https://github.com/katrinleinweber/git-for-bio-scientists
Presentation about digital lab journalling with Git
https://github.com/katrinleinweber/git-for-bio-scientists
collaboration git git-vocabulary gitignore gitlab science scientists
Last synced: about 1 month ago
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Presentation about digital lab journalling with Git
- Host: GitHub
- URL: https://github.com/katrinleinweber/git-for-bio-scientists
- Owner: katrinleinweber
- Created: 2015-04-02T06:49:42.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2022-08-22T13:31:47.000Z (over 2 years ago)
- Last Synced: 2025-03-29T10:05:05.094Z (about 2 months ago)
- Topics: collaboration, git, git-vocabulary, gitignore, gitlab, science, scientists
- Language: TeX
- Homepage:
- Size: 6.92 MB
- Stars: 32
- Watchers: 4
- Forks: 4
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Funding: .github/FUNDING.yml
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README
---
title: Digital Lab Journalling with Git
author: Katrin Leinweber
date: 2015-Apr-13
license: CC-BY-4.0 for own content; image attributions in titles
---
_Slides of this presentation [with recorded audio](http://cdn.podsee.org/konscience/ksl002-digital-lab-journalling-with-git.mp4)_ ([archived notes](http://web.archive.org/web/20200925013644/http://www.konscience.de/2015/04/ksl002-digital-lab-journalling-with-git/))
### Tree of Life
[](https://www.science.org/doi/full/10.1126/science.284.5423.2124)
### Tree of Life
[](http://www.nature.com/nrmicro/journal/v3/n9/fig_tab/nrmicro1253_F1.html)
### Tree of Projects
### Git tracks digital evolution of files
- highlights exactly what changed, line by line
- makes you comment file changes
### Git is your file watchdog.
### Good against: too many files
### Good for: tidy project folders, but...
### Good for: ...version history still accessible
### Version control with Git
#### Technical
- works best for line- or paragraph-based files
- built for source code, but also useful for texts and simple images
- less useful for complex or large file types
- not a substitute for full backups
#### Cultural
- helps build self-explanatory & verifiable project documentation (for your future self, colleagues, students, reviewers...)
- enables less painful collaboration on same set of files
- conflicts only if same lines in same file get changed
- for text files: better than syncing tools
### Basic Git vocabulary: repository/repo
- project folder watched by Git
- is still a normal folder: add, edit & delete files normally
- database of file versions in hidden subfolder
### Basic Git vocabulary: committing
- saving a logical set of file changes in Git, together with meaningful comment
- changes can be within single file, or across different ones
- **commit history:** self-explanatory & verifiable documentation
### Basic Git vocabulary: .gitignore
- file that contains a repo's rules for ignoring files
- No preview of highlighted changes? Large file? Auto-generated? Rather ignore those!
[](http://edc.education.ed.ac.uk/sindhur/2010/10/17/visual-artefact/)
### Basic Git vocabulary: .gitignore in GitHub for Windows
### Vocabulary summary
#### repository/repo
- project folder watched by Git, plus hidden database of file versions
#### committing
- composing logical set of file changes and meaningful commit message
#### .gitignore
- a repo's ignore rules for non-essential files & file types
### How to start using Git?
1. download client from [windows.github.com](https://windows.github.com/) (any other from [git-scm.com/downloads/guis](http://git-scm.com/download/gui/win)) & install
1. start with small sub-project (protocol optimisation, diagram in R, report, etc.)
1. **besides working on the files themselves:** commit logically connected changes often
1. **recommended:** start writing texts in Markdown[^1] format
1. **optional (for collaboration etc.):** create account with Git hosting service like [GitLab](https://gitlab.com/users/sign_in) or [GitHub](https://github.com/join)
[^1]: Possible in Word with [Writage](http://www.writage.com/) add-in
### Thanks to & Further Reading
##### Writing with Git
- "[Markdown Basics](https://help.github.com/articles/markdown-basics/#basic-writing)" and "[Mastering Markdown](https://guides.github.com/features/mastering-markdown/)" by [GitHub](https://github.com/)
- "[Scientific Markdown](https://github.com/JensErat/scientific-markdown)" by Jens Erat
- "[Paper Now](https://github.com/PeerJ/paper-now#paper-now)" by [PeerJ](https://peerj.com/)
##### Git in Science
- "[Git/GitHub: a Primer for Researchers](http://datapub.cdlib.org/2014/05/05/github-a-primer-for-researchers/)" by [Carly Strasser](http://carlystrasser.net/)
- "[We Need a Github of Science](http://marciovm.com/i-want-a-github-of-science/)" by [Marcio von Muhlen](https://twitter.com/marciovm)
- "[Git for Scientists](https://mollygibson.github.io/2014-08-11-wustl/lessons/git-notebook/git-for-scientists.slides.html)" by [Molly Gibson](https://github.com/mollygibson)
##### Git concepts & tech
- "[Learn Version Control with Git](https://www.git-tower.com/learn/git/ebook)" by [Fournova](http://www.fournova.com/)
- "[10 Years of Git: An Interview with Git Creator Linus Torvalds](https://www.linux.com/news/10-years-git-interview-git-creator-linus-torvalds/)" by [Jennifer Cloer](https://twitter.com/JenniferCloer)
### Thanks for your attention! Questions?
