Notes, examples, and outputs from LUMC coding cafés and trainings.
📖 Published at https://lumc-dcc.github.io/research_software_knowledgebase/
This knowledge base is where the output of our coding cafés, workshops, and training sessions is collected and kept. Whenever a topic is worked through at a session — a walkthrough, a worked example, a set of notes, a solution to a problem someone brought along — it is written up here so it stays available afterwards, to the people who were there and to those who were not.
It is written for researchers at LUMC: PhD candidates, MDs, technicians, and data scientists. No prior experience is assumed.
| Section | Covers |
|---|---|
| Version Control | Git basics, the core model, everyday commands, GitHub Flow, branches and pull requests |
| AI-Assisted Coding | The assisted/driven spectrum, prompting habits, AI assistants in the editor, verification and FAIR practice |
| Open & FAIR Software | FAIR principles for code, licensing, citation, packaging (in progress) |
The site is built with MyST.
npm install -g mystmd
myst start # live preview at http://localhost:3000To reproduce a production build, which needs the base path GitHub Pages serves from:
BASE_URL=/research_software_knowledgebase myst build --htmlEvery push to main rebuilds and redeploys through
.github/workflows/deploy.yml. GitHub Pages must be set to
Settings → Pages → Source: GitHub Actions, not "Deploy from a branch".
The workflow sets BASE_URL to the repository path. If the repository is ever renamed, that value
and the baseurl option in myst.yml must be updated together, or every asset and
internal link will 404.
├── index.md # landing page
├── myst.yml # site config and table of contents
├── _static/ # figures and other assets
├── version-control/ # chapter
├── ai-assisted-coding/ # chapter
├── open-science/ # chapter
└── .github/workflows/ # Pages deployment
Contributions from the LUMC community are very welcome — corrections, new topics, or notes from a session you ran. See CONTRIBUTING.md for how to propose a change and the conventions to follow.
If this knowledge base is useful in your teaching or your work, please cite it. Metadata is in
CITATION.cff, and GitHub renders a Cite this repository button from it.
To mint a DOI, connect the repository to Zenodo and publish a release;
Zenodo reads CITATION.cff automatically.
| What | Licence |
|---|---|
| Prose, figures, and teaching material | CC BY 4.0 |
| Code samples and configuration | MIT |
See LICENSE for the details. In short: reuse, adapt, and teach from this freely, including commercially, as long as you give credit.
Some material here is adapted from openly licensed research-software training resources. Each chapter credits its own sources; the fullest list is in AI-Assisted Coding → Verifying & FAIR, and includes:
- CodeRefinery — Responsible Use of Generative AI in Assisted Coding (CC BY 4.0, DOI 10.5281/zenodo.19335927)
- Carpentries Incubator — Coding with LLMs (novice) (CC BY 4.0)
- Southampton RSG — Coding with AI (CC BY 4.0)
- NL eScience Center / Carpentries Incubator — AI-assisted Coding
If you reuse a page that carries its own source note, please carry that attribution with it.
Maintained by the LUMC Research Software Training initiative. For questions, upcoming coding cafés, or training requests, see the training portal or contact the DCC.