q-bio Summer School and Conference, 2022

Detailed UQ-Bio Schedule

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

Events that will be live streamed (and recorded for asynchronous viewing) are marked in bold font. Links to live streams and recordings of these sessions will be provided to registered participants using the summer school’s Slack Channel. 

To ask questions during live stream lectures and tutorials, please use the Slack Channel #live-session-discussions, and to ask questions for previously-recorded sessions, please use the #recorded-session-discussions channel. Please see your welcome email for instructions for join. 

Please register at: https://forms.gle/kNe41izsabaRnTk88 before May to gain access to program materials.

  • 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