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