Scott Cain's website

Bioinformatics, Perl, Cool Stuff
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Email: sco...@scottcain.net

What does this say about my facebook friends, I wonder?

Week of June 1

  • working out kinks in analysis loading and testing with Apollo (8 hours)

week of June 8

  • work on Apollo issues, including improvements to conf files (both for serverside and webstart) (8 hours)
  • gbrowse improvements (2 hours)
  • general testing/debugging (4 hours)

week of June 15

  • last minute troubleshooting (8 hours)
  • attending iplant meeting (16 hours)

46 hours total

Week of May 11:

  • Installing and testing software on the new server (5 hours)
  • Work on GBrowse-related scripts (2 hours)

Week of May 18:

  • Worked on building and testing Apollo webstart (8 hours)

Week of May 25:

  • More work on Apollo webstart (2 hours)
  • Work on Chado loading problems that occur when multiple "versions" of the same data are loaded (6 hours)

total: 23 hours

  • Minor improvements to utility scripts (1 hour)
  • Attended meetings/teleconferences at Dolan (4 hours)

More work on user/Chado scripts, created:

  • create_db.pl
  • create_project.pl
  • load_fasta.pl
  • load_analysis_results.pl

as well as the Utils.pm packages that is used by all of these scripts

6 hours

From the last week:

  • Finished work on create_user_envirnment.pl which does (5 hours):
    • creates and populates a user specific database
    • creates a gmod.conf file for the user
    • Adds an entry to the organism table
    • Loads the user's GFF data into the database
    • Creates a GBrowse conf file
  • After the call on Wednesday, we decided to take this functionality and break it into separate scripts, so that work was started as well (2 hours so far).
  • Created test dna segments from arabidopsis data (1 hour)

Lots of work in the last week:

  • loading tair cDNA and EST data (though it is problematic) (2 hours)
  • Installed and configured GBrowse2 (1 hour)
  • Worked on the outline of the rest of the work needed from my side for creating user spaces (5 hours so far)
    • create new db
      • what about organism?

        INSERT INTO organism (abbreviation,genus,species,common_name) VALUES ('T.testus','Test','testus','test');

      • do we want to have analysis entries pre set up?

Two items:

  • loaded the "fixed" TAIR data into chado (it was fixed by removing "Derived_from" listings that referred to features that didn't exist).
  • created the beginnings of the user-specific database creation script. While it does create the database, this script will probably have to grow to modify/create gbrowse and apollo configuration files.

2 hours.

Needed to fix TAIR's arabidopsis data before it could be loaded into chado; I reported the problems back to the curators at TAIR.

2 hours

Last week (week of 3/23):

  • Investigated the possibility of reuse of code written by Ed Lee for HHMI project. Verdict: won't happen, as there is too tight of a tie in with the confluence wiki.

5 hours

This week (so far):

  • Setting up Chado and loading with ontologies on genestage server

3 hours