Below is the full schedule of the 2024 UQ-Bio Summer School. All lectures and tutorials were recorded, and you can watch the videos using the links provided within the schedule below.
To follow along with the lectures, you will need to download the Python tutorial notebooks and data set from the program GitHub page at: https://github.com/MunskyGroup/uqbio2024
If you have questions about the materials, or if you would like to request to use them in another class, please contact us at brian.munsky@colostate.edu.
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Program at a Glance:
The five modules of the 2024 UQ-bio summer school were:
- Get Started with Scientific Computing in Python
- Single-Cell Optical Microscopy Experiments and Image Processing
- Multivariable Statistics and Machine Learning for Single-Cell Data
- Stochastic Simulations of Single-Cell Gene Regulatory Processes
- Master Equation Analyses of Single-Cell Gene Regulatory Processes
Full Schedule - Week 0
Slides (.pdf): WelcomeVirtualSession
- Welcome Sessions and Review
- Introductions to the course organizers
- Overview of Course Objectives and Philosophy
- Breakout for assistance to find course materials and install key software
- Breakout to go over first tutorial and notebook questions
Review session to go over the first three homework assignments (in three breakout groups). Due to technical difficulties, only the main room was recorded.
Recording of Breakout Session One. This recording primarily focused on helping participants to set up GitHub and VS code.
Review session to go over the first three homework assignments (in three breakout groups).
Video of breakout session zero — further assistance with installing and running github. Work through a few of the problems in the various homework problem sets.
Video of breakout session one — complete review of homework 1, including workflow to stage and commit changes to GitHub and a full step-by-step solution to all problems in Homework 1.
Video of breakout session two: working session to review some of the material covered in Homework 2.
Full Schedule - Week 1
- 12pm-5pm – Check in to dormitories
- 5pm – 7pm – Welcome Reception (Scott Atrium)
- 07:00 – 08:30, Breakfast
- 09:00 – 10:00, Welcome Address, Brian Munsky, Slides: IntroductionJune4, [Link to Video]
- 10:15 – 12:15, Python Tutorial – Image Processing 1 (Basics) – Luis Aguilera, [Link to Video]
- 12:30 – 13:45, Group Lunch
- 14:00 – 15:00, UQ-Bio Challenge Introduction, [Link to Video]
- 15:00 – 17:00, UQ-Bio Challenge, Stage 1 Collaborative Work
- 07:00 – 08:45, Breakfast
- 09:00 – 10:00, Labeling and Imaging Technology Lecture – Eric Ron, [Link to Video]
- 10:15 – 12:15, Python Tutorial – Image Processing 2 (Segmentation/Tracking) – Luis Aguilera, [Link to Video]
- 12:30 – 13:45, Group Lunch
- 14:00 – 14:30, Introduction to interim mini-challenge, [Link to Video]
- 14:30 – 17:00, Project Work
- 07:00 – 08:45, Breakfast
- 09:00 – 10:00, Invited Seminar – Prof. Sabrina Spencer, [Link to Video] (Request access by emailing qbio_summer_school@colostate.edu)
- 10:15 – 12:15, Python Tutorial – Statistics – Prof. Keisha Cook, Link to Video
- 12:30 – 13:45, Group Lunch
- 14:00 – 15:15, Project Work
- 15:30 – 17:00, Career Discussion Panel 1 – DEI In STEM (Dr. Keisha Cook (Moderator), Dr. Will Raymond, Dr. Melisa A. Burt, Dr. Erin Nishimura), [Link to Video]
- 07:00 – 08:45, Breakfast
- 09:00 – 10:00, Invited Seminar – Prof. Keisha Cook, [Link to Video]
- 10:15 – 12:15, Python Tutorial – Machine Learning – Dr. Will Raymond, [Link to Video]
- 12:30 – 13:45, Group Lunch
- 14:00 – 14:30, Example for how to code part of course challenge using GitHub CoPilot, [Link to Video]
- 14:30 — 15:00, Project Work
- 07:00 – 08:45, Breakfast
- Free Time
Full Schedule - Week 2
- 07:00 – 08:45, Breakfast
- 09:00 – 17:00 Experiment Labs and Lab Tours
- 07:00 – 08:45, Breakfast
- 09:00 – 10:00, Invited Seminar – Prof. Doug Shepherd, [Link to video]
- 10:15 – 12:15, Python Tutorial – Stoichiometries, Propensity functions, and ODE Models – Connor King, [Link to Video]
- 12:30 – 13:45, Group Lunch
- 14:00 – 15:00, Project Work, [Link to update video]
- 15:30 – 17:00, Career Discussion Panel 2 – Choosing the right graduate program or team (Dr. Alex Popinga (moderator), Dr. Carol Wilusz, Dr. Doug Shepherd, Dr. Jessica Hill, Dr. Stuart Tobet). [Link to Video]
- 07:00 – 08:45, Breakfast
- 09:00 – 10:00, Invited Seminar – Prof. Erin Nishimura, [Link to Video]
- 10:15 – 12:15, Python Tutorial – Stochastic Simulation – Jack Forman and Alex David, [Link to Video]
- 12:30 – 13:45, Group Lunch
- 14:00 – 17:00, Project Work
- 07:00 – 08:45, Breakfast
- 09:00 – 10:00, Invited Seminar – Prof. Jesse Wilson, [Link to Video]
- 10:15 – 12:15, Python Tutorial – Chemical Master Equation and FSP – Prof. Brian Munsky, [Link to First Part Video], [Link to Second Part Video]
- 12:30 – 13:45, Group Lunch
- 14:00 – 15:00, Project Work
- 15:30 – 17:00, Career Discussion Panel 3 – Industry-Focused Career Discussion (Dmitri Svetlov (moderator), Prof. German Parada, Dr. Reyes Murrieta, Dr. Linda Forero) [Link to Video]
- 07:00 – 08:45, Breakfast
- 09:00 – 10:00, Invited Seminar – Prof. Soham Ghosh, [Link to Video]
- 10:15 – 12:15, Python Tutorial for MCMC – Dr. Kaan Ocal, [Link to Video]
- 12:30 – 13:45, Group Lunch
- 14:00 – 17:00, Project Work
- 07:00 – 08:45, Breakfast
- Free Time
- 07:00 – 08:45, Breakfast
- Free Time
qCMB/UQ-Bio Symposium
- 07:00 – 08:45, Breakfast
- 09:00 – 17:00, qCMB/UQ-Bio Symposium day 1
- 07:00 – 08:45, Breakfast
- 09:00 – 12:30, qCMB/UQ-Bio Symposium day 2, [Link to Brian’s Awful Poetry]
- 12:30 – 14:00, Lunch
- 14:00 – 16:00, UQ-Bio Final Project Presentations, [Link to Video]
- 17:00 – 19:00, qCMB/UQ-Bio Symposium Picnic and Volleyball