diff --git a/html_src_files.lst b/html_src_files.lst index 17bea0b6d0a8dccebdd2728d90725cfdd9c3abef..443a92e3b2ebf0218c92ac2893e412556ed965f0 100644 --- a/html_src_files.lst +++ b/html_src_files.lst @@ -28,9 +28,12 @@ ./module2/ressources/python_r_latex.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/19c2b1de7766484bae73f3ab133463c6 ./module2/exo4/stat_activity.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/b52e4bd2198947a8b28b5e648184048c ./module2/exo4/stat_activity_fr.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/b52e4bd2198947a8b28b5e648184048c -./module2/slides/ressources.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/36723edefc72488ab44e269501cfc9f8 -./module2/slides/ressources_fr.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/36723edefc72488ab44e269501cfc9f8 - +./module2/slides/ressources_S1.org # +./module2/slides/ressources_S1_fr.org # +./module2/slides/ressources_S2.org # +./module2/slides/ressources_S2_fr.org # +./module2/slides/ressources_S5.org # +./module2/slides/ressources_S5_fr.org # ./module3/ressources/iso_date_format.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/316fc24edc1b44278ada4ca531c705be ./module3/ressources/iso_date_format_fr.org # https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/316fc24edc1b44278ada4ca531c705be diff --git a/module2/slides/ressources.org b/module2/slides/ressources.org deleted file mode 100644 index ac3d62f8e6edb31e4fc51683ffd86448ddd81137..0000000000000000000000000000000000000000 --- a/module2/slides/ressources.org +++ /dev/null @@ -1,87 +0,0 @@ -# -*- mode: org -*- -#+TITLE: Computational Documents -#+DATE: June, 2018 -#+STARTUP: overview indent -#+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]] - - [[#economy-austerity-in-fiscal-policy][Economy: Austerity in Fiscal Policy]] - - [[#functional-mri][Functional MRI]] - - [[#incorrect-protein-structures][Incorrect Protein Structures]] - - [[#other-domains][Other domains]] -- [[#m2-s2-why-is-this-so-difficult][M2-S2: Why is This so Difficult?]] - - [[#mistakes][Mistakes]] - - [[#going-public][Going Public?]] -- [[#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]] - - [[#exemples-of-org-mode-documents][Exemples of Org-Mode documents]] - -* M2-S0: Computational Documents -* M2-S1: A few Recent Controversial Studies -** Economy: Austerity in Fiscal Policy -- [[https://en.wikipedia.org/wiki/Growth_in_a_Time_of_Debt][Reinhart et Rogoff]]: /Growth in a Time of Debt/ -- 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 -- 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]] (/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"]]. -** 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/" -- [[http://theconversation.com/we-found-only-one-third-of-published-psychology-research-is-reliable-now-what-46596][Psychology]]: "/attempting to reproduce 100 previously published - findings/, /only one-third of published psychology research was found - to be reliable/" -* M2-S2: Why is This so Difficult? -** Mistakes -- [[http://theconversation.com/how-computers-broke-science-and-what-we-can-do-to-fix-it-49938][Computers broke science]] -- [[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]] -* M2-S3: Computational Documents: Principles -* M2-S5: Collaborating -** Preparing a Document for a Journal or a Conference -Requirements for producing a *pdf*: -- Internally, /pandoc/, /knitr/ or /emacs/org-mode/ -- /LaTeX/ should be installed - - - http://blog.juliusschulz.de/blog/ultimate-ipython-notebook - - https://github.com/kirbs-/hide_code is a must-have - - http://svmiller.com/blog/2016/02/svm-r-markdown-manuscript/ - - https://github.com/balouf/Kleinberg/blob/master/KleinbergsGridSimulator.ipynb -* M2-S6: Comparative Study -** [[file:../ressources/orgmode_examples/README.org][Exemples of Org-Mode documents]] -# ** 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 - -# Les principaux outils actuels: -# - jupyter -# - rstudio -# - org-mode - -# Limitations: -# - Longs calculs -# - Grands documents -# - Solutions wysiwyg pour jupyter - -# Historique/diff un peu compliqué pour jupyter - diff --git a/module2/slides/ressources_S1.org b/module2/slides/ressources_S1.org new file mode 100644 index 0000000000000000000000000000000000000000..e75602e67336d58bb012f5d9f9591059f438f748 --- /dev/null +++ b/module2/slides/ressources_S1.org @@ -0,0 +1,26 @@ +# -*- mode: org -*- +#+TITLE: A few Recent Controversial Studies +#+DATE: June, 2018 +#+STARTUP: overview indent +#+OPTIONS: num:nil toc:t +#+PROPERTY: header-args :eval never-export + + +* Economy: Austerity in Fiscal Policy +- [[https://en.wikipedia.org/wiki/Growth_in_a_Time_of_Debt][Reinhart et Rogoff]]: /Growth in a Time of Debt/ +- 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 +- 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]] (/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"]]. +* 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/" +- [[http://theconversation.com/we-found-only-one-third-of-published-psychology-research-is-reliable-now-what-46596][Psychology]]: "/attempting to reproduce 100 previously published + findings/, /only one-third of published psychology research was found + to be reliable/" diff --git a/module2/slides/ressources_S1_fr.org b/module2/slides/ressources_S1_fr.org new file mode 100644 index 0000000000000000000000000000000000000000..b83fa22d106a049928dc62a79b4b03150ee260c5 --- /dev/null +++ b/module2/slides/ressources_S1_fr.org @@ -0,0 +1,26 @@ +# -*- mode: org -*- +#+TITLE: Exemples récents d'études assez discutées +#+DATE: June, 2018 +#+STARTUP: overview indent +#+OPTIONS: num:nil toc:t +#+PROPERTY: header-args :eval never-export + +* Économie: Politiques d'austérité +- [[https://en.wikipedia.org/wiki/Growth_in_a_Time_of_Debt][Reinhart et Rogoff]]: /Growth in a Time of Debt/ +- Herndon, Ash et Pollin +- Wray: combining data across centuries, exchange rate regimes, +* Les IRM fonctionnelles +- 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.: le saumon mort]] \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][Un bug dans les logiciels d'IRM + pourrait invalider 15 années de recherche sur le cerveau]] (/40 000 articles/) +- 2016: C'est [[https://www.cogneurosociety.org/debunking-the-myth-that-fmri-studies-are-invalid/][plus subtil que ça]]. [[http://blogs.warwick.ac.uk/nichols/entry/bibliometrics_of_cluster/][D'après Nichols, un des auteurs de + l'article d'origine]], c'est plutôt de l'ordre de /3 600 études qui + seraient potentiellement impactées/. +* Les fausses structures de protéines +[[https://people.ligo-wa.caltech.edu/~michael.landry/calibration/S5/getsignright.pdf][A "buggy software"]]. +* Autres domaines +- [[http://www.nature.com/nrd/journal/v10/n9/full/nrd3439-c1.html?foxtrotcallback=true][Oncologie]]: "/half of published studies, even in prestigious journals, + can't be reproduced in industrial labs/" +- [[http://theconversation.com/we-found-only-one-third-of-published-psychology-research-is-reliable-now-what-46596][Psychologie]]: "/attempting to reproduce 100 previously published + findings/, /only one-third of published psychology research was found + to be reliable/" diff --git a/module2/slides/ressources_S2.org b/module2/slides/ressources_S2.org new file mode 100644 index 0000000000000000000000000000000000000000..7c900201b26d2172217273ccfc7b633dce84eadd --- /dev/null +++ b/module2/slides/ressources_S2.org @@ -0,0 +1,14 @@ +# -*- mode: org -*- +#+TITLE: Why is This so Difficult? +#+DATE: June, 2018 +#+STARTUP: overview indent +#+OPTIONS: num:nil toc:t +#+PROPERTY: header-args :eval never-export + +* Mistakes +- [[http://theconversation.com/how-computers-broke-science-and-what-we-can-do-to-fix-it-49938][Computers broke science]] +- [[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]]. The most cited papers are + those describing a new technique or some software that