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Topics in GBrowse web:
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Changed: now 01:25 GMT
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Changed by:
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WebStatistics
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07 Oct 2008 - 15:04 - r1.455
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TWikiGuest
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// Statistics for Web // Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: // // Oct 2008 3250 0 0 996 508 WebRss 387 101 WebIndex 98 96 WebChanges 89 61 TiledImagePanel 51 41 PrototypeGBrowse 39 SkinnerUzilovMungallHolmesRecomb2007Poster // Sep 2008 24088 102 1 8012 2588 WebStatistics 2039 1820 WebIndex 1810 1526 WebRss 932 522 WebChangesGroup 352 351 BoscAjaxGbrowseAbstract2007 302 TestPage ...
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HackMeeting16Sept08
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25 Sep 2008 - 11:09 - r1.57
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IanHolmes
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// Hackathon/Tutorial/Progress Meeting // Main.IanHolmes 16 Sep 2008 // Met from 4-5pm in Ian's office. // added notes on in-memory GFF adaptor to BioStore page // Reviewed location of some source files // BrowserSrc:GenomeView.js everything below the gray co-ordinate bar; divided into slices (vertical column with co-ordinate number at the top left) and blocks (intersection of a slice a track) // BrowserSrc:Track.js currently subclassed into feature tracks ...
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NameIdeas
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19 Sep 2008 - 09:35 - r1.6
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IanHolmes
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// Browser name ideas // Click Here to take survey // Need a kick-ass name other than "AJAX GBrowse". // Perhaps we can pick a "development name" and save the final pick till when it's more fleshed out. // Suggestions: // Oxygene (er, the Jean-Michel Jarre tune Wikipedia:Oxygene? Also sounds a bit like doxygen) // Jaga // for aJAx Gbrowse // also in honor of one of the greatest jazz orchestras of all time, a Russian fairy tale, and some minor unrelated things ...
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BioStore
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16 Sep 2008 - 23:06 - r1.36
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IanHolmes
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// BioStore // "Bio Store" // also known (in more rigorously-namespaced circles) as // Bio::DB::SeqFeature::Store // A thin Perl/SQL layer for working with feature annotation data, such as GFF. //
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WebPreferences
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01 Sep 2008 - 17:00 - r1.38
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IanHolmes
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// Web Preferences // The following settings are web preferences of the web. These preferences overwrite the site-level preferences in ., and can be overwritten by user preferences (your personal topic, eg: .TWikiGuest in the web). // Preferences: // Set SKIN koala // Set NAVBARH // Set NAVBARF // Set NOWEBSBAR // Set WIKILOGOIMG /TWiki/TWikiLogos/BioWikiLogo.png // Set WIKILOGOURL http://biowiki.org/ // List of topics of the . web: //
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WebHome
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19 Aug 2008 - 17:05 - r1.108
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MitchSkinner
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// Welcome to the AJAX GBrowse wiki // This wiki is for everything pertaining to the AJAX GBrowse project: info, discussion, development, documentation, feature requests, etc. // As this is a wiki, feel free to edit any part of it, especially the feature requests page. // The demo itself is at http://genome.biowiki.org/. // Please leave feedback on the general project info page. // Download //
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PrototypeGBrowse
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20 Jul 2008 - 04:16 - r1.70
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IanHolmes
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// Prototype Generic Genome Browser // We are extending the Main.GenericGenomeBrowser (GBrowse) // with AJAX, community annotation and other "Web 2.0"-y ideas. // You can see what we have so far at genome.biowiki.org. // Documentation // See: GBrowse.AJAXGBrowseDocs // Feature requests // Please see our Prototype GBrowse Wish List for what we intend to add and other info. //
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WishList
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26 Jun 2008 - 23:20 - r1.99
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MitchSkinner
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// Table of Contents: // // AJAX GBrowse list // Feature and improvement wishlist for AJAX GBrowse (Prototype GBrowse, demo at http://genome.biowiki.org ). // This is also the development outline; tasks are listed approximately in the order they need to be done. // High-level goals // At a high level, the goals of the project are as follows: //
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AJAXGBrowseDocs
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26 Jun 2008 - 23:11 - r1.35
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MitchSkinner
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// Table of Contents: // // Documentation for the AJAX GBrowse // This is the repository for every scrap of documentation on the AJAX GBrowse framework ( aka GBrowse). // Most everything below is out of date, stay tuned for doc work. Sorry. // Main.MitchSkinner 27 Jun 2008 //
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GettingStarted
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14 Mar 2008 - 06:20 - r1.17
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TWikiGuest
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// Install Bioperl // From CPAN is probably easiest: // cpan 1 install S/SE/SENDU/bioperl-1.5.2 102.tar.gz // You want a recent 1.5-series release; the one above should work fine. // Get GBrowse 1 code // You don't have to actually install "regular" GBrowse to use AJAX GBrowse; you can if you want to, but installing it is somewhat involved. If you do choose to install it, read the GBrowse installation instructions. // AJAX GBrowse does use some modules from ...
