Git and GitHub at INBO

Open Science Café session on 25 November 2025 dedicated to introduce the concepts of (distributed) version control and how impactful it is at INBO, Research Institute for Nature and Forest. Some participants will participate to the hands-on workshop following this event.

Transcript

1. 25-11-2025 - Damiano Oldoni Git and GitHub @ INBO Git logo by Jason Long, CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=19329352 GitHub logo by GitHub, CC BY 4.0
2. Imagine a place where: - Working collaboratively is easy and fun - No files are lost Welcome to distributed (GitHub) version control (git). Imagine Photo by Ben Potter / UAF Jan 2018 - Ancient DNA discovery reveals previously unknown population of native Americans
3. - A Git world is a better world (Open Science Café) - GitHub at INBO (Open Science Café) - Hands-on workshop using Github Desktop Agenda Photo by Ben Potter / UAF
4. Do not reinvent the wheel: give a look to our Git course, made-in-INBO. A Git world is a better world Commits and branches history of some repositories. From top: trias R package, craywatch website and alien species portal.
5. - github.com/inbo: Open source, data and science initiatives of INBO - 510 repositories (217 private) - 26 projects (4 private) - 140 people - 27 teams - INBO > INBO’s GitHub organisation Git + GitHub + INBO = ♡ INBO GitHub homepage.
6. - Craywatch, vespawatch and INBO coding club websites - Petridish website theme - INBO protocols - {rgbif}, {digest} R packages - {qgisprocess}, {git2rdata} R packages - Camtrap DP data exchange format Git + GitHub + INBO = ♡
7. - Citizen science project - Project website is a repository on GitHub - Collections of (Markdown) pages + (yaml) settings - Website rendered and hosted by GitHub via GitHub Pages Craywatch Crawywatch species webpage.
8. - Oscibio: tech know-how - Oscibio: “Crash course Git & GitHub” (100% hands-on) - Goal: self-reliance 💪 - 1738 commits, 245 closed Pull Requests 😲 Craywatch Screenshot of Crash course event from my Google Calendar on top of craywatch GitHub repository.
9. Petridish - Petridish is a Jekyll (website generator) theme for research project websites, personal blog or lab website󰟾 - mobile-friendly, free, easy to customize - works well with GitHub Pages - Petridish is a GitHub repo itself - 56 stars, 45 forks Petridish homepage.
10. Vespa-Watch - Flemish reporting centre for nests and individuals of Asian hornets. - Another petridish-based website maintained via GitHub and GitHub Pages - Vespa-Watch repository Vespa-Watch homepage.
11. INBO Coding Club - Static website - Hosted on GitHub Pages - Earlier on INBO’s Google Drive - Problems with file permissions (external invites) - Cut&Paste phobia😨 - 2314 commits INBO Coding Club session page with reference material.
12. INBO Protocols - Ecosystem of GitHub repositories - protocolsource: protocols development, source files (Rmarkdown) - protocols: generated html/PDFs, shown on protocols.inbo.be - {protocolhelper} R package: helper functions and templates to manage the protocolsource repository INBO protocols homepage (left, top), {protocolhelper} functions page (right, back).
13. Contribute 🤝 Is there an useful, open R package available? Would you like to: - Extend its functionality? - Improve its documentation? CONTRIBUTE! Examples: - {rgbif} (Damiano, Peter) - {digest} (Thierry) Damiano Oldoni’s pull requests for {rgbif} (left, back) Thierry Onkelinx’s pull request for {digest} (right, top)
14. INBO ♡ open science - R packages hosted by worldwide important GitHub organizations - {qgisprocess}: hosted by r-spatial Floris Vanderhaeghe (INBO) is maintainer of {qgisprocess}: an R package to use QGIS processing algorithms.
15. INBO ♡ open science - R packages hosted by worldwide important open software organizations - {qgisprocess}: hosted by r-spatial - {git2rdata}: hosted by rOpenSci Thierry Honkelinx (INBO) is maintainer of {git2rdata}: an R package for storing and retrieving data.frames in git repositories.
16. INBO ♡ open science - R packages hosted by worldwide important GitHub organizations - {qgisprocess}: hosted by r-spatial - {git2rdata}: hosted by rOpenSci - {frictionless}: hosted by Frictionless Data Peter Desmet (INBO) is maintainer of {frictionless}: an R package to read and write Frictionless Data Packages.
17. How to develop standards together Git and GitHub help developing community driven data standards, e.g. TDWG’s standards: - Darwin Core, see dwc (GitHub repository) - Camtrap DP, see camtrap-dp (GitHub repository) Don’t you notice something familiar? Yes, two other “petridish websites” 🧫
18. Thank you! @damianooldoni.bsky.social damiano.oldoni@inbo.be 0000-0003-3445-7562 bit.ly/github-inbo ♡ + + =