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3rd Annual Undergraduate Quantitative Biology (UQ-bio) Summer School

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Welcome to the 3rd Annual UQ-Bio Summer School!

Below is the Github repository holding all the links to Colab Notebooks and files needed during the course.

Authors

Brian Munsky, Luis Aguilera, William Raymond, 
Joshua Cook, Michael May, Zachary Fox, 
Eric Ron, Keisha Cook, Kaan Ocal, 
Ania Baetica, and Ana Carolina Padua.
                

uqbio.summer.school@gmail.com 2023 Undergraduate Summer School ScheduleUQ-BioMunsky Group


Modules

Module 0 (Online) : Getting Started with Basic Scientific Computing in Python.

Date (MST) Location Description Link
May 22 Online Intro to Python: Hello (Python) World, Types, Arithmetic Operations, Iterables, and Containers (Instructor: Zach Fox) Open In Colab
May 22 Online Intro to Python: Loops, Ranges, Functions, Lambdas, List Comprehension (Instructor: Luis Aguilera) Open In Colab
May 22 Online Intro to Python: importing packages, classes/modules, os navigation, reading files (Instructor: Will Raymond) Open In Colab
May 22 Online Intro to Python: Google Colab environment setup and navigation (Instructor: Will Raymond) Open In Colab
May 22 Online Intro to Python: Matplotlib visualization (Instructor: Will Raymond) Open In Colab
May 22 Online Intro to Python: NumPy and Linear Algebra Review (Instructor: Michael May) Open In Colab
May 22 Online Intro to Python: Using OpenAI's GPT3.5 in Python (Instructor: Brian Munsky) Open In Colab

Module 1 : Optical Microscopy Experiments and Image Processing .

Date (MST) Location Description Link
May 24 Online Python Preliminary Image Loading and Processing (Instructor: Luis Aguilera) Open In Colab
May 31 in person Tutorial 1.1 — Basics of Image Processing, Dr. Luis Aguilera (Colorado State University) Open In Colab
June 1 In person Tutorial 1.2 — Image Segmentation and Tracking, Dr. Carolina Padua (Champalimaud Center for the Unknown, Lisbon, Portugal) Open In Colab

Module 2 : Multivariable Statistics and Machine Learning for Biological Data.

Date (MST) Location Description Link
June 2 in person Tutorial 2.1 — Basic statistics, Prof. Ania Baetica (Drexel University) Open In Colab
June 5 in person Tutorial 2.2 – Basics of Regression, Classification and Machine Learning, Dr. Zachary Fox (Oak Ridge National Laboratory) Open In Colab

Module 3 : Stochastic Simulations of Biological Processes.

Date (MST) Location Description Link
June 6 in person Tutorial 3.1 – Formulating and solving models for gene regulation dynamics, Joshua Cook (Colorado State University) Open In Colab
June 7 in person Tutorial 3.2 – Sampling from Probability Distributions and Generating Stochastic Simulations, Prof. Keisha Cook (Clemson University) Open In Colab

Module 4 : Master Equation Analyses of Biological Processes.

Date (MST) Location Description Link
June 8 in person Tutorial 4.1 – Chemical Master Equation, Michael May (Colorado State University) Open In Colab
June 9 in person Tutorial 4.2 – Markov Chain Monte Carlo and Model Inference, Kaan Ocal (Edinburgh University) Open In Colab

UQ-Bio23 Drug Discovery Challenge

drawing

Drug Discovery Challenge Presentation

Date (MST) Location Description Link
May 31 NT135 Stage 1: Experimental Quantification (Instructor: Luis Aguilera) Open In Colab
June 2 NT135 Stage 2: Statistical Analysis (Instructor: Ania Baetica and Brian Munsky ) Open In Colab
June 5 NT135 Stage 3: Regression Analysis (Instructor: Zach Fox and Brian Munsky ) Open In Colab
June 7 NT135 Stage 4: Models and Stochastic Simulation (Instructor: Michael May, Joshua Cook, and Keisha Cook ) Open In Colab
June 13 BSB 107 Final Predictions and Presentations Open In Colab

Breaking news

Newsletter Link to the complete story

Newsletter Link to the complete story


Closing time 🎶

Newsletter Link to the complete story


Licensing

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