Moore Notes 3 12 14

From OpenWetWare
Jump to navigationJump to search

Group Call

  • Participants: Katie, Jonathan, Tom, Stacia, Stephen, Dongying, Guillaume, Josh, Sarah
  • Guillaume did not find any new datasets in CAMERA or MG-RAST
  • Tom: Data Driven Discovery early career investigator application (slides)
    • Protein function annotation
      • High-throughput experimental assays for proteins (enzymes) and organisms (Biolog colorametric assay)
      • Sequence/phylogenetic inference
      • Evolutionary (selection) annotation
      • Ecological annotation (correlation with other proteins and with ecological properties)
    • Graph databases enable network analyses (e.g., social network analysis)
      • Protein graph with nodes (tables) and edges (annotated pointers)
      • Extend Bio4j GraphDB (e.g., with SFams sequence similarity results)
      • Phylogeny of genomes using GEBA markers
    • Network neighborhood based inferences
      • Functional annotation, potentially in collaboration with Ladan
      • Horizontal gene transfer identification and quantification
      • Lineage specific selection and gain/loss
    • Computational issues
      • Many graph algorithms implemented
      • Most compute is up front with results (summary statistics) stored in db
      • Relationship to regression problems, other types of regression models