Topics in JBrowse web
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For information on JBrowse, please see the JBrowse website at http://jbrowse.org/.
JBrowse priorities Stabilization Basic documentation. Generate technical documentation for (a) users (b) developers. The GMOD wiki is a good start. Developer documentation ...
Goal: Fix current sub optimal aspects of the JSON format, allowing us to: 1. support it into the future, and 1. start encouraging other people to generate it ...
Misc JBrowse related sysadmin stuff: My crontab: 0 cd /var/www/code/jbrowse master git pull git submodule update It keeps ...
Existing tests: some client side tests (e.g., here), there are some more in the web apollo fork that we should probably fold back in when we fold in the NCList ...
update VERSION file update release notes.txt tag release $ git tag a release name minimize JS $ make minify js create ZIP (I've been removing ...
Input: set of N half open intervals %$\{(s 1, e 1), (s 2, e 2), ..., (s N, e N)\ \ i start position is monotonically non decreasing and end position is monotonically ...
Home Login Register Tutorial Changes http://jbrowse.org/ jbrowse.org
Goals: Store in filesystem or S3 (cheap hosting for users? How hard will it be to explain to less technical users?) S3 advantages over EBS: don ...
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 ...
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 ...
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 ...
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 ...
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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 BioPerl, JSON (e.g ...
IanHolmes 01 Apr 2009
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 ...
This page is an out of date tutorial for an older prototype of JBrowse.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 ...
First Name: Rickie Last Name: Brown Login Name: RickieBrown Email: rbrown #64;whid.org Country: Germany Location: Other My Links ...
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 ...
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How to use generate tiles.pl TODO: write me! Until then, run: ./generate tiles.pl ? to get a help prompt. Sample use (ancient history?) ./generate tiles ...
Prototype Generic Genome Browser We are extending the GenericGenomeBrowser (GBrowse) with AJAX, community annotation and other "Web 2.0" y ideas. You can see what ...
Table of Contents: Documentation for the AJAX GBrowse This is the repository for every scrap of documentation on the AJAX GBrowse framework ( aka Prototype GBrowse ...
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 ...
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 ...
Abstract: AJAX GBrowse: Community Genome Annotation Made Easy Mitch Skinner1, Andrew Uzilov1, Lincoln Stein2, Chris Mungall3, Ian Holmes1 1: Department of ...
Notes on our GBrowse RECOMB 2007 poster EDITING OF THE POSTER CONTENT IS NOW CLOSED FINAL POSTER: format Illustrator .ai format We presented at A: ...
How I made the components graphic for the AJAX GBrowse RECOMB 2007 poster. This is a transcript from the firebug javascript console: tileDiv document.getElementById ...
using cpan: Catalyst relevant plugins install Catalyst::Runtime Catalyst::Plugin::Session Catalyst::Plugin::Session::State::Cookie Catalyst::Plugin::Session::Store ...
#UseCases Use Cases Computational user runs analysis on genome, wants to visualize. Uploads GFF3 file with analysis results, views in browser, tweaks code, re ...
based on FeatureUploadRequirements Browser has "upload" button User clicks on upload button, gets page with: track name field file input field (for choosing ...
CVS repository access Our code is now a part of the SourceForge project. Specifically, we are in the subdirectory ajax of the Generic Genome Browser module ...
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 ...
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 ...
JavaScript resources The Prototype library is quite awesome: http://prototype.conio.net/ My favorite documentation for it is here: http://www.sergiopereira.com/articles ...
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... ...
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 ...
TiledImageDemoScriptOutput (See TiledImage) yoko:~/TiledImage yam% ./demo tiledimage.pl Recording colorAllocate (255 255 255) with bounding box (0 0 100 100) Recording ...
TileIndexDemoScriptOutput (See TileIndex) yoko:~/TiledImage yam% ./demo tileindex.pl Generated index file: md5 map/e0d685342d685256e61bd028e3de513a.xml yoko:~ ...
(go back to InstallTileRendering) The files that you need to have on /mnt/nfs prior to doing this are: install drosophila stuff.bash script that automates configuration ...
Number of topics: 50
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