We will have several computational tutorials throughout the course. As the course progresses, these materials will be posted below. Note: In some browsers (Firefox primarily), the end of each sentence is clipped off, making it difficult to read. If this is occurring, please try using another browser (Chrome, Safari, etc).
Tutorial 0a: Configuring your computer | This tutorial will walk you through how to install a Python 3.7 scientific computing environment.
Tutorial 0b: Using the Jupyter notebook | This tutorial will teach you how to write code and text in Jupyter notebooks.
Tutorial 0c: A Primer on Python Syntax | This tutorial will walk you through the basics of programming in Python.
Please download the following data sets, unzip them, and place them in your
pboc/data folder as described in the setting up Python tutorial.
As sometimes syntax can be difficult, we have written a file with a few functions written in Python that will make some of the in-class exercises less cumbersome. Please download them below and place them in your root
- pboc_utilities.py | Course utilities.
As we progress through the course, the code written in class will be posted here, along with the polished version of the same material.
- Tutorial 1 | Numerical Integration of Biological Growth
- Tutorial 2 | Measuring Bacterial Growth Via Microscopy
- Tutorial 3 | Stochastic Simulations
- Tutorial 4 | Integrating the Master Equation
Below is a list of useful online resources for learning the Python programming language and principles of programming in general.
How bad is your colormap. Interesting blog that discusses how the jet colormap is actually bad for displaying data.
A better default colormap. Talk at the Scipy 2015 meeting where they explain the caveats behind colormaps.