has allowed a + community of researchers to evolve and go farther. diff --git a/module2/slides/ressources_S2_fr.org b/module2/slides/ressources_S2_fr.org new file mode 100644 index 0000000000000000000000000000000000000000..ddf772731b2969ab0d7ea7de41e2ade8cb7ff527 --- /dev/null +++ b/module2/slides/ressources_S2_fr.org @@ -0,0 +1,14 @@ +# -*- mode: org -*- +#+TITLE: Pourquoi est-ce difficile? +#+DATE: June, 2018 +#+STARTUP: overview indent +#+OPTIONS: num:nil toc:t +#+PROPERTY: header-args :eval never-export + +* Les erreurs classiques +- [[http://theconversation.com/how-computers-broke-science-and-what-we-can-do-to-fix-it-49938][Enquoi les ordinateurs ont "cassé" la science]] +- [[https://qz.com/768334/years-of-genomics-research-is-riddled-with-errors-thanks-to-a-bunch-of-botched-excel-spreadsheets/][Erreurs de programmation et de manipulation de données en génomique]] +* Tout rendre publique ? +- Quelqu'un pourrait [[http://www.nature.com/news/the-top-100-papers-1.16224][tirer parti de mon dur labeur]]. Les papiers les + plus cités sont des papiers qui décrivent une nouvelle technique ou + un logiciel permettant à une communauté de recherche d'avancer. diff --git a/module2/slides/ressources_S5.org b/module2/slides/ressources_S5.org new file mode 100644 index 0000000000000000000000000000000000000000..986d9a3b712bfaecd04ff9e4f127ec25694402cc --- /dev/null +++ b/module2/slides/ressources_S5.org @@ -0,0 +1,16 @@ +# -*- mode: org -*- +#+TITLE: Collaborating +#+DATE: June, 2018 +#+STARTUP: overview indent +#+OPTIONS: num:nil toc:t +#+PROPERTY: header-args :eval never-export + +* Preparing a Document for a Journal or a Conference +Requirements for producing a *pdf*: +- Internally, /pandoc/, /knitr/ or /emacs/org-mode/ +- /LaTeX/ should be installed + + - http://blog.juliusschulz.de/blog/ultimate-ipython-notebook + - https://github.com/kirbs-/hide_code is a must-have + - http://svmiller.com/blog/2016/02/svm-r-markdown-manuscript/ + - https://github.com/balouf/Kleinberg/blob/master/KleinbergsGridSimulator.ipynb diff --git a/module2/slides/ressources_S5_fr.org b/module2/slides/ressources_S5_fr.org new file mode 100644 index 0000000000000000000000000000000000000000..6653eb77b6fce909a140df4fbb84f2246ea798d9 --- /dev/null +++ b/module2/slides/ressources_S5_fr.org @@ -0,0 +1,16 @@ +# -*- mode: org -*- +#+TITLE: Travailler avec les autres +#+DATE: June, 2018 +#+STARTUP: overview indent +#+OPTIONS: num:nil toc:t +#+PROPERTY: header-args :eval never-export + +* Préparation d'un document pour un journal ou pour une conférence +De quoi aurez-vous besoin pour produire un document *pdf*: +- En interne: /pandoc/, /knitr/ ou /emacs/org-mode/. +- /LaTeX/ devra aussi être installé +Voici quelques billets intéressants sur le sujet: + - http://blog.juliusschulz.de/blog/ultimate-ipython-notebook + - https://github.com/kirbs-/hide_code is a must-have + - http://svmiller.com/blog/2016/02/svm-r-markdown-manuscript/ + - https://github.com/balouf/Kleinberg/blob/master/KleinbergsGridSimulator.ipynb diff --git a/module2/slides/ressources_fr.org b/module2/slides/ressources_fr.org deleted file mode 100644 index 7174d072b30f8a4181d83dab24e53e25bda4494b..0000000000000000000000000000000000000000 --- a/module2/slides/ressources_fr.org +++ /dev/null @@ -1,89 +0,0 @@ -# -*- mode: org -*- -#+TITLE: Le document computationnel -#+DATE: June, 2018 -#+STARTUP: overview indent -#+OPTIONS: num:nil toc:t -#+PROPERTY: header-args :eval never-export - -Ce document rassemble la plupart des références mentionnées dans les -vidéos. C'est une liste relativement grossière qui mériterait d'être -améliorée. - -* Table des matières :TOC: -- [[#m2-s0-le-document-computationnel][M2-S0: Le document computationnel]] -- [[#m2-s1-exemples-récents-détudes-assez-discutées][M2-S1: Exemples récents d'études assez discutées]] - - [[#économie-politiques-daustérité][Économie: Politiques d'austérité]] - - [[#les-irm-fonctionnelles][Les IRM