diff --git a/module2/slides/Makefile b/module2/slides/Makefile index 5b13068d64e137f7269f728f6274fa16ddae86af..1eeb584d78cbdb3efd3a4185edb1a9331a300c47 100644 --- a/module2/slides/Makefile +++ b/module2/slides/Makefile @@ -1,3 +1,7 @@ +ressources-md: ressources.md ressources_fr.md + +include ../../Makefile.ressources + C028AL_slides_module2-en-gz.pdf: slides_module2.pdf mv $< $@ diff --git a/module2/slides/ressources.md b/module2/slides/ressources.md new file mode 100644 index 0000000000000000000000000000000000000000..04f293368b2028853d56b714d734b07fc387525c --- /dev/null +++ b/module2/slides/ressources.md @@ -0,0 +1,122 @@ +--- +TITLE: Computational Documents +--- + +Table of Contents +============================================================== + +- [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) + - [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) + +M2-S0: Computational Documents +============================== + +M2-S1: A few Recent Controversial Studies +========================================= + +Economy: Austerity in Fiscal Policy +----------------------------------- + +- [Reinhart et Rogoff](https://en.wikipedia.org/wiki/Growth_in_a_Time_of_Debt): *Growth in a Time of Debt* +- Herndon, Ash et Pollin +- Wray: combining data across centuries, exchange rate regimes, + +Functional MRI +-------------- + +- 2010: [Bennett et al. and the dead salmon](https://www.researchgate.net/publication/255651552_Neural_correlates_of_interspecies_perspective_taking_in_the_post-mortem_Atlantic_Salmon_an_argument_for_multiple_comparisons_correction) ☺ +- 2016: [Eklund, Nichols, and Knutsson](http://www.pnas.org/content/113/28/7900.abstract). [A bug in fmri software could invalidate 15 years of brain research](http://www.sciencealert.com/a-bug-in-fmri-software-could-invalidate-decades-of-brain-research-scientists-discover) (*40 000 articles*) +- 2016: But it's [more subtle than it looks like](https://www.cogneurosociety.org/debunking-the-myth-that-fmri-studies-are-invalid/). [Nichols](http://blogs.warwick.ac.uk/nichols/entry/bibliometrics_of_cluster/). *≈ 3 600 impacted studies* + +Incorrect Protein Structures +---------------------------- + +[a "buggy software"](https://people.ligo-wa.caltech.edu/~michael.landry/calibration/S5/getsignright.pdf) + +Other domains +------------- + +- [Oncology](http://www.nature.com/nrd/journal/v10/n9/full/nrd3439-c1.html?foxtrotcallback=true): "*half of published studies, even in prestigious journals, can't be reproduced in industrial labs*" +- [Psychology](http://theconversation.com/we-found-only-one-third-of-published-psychology-research-is-reliable-now-what-46596): "*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 +-------- + +- [Computers broke science](http://theconversation.com/how-computers-broke-science-and-what-we-can-do-to-fix-it-49938) +- [Programming and data manipulation mistakes in Genomics](https://qz.com/768334/years-of-genomics-research-is-riddled-with-errors-thanks-to-a-bunch-of-botched-excel-spreadsheets/) + +Going Public? +------------- + +- Someone may [benefit from my hard work](http://www.nature.com/news/the-top-100-papers-1.16224) + +Tools to Avoid and Possible Alternatives +---------------------------------------- + +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 + + - + - is a must-have + - + - + +M2-S6: Comparative Study +======================== + +See 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 + - +- 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.org b/module2/slides/ressources.org new file mode 100644 index 0000000000000000000000000000000000000000..a47c835ebbf6bf9a59c5582d673cd50d366dacd7 --- /dev/null +++ b/module2/slides/ressources.org @@ -0,0 +1,87 @@ +# -*- mode: org -*- +#+TITLE: Computational Documents +#+DATE: June, 2018 +#+STARTUP: overview indent +#+OPTIONS: num:nil toc:t +#+PROPERTY: header-args :eval never-export + +* 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?]] + - [[#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]] + +* 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]] \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/ +** 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]] +** Tools to Avoid and Possible Alternatives +* 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 +** See 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_fr.md b/module2/slides/ressources_fr.md new file mode 100644 index 0000000000000000000000000000000000000000..4e1a8e18517b1f0d46f803d0ff4e7c1cc0da093d --- /dev/null +++ b/module2/slides/ressources_fr.md @@ -0,0 +1,6 @@ +--- +TITLE: FIXME Computational Documents +--- + +Table des matières +=============================================================== diff --git a/module2/slides/ressources_fr.org b/module2/slides/ressources_fr.org new file mode 100644 index 0000000000000000000000000000000000000000..bbb334d4733dc3f6a60286283cf067ff65402e4b --- /dev/null +++ b/module2/slides/ressources_fr.org @@ -0,0 +1,8 @@ +# -*- mode: org -*- +#+TITLE: FIXME Computational Documents +#+DATE: June, 2018 +#+STARTUP: overview indent +#+OPTIONS: num:nil toc:t +#+PROPERTY: header-args :eval never-export + +* Table des matières :TOC: