ChiTownBio presents Python 101

Aims

This course is designed to introduce the basic of Python programming to a Bioinformatics audience.

Presented by ...

• ChiTownBio
• Censibal

Terminology

Languages

• Command Line: A text-based interface for interacting with a computer system, often bash on Unix-like systems, including Mac, and cmd or powershell on Windows.
• Python: A high-level programming language known for its readability and simplicity.
• Markdown: A lightweight markup language with plain text formatting syntax.
• Jupyter Notebook: An document format that combines python and markdown code in a single document, via 'cells'.

Tools

• Repository: A storage location for software packages, often hosted on platforms like GitHub.
• Codespace: An online development environment provided by GitHub, allowing users to write and run code directly in the browser, mimicking VS Code.
• VS Code: A popular editor and IDE (Integrated Development Environment) for writing and debugging code.

Course Structure

Overview

After an initial setup, each session will consist of:

• Bio Blurb: A short presentation on a biology topic, and the broader scientific context.
• Python Primer: A brief introduction to a relevant Python concept.
• Hands-on: A practical coding challenge from the Rosalind Project, where participants will work on exercises and/or personal projects.
• Wrap-up: A summary of the session, including key takeaways and additional resources.

Our goal is to provide a solid foundation in Python programming, enabling participants to tackle bioinformatics challenges and projects with confidence.

Prelimary Schedule

Session	Date	Bio Blurb	Python Primer	Hands-on
0	6/19/25	n/a	Tooling, Data Types	Codespaces
1	TBD	DNA	Iteration	Counting Nucleotides
2	TBD	Transcription	String Operations	Transcribing DNA

Getting Started

This course is designed to be run in a GitHub Codespace, which is an online development environment. This allows you to run Python code directly in your browser, without needing to install anything on your local machine. Every GitHub user gets 60 free hours per month, well beyond what we will need for this course, but you will need to remember to stop your codespace when you are done with it to avoid unnecessary use of your free hours.

1. Sign up for a GitHub account: If you don't already have one, go to GitHub and sign up for a free account.
2. Create a Codespace: Go to the ChiTownBio Python 101 repository and click on the green "Code" button. Select "Open with Codespaces" and then "New codespace". This will create a new codespace for you, which may take a few minutes to set up.
3. Open the Codespace: Once the codespace is created, it will open in a new tab. You will see a file explorer on the left side, and a terminal at the bottom. The file explorer shows the files in your codespace, and the terminal allows you to run commands.
4. Open the Jupyter Notebook: In the file explorer, navigate to the notebooks folder and open the 00_Intro.ipynb file. This is a Jupyter Notebook, which allows you to run Python code and write markdown in the same document.
5. Stop the Codespace: When you are done with your codespace, make sure to stop it by clicking the green button again, and then the three dots next to 'Acdive', and selecting "Stop Codespace". Alternatively, you can follow these instructions to interact with any of your codespaces.