Cosmetics

module2/slides/ressources.org

@@ -5,6 +5,9 @@
 #+OPTIONS: num:nil toc:t
 #+PROPERTY: header-args :eval never-export
 
+This document gathers most references mentioned in the videos. This is
+a rather crude list.
+
 * Table of Contents                                                     :TOC:
 - [[#m2-s0-computational-documents][M2-S0: Computational Documents]]
 - [[#m2-s1-a-few-recent-controversial-studies][M2-S1: A few Recent Controversial Studies]]
@@ -15,13 +18,11 @@
 - [[#m2-s2-why-is-this-so-difficult][M2-S2: Why is This so Difficult?]]
   - [[#mistakes][Mistakes]]
   - [[#going-public][Going Public?]]
-  - [[#tools-to-avoid-and-possible-alternatives][Tools to Avoid and Possible Alternatives]]
 - [[#m2-s3-computational-documents-principles][M2-S3: Computational Documents: Principles]]
 - [[#m2-s5-collaborating][M2-S5: Collaborating]]
   - [[#preparing-a-document-for-a-journal-or-a-conference][Preparing a Document for a Journal or a Conference]]
 - [[#m2-s6-comparative-study][M2-S6: Comparative Study]]
-  - [[#see-org-mode-documents][See org-mode documents.]]
-  - [[#bonus-expériences-vécues][Bonus: expériences vécues]]
+  - [[#examples-de-document-org-mode][Examples de document Org-Mode]]
 
 * M2-S0: Computational Documents
 * M2-S1: A few Recent Controversial Studies
@@ -30,13 +31,13 @@
 - Herndon, Ash et Pollin
 - Wray: combining data across centuries, exchange rate regimes,
 ** Functional MRI
-- 2010: [[https://www.researchgate.net/publication/255651552_Neural_correlates_of_interspecies_perspective_taking_in_the_post-mortem_Atlantic_Salmon_an_argument_for_multiple_comparisons_correction][Bennett et al. and the dead salmon]] $\smiley$
+- 2010: [[https://www.researchgate.net/publication/255651552_Neural_correlates_of_interspecies_perspective_taking_in_the_post-mortem_Atlantic_Salmon_an_argument_for_multiple_comparisons_correction][Bennett et al. and the dead salmon]] \smiley
 - 2016: [[http://www.pnas.org/content/113/28/7900.abstract][Eklund, Nichols, and Knutsson]]. [[http://www.sciencealert.com/a-bug-in-fmri-software-could-invalidate-decades-of-brain-research-scientists-discover][A bug in fmri software could
-  invalidate 15 years of brain research]] \newline (/40 000 articles/)
-- 2016: But it's [[https://www.cogneurosociety.org/debunking-the-myth-that-fmri-studies-are-invalid/][more subtle than it looks like]]. [[http://blogs.warwick.ac.uk/nichols/entry/bibliometrics_of_cluster/][Nichols]].\newline /\approx 3 600
-    impacted studies/
+  invalidate 15 years of brain research]] (/40 000 articles/)
+- 2016: But it's [[https://www.cogneurosociety.org/debunking-the-myth-that-fmri-studies-are-invalid/][more subtle than it looks like]]. [[http://blogs.warwick.ac.uk/nichols/entry/bibliometrics_of_cluster/][Nichols]]. /\approx
+  3 600 impacted studies/
 ** Incorrect Protein Structures
-   [[https://people.ligo-wa.caltech.edu/~michael.landry/calibration/S5/getsignright.pdf][a "buggy software"]]
+[[https://people.ligo-wa.caltech.edu/~michael.landry/calibration/S5/getsignright.pdf][A "buggy software"]].
 ** Other domains
 - [[http://www.nature.com/nrd/journal/v10/n9/full/nrd3439-c1.html?foxtrotcallback=true][Oncology]]: "/half of published studies, even in prestigious journals,
   can't be reproduced in industrial labs/"
@@ -49,7 +50,6 @@
 - [[https://qz.com/768334/years-of-genomics-research-is-riddled-with-errors-thanks-to-a-bunch-of-botched-excel-spreadsheets/][Programming and data manipulation mistakes in Genomics]]
 ** Going Public?
 - Someone may [[http://www.nature.com/news/the-top-100-papers-1.16224][benefit from my hard work]]
-** Tools to Avoid and Possible Alternatives
 * M2-S3: Computational Documents: Principles
 * M2-S5: Collaborating
 ** Preparing a Document for a Journal or a Conference
@@ -62,26 +62,26 @@ Requirements for producing a *pdf*:
   - http://svmiller.com/blog/2016/02/svm-r-markdown-manuscript/
   - https://github.com/balouf/Kleinberg/blob/master/KleinbergsGridSimulator.ipynb
 * M2-S6: Comparative Study
-** See org-mode documents.
-** Bonus: expériences vécues 
+** [[file:../ressources/orgmode_examples/README.org][Examples de document Org-Mode]]
+# ** Bonus: expériences vécues 
 
-Éléments clés lors du choix:
-- Simplicité de prise en main vs. vrai éditeur
-- Où sont fait les calculs 
-- Multi-langage
-  - http://carreau.github.io/posts/23-Cross-Language-Integration.html
-- Gestion des langages compilés
-- Notions de caches et d'état
+# Éléments clés lors du choix:
+# - Simplicité de prise en main vs. vrai éditeur
+# - Où sont fait les calculs 
+# - Multi-langage
+#   - http://carreau.github.io/posts/23-Cross-Language-Integration.html
+# - Gestion des langages compilés
+# - Notions de caches et d'état
 
-Les principaux outils actuels:
-- jupyter
-- rstudio
-- org-mode
+# Les principaux outils actuels:
+# - jupyter
+# - rstudio
+# - org-mode
 
-Limitations:
-- Longs calculs
-- Grands documents
-- Solutions wysiwyg pour jupyter
+# Limitations:
+# - Longs calculs
+# - Grands documents
+# - Solutions wysiwyg pour jupyter
 
-Historique/diff un peu compliqué pour jupyter
+# Historique/diff un peu compliqué pour jupyter