist +995 WS188 update checklist
- 11:46, 22 March 2008 diff hist -70 Release Schedule →Upcoming Releases
- 11:45, 22 March 2008 diff hist +82 Release Schedule →Release History
- 11:40, 22 March 2008 diff hist -430 Project Calendar current
- 11:14, 22 March 2008 diff hist +382 Project Calendar
- 11:11, 22 March 2008 diff hist +312 N Project Calendar New page: <googlecalendar>ht3jlfaac5lfd6263ulfh4tql8%40group.calendar.google.com</googlecalendar> What is it <iframe src="http://www.google.com/calendar/embed?src=pgo1792vogc66levsk3no4g6sc%40group...
- 11:05, 22 March 2008 diff hist +22 Main Page →For Developers
- 10:57, 22 March 2008 diff hist +69 Formal development strategy →Sample Development Timeline
- 10:57, 22 March 2008 diff hist -1 Formal development strategy →Sample Development Timeline
- 10:56, 22 March 2008 diff hist +59 Formal development strategy →3. Step 3. Releasing new software and databases into production
- 10:49, 22 March 2008 diff hist +12 Update checklist template →Update checklist for www.wormbase.org
- 10:48, 22 March 2008 diff hist +64 CSHL documentation →Update Checklist
- 10:46, 22 March 2008 diff hist +978 N Update checklist template New page: == Update checklist for www.wormbase.org== {| border=1 ! Task ! Description ! Status |- | Check diskspace on available nodes | ssh [node] df -h | |- | Checkout new code | Checkout changes...
- 10:45, 22 March 2008 diff hist +21 CSHL documentation →Update Checklist
- 10:45, 22 March 2008 diff hist +13 CSHL documentation →Update Checklist
- 10:45, 22 March 2008 diff hist +9 Template:Update checklist template current
- 10:44, 22 March 2008 diff hist +965 N Template:Update checklist template New page: Update checklist for www.wormbase.org. {| ! Task ! Description ! Status |- | Check diskspace on available nodes | ssh [node] df -h | |- | Checkout new code | Checkout changes into brie3:/...
- 10:35, 22 March 2008 diff hist +29 N WS188 update checklist New page: {{update_checklist_template}}
- 10:31, 22 March 2008 diff hist +51 CSHL documentation
- 18:47, 21 March 2008 diff hist +339 Log file management and analysis →Analog
- 18:42, 21 March 2008 diff hist +165 Log file management and analysis →Mint
- 18:31, 21 March 2008 diff hist +980 N Log file management and analysis New page: =Approaches= I've used just about every logfile analysis tool known to man. Here are a few I use regularly. ==Analog== ==awstats== ==Visitors== Website: http://hping.org/visitors Li...
- 18:11, 21 March 2008 diff hist +39 CSHL documentation →General Admin
- 18:24, 15 March 2008 diff hist +67 Developer documentation →Software platform
- 17:28, 11 March 2008 diff hist -8 User:Tharris
- 09:16, 28 February 2008 diff hist +152 C.remanei minor edits and formatting
- 10:15, 24 February 2008 diff hist +85 Converting GFF2 to GFF3
- 01:45, 16 February 2008 diff hist +43 Release Schedule →Release History
- 01:44, 16 February 2008 diff hist +41 Release Schedule →Release History
- 01:42, 16 February 2008 diff hist -71 Release Schedule →Upcoming Releases
- 01:42, 16 February 2008 diff hist +84 Main Page →Using WormBase
- 13:07, 13 February 2008 diff hist +2,599 HOWTO migrate a CGI
- 23:08, 12 February 2008 diff hist +217 Developer documentation →Presentations
- 23:07, 12 February 2008 diff hist +35 N File:2008.02.13-on configuration.key.tgz Part II: On Configuration (keynote) current
- 23:05, 12 February 2008 diff hist +43 N File:2008.02.13-on configuration.pdf Part II of CSHL introduction: configuration current
- 22:06, 12 February 2008 diff hist -5 Developer documentation →Presentations
- 22:05, 12 February 2008 diff hist -1 Developer documentation →Presentations
- 22:04, 12 February 2008 diff hist +293 Developer documentation
- 22:03, 12 February 2008 diff hist +58 N File:2008.01.23-site intro.pdf CSHL conference call, 2008.01,23: Pt 1: Introduction - pdf current
- 21:53, 12 February 2008 diff hist +51 N File:2008.01.23-CSHL call intro.key.tgz 2008.01.23: Reimplementation, Pt 1: Intro (keynote) current
- 20:50, 10 February 2008 diff hist +460 N HOWTO migrate a CGI New page: conversion outline: 1. create model and controller script/wormbase_create.pl controller Your_class script/wormbase_create.pl model Your_class 2. rip code from CGI, marking cleared c...