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BoscAjaxGbrowseAbstract2007
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28 Jun 2007 - 13:57 - r1.6
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TWikiGuest
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// Abstract: // AJAX GBrowse: Community Genome Annotation Made Easy // Mitch Skinner1, Andrew Uzilov1, Lincoln Stein2, Chris Mungall3, Ian Holmes1 // 1: Department of Bioengineering, University of California, Berkeley // 2: Cold Spring Harbor Laboratory // 3: Lawrence Berkeley National Laboratory // The current standard for genome browser software involves a user interface based on static web pages. These pages are created on a server from a pre-loaded database ...
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BiologyOfGenomes2007GenomeWikiPoster
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03 May 2007 - 18:33 - r1.7
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MitchSkinner
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// Genome browser/wiki poster for Biology of Genomes 2007 // See the RECOMB 2007 poster. // Note that the order of authors is different in this abstract. // The submitted abstract // A PROTOTYPE “GENOME WIKI” FOR COMMUNITY ANNOTATION // Mitch Skinner1, Andrew Uzilov1, Lincoln Stein2, Chris Mungall3, Ian Holmes1 // 1: Department of Bioengineering, University of California, Berkeley // 2: Cold Spring Harbor Laboratory // 3: Lawrence Berkeley National Laboratory ...
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LivePageFiddling
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20 Apr 2007 - 16:44 - r1.5
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MitchSkinner
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// How I made the client components graphic for the AJAX-GBrowse RECOMB 2007 poster. // This is a transcript from the firebug javascript console: // tileDiv document.getElementById("3 mRNA tileDiv") // tileHighlight document.createElement("div"); // tileHighlight.style.cssText "background-color: rgb(56, 117, 215); position: absolute; left: 0 ; top: 0 ; width: 100 ; height: 100 ; opacity: 0.8; text-align: center; padding-top: 100px; font-size: 40pt;" // "background ...
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InstallFeatureUpload
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13 Apr 2007 - 00:50 - r1.2
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MitchSkinner
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// using cpan: // Catalyst relevant plugins // install Catalyst::Runtime Catalyst::Plugin::Session Catalyst::Plugin::Session::State::Cookie Catalyst::Plugin::Session::Store::FastMmap Catalyst::Plugin::StackTrace Catalyst::Plugin::Static::Simple Catalyst::Plugin::ConfigLoader Catalyst::View::TT Catalyst::Action::RenderView // for fastCGI: // install FCGI FCGI::ProcManager //
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InstallTileRendering
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13 Apr 2007 - 00:41 - r1.69
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TWikiGuest
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// See GettingStarted // Most of the information below is out of date. We might bring some parts of it back in the future, so I'm leaving it here, but GettingStarted is a better place to start. MS 4/13/07 // THE GOAL // This is just a log of how I installed everything necessary to run generate-tiles.pl on the Main.SixtyFourBitCluster. This is here for reference in case I need to look something up or if the procedure needs to be repeated on some other system ...
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FeatureUploadRequirements
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22 Mar 2007 - 15:02 - r1.14
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IanHolmes
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// #UseCases // Use Cases // Computational user runs analysis on genome, wants to visualize. Uploads GFF3 file with analysis results, views in browser, tweaks code, re-runs analysis, re-uploads. // later uploads overwrite previous data (for this user/track combo) // Versioning in future? (definitely not at first) (but easy to implement hackily on filesystem using RCS; that's how TWiki does it IH) // Computational user runs analysis on one chromosome. Uploads ...
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FeatureUploadDesign
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22 Mar 2007 - 14:38 - r1.4
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IanHolmes
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// based on FeatureUploadRequirements // Browser has "upload" button // User clicks on upload button, gets page with: // track name field // file input field (for choosing a file to upload from the local filesystem) // URL field (for getting data from a URL) // submit button // User clicks submit button, upload script on server: // checks validity (possibly future) // checks if user has uploaded features for this track before // how does server know who the ...
