Integrated Breeding Databases (HS 863 (HS 790))

5 weeks (14 laboratories), 1 credit

Todd Wehner, Instructor

  • Breeding Databases
    • Agrobase (Agronmix)
      • Well-established (1990) commercial database (Windows, Windows server, SQL).
    • GeneFlow
      • Good for marker data, genomics and QTLs
    • GBrowse
      • Genome browser
    • ICIS (CGIAR)
      • ICIS is an Open Community of Practice; it is not a plug and play solution to the crop information problem. All partners in ICIS contribute intellectual capital in designing and testing, and in curating public and private data; some contribute funds to support programmers to improve ICIS
    • Integrated Breeding Platform
      • A project of the Generation Challenge Program of the CGIAR system. Involves tool development to improve the operation of plant breeding programs. Uses open standards such as web browsers, R-project software, and Excel spreadsheets (Windows, Linux, Mac, web).
      • Seed inventory, germplasm management system
    • CyVerse (formerly the iPlant Collaborative)
      • Genotype to phenotype storage, visualization, analysis
    • LabKey Software
      • Uses SAS and R for data analysis
      • Excel worksheet export
  • Phenome Networks
    • Commercial database system.
    • Uses open standards (web browser, SQL, Apache, R-project, ICIS) to be flexible and expandable.
  • Items needed by students for HS 863 course
    • Phenome database access permission
    • Computer (Linux, Mac, Windows) with network connection
    • Excel spreadsheet and web browser (Firefox or Chrome, not IE)
    • Optional: label printer (laser printer with label paper)
  • Resources for HS 863 course