usecases

PREPARATIONS.md

@@ -27,7 +27,7 @@ Very preliminary, please update, extend, or comment.
 | 13:00 | **Git conflicts** | Martijn Vermaat?  | Merge conflicts, protected branches |
 | 13:30 | *Practical*       |                   |                           |
 | 14:00 | Break             |                   |                           |
-| 14:30 | **Data analysis** | Szymon Kiełbasa   | Project template, R-Studio, GitLab |
+| 14:30 | **Data analysis** | Szymon Kiełbasa   | [GitLab use cases: markdown, reproducible reports from Rstudio](usecases/) |
 | 15:00 | *Practical*       |                   |                           |
 | 15:30 | Leftover minutes  |                   | TODO: assign to some lecture or practical |
 | 16:00 | Questions, drinks |                   |                           |
@@ -85,4 +85,4 @@ is more than enough, or you could go though [tutorials 1-3 here](http://www.ee.s
 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
-installed. The lessons are interactive, meaning that you really need a laptop.
\ No newline at end of file
+installed. The lessons are interactive, meaning that you really need a laptop.

README.md

@@ -9,7 +9,7 @@ The Git system is widely used by software developers, but can also be used for
 project management. In the LUMC we use [GitLab](https://git.lumc.nl) as a
 collaborative environment on top of Git. By keeping track of all versions,
 history, etc, GitLab makes your projects more reproducible and collaboration
-with colleagues easy.
+with colleagues easy ([introduction](http://doc.gitlab.com/ce/gitlab-basics/README.html)). 
 
 
 ## Course dates
@@ -39,4 +39,4 @@ First clone this repository, then fetch the data from the submodule:
 A new presentation can be added like this:
 
     cd presentation
-    bash mkpres.sh ../mypresentation
\ No newline at end of file
+    bash mkpres.sh ../mypresentation

usecases/README.md

+# [gitlab](https://www.gitlab.com) and `git` use cases live demo
+
+- [markdown](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet) language
+- `README.md` file
+  - editing in the browser
+- use case: meeting minutes
+- project location and access permisions:
+  - access levels
+  - groups and individuals
+- use case: bioinformatics analysis:
+  - project skeletons
+  - integration with [Rstudio](https://www.rstudio.com/):
+    - example report in R/[Rmarkdown](http://rmarkdown.rstudio.com/)
+  - interaction with collaborators:
+    - delivering reports through [gitlab](https://www.gitlab.com)
+    - checking updates (commit logs and graphs)
+    - [tagging](https://git-scm.com/book/en/v2/Git-Basics-Tagging) repository states
+    - requesting changes ([issues](http://doc.gitlab.com/ce/gitlab-basics/create-issue.html))
+