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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 Quick Tutorial on how to set up the JBrowse server. Goes into slightly more detail.
Download
- The latest code is available on GitHub.
Reference
Please cite the following:
Mailing lists
- gmod-ajax: Development discussion/announcements/etc. Sign up for this to receive the latest news and discussion
New stuff
Recent new pages
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Topics in JBrowse web:
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Changed: now 13:16 GMT
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Changed by:
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LazyFeatureLoading
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30 Oct 2009 - 22:08 - r1.18
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MitchSkinner
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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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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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Number of topics: 6
Recent changes
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Topics in JBrowse web:
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Changed: now 13:16 GMT
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Changed by:
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WebStatistics
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23 Nov 2009 - 10:28 - r1.1080
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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: // // Nov 2009 5534 0 0 1024 374 QuickTutorial 314 235 WebRss 211 208 TWikiPlugin 187 153 AmazonMachineImage 141 128 PrototypeGBrowse 105 InstallTileRendering // Oct 2009 7289 18 7 1154 825 WebStatistics 450 295 WebRss 227 207 AmazonMachineImage 195 181 PrototypeGBrowse 158 148 WebChanges 145 HowToGenerateTiles 25 Main ...
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LazyFeatureLoading
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30 Oct 2009 - 22:08 - r1.18
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MitchSkinner
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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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WebHome
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09 Jul 2009 - 00:04 - r1.129
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IanHolmes
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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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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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Number of topics: 6
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