Python Programming for Biologists is an open set of teaching materials built from a seminar series that started at NIAID/NIH in 2015 to help wet-lab scientists, analysts, and staff learn Python for real biological data. These sessions have been used to train researchers at NIH (2015-2025) in Bethesda, Maryland and at NIEHS (2015 to present) in Research Triangle Park, North Carolina.
The notebooks and slides in this repository walk through the core skills needed to move from zero Python experience to doing data analysis, visualization, and bioinformatics workflows in a reproducible way.
- Working at the command line (UNIX shell)
- Using Jupyter Notebooks for interactive analysis
- Python fundamentals for new programmers
- Python language essentials for experienced coders
- Data analysis with pandas
- Plotting and visualization in Python
- Intermediate Python and best practices
- Bioinformatics scripting and pipelines
- Building automated workflows
- Storing and querying biomedical data with SQL & NoSQL
- Principles and tools for reproducible science
Created and maintained by R. Burke Squires (Computational Genomics, bioinformatics training, and reproducible workflows).
This project grew out of seminars originally offered, at no cost, by the NIAID Bioinformatics and Computational Biosciences Branch (BCBB) within the Office of Cyberinfrastructure and Computational Biology (OCICB).