Monday, July 9, 2007

Weekly Update

Hi all...been busy last few weeks.

PROJECT: Command Line Topological Query Apps for BioSQL

Last TWO weeks:
  • Completed a Working version of PhyOpt. The core of this comes from H. Lapp's tree-precompute script. This put me ahead of my original timeline on the front of having working transitive closure precomputes available. I am using the precomputed values for PhyExport and PhyQry.
  • Upgraded my version of MySQL from 4.0 to 4.1. This allows me to use nested queries. It looks like nested queries are going to be the easiest way for me to do the optimization as well as use the optimization info. I may upgrade again to 5.0, but I would like the program to run on the oldest version of the database possible. (I also don't want to kill the 40 other databases I have on my machine.)
  • Started PhyMod to modify trees in the database .. this is making use of the precomputations from above in PhyOpt.
  • Updated info on the project web page to reflect some changes in the command line options.
  • I have been reading Perl Best Practices by D. Conway... I wish I had this book years ago!
  • I have also been dealing with genome annotation problems that have nothing to do with this project (I really would like bioperl to support computational results in game xml or Apollo to support Chado better..)

For this week:
  • Finish subtree Delete query in phymod based on a node ID passed to the program.
  • Add subtree export to PhyExport ... It made more sense for me to get PhyOpt fully working before doing this.

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