From 1bf0ff7d3b43aeea229541fe815c9cdc55a70f03 Mon Sep 17 00:00:00 2001 From: Arnaud Legrand Date: Wed, 20 Mar 2019 12:54:39 +0100 Subject: [PATCH] Cosmetics --- module2/slides/ressources.org | 54 +++++++++++++++++------------------ 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/module2/slides/ressources.org b/module2/slides/ressources.org index 2ed1954..2a1496a 100644 --- a/module2/slides/ressources.org +++ b/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 -- 2.18.1