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Bioinformatics, Perl, Cool Stuff
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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:


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

6 hours

From the last week:

  • Loaded septoria SNPs (.5 hours)
  • Installed GBrowse and configured it to browse septoria data (1.5 hours)
  • Identified the issues with missing maize bacs and loaded them (2 hours)
  • Deleted septoria SNPs, reloaded new SNP file, and reconfigured GBrowse to use it (1 hour)
  • Loaded maize chip and probe data (2 hours)

Total: 7 hours

From the last week:

  • Finished work on 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)

This week:

  • Struggled with getting GBrowse2 installed on Chado server. It isn't working and I think it is because the server has a rather odd hybrid of package managed and source installed software (3 hours)
  • While checking the loaded data for consistency, found that many (about 1/3) of the maize sequences are missing. Looking into where they might be obtained from (1 hour)
  • parsed and loaded sunflower contigs (2 hours)

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?

Checked that the maize load completed successfully (though assembly sequences still need to be added) and loaded septoria genes and sequences (v.2).

1 hour

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.