Difference between revisions of "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 http://cas.gmod.org/ | + | This is placeholder page for the community annotation system information page. The live version of the CAS is running at http://cas.gmod.org/ |
| − | You can download a copy of the currently running annoation server from here: | + | You can download a copy of the currently running annoation server from here: http://www.gmod.org/live_annotation_server.tar.bz2 (it's big: 1.3GB). Be warned however that this virtual appliance is still quite rough. |
| − | *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). | + | Items that are working: |
| − | *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). | + | *A recent (pre-1.69) instance of [http://cas.gmod.org/cgi-bin/gbrowse/dicty 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. | ||
| + | *<strike>Hook up the cgi for generating GameXML from [[GBrowse]] (so that the click to edit with [[Apollo]] will work).</strike>DONE! | ||
*Documentation, Documentation, Documentation! | *Documentation, Documentation, Documentation! | ||
| − | For more information or help, send email to the GMOD | + | For more information or help, send email to the [[GMOD Help Desk]] at [mailto:help@gmod.org help@gmod.org]. |
| + | |||
| + | [[Category:GMOD Components]] | ||
| + | [[Category:Community Annotation]] | ||
Latest revision as of 18:57, 29 February 2008
This is placeholder page for the community annotation system information page. The live version of the CAS is running at http://cas.gmod.org/
You can download a copy of the currently running annoation server from here: http://www.gmod.org/live_annotation_server.tar.bz2 (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 help@gmod.org.
