Throughout the course, we will break out of the lecture to explore concepts more thoroughly through computational analysis. We’ll write a wide variety of code covering concepts such as mathematical techniques, stochastic simulations, and image processing. Furthermore, we will work through an experimental data set to quantify gene expression in bacterial cells.
Please work through the following tutorials before the beginning of class. The TAs will hold a special session covering these topics on Sunday, January 15th from 16:00 to 17:00 in College C.102.
Below are links to some courses you may find useful for learning programming and data analysis in biology.
Introduction to Programming in the Biological Sciences | A pboc-style course in which you learn practical programming in one weeks’ time.
Data Analysis in the Biological Sciences | A wonderful course which teaches the theory and practice of Bayesian statistics using biological data. The tutorials are shown in detail 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.
- Data Set 1 | A phase contrast image of bacteria and a graticule.
- Data Set 2 | A series of phase contrast and fluorescence images of a growing E. coli colony
- Data Set 3 | Images of developing fly embryos for identification of the position of the cephalic furrow.
- Data Set 4 | A large image set of E. coli strains with varying copy numbers of the lacI repressor molecule.
- Data Set 5 | An image set of 5’ and 3’ labeled mRNA expressing in the developing Drosophila embryo.
Course Python Utilities
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 folder as described in the setting up Python tutorial.
pboc_utils.py| Course utilities.
As we go through the course, the code we write in class will be posted here. When possible, extra tutorials with more detail and explanation will be posted as well.
Below are some coding exercises that were not performed in class, but are relevant to our discussions.