💼 Modern Programming in Genome to Phenome

August 1 - 5, 2022, Meyer Hall, University of California, Davis

• Instructors:

  • Dr. Hao Cheng, University of California, Davis
  • Dr. Rohan Fernando, Iowa State University
  • Dr. James Chen, Virginia Tech
  • Dr. Daniel Runcie, University of California, Davis

• Topics: Learn to code for the genome to phenome analysis from scratch. The following topics will be covered:

  • Genomic Prediction
    • Mixed-effects models with polygenic, maternal, and permanent environment effects
    • Iterative methods for solving linear systems
    • GBLUP and Bayesian alphabet
    • Variance component estimation
    • Multi-environment trials
  • Phenomics
    • Image matrix manipulation
    • Computer vision algorithms and applications

  The workshop will provide an introduction to programming and how to use it to code algorithms listed above from scratch for genomics to phenomics analyses. The course consists of lectures and practical components with hands-on exercises.

• Attendance:

  • The attendance is limited to 25 to preserve a high TA-to-student ratio to offer more personalized instruction and feedback.

• Prerequisites:

  • Knowledge of quantitative genetics
  • Prior programming knowledge

• Fees:

  • Industry - $500
  • Academic - $400
  • Graduate student - $300

• Registration:

  • Please go to the following site: https://ces-apps.ucdavis.edu/confreg/?confid=1204

• Logistics:

  • UC Davis is located near two airports - Sacramento International Airport (SMF) and San Francisco International Airport (SFO). Transportation options from each airport can be found at https://siss.ucdavis.edu/airport-transportation.

• Housing:

  • Summer visitor housing in the UC Davis residence halls is available at https://conferencehousing.ucdavis.edu/summer-visitor-housing. Other housing options are available through regular booking websites and Airbnb.

• Davis:

  • Interesting sites on campus can be found at https://www.ucdavis.edu/campus-life/things-to-do. Davis is close to San Francisco, Lake Tahoe, Napa Valley, Yosemite and many other interesting places.

• Special requirements:

  • Please email qtlcheng@ucdavis.edu if you have any special requirements (e.g., registration, lodging, visa, invitation letters, international travel).

• What do people say about our past workshop?

I really like that we get to build our own package 'miniJWAS' from scratch. This actually helps me understand the complexity underlying other public packages/software out there much better. I'm not saying I understand 100% of what we went over in the past week, but I enjoy it and feel quite proud to have come this far!

I love this workshop!!!!!!

I want to participate in the same course once more.

The course instructors are incredibly compassionate, positive, and supportive.

I like TAs most. They are willing to help you and patient. Also, they understand the material well so their explanation are easy to understand.

It is interesting and relevant to many parts of breeding, and hands on coding is always the best way to learn how to best use a program.

I learnt a very efficient language and in the process, learnt the programming of mixed linear model. Every topic is very well integrated with both learning goals.

💼 Past Short Courses

Past Short Courses