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Topics in JBrowse web:
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Changed: now 23:33 GMT
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Changed by:
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WebStatistics
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01 Sep 2010 - 18:58 - r1.2129
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Main.guest
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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: // // Sep 2010 253 0 0 109 60 WebHome 12 5 QuickTutorial 4 4 WebChanges 3 3 GenomeViewDesignNotes 3 3 TWikiPlugin 3 TiledImageDemoScriptOutput // Aug 2010 10163 0 0 3401 1700 WebHome 542 538 WebRss 323 210 AmazonMachineImage 155 153 LazyFeatureLoading 151 149 RecentRecent 146 TWikiPlugin // Jul 2010 16139 2 0 7816 2949 ...
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GenomeViewDesignNotes
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02 Jul 2010 - 17:31 - NEW
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MitchSkinner
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// Constraints on block sizing/positioning // Assumption: percentages of blocks should be round numbers to avoid rounding error // If blocks are positioned and sized in round percentages, then scroll updates must move the scrolling element by round percentages as well. // Question: do scroll updates need to move the scrolling element by multiples of block size? Currently this is done, would relaxing this requirement buy us anything? // If we keep the scroll ...
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WebHome
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02 Jul 2010 - 17:22 - r1.132
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MitchSkinner
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// Welcome to the JBrowse wiki // This wiki is for the JBrowse genome browser. // Feel free to edit, update, correct and expand. // The demo itself is at http://jbrowse.org/. // Tutorials // The tutorial included in the docs/tutorial directory describes how to set up JBrowse for the example data in the source distribution. // This wiki includes another QuickTutorial on how to set up the JBrowse server. Goes into slightly more detail. //
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JSONFeatureFormat
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07 Jun 2010 - 11:16 - NEW
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MitchSkinner
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// Unlike data formats where each item's attributes have defined positions, like GFF, where the meaning of each column is fixed by a pre-arranged agreement, or formats with named attributes like XML, in JBrowse each feature is represented by an array where each position is named. So it's sort of a named-positional hybrid. The names are specified in the track-wide metadata, which includes a "headers" array that names the positions, e.g.: // "start", "end", "strand ...
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LazyFeatureLoading
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29 Jan 2010 - 16:21 - r1.19
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Main.guest
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// Scaling to large numbers of features by lazily loading chunks of data // Applications: human SNP and EST tracks, short-read sequencing reads, etc. Any data with large numbers of features. // Range Queries // When I first started thinking about lazy feature loading in JBrowse, I imagined taking a DAS-like approach: doing some kind of range query for features in the region being viewed. But there are two problems with that approach: // Problem 1: dynamic queries ...
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QuickTutorial
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25 Jun 2009 - 13:42 - r1.229
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IanHolmes
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// Quick JBrowse tutorial // This quick guide on how to set up JBrowse should no doubt be regarded as experimental, etc. // install pre-requisites // Main.BioPerl, JSON (e.g. from Main.CPAN command-line client) // or skip to next step and get an Amazon EC2 machine image // Installing Bioperl on an Apple OS X machine can be problematic; you may find it necessary to do a force install from CPAN, if the regular installation fails repeatedly. // download the source ...
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AmazonMachineImage
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02 Apr 2009 - 11:38 - r1.6
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IanHolmes
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// Running the Jbrowse AMI // Notes // Amazon's EC2 allows for the deployment of a webserver without the overhead of running a machine yourself. In particular, this may have applications for demonstrations, prototyping, and short-term use. To this end, we've provided an AMI based on Amazon's Fedora 8 AMI, and including a pre-installed and configured instance of Jbrowse. This page will give a brief intro on getting the instance running. For more information, ...
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TWikiPlugin
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23 Mar 2009 - 14:58 - r1.24
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IanHolmes
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// The JBrowse TWiki plugin // We have created a minimal TWiki plugin for JBrowse, located in the twiki/ directory of the JBrowse source tree. // Install TWiki in /usr/local/twiki // Install JBrowse in /usr/local/jbrowse // Create symlinks to JBrowse from TWiki: cd /usr/local/jbrowse/twiki; make // Internally, the plugin regularly runs a Makefile to automatically maintain prepared JBrowse server files for uploaded FASTA, GFF, BED WIG-format attachments to wiki ...
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HackMeeting16Sept08
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20 Mar 2009 - 20:25 - r1.59
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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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GettingStarted
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20 Mar 2009 - 17:51 - r1.18
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IanHolmes
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// This page is an out-of-date tutorial for an older prototype of JBrowse. // Please see QuickTutorial for a more recent tutorial. // This page is retained in case the older TiledImage code may be of historical or other interest. // Install Bioperl // From CPAN is probably easiest: // cpan 1 install S/SE/SENDU/bioperl-1.5.2 102.tar.gz //
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WebPreferences
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04 Feb 2009 - 06:55 - r1.39
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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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RickieBrown
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29 Jan 2009 - 21:32 - r1.2
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Main.guest
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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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BatchTiledImage
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29 Jan 2009 - 21:07 - r1.2
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Main.guest
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// BatchTiledImage.pm is a subclass of JBrowse.TiledImage with a little extra logic for rendering tracks of tiles. // It implements a particular hack as a potential speedup for JBrowse.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 ...
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PrototypeGBrowse
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16 Jan 2009 - 10:55 - NEW
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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: JBrowse.AJAXGBrowseDocs // Feature requests // Please see our Prototype GBrowse Wish List for what we intend to add and other info. //
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AJAXGBrowseDocs
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16 Jan 2009 - 10:54 - r1.36
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IanHolmes
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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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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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BoscAjaxGbrowseAbstract2007
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28 Jun 2007 - 13:57 - r1.6
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Main.guest
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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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Main.guest
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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 - 16:02 - 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 - 15:38 - 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 - 23:36 - 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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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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BiowikiInfo
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14 Apr 2006 - 20:40 - NEW
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Main.guest
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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 JBrowse.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 JBrowse.TileIndex class (see also JBrowse.TiledImage). // See also JBrowse.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 JBrowse.TileIndex) // yoko:~/TiledImage yam ./demo-tileindex.pl // Generated index file: md5 map/e0d685342d685256e61bd028e3de513a.xml // yoko:~/TiledImage yam more md5 map/ //
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Number of topics: 50
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