Reference Genome April 2010-monthly (Archived)

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PAINT SOP meeting

We held a meeting in Princeton with Kara Dolinski, Mike Livestone, Mary Dolan, Li Ni, Pascale Gaudet, Paul Thomas, Ed Lee, as well as Suzi Lewis and Judy Blake (both attending remotely). A lot of the SOPs have now been defined. The minutes are here: RefG_Princeton_April_12-13_2010

PAINT beta 28

  • GAFs generated are now GAF 2.0 compliant -- note that there was a bug
  in the previous versions where generated GAFs had the wrong number
  of columns, so if you have any GAFs that you have saved in previous
  versions of PAINT, they won't work with the current version
  (to fix the files is fairly trivial, so if you have any issues,
  feel free to contact me).  The GAF parser supports both GAF 1.0
  and GAF 2.0 formats.
  • Issues with timing out connections to the GO database have
  *hopefully* been resolved.  The side effect of this issue was
  that PAINT instances that were idle for long periods of time
  would hang, causing the user to need to restart the application.
  Please provide feedback on whether PAINT is still hanging after
  long periods of time (although with how much faster it now is, you
  might not just let PAINT sit while you go grab a cup of coffee
  when waiting for PAINT to propagate annotations -- sorry Paul =P ).


PAINT beta 24-27

We've just released beta 27, but first is a summary of the changes between 24 and 26:

  • Importing GAF files and the annotating is MUCH faster now.
  We're talking orders of magnitude here, folks.  Some pretty
  clever tricks were used to speed things up, but since a lot of
  the code had to be rewritten, hopefully it didn't break anything.
  Let us know if something has gone awry after the massive
  rewriting.
  • Hyperlinks for E.coli genes now work (they were broken after we
  had to change the database from ECOLI to EcoCyc as expected in
  the GO database)
  • Fixed issues where experimental evidence from the GO database
  sometimes wouldn't show up in PAINT.  Changed the behavior
  so that all experimental evidence shows up, even if they're to
  the same term (as long as the SOURCE and/or ECO are different).
  • Fixed issues with weird colored nodes when restoring data from
  a GAF that contained NOT annotations in a particular aspect but
  not other(s)
  • Fixed scrolling issues with MSA viewer when using the horizontal
  scroll bar (worked fine when using the mouse wheel).

Phew, now on to beta 27...

  • Fixed some issues with how associations are generated that was
  preventing multiple annotations to certain nodes
  • After some feedback from the GO meeting and discussion with Paul,
  we've decided to change how NOTs are displayed in the
  annotation matrix.  In the past, NOTs would display up the the
  GO graph as long as there was no positive annotation to
  contradict.  That turned out to be confusing, as NOTs don't
  propagate up, but rather down.  So the behavior has been changed
  to reflect that.  Implied NOTs are only applied to descendants.
  Since this is a new feature, I'd like to get some feedback to
  make sure that it's behaving correctly.  This also brings up
  another question.  Should we expand the headers (GO terms) in
  the matrix to display all descendant terms to currently annotated
  terms?  We probably wouldn't annotate to those terms directly,
  but they would show the NOT downwards propagation.  The downside
  of that is it will fatten up the matrix even further.

Back to Reference_Genome_Annotation_Project#Progress_Reports

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