During this course, you will develop a computational prowess that will aid in your understanding of physical biology. These will be done using Jupyter notebooks through Google Colab, so you will need to sign into a Google Account to create new notebooks.

We will post links to Jupyter Notebooks hosted on colab of the tutorial sessions here.

Tutorials

Tutorial 0.0 – A Primer On Jupyter Notebooks and Google Colab | This tutorial expalins what a Jupyter Notebook is and how to use it on Google Colab
Tutorial 0.1 – A Primer On Python Syntax | This tutorial gives a quick intro to programming in Python.

Exercises

Day 2 – Tutorial 1: Update rules applied for exponential growth and constitutive expression | In this exercise, we learn apply the simplest numerical scheme to integrate an ordinary differential equation.
Day 2 – Tutorial 2: Dynamics and Stochasticity of Constitutive Expression | In this exercise, we use a chemical master equation to dissect dynamics of constitutive expression.
Day 3 – Tutorial 3: A random walker diffusing away | In this exercise, we write master equations for a random walk, giving rise to diffusion.
Day 4 – Tutorial 4: The theory of least mean square | Doing a regression on a desert island (nearly).
Day 4 – Tutorial 5: Principle component analysis of a mystery dataset | In this exercise, we find the ‘natural coordinates’ of a dataset.

Data file: trajectory.txt
Day 5– Tutorial 6: The danse of the worm | In this exercise, we will break down the danse of the worm in a couple of its favorite steps. For this we will apply principal component ananlysis to its movement as a function of times.
Day 6– Tutorial 7: The ion channel | In this exercise, we will derive the probability of an ion channel being open and closed, through data and through statistical mechanics.

Data file: Keller1986Interpolated.xls
Day 6– Tutorial 8: Cefalic Furrow | In this exercise, we will look at the position of the Cefalic Furrow as a function of the Bicoid dosage in different mutants.