- 20:49, 10 February 2008 diff hist +124 Developer documentation →Migration documentation
- 00:47, 10 February 2008 diff hist -5,681 Coding standards →Documentation
- 00:46, 10 February 2008 diff hist +14 Coding standards →Function braces
- 00:45, 10 February 2008 diff hist 0 Coding standards
- 00:44, 10 February 2008 diff hist -238 Coding standards
- 00:37, 10 February 2008 diff hist -2,509 Coding standards
- 23:39, 9 February 2008 diff hist -1,035 Coding standards →Variable names
- 12:13, 9 February 2008 diff hist -1 Release Schedule →Release History
- 12:04, 9 February 2008 diff hist +94 Developer documentation →Migration documentation
- 12:59, 6 February 2008 diff hist -103 Release Schedule →Access Statistics
- 12:52, 6 February 2008 diff hist -2 Release Schedule →Access Statistics
- 12:51, 6 February 2008 diff hist +4,703 Release Schedule
- 11:35, 6 February 2008 diff hist +9 Main Page →Using WormBase
- 11:34, 6 February 2008 diff hist +30 N Release Release moved to Release Schedule: more informative name! current
- 11:34, 6 February 2008 diff hist 0 m Release Schedule Release moved to Release Schedule: more informative name!
- 15:42, 5 February 2008 diff hist +552 Release Schedule →Release Schedule
- 19:44, 17 January 2008 diff hist -8 2008.01-Toronto →Thursday
- 19:43, 17 January 2008 diff hist +252 2008.01-Toronto →Thursday
- 13:17, 17 January 2008 diff hist +1,279 Website:Application overview →Generic Controller Actions
- 13:08, 17 January 2008 diff hist -30 Website:Application overview →Specifying configuration
- 13:07, 17 January 2008 diff hist -810 Website:Application overview →Setting up a new page
- 13:07, 17 January 2008 diff hist +1,070 Website:Application overview →Creating new Models and Controllers
- 13:04, 17 January 2008 diff hist +1,056 Website:Application overview →Creating new Models and Controllers
- 12:48, 17 January 2008 diff hist -219 Website:Application overview →Widgets
- 12:48, 17 January 2008 diff hist +145 Website:Application overview →Example
- 12:47, 17 January 2008 diff hist +94 Website:Application overview →Pages
- 12:46, 17 January 2008 diff hist 0 Website:Application overview →PAGES
- 12:45, 17 January 2008 diff hist -345 Website:Application overview →Quick Overview
- 12:43, 17 January 2008 diff hist -7 Website:Application overview →Application structure
- 12:40, 17 January 2008 diff hist +2,530 Website:Application overview →Application structure
- 10:10, 17 January 2008 diff hist -1 2008.01-Toronto →Wednesday
- 10:06, 17 January 2008 diff hist +141 2008.01-Toronto →Wednesday
- 10:05, 17 January 2008 diff hist +17 2008.01-Toronto →Accomplishments
- 10:04, 17 January 2008 diff hist +260 2008.01-Toronto →Wednesday
- 10:02, 17 January 2008 diff hist +24 2008.01-Toronto →AM
- 15:01, 16 January 2008 diff hist +150 Website:Application overview →Creating new Models and Controllers
- 14:37, 16 January 2008 diff hist +1,010 Website:Application overview →Directory Structure
- 13:38, 16 January 2008 diff hist +2 Developer documentation →Software platform
- 13:37, 16 January 2008 diff hist -79 Developer documentation →Software platform
- 13:36, 16 January 2008 diff hist 0 Developer documentation →Software platform
- 13:36, 16 January 2008 diff hist +15,568 Coding standards
- 13:29, 16 January 2008 diff hist +53 2008.01-Toronto →Wednesday
- 13:27, 16 January 2008 diff hist -28 Developer documentation →Software platform
- 13:22, 16 January 2008 diff hist +631 Website:Application overview
- 13:17, 16 January 2008 diff hist +91 2008.01-Toronto →Wednesday
- 13:15, 16 January 2008 diff hist +638 Website:Application overview
- 13:06, 16 January 2008 diff hist -1 2008.01-Toronto →Accomplishments
- 13:06, 16 January 2008 diff hist +112 2008.01-Toronto →Wednesday
- 13:06, 16 January 2008 diff hist +132 Developer documentation
- 13:03, 16 January 2008 diff hist +77 2008.01-Toronto →Wednesday
- 13:02, 16 January 2008 diff hist +850 N Website:Application overview New page: = Configuration = Catalyst offers a powerful configuration system. We use it to provide application-wide, per-page, and per-session configuration. In addition, local configuration files...
- 12:09, 16 January 2008 diff hist +3 Developer documentation →Software platform
- 11:32, 16 January 2008 diff hist +7 2008.01-Toronto →Accomplishments
- 11:23, 16 January 2008 diff hist +131 2008.01-Toronto →Accomplishments
- 10:39, 16 January 2008 diff hist +23 2008.01-Toronto →AM
- 10:39, 16 January 2008 diff hist +103 2008.01-Toronto →PM
- 10:21, 16 January 2008 diff hist -1,110 CSHL documentation
- 10:21, 16 January 2008 diff hist +121 CSHL documentation
- 10:20, 16 January 2008 diff hist -30 Developer documentation
- 10:18, 16 January 2008 diff hist +28 Developer documentation
- 10:17, 16 January 2008 diff hist -829 Developer documentation
- 10:14, 16 January 2008 diff hist +29 Main Page →For Developers
- 10:13, 16 January 2008 diff hist +1,956 N Developer documentation New page: This page contains information pertinent to developers of WormBase. = Reimplementation = == Hardware platform == * Logical structure * Physical structure * [[Performance optimiz...
- 09:05, 16 January 2008 diff hist +70 CSHL documentation →Software platform
- 16:47, 15 January 2008 diff hist 0 CSHL documentation →[[Developer_meetings|Developer Meetings]]
- 16:46, 15 January 2008 diff hist +51 CSHL documentation →[[Developer_meetings|Developer Meetings]]
- 16:46, 15 January 2008 diff hist +21 CSHL documentation →Developer Meetings
- 16:44, 15 January 2008 diff hist +1,587 N 2008.01-Toronto New page: __TOC__ = Toronto, 14 January - 18 January 2008 = == Agenda == ===OBJECTIVES=== * Describe how to develop for the WormBase implementation * Decide on best practices for team developmen...
- 16:43, 15 January 2008 diff hist +26 CSHL documentation
- 15:45, 15 January 2008 diff hist -6 Establishing the SVN repository
- 15:45, 15 January 2008 diff hist +10 Establishing the SVN repository
- 15:44, 15 January 2008 diff hist +299 N Establishing the SVN repository New page: Here's how the WormBase subversion repository was established. <nowiki> ssh brie3 cd /usr/local sudo mkdir svn sudo chgrp wormbase svn sudo chmod 2775 svn cd projects mkdir temp mv wormb...
