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# Preparations for course: Code and data management with Git
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- Date: December 1st, 2015
- Time: 9:00 - 17:00
- Location: T-0-010
- Teachers:
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  - Martijn Vermaat (m.vermaat.hg@lumc.nl)
  - Jeroen Laros (j.f.j.laros@lumc.nl)
  - Wibowo Arindrarto (W.Arindrarto@lumc.nl)
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  - Szymon M. Kiełbasa (S.M.Kielbasa@lumc.nl)
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## Program

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Very preliminary, please update, extend, or comment.

| Time  | Subject           | Teacher           | Contents                  |
| ----- | ----------------- | ----------------- | ------------------------- |
| 09:00 | **Introduction**  | Jeroen Laros      | Welcome, GitLab overview  |
| 09:30 | *Practical*       |                   |                           |
| 09:45 | **Git basics**    | Wibowo Arindrarto | Basic Git command line fu |
| 10:15 | *Practical*       |                   |                           |
| 10:45 | Coffee            |                   |                           |
| 11:00 | **Git remotes**   | Martijn Vermaat   | Collaborating via GitLab  |
| 11:30 | *Practical*       |                   |                           |
| 12:00 | Lunch             |                   |                           |
| 13:00 | **Git conflicts** | Martijn Vermaat?  | Merge conflicts, protected branches |
| 13:30 | *Practical*       |                   |                           |
| 14:00 | Break             |                   |                           |
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| 14:30 | **Data analysis** | Szymon M. Kiełbasa | [GitLab use cases: markdown, reproducible reports from Rstudio](usecases/) |
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| 15:00 | *Practical*       |                   |                           |
| 15:30 | Leftover minutes  |                   | TODO: assign to some lecture or practical |
| 16:00 | Questions, drinks |                   |                           |

- Branches: not in this course
- Git annex: not in this course
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## Participants

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Confirmed:

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1. Tom van Bavel
2. Ekrem Sabir
3. Haoyu Wu
4. Nicolas Bastidas
5. Vincent de Bakker
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Cancelled:
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1. Johan den Dunnen
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2. Martijn Eenink
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3. Roel Zinkstok
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4. Saeed Katiraei
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5. Tarek Malas
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6. Roberta Rivoto
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## Course materials
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We can reuse many slides from last year, see the contents of this repository.

We will provide the course materials and program via GitLab. So this GitLab
project will be the course homepage.

The old course homepage can still be found here, but will be deleted before the
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course starts: https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/gitcourse


# Prerequisites

Affinity with the UNIX shell is required before taking the course. For example,
our [scripting course](https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/scripting)
is more than enough, or you could go though [tutorials 1-3 here](http://www.ee.surrey.ac.uk/Teaching/Unix/).

We encourage you to bring your own laptop, but make sure it has the necessary
software installed (see [Software installation](https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/gitcourse/SoftwareInstallation)).
We can also provide you with a laptop that has all the required software
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installed. The lessons are interactive, meaning that you really need a laptop.