Python for Biologists — Workshop Tutorial

Muhammad Bilal Department of Biological Sciences, Oakland University, Rochester MI

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hey everyone! this is the complete workshop tutorial notebook.

everything is in one place — no jumping between files. open the notebook, start from the top, and work through it at your own pace.

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the notebook covers

section	what you learn
Session 1	variables, data types, strings, lists, loops, functions
Session 2	dictionaries, reading FASTA files, reading/writing CSV
Session 3	pandas for data analysis, making publication-ready plots
Mini Project	build a complete sequence analyser from scratch
Error Reference	common errors and how to fix them

biology examples throughout — GC content, genome stats, growth curves, FASTA parsing. every error shown comes with an explanation and a fix.

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how to open the notebook

option 1 — google colab (easiest, no install needed)

1. go to https://colab.research.google.com
2. click File > Open notebook > GitHub
3. paste this URL: https://github.com/mbilal-OU/python_workshop
4. open Python_Workshop_Biology.ipynb

option 2 — run on your own computer

# install what you need
pip install jupyter notebook pandas matplotlib

# get the files
git clone https://github.com/mbilal-OU/python_workshop.git
cd python_workshop

# start jupyter
jupyter notebook

then click Python_Workshop_Biology.ipynb.

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before you start

run cells from top to bottom jupyter runs cells in the order you tell it to. if you skip cells, later ones might fail because earlier code never ran. if things break, go to Kernel > Restart & Run All.

errors are normal everyone gets them. even experienced programmers. when you see a red error box, read what it says — Python usually tells you exactly what's wrong. the Error Reference section at the bottom of the notebook covers the most common ones.

type the code yourself copy-paste works but typing it helps you remember it. and changing values to see what happens is honestly the best way to learn.

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what you need installed

for most of the notebook, just Python + Jupyter is enough.

for Session 3 (pandas and plotting):

pip install pandas matplotlib

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files in this repo

Python_Workshop_Biology.ipynb   <- the main tutorial (start here)
data/
  example_sequences.fasta       <- sample FASTA file to practice with
  example_data.csv              <- sample growth curve data
README.md
requirements.txt

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questions?

if something doesn't make sense, ask in class. if you find a mistake, let me know.

good luck :)