What's new today

  • A BIMS traning working workshok will be held at the annual RosBREEDS participants meeting in East Lansing on March 26th, 2019.

    Trainers: Soook Jung, Taein Lee, Daniel Edge-Garza, Ksenija Gasic and Dorrie Main

    Participants:
    Amy Iezzoni, Audrey Sebolt (tart cherry breeding, Michigan State University); Per McCord (sweet cherry breeding, Washington State University); Lis Mahoney (strawberry breeding, University of New Hampshire); Dave Byrne, Zena Rawandoozi, Ellen Yong, Stella Kang, Jeekin Lau (rose breeding, Texas A&M University); Margaret Worthington (University of Arkansas (Peach, blackberry and muscadine breeding); Soon Li Teh (apple breeding, Washington State University) 

    Agenda

    • Introduction to Workshop and BIMS (Dorrie): 9.00 AM
    • Hands on training (Taein): 9.30 AM
      • Browsing trait/cross/trial data with statistical values
      • Data editing
    • Beverage Break: 10.15 AM
    • Hands on training (Taein): 10.30 AM
      • Search/Download/Comparison/Archive
      • Data editing
    • Lunch: 12.00 -1.00 PM
    • Training on how to create a program and load data (Taein): 1.00 PM
      • Create a program and add members
      • Load data in template
      • Load data in FieldBook output
      • Browse/Search your own data
      • Create an input file for FieldBook App
    • Beverage Break: 3.00 PM
    • Questions on Field Book (Ksenija): 3.30 PM
    • Overview of Templates (Sook) 4 PM
    • Future Plans (Sook) 4.30 PM
    • Open discussion on BIMS: 4.30 – 5.00PM
  • Title:  CottonGen BIMS Training Workshop at Cotton Beltwide Conference, New Orleans, January 8-10, 2019 

    When: Tuesday, January 8, 9-11 AM
    Where: Balcony I

    Who: Cotton Breeders and support staff/students
    Required: Bring a laptop
    Sign up: by adding your information at
    https://docs.google.com/spreadsheets/d/1qZhcBUYTjOWbw9YXfQVQ3lWY1jRXpyJ_g5yCv2NZqnQ/edit?usp=sharing


    Overview:

     

    This workshop will provide breeders (and program personnel) with practical training on how to use BIMS to manage their breeding program data using sample data. Participants will learn how to create a private breeding program within BIMS, control access levels to their program people, load data in templates and/or Field Book App output, view/search/download data, perform various searches, and create input files for the Field Book App. There will be time at the end to discuss functionality needs for BIMS. Participants will need to bring a laptop.

     

    BIMS Trainers: Taein Lee, Sook Jung, Jing Yu, Dorrie Main

     

    Agenda

    • Introduction to BIMS (Dorrie) (10 min)
    • Hands on training using sample data (Taein) (40 min)
      • Browsing trait/cross/trial data with statistical values
      • Search/Download/Comparison/Archive
    • Demo on how to create a private program and how to load sample data (Taein): (40 min)
      • Create a program and add members
      • Load data in template
      • Load data in FieldBook output
      • Create an input file for FieldBook App
      • Overview of Templates (Sook) (10 min)
    • Open discussion on BIMS (15 min)
  • We will hold a NRSP10 Training workshop at PAG, 2019

    The workshop will be held Sunday 1.10 - 3.40 in the California Room

  • Gensas Version 6.0 Now Available. new features include: 

     

    • Addition of BUSCO, HISAT2, DIAMOND, pBLAT (version of BLAT that runs multi-threaded), BRAKER2
    • Option to use soft-masked sequence with some gene prediction tools added
    • Summary report of tools and setting used to generate OGS produced at Publish step
    • BLAT, BLAST+, InterPRoScan, HISAT2, DIAMOND, BRAKER2, GeneMark-ES, TopHat2, PASA now all run multi-threaded on the cluster
    • Assembly sequence names processed to remove special characters and for length
    • Option to make combined GFF3 file with OGS, repeats, rRNA, tRNA data and functional annotation info in column 9 added to Publish step