Welcome to Arizona State University Center for Biological Physics Summer School 2025!
Below is the GitHub repository with the course schedule and links to Jupyter Notebooks plus other files we will use during the course.
Authors: Douglas Shepherd
Materials adapted from: uqbio2024 Summer School and CSU BIOM 480A5.
Summer school location
Setting up Google Colab
Course Materials
The summer school will be held in Bateman Physical Sciences Building H (PSH) Room 563. A map to the school is found here
Before the summer school begins, please make sure you have an active Google account so that you can access Google Colaboratory. You do not need the "pro" account for the summer school. If you do not have a Google account, you will need to make one for the school.
Below are the course materials for the 2025 CBP Summer School. Please refresh this repository often as these materials may change at any time up to the actual lecture date! The dates for each module may change as we get started.
| Date | Description | Links to Notebooks(s) |
|---|---|---|
| August 4th, 2025 | Google Colab and Python introduction | Module 1A ➡️ |
| August 4th, 2025 | Python basics and data types | Module 1B ➡️ |
| August 4th, 2025 | Loops, ranges, functions | Module 1C ➡️ |
| August 4th, 2025 | Loops and functions practice | Module 1C practice ➡️ |
| August 5th, 2025 | Numpy and linear algebra review | Module 1D ➡️ |
| August 5th, 2025 | Eigenvalues, vectors, decompositions, and transformations | Module 1E ➡️ |
| August 5th, 2025 | PCA example | Module 1E* ➡️ |
| August 5th, 2025 | Visualing data using matplotlib and seaborn | Module 1F ➡️ |
| Date | Description | Links to Notebooks(s) |
|---|---|---|
| August 6th, 2025 | Probability Puzzle slides | Module 2 lecture ➡️ |
| August 6th, 2025 | Distributions | Module 2A ➡️ |
| August 6th, 2025 | A primer on the normal distribution | Example 2 ➡️ |
| August 6th, 2025 | Likelihooods | Module 2B ➡️ |
| August 6th, 2025 | Signficance testing | Module 2C ➡️ |
| August 6th-7th, 2025 | Practice exercises (group work) | Modules 2A-C Practice ➡️ |
| Optional | Machine Learning and Regression | Module 2D ➡️ |
| Optional | Classification | Module 2E ➡️ |
| Date | Description | Links to Notebooks(s) |
|---|---|---|
| August 7th, 2025 | Stoichometries, Propensity functions, and ODE models | Module 3A ➡️ |
| August 7th, 2025 | Practice exercises (group work) | Module 3A practice ➡️ |
| August 7th, 2025 | Stochastic simulation | Module 3B ➡️ |
| August 7th, 2025 | Practice exercises (group work) | Module 3B practice ➡️ |
| August 8th & 11th, 2025 | Chemical Master Equations | Module 3C ➡️ |
| August 8th & 11th, 2025 | Practice exercises (group work) | Module 3C practice ➡️ |
| August 11th, 2025 | Fitting Models to Data | Module 3D ➡️ |
| August 11th, 2025 | Fitting CME to Data | Module 3E ➡️ |
| Date | Description | Links to Notebooks(s) |
|---|---|---|
| August 12th, 2025 | Introduction to bacteria division | Module 4A ➡️ |
| August 12-13th, 2025 | Comparing models to experiments for bacteria populations | Module 4B ➡️ |
| August 13th, 2025 | Stochastic modeling of bacteria growth | Module 4C ➡️ |
| Date | Description | Links to Notebooks(s) |
|---|---|---|
| Optional | Bayesian Thinking | Module 5A ➡️ |
| Optional | Markov Chain Monte Carlo | Module 5B ➡️ |