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Gene Ontology applet beta-test

John Richter jrichter at bdgp.lbl.gov
Wed Aug 30 14:45:31 PDT 2000


The new SWING-ified version of the Gene Ontology applet is now ready for
beta testing. There is currently no documentation, but most of the
functionality is fairly clear (if you disagree, please tell me and I'll
try to make things easier to understand).

The beta test version is at 

http://www.fruitfly.org/annot/go/beta.html

In a few days (as soon as any bug reports are fixed and documentation
written) the beta test version will be promoted to the main page.

The beta-test version features:
-------------------------------

* Entirely revised layout. GO terms are now organized in a single tree on
  the left of the screen. Selecting a term causes the term's information
  to be loaded in the info pane to the right. If multiple terms are
  selected, they will each appear in a tabbed pane. Multiple terms are
  selected by holding down the Control key and clicking. (Holding down the
  shift key and clicking causes a span of terms to be selected)

* Regular expressions. Term searches are now done using regular
  expressions, which are much more expressive and much faster than the
  old wildcard approach. If you don't know what regular expressions are,
  take a look at "Using Regular Expressions" at

  http://etext.lib.virginia.edu/helpsheets/regex.html

  (You can still use the regular expression searcher the way you used the
  wildcard searcher. Just use a .* (period-asterick) when you would have
  used an * (asterick)).

* Search synonynms and refine search. Term searches can now search term
  synonyms (if you tell it to). Also, searches can either search all terms
  or only the currently selected terms, allowing you to refine a search
  you have already done.

* Works on the Mac. We have successfully run the GO applet on the
  Macintosh under Internet Explorer. We are working on getting it to run
  on Netscape Navigator.


Still working on:
-----------------

* All of the save mechanisms are currently unavailable

* Organism database entries are only available for FlyBase

* Still trying to trim startup time


Getting the most out of the GO applet:
---------------------

The GO applet runs TEN TIMES faster in browsers other than Netscape
Navigator. I am not sure why this happens, but on a fast network
connection the applet can start up in under 8 seconds in Internet Explorer
or appletviewer, but takes serveral minutes to start in Netscape
Navigator.

If your machine does not have a non-Netscape browser installed but you
have an installation of Java, you can use the Java appletviewer to use the
applet. To do this:

1) Go to a command line and type

   java -version

   The result will look something like

   java version "1.1.8"

   The version number must be higher than 1.1.3 for this to work.

2) Type

   appletviewer http://www.fruitfly.org/annot/go/beta.html

3) The familiar green GO button should appear in a little window. (If this
   is the first time you have run appletviewer, you may see a window
   containing licensing information for appletviewer. Click ok)



Please send any comments/bug reports/questions to go_admin at bdgp.lbl.gov


	Enjoy the ontology,

		John


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