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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 pages.

If the string %JBROWSE% appears anywhere in the wiki "plaintext" for the page (e.g. in an automatically-included header), the rendered page will contain an embedded JBrowse browser, serving up the page's attachments as tracks.

JBrowse configuration files can also be attached, with the filename config.js, to split .gff file attachments into multiple tracks using various glyphs & styles.

This plugin stops some way short of being everything that one would hope for in a GenomeWiki. It lacks fine-grained access controls, an intuitive JBrowse-integrated UI, robust Wikipedia:ACID properties, a Wikipedia:distributed_database, and other features.

Primarily it's meant to illustrate a simple declarative-dependency approach to creating a JBrowse Wikipedia:plugin for a web Wikipedia:content_management_system.

However, it could feasibly be used as a view onto a genome consortium wiki, such as this 12-fly wiki. (NB: that wiki uses the Wikipedia:MediaWiki engine, but the Makefile approach used here would be easy to port to MediaWiki.)

The plugin is up & running here on a TWiki 4.0 installation:

We have not yet integrated it into the main biowiki.org TWiki, since it's experimental software. (Also, the main wiki engine @biowiki.org is a modified TWiki 2004 release as of 20 Mar 2009).

-- IanHolmes - 20 Mar 2009

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