Introductory Materials

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.

Data sets

Please download the following data sets, unzip them, and place them in your pboc/data folder.

• Data Set 1 | A series of Phase contrast images of growing E. coli colony.
• Data Set 2 | A sample phase contrast and fluorescence image of bacteria.
• Data Set 3 | A large image set of E. coli strains with varying copy numbers of the lacI repressor molecule.

Course Exercises

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.

(Exercise 1 | Measuring the growth rate of bacteria.[in class segmentation][Image segmentation to find the area][in class][Growth rate fit]

(Exercise 2 | Diffusion and random walk.[in class random walker][Coin flip for a random walker]

(Exercise 3 | Gene Expression.[in class mRNA spread the butter][Gene Expression Measurement]

(Exercise 4 | Genetic Switch.[in class dynamical system of mutual repression]