Org-mode examples

module2/ressources/video_examples/README.org

+# -*- coding: utf-8 -*-
+# -*- mode: org -*-
+
+#+TITLE:       Org document examples
+#+AUTHOR:      Arnaud Legrand
+#+STARTUP: overview indent inlineimages logdrawer
+#+LANGUAGE:    en
+
+In the MOOC video, I quickly demo how org-mode can be used in various
+contexts. Here are the (sometimes trimmed) corresponding
+org-files. These documents depend on many other external data files
+and are not meant to lead to reproducible documents but it will give
+you an idea of how it can be organized:
+
+1. [[file:journal.org][journal.org]]: an excerpt (I've only left a few code samples and links
+   to some resources on R, Stats, ...) from my own journal. This is a
+   personal document where everything (meeting notes, hacking, random
+   thoughts, ...) goes by default. Entries are created with the =C-c c=
+   shortcut.
+2. [[file:labbook_single.org][labbook_single.org]]: this is an excerpt from the laboratory notebook
+   [[https://cornebize.net/][Tom Cornebize]] wrote during his Master thesis internship under my
+   supervision. This a personal labbook. I consider this notebook to be
+   excellent and was the ideal level of details for us to communicate
+   without any ambiguity and for him to move forward with confidence.
+3. [[file:paper.org][paper.org]]: this is an ongoing paper based on the previous labbook of
+   Tom Cornebize. As such it is not reproducible as there are hardcoded
+   paths and uncleaned dependencies but writing it from the labbook was
+   super easy as we just had to cut and paste the parts we
+   needed. What may be interesting is the organization and the org
+   tricks to export to the right LaTeX style.
+4. [[file:labbook_several.org][labbook_several.org]]: this is a labbook for a specific project shared
+   by several persons. As a consequence it starts with information
+   about installation, common scripts, has section with notes about all
+   our meetings, a section with information about experiments and an
+   other one about analysis. Entries could have been labeled by who
+   wrote them but there were only a few of us and this information was
+   available in git so we did not bother. In such labbook, it is common
+   to find annotations indicating that such experiment was :FLAWED: as
+   it had some issues.
+5. [[file:technical_report.org][technical_report.org]]: this is a short technical document I wrote
+   after a colleague sent me a PDF describing an experiment he was
+   conducting and asked me about how reproducible I felt it was. It
+   turned out I had to cut and paste the C code from the PDF, then
+   remove all the line numbers and fix syntax, etc. Obviously I got
+   quite different performance results but writing everything in
+   org-mode made it very easy to generate both HTML and PDF and to
+   explicitly explain how the measurements were done.
+
+