UQ-Bio Schedule 2023

Below is the schedule for the 2023 UQ-Bio Summer School. Please toggle to expand each section and view the events that we held each day.

Events that were be live streamed (and recorded for asynchronous viewing) are marked in bold font.

*Afternoon Project Sessions and Hack-a-thons (MWF) will meet together (in person and online) for 20 minutes at the start of each session to discuss the day’s challenge.  Then we will break into teams to work on the problem, and we will reconvene for 30 minutes at the end to discuss solutions and progress.

** All listed times are in Mountain Daily Time (MDT, UTC/GMT -6 hours).

*** To obtain links to join the program Slack team or to view lecture materials, you must apply/register at: https://forms.gle/zPH69KzYbYERXDRY7

  • 16:00 – Check in opens for dormitories (please see instructions in lodging confirmation email)
  • 17:30 – 19:00, Welcome Reception (W Scott Jr Bioengineering Atrium)

All meetings in Nutrien, Room 135, See Campus Map Here

  • 09:00 – 10:00, Welcome Address and Overview Lecture, The UQ-Bio Summer School Team [Slides .pdf], [Video]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Python Tutorial 1.1 —  Basics of Image Processing, Dr. Luis Aguilera (Colorado State University) [Colab Notebook], [Video]
  • 12:30 – 13:45, Group Lunch
  • 14:00 – 17:00, *Project Session and Hack-a-thon — Image Processing Basic Skills [Colab Notebook]

All meetings in Nutrien, Room 135, See Campus Map Here

All meetings in Nutrien, Room 135, See Campus Map Here

  • 09:00 – 10:00, Invited Lecture, Prof. Soham Ghosh (Colorado State University) [Video]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Python Tutorial 2.1 — Basic statistics, Prof. Ania Baetica (Drexel University) [Colab Notebook], [Video]
  • 12:30 – 13:45, Group Lunch
  • 14:00 – 17:00, *Project Session and Hack-a-thon — Statistical Analyses of Images, [Blank Colab Notebook]

All meetings in Nutrien, Room 135, See Campus Map Here

  • 09:00 – 12:00, Group Laboratory tour and experiment demonstrations
  • 12:30 – 13:45, Group Lunch

All meetings in Nutrien, Room 135, See Campus Map Here

  • 09:00 – 10:00, Invited Seminar, Prof. Douglas Shepherd (Arizona State University) [Slides .pdf] [Video]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Python Tutorial 2.2 – Basics of Regression, Classification and Machine Learning, Dr. Zachary Fox (Oak Ridge National Laboratory) [Colab Notebook] [Video] [Video-Part 2]
  • 12:30 – 13:45, Group Lunch
  • 15:15 – 17:00, *Project Session and Hack-a-thon — Machine Learning for Single-Cell Data

All meetings in Nutrien, Room 135, See Campus Map Here

  • 09:00 – 09:30, Invited Seminar, Prof. Keisha Cook (Clemson University) [Video – First Half] 
  • 09:30 – 10:00, Invited Seminar, Dr. Hanieh Mazloom Farsibaf (UT Southwestern Medical Center.) [Video – Second Half]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Python Tutorial 3.1 – Formulating and solving models for gene regulation dynamics, Joshua Cook (Colorado State University) [Colab Notebook], [Video]
  • 12:30 – 13:45, Group Lunch
  • 14:00 – 15:00, “ODE Modeling” Group Exercises
  • 15:30 – 17:00, Career Discussion Panel 2 – Student Life and Diversity Equity and Inclusion in STEM [Video]
    • Prof. Keisha Cook, Clemson University
    • Prof. Naomi Nishi, Colorado State University
    • Prof. Erin Nishimura, Colorado State University
    • Prof. German Parada, Colorado State University

All meetings in Nutrien, Room 135, See Campus Map Here

  • 09:00 – 10:00, Invited Seminar, Prof. Phillip Nelson (University of Pennsylvania) [Slides] [Video]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Python Tutorial 3.2 – Sampling from Probability Distributions and Generating Stochastic Simulations, Prof. Keisha Cook (Clemson University) [Colab Notebook][Video]
  • 12:30 – 13:45, Group Lunch
  • 14:00 – 17:00, *Project Session and Hack-a-thon — Modeling Gene Regulation with Stochastic Simulations

All meetings in Nutrien, Room 135, See Campus Map Here

  • 09:00 – 10:00, Invited Seminar, Prof. Eric Deeds (University of California, Los Angeles) [Video]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Python Tutorial 3.3 –  Chemical Master Equation, Michael May (Colorado State University) [Link to Colab][Video]
  • 12:30 – 13:45, Group Lunch
  • 14:00 – 15:00, “Chemical Master Equation” Group Exercises
  • 15:30 – 17:00, Career Discussion Panel 3 — Quantitative and Computational Biology Beyond Academia [Video]
    • Dr. Phil Fox, Darwin Biosciences, Boulder CO
    • Dr. Zachary Fox, Oak Ridge National Laboratory, Oak Ridge, TN
    • Dr. Jerome Lee, Invitae, Boulder, CO
    • Murrieta Reyes, Zoetis, Fort Collins, CO

All meetings in Nutrien, Room 135, See Campus Map Here

  • 09:00 – 09:30, Invited Lecture, William Raymond (Colorado State University) [Video]
  • 09:30 – 10:00, Invited Lecture, Prof Ania Baetica (Colorado State University) [Video]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Python Tutorial 4.1 – Markov Chain Monte Carlo and Model Inference, Kaan Ocal (Edinburgh University) [Video]
  • 12:30 – 13:45, Group Lunch
  • 14:00 – 17:00, *Project Session and Hack-a-thon — Bayesian Inference for Single-Cell model
  • 09:00 – 12:00, Group Laboratory tour and experiment demonstrations
  • 12:30 – 13:45, Group Lunch
  • 14:00 – Free Time

Please visit https://cmb.colostate.edu/qcmb/qcmb-symposium/ for the complete, up-to-date schedule for the qCMB/UQ-Bio Computational and Systems Biology Symposium.

Please visit https://cmb.colostate.edu/qcmb/qcmb-symposium/ for the complete, up-to-date schedule for the qCMB/UQ-Bio Computational and Systems Biology Symposium.

  • 09:00 – 12:00, Check out and departure.
q-bio