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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
- The code is available using git like so:
git clone http://genome.biowiki.org/test/divbrowser/.git
- You can also download a working installation with sample data from D. melanogaster here.
Mailing lists
- gmod-ajax: Development discussion/announcements/etc. Sign up for this to receive the latest news and discussion
Recent new pages
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Topics in GBrowse web:
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Changed: now 01:27 GMT
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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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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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NameIdeas
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18 Apr 2007 - 21:00 - r1.5
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IanHolmes
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// 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 ...
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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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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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Number of topics: 6
Recent changes
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Topics in GBrowse web:
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Changed: now 01:27 GMT
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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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WebStatistics
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17 Aug 2008 - 22:16 - r1.277
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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: // // Aug 2008 6815 1 0 829 819 WebHome 713 540 WebRss 166 160 GettingStarted 153 152 SkinnerUzilovMungallHolmesRecomb2007Poster 145 137 TiledImagePanel 133 RecentRecent 1 Main.IanHolmes // Jul 2008 8383 3 0 1293 917 WebHome 689 524 WebChanges 400 264 PrototypeGBrowse 248 238 GettingStarted 183 178 BiologyOfGenomes2007GenomeWikiPoster ...
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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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Number of topics: 6
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