Course materials for IDS3932 Beginners Programming for Biology, taught at Florida Atlantic University's Wilkes Honors College. Designed by Yaouen Fily (physicist), Nick Dickens (genomicist), and Andia Chaves-Fonnegra (marine ecologist).
The course is revolves around a series of Jupyter notebooks. Each notebook introduces new concepts, illustrates them with examples, and contains tasks to complete. Solutions are not included.
The wolf GPS data is not included. I promised the good people of the Voyageurs Wolf Project that I wouldn't share it willy nilly.
Week 1: Installing python/jupyter. Variables. Numbers. Strings. Task: Count the bases in a DNA sequence.
Week 2-5: Write and use a RNA translator.
Week 2: Slicing. Reading text files. Lists. Loops. Task: Parse a codon table.
Week 3: More loops. If statements. Task: Split a RNA sequence into codons. Translate a single codon.
Week 4: Functions. Task: Write a RNA translator.
Week 5: Using automatic RNA translation to analyze mutations. Task: Search HBB sequences for common mutations including sickle-cell anemia.
Week 6-7: Installing and using modules. Plotting. Statistics. Numpy. Matplotlib. Pandas. Task: Plot various biological data sets (microhabitat stats, fish trajectories, map of data collection sites, etc).
Week 8-10: Collecting and working with GPS data. Computing distances and speeds. Task: Analyze animal displacement patterns.
Week 11: Working with video and image data. Task: Analyze a video of zebrafish brain activity.
Week 12-14: Final Project.