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SchemaOptions
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20 Mar 2007 - 22:36 - r1.5
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MitchSkinner
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// Chado // Flexible, can handle a variety of things // Complex // Used differently by different groups // GBrowse integration needs work // Bio::DB::SeqFeature::Store // Works well with GBrowse // Contains serialized Perl objects (is this necessary if you're storing subfeatures separately?) // Less flexible than Chado // Specialized for GFF3? // How widely used? //
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RickieBrown
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28 Feb 2007 - 05:39 - NEW
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TWikiGuest
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// First Name: Rickie // Last Name: Brown // Login Name: RickieBrown // Email: rbrown@whid.org // Country: Germany // Location: Other // My Links // .WelcomeGuest to learn TWiki // Sandbox.WebHome web to try out TWiki // Sandbox.Sandbox just for me // // //
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CVSRepositoryAccess
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18 Feb 2007 - 14:31 - r1.21
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AndrewUzilov
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// CVS repository access // Our code is now a part of the GMOD SourceForge project. Specifically, we are in the subdirectory ajax of the Generic-Genome-Browser module. // Check out for developers // export CVS RSH ssh // To check out the whole thing (includes complete GBrowse, etc.): // cvs z3 d :ext:YOUR SF LOGIN@gmod.cvs.sourceforge.net:/cvsroot/gmod co P Generic-Genome-Browser // To check out AJAX subdir only (includes client and server code), e.g. to the ...
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CommunityAnnotation
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05 Feb 2007 - 18:05 - NEW
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MitchSkinner
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// Table of Conents: // // see also: the WishList // There are three kinds of community annotation that have been talked // about: // Bulk annotation upload // Lots of people have GFF/BED/etc. files that they'd like to see rendered. // We ought to make this dead simple. // Existing examples include Santa Cruz's upload functionality: //
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SinclairBioperlUpdate
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01 Feb 2007 - 16:15 - r1.13
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MitchSkinner
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// in CPAN shell (as root): // install Bundle::CPAN // restarted CPAN shell, was asked for Module::Build special parameters. I only set uninst 1 (and used the default of nothing for the other parameters). // o conf commit // The CPAN 'r' command produced a list of modules with updated versions. I randomly chose to update these: // install CGI CGI::Session CGI::Session::Driver DBD::Pg DBD::mysql GD GD::SVG XML::SAX XML::Twig // accepted the defaults for everything ...
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TiledImage
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07 Nov 2006 - 12:24 - r1.212
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AndrewUzilov
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// TiledImage // What it does // TiledImage is a proxy for GD::Image that "records" GD method calls (primitives), storing them in a SQL database, then "replays" them to geometrically-translated, cropped GD child objects, or "tiles". // An included demo script, demo-tiledimage.pl , is loosely based on the example code from the GD::Image manpage. // Getting the source code // CVS repository access // Perl modules //
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JavaScript
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02 Nov 2006 - 11:05 - r1.3
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AndrewUzilov
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// JavaScript resources // The Prototype library is quite awesome: // http://prototype.conio.net/ // My favorite documentation for it is here: // http://www.sergiopereira.com/articles/prototype.js.html // // Created by: Main.AndrewUzilov on 02 Nov 2006 //
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TiledImageOptimisation
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15 Apr 2006 - 01:02 - r1.7
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IanHolmes
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// optimisation seems to be a recurrent issue... // BatchTiledImage is the latest attempt to address poor performance when fetching-and-rendering primitives from the database. // (See below for some older discussion motivating the use of SQL in the first place.) // Lincoln has noted that current speed issues may be due to mysql's dire handling of range searches. // Suggestions for a fix: use a binning strategy, // or take advantage of MySQL 5.0's geometric primitives ...
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TiledImagePanel
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14 Apr 2006 - 20:58 - NEW
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IanHolmes
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// TiledImagePanel is a hacked version of Bio::Graphics::Panel with a few minor alterations to work with the TiledImage class. // Can we enumerate these changes.... // ...and roll them back in as a subclass of Panel? // Main.IanHolmes 15 Apr 2006 //
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BatchTiledImage
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14 Apr 2006 - 20:57 - NEW
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IanHolmes
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// BatchTiledImage.pm is a subclass of TiledImage with a little extra logic for rendering tracks of tiles. // It implements a particular hack as a potential speedup for TiledImage's track rendering: // a renderAndWipe method that renders all the tiles up to a particular X co-ordinate, // then wipes all primitives to the left of that co-ord. // It may be unnecessary to pursue this line of optimization if SQL tricks, // such as Lincoln's idea of "binning" primitives ...
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BiowikiInfo
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14 Apr 2006 - 20:40 - NEW
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TWikiGuest
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// Access control // This wiki does not require registration to edit pages or create new pages: // click on the "Edit" link (top right of page) to edit any page. // However, unregistered users are prohibited from adding URLs to external sites (antispam technique). // To add external URLs, please first register, and then contact Main.IanHolmes requesting URL-adding privileges. However, note that you can do quite a lot without entering URLs. // For example, you ...
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TiledImageDemoScriptOutput
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14 Apr 2006 - 20:33 - r1.4
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IanHolmes
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// TiledImageDemoScriptOutput // (See GBrowse.TiledImage) // yoko:~/TiledImage yam ./demo-tiledimage.pl // Recording colorAllocate (255 255 255) with bounding box (0 0 100 100) // Recording colorAllocate (0 0 0) with bounding box (0 0 100 100) // Recording colorAllocate (255 0 0) with bounding box (0 0 100 100) // Recording colorAllocate (0 0 255) with bounding box (0 0 100 100) // Recording transparent (0) with bounding box (0 0 100 100) // Recording interlaced ...
