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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. Hunt around a bit to find the right button to click on to download the source, or go directly to this page.
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 22:46 GMT
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Changed by:
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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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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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Number of topics: 6
Recent changes
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Topics in JBrowse web:
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Changed: now 22:46 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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Number of topics: 6
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