1. Data analyses
   1. Microarray 12th vs SSP
   2. Solexa RnaSeq alignments, quantitation
   3. Gene annotations
   4. Microarray cross-species
   5. Avian cross-species CGH data
2. GBrowse work enabling data analysis
3. GBrowse, finch data, enhancements
   1. GMOD/GBrowse/Chado introduction
   2. GMOD/Chado architecture slide
   3. Songbird DB architecture (w/ Chado?)
   4. GBrowse content: finch genes, predictions, 454 ESTs, Budgie genome, xenoRefGene, Duke clones, oligoarray oligos
   5. GBrowse functions
      1. Text search -- using PostgreSQL full-text search heuristics
      2. BLAT/BLAST sequence alignments
      3. Feature-feature comparisons/overlaps/etc.
      4. Balloon hover content -- cross-links
   6. Interesting GBrowse views -- conclusions "seen"
      1. 454 ESTs and Duke clones suggest another exon
      2. Budgie genome alignment, mostly over the exons (also 454 ESTs)
      3. GBrowse search with multiple hits
4. Gene annotations
   1. Exonerate clones to genome (intron boundary-aware)
   2. Download latest EnsEMBL gene coordinates
   3. Download latest xenoRefGene
   4. Describe heuristic used in latest annotations
      1. If Duke name/descr, use that
      2. Gene name majority -- xenoRefGene, finch EnsEMBL name, human/chicken BLAST, Duke name
5. Budgie 454 genome sequence assembly
   1. estimating coverage by bases, contigs, exons, extended alignments