- 15:42, 15 January 2008 diff hist +81 CSHL documentation →Development
- 14:48, 15 January 2008 diff hist 0 CSHL documentation →Software platform
- 14:47, 15 January 2008 diff hist -103 CSHL documentation →Software platform
- 14:36, 15 January 2008 diff hist +103 CSHL documentation →Software platform
- 09:37, 8 January 2008 diff hist -38 Release notes →Statistics by release
- 15:16, 23 December 2007 diff hist +312 Release notes →Statistics by release
- 10:07, 19 December 2007 diff hist -247 Mailing lists
- 10:06, 19 December 2007 diff hist +104 Mailing lists →Internal Mailing Lists
- 10:05, 19 December 2007 diff hist +209 Mailing lists →Public Mailing Lists
- 10:03, 19 December 2007 diff hist -66 Mailing lists →Archives
- 10:02, 19 December 2007 diff hist +633 Mailing lists →Archives
- 12:29, 2 December 2007 diff hist 0 Release notes →Statistics by release
- 12:29, 2 December 2007 diff hist +312 m Release notes →Statistics by release
- 18:59, 30 November 2007 diff hist +528 N Editorial policy New page: ==WormBase Policy on changing meeting abstracts== Paul Sternberg (with consultation with Tim Schedl, Martin Chalfie, Cori Bargmann, and Jonathan Hodgkin; November 2007) Typos can be fixe...
- 18:58, 30 November 2007 diff hist +54 Main Page →Using WormBase
- 11:13, 30 November 2007 diff hist +122 How to build a frozen release →Configuring VMXs as hosted frozen releases
- 09:03, 12 November 2007 diff hist +312 Release notes →Statistics by release
- 21:53, 11 November 2007 diff hist -156 RSS implementation
- 21:30, 11 November 2007 diff hist +3,763 N RSS implementation New page: ==OBJECTIVE== Create a simple RSS based notification system to easily track changes to any given object in the database. ==Approach== Since our databases are build-use-discard, the RSS ...
- 20:51, 11 November 2007 diff hist +100 CSHL documentation →Development
- 20:49, 11 November 2007 diff hist +614 RSS news feeds
- 11:20, 7 November 2007 diff hist +28 Main Page →Using WormBase
- 10:50, 7 November 2007 diff hist +26 Main Page →Using WormBase
- 10:49, 7 November 2007 diff hist +1 Main Page →Community Resources
- 10:58, 1 November 2007 diff hist 0 CSHL documentation →Software platform
- 10:15, 1 November 2007 diff hist +11 CSHL documentation →Software platform
- 10:14, 1 November 2007 diff hist -1 CSHL documentation →Software platform
- 10:13, 1 November 2007 diff hist +44 N Installing Catalyst Installing Catalyst moved to Installing the Web Application: better name current
- 09:59, 1 November 2007 diff hist +98 CSHL documentation →Software platform
- 09:57, 1 November 2007 diff hist +25 CSHL documentation →Software platform
- 09:27, 25 October 2007 diff hist +88 Release notes →Statistics by release
- 14:10, 16 October 2007 diff hist +377 Virtual Machines →Updating the Software
- 13:44, 16 October 2007 diff hist +67 Virtual Machines →Navigating WormBase
- 13:44, 16 October 2007 diff hist +66 Virtual Machines →Download Instructions
- 13:43, 16 October 2007 diff hist -197 Virtual Machines →Download Instructions
- 13:40, 16 October 2007 diff hist -21 Virtual Machines →Downloading
- 13:39, 16 October 2007 diff hist -23 Virtual Machines →Downloading via the command line client curl
- 13:35, 16 October 2007 diff hist +3 How to build a WormBase Virtual Machine →Users and groups
- 13:30, 16 October 2007 diff hist +2 Main Page →Staying up-to-date
- 13:29, 16 October 2007 diff hist +1 Main Page →Staying up-to-date
- 13:29, 16 October 2007 diff hist -1 Virtual Machines →Updating the Software
- 13:28, 16 October 2007 diff hist -11 Virtual Machines →Logging in
- 13:28, 16 October 2007 diff hist -21 Virtual Machines →Unpacking a downloaded torrent
- 13:27, 16 October 2007 diff hist -2,746 Virtual Machines →Available Virtual Machines
- 13:25, 16 October 2007 diff hist -36 Main Page →For Developers
- 20:09, 9 October 2007 diff hist +122 How to build a WormBase Virtual Machine →Quick Start Guide
- 15:59, 8 October 2007 diff hist -1 Downloads →GFF2
- 23:03, 6 October 2007 diff hist -16 How to build a frozen release →Configuring VMXs as hosted frozen releases
- 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...