This handbook is a practical, open resource for researchers at LUMC who write code — whether you script your analysis in Python, manage pipelines in Snakemake, or build tools shared with colleagues. It is inspired by The Turing Way and adapted for the daily realities of biomedical research software.
Who is this for?¶
This handbook is for:
Researchers who write analysis scripts and want to make them more reproducible
PhD students and postdocs getting started with collaborative coding
Lab leads looking to establish good software practices in their group
Anyone who has ever lost a week of work because they forgot what their code did
No prior software engineering experience required. We assume you know some programming — the rest we will explain.
How to use this book¶
Each chapter is self-contained. Start with Git Basics if you are new to version control, or jump to the topic most relevant to your current work. Code examples are copy-paste ready. Commands shown in code blocks are meant to be run in your terminal.
Track changes, collaborate without chaos, and never lose work again. Covers Git from the ground up and GitHub Flow for teams.
Make your software findable, accessible, interoperable, and reusable. Covers licensing, citation, README best practices, and packaging.
Contributing¶
This handbook is a living document. If you spot an error, have a suggestion, or want to add a section, please open an issue or pull request on GitHub. Contributions from the LUMC community are very welcome.