fonctionnelles]] - - [[#les-fausses-structures-de-protéines][Les fausses structures de protéines]] - - [[#autres-domaines][Autres domaines]] -- [[#m2-s2-pourquoi-est-ce-difficile][M2-S2: Pourquoi est-ce difficile?]] - - [[#les-erreurs-classiques][Les erreurs classiques]] - - [[#tout-rendre-publique][Tout rendre publique ?]] -- [[#m2-s3-le-document-computationnel-principe][M2-S3: Le document computationnel : principe]] -- [[#m2-s5-travailler-avec-les-autres][M2-S5: Travailler avec les autres]] - - [[#préparation-dun-document-pour-un-journal-ou-pour-une-conférence][Préparation d'un document pour un journal ou pour une conférence]] -- [[#m2-s6-analyse-comparée-des-différents-outils][M2-S6: Analyse comparée des différents outils]] - - [[#exemples-de-document-org-mode][Exemples de document Org-Mode]] - -* M2-S0: Le document computationnel -* M2-S1: Exemples récents d'études assez discutées -** Économie: Politiques d'austérité -- [[https://en.wikipedia.org/wiki/Growth_in_a_Time_of_Debt][Reinhart et Rogoff]]: /Growth in a Time of Debt/ -- Herndon, Ash et Pollin -- Wray: combining data across centuries, exchange rate regimes, -** Les IRM fonctionnelles -- 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.: le saumon mort]] \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][Un bug dans les logiciels d'IRM - pourrait invalider 15 années de recherche sur le cerveau]] (/40 000 articles/) -- 2016: C'est [[https://www.cogneurosociety.org/debunking-the-myth-that-fmri-studies-are-invalid/][plus subtil que ça]]. [[http://blogs.warwick.ac.uk/nichols/entry/bibliometrics_of_cluster/][D'après Nichols, un des auteurs de - l'article d'origine]], c'est plutôt de l'ordre de /3 600 études qui - seraient potentiellement impactées/. -** Les fausses structures de protéines -[[https://people.ligo-wa.caltech.edu/~michael.landry/calibration/S5/getsignright.pdf][A "buggy software"]]. -** Autres domaines -- [[http://www.nature.com/nrd/journal/v10/n9/full/nrd3439-c1.html?foxtrotcallback=true][Oncologie]]: "/half of published studies, even in prestigious journals, - can't be reproduced in industrial labs/" -- [[http://theconversation.com/we-found-only-one-third-of-published-psychology-research-is-reliable-now-what-46596][Psychologie]]: "/attempting to reproduce 100 previously published - findings/, /only one-third of published psychology research was found - to be reliable/" -* M2-S2: Pourquoi est-ce difficile? -** Les erreurs classiques -- [[http://theconversation.com/how-computers-broke-science-and-what-we-can-do-to-fix-it-49938][Enquoi les ordinateurs ont "cassé" la science]] -- [[https://qz.com/768334/years-of-genomics-research-is-riddled-with-errors-thanks-to-a-bunch-of-botched-excel-spreadsheets/][Erreurs de programmation et de manipulation de données en génomique]] -** Tout rendre publique ? -- Quelqu'un pourrait [[http://www.nature.com/news/the-top-100-papers-1.16224][tirer parti de mon dur labeur]] -* M2-S3: Le document computationnel : principe -* M2-S5: Travailler avec les autres -** Préparation d'un document pour un journal ou pour une conférence -De quoi aurez-vous besoin pour produire un document *pdf*: -- En interne: /pandoc/, /knitr/ ou /emacs/org-mode/. -- /LaTeX/ devra aussi être installé -Voici quelques billets intéressants sur le sujet: - - http://blog.juliusschulz.de/blog/ultimate-ipython-notebook - - https://github.com/kirbs-/hide_code is a must-have - - http://svmiller.com/blog/2016/02/svm-r-markdown-manuscript/ - - https://github.com/balouf/Kleinberg/blob/master/KleinbergsGridSimulator.ipynb -* M2-S6: Analyse comparée des différents outils -** [[file:../ressources/orgmode_examples/README_fr.org][Exemples 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 - -# Les principaux outils actuels: -# - jupyter -# - rstudio -# - org-mode - -# Limitations: -# - Longs calculs -# - Grands documents -# - Solutions wysiwyg pour jupyter - -# Historique/diff un peu compliqué pour jupyter -