• Welcome to the AJAX GBrowse wiki
  • Download
  • Mailing lists
  • Howto and documentation
  • Development
    • Perl modules and scripts
    • Tests, benchmarks and builds
    • Bug reporting
    • Recent new pages
    • Recent changes

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/.

Another copy of the demo is running at the CBRG in Oxford.

Please leave feedback on the general project info page.

This project is in early stages of development. Expect changes often!

Download

• The code is available using git like so:
  
  git clone http://genome.biowiki.org/test/divbrowser/.git

Mailing lists

• gmod-ajax: Development discussion/announcements/etc. Sign up for this to receive the latest news and discussion
• gmod-gbrowse-ajax-commits: CVS commits list

Howto and documentation

• Getting Started
• Install Feature Upload
• General information/overview
• Documentation: an attempt to aggregate all the documentation for the project into one place
• Install tile rendering: how to install the tile rendering framework
• How to generate tiles
• Biowiki info: how to abuse this TWiki installation

Development

Contact IanHolmes or MitchSkinner if you are interested in contributing to the project. We welcome and are thankful for everyone's help!

• Wish list: braindump your ideas and feature requests here
  • also serves as a development outline
• JavaScript resources

Perl modules and scripts

• TiledImage: Perl module for intercepting GD primitives and replaying to tiles
  • BatchTiledImage: subclass of TiledImage for batch-rendering tiles
• TiledImagePanel: hacked version of Bio::Graphics::Panel for creating tiled tracks

Tests, benchmarks and builds

• GenerateTiles cluster benchmarks
  • TiledImage optimisation: discussion of ways to improve performance

Bug reporting

Please use the SourceForge bug tracker (category GBrowse-ajax) to report bugs and problems.

Recent new pages

Topics in GBrowse web:

Changed: now 02:54 GMT

Changed by:

WebChangesGroup	18 Jun 2007 - 23:01 - NEW	TWikiGuest
Pages most recently changed in this group of webs: // URLPARAM{"web"} "} //

BoscAjaxGbrowseAbstract2007	28 Jun 2007 - 13:57 - r1.6	TWikiGuest
// 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 ...

LivePageFiddling	20 Apr 2007 - 16:44 - r1.5	MitchSkinner
// 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 ...

NameIdeas	18 Apr 2007 - 21:00 - r1.5	IanHolmes
// Browser name ideas // 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 // unfortunately clashes with ...

BiologyOfGenomes2007GenomeWikiPoster	03 May 2007 - 18:33 - r1.7	MitchSkinner
// 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 ...

InstallFeatureUpload	13 Apr 2007 - 00:50 - r1.2	MitchSkinner
// 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 //

Number of topics: 6

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Recent changes

Topics in GBrowse web:

Changed: now 02:54 GMT

Changed by:

WebStatistics	03 Jul 2008 - 21:41 - r1.204	TWikiGuest
// Statistics for Web // Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: // // Jul 2008 509 0 0 103 36 WebRss 30 21 AJAXGBrowseDocs 18 18 BiologyOfGenomes2007GenomeWikiPoster 17 17 InstallFeatureUpload 14 13 WishList 12 WebNotify // Jun 2008 5737 7 0 903 632 WebRss 543 182 PrototypeGBrowse 157 156 BioStore 131 129 BiologyOfGenomes2007GenomeWikiPoster 112 111 WebPreferences 111 GettingStarted ...

WebHome	26 Jun 2008 - 23:23 - r1.103	MitchSkinner
// 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/. // Another copy of the demo is running at the CBRG in Oxford. // Please leave feedback on the general project info page. //

WishList	26 Jun 2008 - 23:20 - r1.99	MitchSkinner
// 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: //

AJAXGBrowseDocs	26 Jun 2008 - 23:11 - r1.35	MitchSkinner
// 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 //

PrototypeGBrowse	26 Jun 2008 - 23:07 - r1.68	MitchSkinner
// 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 // The Times They Are A-Changin' // Please see our Prototype GBrowse Wish List for what we intend to add and other info. //

GettingStarted	14 Mar 2008 - 06:20 - r1.17	TWikiGuest
// 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 ...

Number of topics: 6

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