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TileIndexFilenameMangling
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14 Apr 2006 - 20:33 - r1.17
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IanHolmes
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// TileIndexFilenameMangling // Details of the filename mangling in the GBrowse.TileIndex class (see also GBrowse.TiledImage). // See also GBrowse.TileIndexDemoScriptOutput for an example of this evil munging in action. // coord-munged symbolic links in subdirectory tiles // the filename stub for a co-ordinate pair ($x,$y) is "${x} ${y}" // e.g. for $(x,y) (0,15)$ the filename stub is 0 15 // the filename is the filename stub followed by .png // i.e. 0 15.png ...
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TileIndexDemoScriptOutput
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14 Apr 2006 - 20:33 - r1.5
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IanHolmes
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// TileIndexDemoScriptOutput // (See GBrowse.TileIndex) // yoko:~/TiledImage yam ./demo-tileindex.pl // Generated index file: md5 map/e0d685342d685256e61bd028e3de513a.xml // yoko:~/TiledImage yam more md5 map/ //
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InstallTileRenderingExactSteps
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14 Apr 2006 - 20:33 - r1.11
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IanHolmes
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// (go back to GBrowse.InstallTileRendering) // The files that you need to have on /mnt/nfs prior to doing this are: // install-drosophila-stuff.bash script that automates configuration of MySQL and copying of Drosophila melanogaster files to host, and also copies the CPAN configuration files to host so you can use CPAN // my.cnf the MySQL config file // gdtile.sql MySQL schema for 'gdtile' database // dmel-4-r4.2.1.conf Apache/GBrowse Drosophila melanogaster ...
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DotplotTracks
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14 Apr 2006 - 20:32 - r1.31
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IanHolmes
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// How about tracks for the genome browser? // No need to go through the GBrowse.TiledImage layer for this, either: we could generate the dotplot tiles independently, direct from sequence. // Simple tracks could just show dotplots a la dotlet. // Or dotter // (Erik Sonnhamer's cool X utility with nice, responsive contrast widget.... sadly don't think javascript is up to this!). // More advanced tracks could show posterior probabilities for local direct repeats ...
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GenerateTilesClusterBenchmarks
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14 Apr 2006 - 20:32 - r1.16
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IanHolmes
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// Benchmarks of generate-tiles.pl on Drosophila melanogaster chromosome 4 on the Main.SixtyFourBitCluster // (go back to the Main.SixtyFourBitCluster page) // It's 11:15PM, and all of the 208 rendering jobs launched yesterday are done, except for one (track 11, coding sequences at 100bp zoom level, about half done). // Today Main.IanHolmes mentioned that he noticed some lag over the NFS on the cluster... is this lag hampering the rendering, since all the PNG ...
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TileIndex
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14 Apr 2006 - 20:28 - r1.22
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IanHolmes
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// TileIndex // What it is // TileIndex is a module for generating index files for rectangular tile grids, using Main.GBrowse.TiledImage. // The hope is that this generic example may inform design of customized pre-rendered apps, e.g. for the GenericGenomeBrowser. // However, as it stands, TileIndex is not really suitable for a track-based browser, because it assumes a rectangular grid of tiles, each tile having the same x- and y-dimensions. // That is, it doesn ...
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TiledImageMySQLDatabaseSchema
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14 Apr 2006 - 20:27 - r1.12
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IanHolmes
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// This is the Main.MySQL schema (written by Main.IanHolmes and Main.ChrisMungall) for the gdtile database used by GBrowse.TiledImage. // GRANT ALL ON gdtile. TO ''@'localhost'; // CREATE DATABASE gdtile; // USE gdtile; // CREATE TABLE tiledimage ( // tiledimage id INT UNSIGNED NOT NULL AUTO INCREMENT, // width INT UNSIGNED, // height INT UNSIGNED, // PRIMARY KEY (tiledimage id) // ); // CREATE TABLE primitive ( //
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WebNotify
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04 Apr 2006 - 02:48 - r1.6
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IanHolmes
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// This is a subscription service to be automatically notified by e-mail when topics change in this web. This is a convenient service, so you do not have to come back and check all the time if something has changed. To subscribe, please add a bullet with your .WikiName in alphabetical order to this list: // Main.TWikiGuest example@your-company.com // TWIKIWEB .WebChangesAlert"} // Related topics: .WebChangesAlert, ., .TWikiRegistration //
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WebRss
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15 Aug 2004 - 20:27 - r1.2
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PeterThoeny
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// 's web // /view/ // The web of TWiki. TWiki is a Web-Based Collaboration Platform for the Corporate World. // TWIKIWEB .WebRssBase"} //
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Number of topics: 50
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