Community Annotation System

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This is placeholder page for the community annotation system information page. The live version of the CAS is running at

You can download a copy of the currently running annoation server from here: (it's big: 1.3GB). Be warned however that this virtual appliance is still quite rough.

Items that are working:

  • A recent (pre-1.69) instance of GBrowse, with popup balloons enabled, that provide:
    • A gene popup balloon that gives an 'Edit in the wiki' option
    • An overview selection balloon that gives an 'Edit in Apollo' option
  • A CGI that takes a gene name and copies name, description and synonym data from Chado to the MediaWiki database and then redirects to the newly created page.
  • A CGI that takes a chromosomal range and creates GAME-XML and jnlp files and a link to download and run Apollo WebStart.

Items that need to be addressed soon are:

  • Make networking generic again (currently it is hard coded to run at CSHL). This should be pretty easy (writing a bash script similar to what Eric wrote for the original Modware VM).
  • Address the hard coding of stuff in the Chado -> Mediawiki and Mediawiki -> Chado scripts.
  • Hook up the cgi for generating GameXML from GBrowse (so that the click to edit with Apollo will work).DONE!
  • Documentation, Documentation, Documentation!

For more information or help, send email to the GMOD Help Desk at