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
- Asynchronous — Watch the preliminary getting started with python tutorial videos and complete the asynchronous Google Colab workbooks.
- May 22, 10:00 – 12:00 – Welcome and Python Online Warm-Up Session — [Link to Recorded Session], [Slides], [Link to UQ-Bio GitHub Page]
- May 24, 10:00 – 12:00 – Python Preliminary Image Loading and Processing –– [Link to Recorded Session], [Link to UQ-Bio GitHub Page]
- May 26, 10:00 – 12:00 – Python Online Help Session –– [Link to Recorded Session], [Link to UQ-Bio GitHub Page]
- 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
- 10:00 – 10:15, Coffee Break
- 10:15 – 12:15, Python Tutorial 1.1 — Basics of Image Processing, Dr. Luis Aguilera (Colorado State University)
- 12:30 – 13:45, Group Lunch
- 14:00 – 17:00, *Project Session and Hack-a-thon — Image Processing Basic Skills
All meetings in Nutrien, Room 135, See Campus Map Here
- 09:00 – 10:00, Lecture — Fluorescent Labeling Techniques used in Single-Cell Research, Eric Ron (Colorado State University)
- 10:00 – 10:15, Coffee Break
- 10:15 – 12:15, Python Tutorial 1.2 — Image Segmentation and Tracking, Dr. Carolina Padau (Champalimaud Center for the Unknown, Lisbon, Portugal)
- 12:30 – 13:45, Group Lunch
- 14:00 – 15:00, “Image Segmentation” Group Exercises
- 15:30 – 17:00, Career Discussion Panel 1 — Finding and Joining the Right Research Team or Project
All meetings in Nutrien, Room 135, See Campus Map Here
- 09:00 – 10:00, Invited Lecture, Prof. Soham Ghosh (Colorado State University)
- 10:00 – 10:15, Coffee Break
- 10:15 – 12:15, Python Tutorial 2.1 — Basic statistics, Prof. Ania Baetica (Drexel University)
- 12:30 – 13:45, Group Lunch
- 14:00 – 17:00, *Project Session and Hack-a-thon — Statistical Analyses of Images
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)
- 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)
- 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)
- 09:30 – 10:00, Invited Seminar, Dr. Hanieh Mazloom Farsibaf (UT Southwestern Medical Center.)
- 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)
- 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
All meetings in Nutrien, Room 135, See Campus Map Here
- 09:00 – 10:00, Invited Seminar, Prof. Phillip Nelson (University of Pennsylvania)
- 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)
- 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)
- 10:00 – 10:15, Coffee Break
- 10:15 – 12:15, Python Tutorial 3.3 – Chemical Master Equation, Michael May (Colorado State University)
- 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
All meetings in Nutrien, Room 135, See Campus Map Here
- 09:00 – 09:30, Invited Lecture, William Raymond (Colorado State University)
- 09:30 – 10:00, Invited Lecture, Prof Ania Baetica (Colorado State University)
- 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)
- 12:30 – 13:45, Group Lunch
- 14:00 – 17:00, *Project Session and Hack-a-thon — Bayesian Inference for Single-Cell models
- 09:00 – 12:00, Group Laboratory tour and experiment demonstrations
- 12:30 – 13:45, Group Lunch
- 14:00 – Free Time
Symposium in Lory Student Center, Grand Ballroom, See Campus Map Here
- 08:00 – 09:00, Coffee and Poster Set up
- 09:00 – 10:15, Invited Tutorial, Prof. Andrew Mugler (University of Pittsburgh)
- 10:15 – 10:30, Break
- 10:30 – 11:30, Session 1
- 10:30 – 10:45, Contributed Talk 1, TBA
- 10:45 – 11:15, Invited Talk, Dr. Tatsuya Morisaki, Colorado State University
- 11:15 – 11:30, Contributed Talk 2, TBA
- 11:30 – 12:00, Lightning Talks 1-8 (2.5 min each)
- 12:00 – 14:00, Lunch and Poster Session I
- 14:00 – 15:30, Session 2
- 14:00 – 14:30, Invited Talk, Prof. Megan McClean, University of Wisconsin Madison
- 14:30 – 14:45, Contributed Talk 3, TBA
- 14:45 – 15:15, Invited Talk, Prof Daniel Reker, Duke University
- 15:15 – 15:30, Contributed Talk 4, TBA
- 14:00 – 14:30, Invited Talk, Prof. Megan McClean, University of Wisconsin Madison
- 15:30 – 15:40, Coffee Break
- 15:40 – 16:35, Session 3
- 15:40 – 16:25, Keynote Talk, Prof. Thomas Yankeelov, University of Texas at Austin
- 16:25 – 16:35, Lightning Talks 9-12
- 16:35 – 19:00, Dinner and Poster Session II
Symposium in Lory Student Center, Grand Ballroom, See Campus Map Here
- 08:00 – 09:15, Coffee, Conversations and Collaborations
- 09:15 – 15:30, Session 4
- 09:15 – 09:45, Invited Talk, Prof. Olivia Rissland, University of Colorado, Anschutz
- 09:45 – 10:00, Contributed Talk 5, TBA
- 10:00 – 10:30, Invited Talk, Prof. Pablo Iglesias, Johns Hopkins University
- 10:30 – 10:45, Contributed Talk 6, TBA
- 09:15 – 09:45, Invited Talk, Prof. Olivia Rissland, University of Colorado, Anschutz
- 10:45 – 11:00, Coffee Break
- 11:00 – 12:00, Panel Discussion, Future of Artificial Intelligence and Large Language Models in Biological and Biomedical Education and Practice.
- Asa Ben Hur, Colorado State University (discussion chair)
- Mayla R Boguslav, Colorado State University
- Arjun Krishnan, University of Colorado Anschutz Medical Campus
- Zachary R Fox, Oak ridge National Laboratory
- Thomas Yankeleev, University of Texas at Austin
- 12:00 – 12:15, Wrap up
- 17:00 – ??? Farewell Celebration.
- 09:00 – 12:00, Check out and departure.