UQ-bio Summer School

2022 UQ-Bio Schedule

Below is the schedule for the 2022 UQ-Bio Summer School. Please toggle to expand each section and view the events that we held each day.

Events that were live-streamed (and recorded for asynchronous viewing) are marked in bold font. Please use links to view videos.

  • May 19, 13:00 – 14:30, Python Online Warm-Up Session 1 — see email or slack for links to join live.
  • May 25, 14:00 – 15:30, Python Online Warm-Up Session 2 — see email or slack for links to join live.
  • 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)
  • 07:00 – 08:30, Breakfast
  • 09:00 – 10:00, Welcome Address and Overview Lecture (Prof. Brian Munsky, Prof. Ashok Prasad, Dr. Luis Aguilera) [Link to Recording] [Slides]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Tutorial 1.1 – Python Review and Basic Image Processing — Dr. Luis Aguilera [Link to Recording] [Link to Notebook]
  • 12:30 – 13:45, Group Lunch
  •  14:00 – 15:00, Icebreakers and Team Building Exercises
  • 15:15 – 17:00, Hack-a-thon (Basic Python Skills) [Link to Recording]
  • 07:00 – 08:45, Breakfast
  • 09:00 – 10:00, Lecture — Fluorescent Labeling Techniques used in Single-Cell Research – Dr. Linda Forero [Link to Abstract, Biosketch, and Recording]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Tutorial 1.2 – Python Tutorial for Cell Segmentation and smFISH – Dr. Luis Aguilera [Link to Live/Recorded Video] [Link to Notebook]
  • 12:30 – 13:45, Group Lunch
  • 14:00 – 15:00, Image Segmentation Group Exercises
  • 15:30 – 17:00, Career Discussion Panel 1 – Finding, Applying to, and Choosing the Right Graduate Program or Postdoc Position [Link to Live/Recorded Video]
  • 07:00 – 08:45, Breakfast
  • 09:00 – 10:00, Invited Lecture — Scalable High-Speed Imaging of Molecular Biology in Action – Prof. Douglas Shepherd [Link to Abstract, Biosketch, and Recording]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Tutorial 1.3 – Python Tutorial for Particle Tracking – Dr. Luis Aguilera [Link to Recording] [Link to Notebook]
  • 12:30 – 13:45, Group Lunch
  • 14:00 – 15:00, Particle Tracking Group Exercises
  • 15:15 – 17:00, Hack-a-thon (Python for Image Processing)
  • 07:00 – 08:45, Breakfast
  • 09:00 – 12:00, Group Laboratory tour and experiment demonstrations
  • 12:30 – 13:45, Group Lunch
  • 07:00 – 08:45, Breakfast
  • 09:00 – 10:00, Invited Seminar — Dr. Christian Meyer, University of Colorado Boulder, Bacteria Regulate Calcium Flux using the Physics of Phase Transitions, [Link to Abstract, Biosketch, and Recording]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Tutorial 2.1 – Python Tutorial for Basic Probability Distributions and Sampling – Prof. Ania Baetica [Link to Recording] [Link to Notebook] [Link to Notebook 2]
  • 12:30 – 13:45, Group Lunch
  • 14:00 – 15:00, Statistical Analyses Group Exercises
  • 15:15 – 17:00, Hack-a-thon (Statistics in Python)
  • 07:00 – 08:45, Breakfast
  • 09:00 – 10:00, Invited Seminar – Fast, Smart Therapeutic Solutions for Pandemic Response – Prof. Anushree Chaterjee, University of Colorado Boulder [Link to Abstract, Biosketch, and Recording]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Tutorial 2.2 – Python Tutorial for Supervised Learning – Will Raymond [Link to Recording] [Link to Notebook]
  • 12:30 – 13:45, Group Lunch
  • 14:00 – 15:00, “Supervised Learning” Group Exercises
  • 15:30 – 17:00, Career Discussion Panel 2 – Responsible Conduct in Research [Link to Recording]
  • 07:00 – 08:45, Breakfast
  • 09:00 – 10:00, Invited Seminar — Prof. Soham Ghosh, Colorado State University [Link to Abstract, Biosketch, and Recording]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Tutorial 3.1 – Python Tutorial for Stoichiometries and Propensity Functions – Michael May [Link to Slides, Notebook, and Recording]
  • 12:30 – 13:45, Group Lunch
  • 14:00 – 15:00, Supervised Learning Group Exercises
  • 15:15 – 17:00, Hack-a-thon (Machine Learning in Python)
  • 07:00 – 08:45, Breakfast
  • 09:00 – 10:00, Invited Seminar – Prof. Ashok Prasad [Link to Abstract, Biosketch, and Recording]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Tutorial 3.2 –  Python Tutorial for Stochastic Simulation Algorithm – Joshua Cook [Link to Recording] [Link to Notebook]
  • 12:30 – 13:45, Group Lunch
  • 14:00 – 15:00, Stochastic Simulation Algorithm Group Exercises
  • 15:30 – 17:00, Career Discussion Panel 3 – Diversity, Equity and Inclusion in STEM [Link to Recording]
  • 07:00 – 08:45, Breakfast
  • 09:00 – 10:00, Single Molecule Transcription and Translation Dynamics Lecture – Dr. Tatsuya Morisaki [Link to Abstract, Biosketch, and Recording]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Tutorial 3.3 – Python Tutorial for Totally Asymmetric Exclusion Processes – Will Raymond [Link to Notebook] [Link to Recording]
  • 12:30 – 13:45, Group Lunch
  • 14:00 – 15:00, TASEP Group Exercises

15:15 – 17:00, Hack-a-thon (Python for Statistical Process Simulation)

  • 07:00 – 08:45, Breakfast
  • 09:00 – 12:00, Group Laboratory tour and experiment demonstrations
  • 12:30 – 13:45, Group Lunch
  • 14:00 – Free Time
  • 07:00 – 08:45, Breakfast
  • 09:00 – 10:00, Invited Lecture — Bridging Stochastic Mechanistic Modeling and Statistical Inference to Shed Light on Epigenetic Regulation – Prof. Elizabeth Read [Link to Abstract, Biosketch, and Recording]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Tutorial 4.2 – Python Tutorial for Model Optimization and Data Fitting – Dr. Zachary R Fox [Link to Recording] [Link to Notebook]
  • 12:30 – 13:45, Group Lunch
  • 14:00 – 15:00, Optimization and Data Fitting Group Exercises
  • 15:30 – 17:00, Career Discussion Panel 4 – Navigating Graduate School while Balancing Work and Life [Link to Recording]
  • 07:00 – 08:45, Breakfast
  • 09:00 – 10:00, Invited Seminar – Kaan Ocal [Link to Abstract, Biosketch, and Recording]
  • 10:00 – 10:15, Coffee Break
  • 10:15 – 12:15, Tutorial 4.3 – Python Tutorial for MCMC and Metropolis Hastings Analysis
  • 12:30 – 13:45, Group Lunch
  • 14:00 – 20:00, q-bio Conference