# Journal de bord du Mooc / Mooc's logbook

FR

Espace réservé au journal de bord du Mooc

EN

Reserved for the Mooc's logbook

----

# Module 1

Some important points to remember and consider later on:

- Note taking of today is the summary of the long path of different approaches realized in the past
- "The Measure of All Things: The Seven-Year Odyssey and Hidden Error that Transformed the World", a must read describing a notebook example.
- Besides text: _metadata_ can be stored within images and other media (__exiftool__)
- Find the right note is crucial: necessary relevant tools use indexing to speed up search (eg. __docFetcher__)
- GitLab is used for versioning of notes
- [Markdown essentials](https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/-/blob/00c0d630fea6a1d91fc0d3e6ea1632541c63e407/module1/ressources/introduction_to_markdown.org)
- Markdown processing and PanDoc.

# Module 2

Strictness and transparency in research presentation is necessary for its reproducibility which is very important for a reputable scientific source.

Etreme power and ease of computer-based methods' use leads to more common misuse and errors due.

Reproducibility issues (in calculation, in data acquisition and representation...) can be addressed with:

1. Use a lab notebook.
2. exclude as much as possible proprietary formats and software - use text formats.
2. use open software and programming languages.
3. replicate data over several locations.
4. beware of spreadsheets and graphical tools.

On data publication (=transparency):

1. calculation errors: transparency leads to better cross-checking = help from other researchers.
2. publicly available data and methods' decriptions lead to more quotation and popularity within the scientific community (respected intellectual property).
3. sensitive data should be respected (ethical dimension): encryption with limited access.

A computational document (presentation of data + calculation code):

- Jupyter notebook: R, python, Ruby (output with Markdown, not flexible, but configurable).
- Rstudio: R, python (output with Markdown, not flexible, but configurable).
- OrgMode: any language (output with Org, very flexible with native LaTeX).

## Jupyter notebook

- careful with cell running, the environment is not changed for other cells. better run the whole document.
- lsmagic = lists commands useful in some cases (ex. to plot data).
- turning on a language works cell-wide (see %%... in lsmagic output).