2025-CBP-SummerSchool

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
Some materials adapted from: uqbio2024 Summer School

Course Materials
Setting up Google Colab
Getting started with GitHub
Licensing

Course Materials

Below are the course materials for the 2025 CBP Summer School. Please pull to refresh this repository often as these materials may change at any time up to the actual lecture date!

Module 1: Getting started with numerical simulations and scientific computing in Python.

Date	Description	Links to Notebooks(s)
August 4th, 2025	Google Colab introduction	Module 1A ➡️
August 4th, 2025	Python basics and data types	Module 1B ➡️
August 4th, 2025	Loops, ranges, functions	Module 1C ➡️
August 4th, 2025	Packages, classes & modules, file management basics	Module 1D ➡️
August 5th, 2025	Numpy and linear algebra review	Module 1E ➡️
August 5th, 2025	Visualing data using matplotlib and seaborn	Module 1F ➡️

Module 2: Multivariable statistics

Date	Description	Links to Notebooks(s)
August 6th, 2025	Distributions	Module 2A ➡️
August 6th, 2025	Likelihooods	Module 2B ➡️
August 6th, 2025	Signficance testing	Module 2C ➡️
August 6th, 2025	Machine Learning and Regression	Module 2D ➡️
August 6th, 2025	Classification	Module 2E ➡️

Module 3: Computational modeling: from continuous to stochastic models

Date	Description	Links to Notebooks(s)
August 7th, 2025	Stoichometries, Propensity functions, and ODE models	Module 3A ➡️
August 8th, 2025	Stochastic simulation	Module 3B ➡️
August 11th, 2025	Chemical Master Equations	Module 3C ➡️

Module 4: Computational modeling: Bayesian approaches

Date	Description	Links to Notebooks(s)
August 11th, 2025	Bayesian Thinking	Module 4A ➡️
August 12th, 2025	Markov Chain Monte Carlo	Module 4B ➡️

Module 5: Modeling bacteria cell division

Date	Description	Links to Notebooks(s)
August 12th, 2025	Continuous models of bacteria populations
August 13th, 2025	Stochastic models of bacteria populations

Setting up Google Colab

Getting started with GitHub

Licensing