Agenda

• Progress reports
  • Status of compilation of assemblies for deep green (Norm):
    • First 40 data sets are currently being run through Mike Barker's DupPipe and TransPipe at Arizona, running at a rate of 3-4 taxa/day.
    • Michael Gonzales has installed Hamstr on TACC cluster(s). Mike will test installation, and Norm will start using Hamstr to sort uniscripts next week.
  • Ks Plots and transpipe - Now running on Mike B's cluster at Arizona.
  • TACC repository for OneKp data needs to be synced with WestGrid repository (Mike G. and Chris J.)
  • BLAST portal (Mike G.) - Next on Mike's priority list (after testing Hamstr and updating TACC data repository). Raj can help.
  • Portal for searching terms of best BLAST hits (Mike G.) - Mike has a database of BLASTX results including (Query = 1kp assembly sequence, Hit = sequence from 25 genome database):
    • Query_name
    • Query_sequence
    • Query_accession
    • Query_description
    • Query_number_of_hits
    • Hit_name
    • Hit_accession
    • Hit_description
    • Hit_significance (e-value)
    • Hit_num_hsp (number of hsp)
      • Alignments not included - too bad but simply reporting hits with Query sequence would be useful for OneKp consortium.
  • Installation of SATe on TACC cluster(s) (Mike G.) - Mike talking with Tandy Warnow.
• Brief demo of Tree Reconciliation Viewer (Jim and Naim)
  • Folks were impressed with Naim's demo. Questions discussed including:
    • Font size and node symbols too small.
    • Nodal support values for trees - Database can accommodate support values.
    • How will tree reconciliations be done for OneKp data:
      • Notung would use estimated gene trees and species tree
      • TreeBEST and PrIME-GSR would assume the estimated species tree is correct and re-estimated gene trees with reconciliations using penalized likelihood and a Bayesian approach, respectively.
    • Accuracy of reconciliations - Jamie Estill is comparing TreeBEST reconciliations with six-taxon synteny-based reconciliation constructed by John Bowers.
• Action Items:
  • Norm - Run Hamstr on translations coming from Mike B's TransPipe; Assess differences between SOAP and CLC+ assemblies for exemplar taxa; work with Jim and Raj to complete compilation cDNA data sets for all taxa in "deep green" study.
  • MIke G. - Complete installation of Hamstr ; Sync TACC OneKP data repository with Westgrid repository; Finalize OneKp blast portal (Jim and Raj could help could help simplify blast database - e.g. split into smaller taxon databases, remove all database sequences shorter than some threshold (???)); Develop front end for blast results database (Raj could help).