- [[#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/
- [[https://en.wikipedia.org/wiki/Growth_in_a_Time_of_Debt][Reinhart et Rogoff]]: /Growth in a Time of Debt/
- Herndon, Ash et Pollin
- Herndon, Ash et Pollin
- Wray: combining data across centuries, exchange rate regimes,
- Wray: combining data across centuries, exchange rate regimes,
** Functional MRI
* 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
- 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/)
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
- 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
- [[http://www.nature.com/nrd/journal/v10/n9/full/nrd3439-c1.html?foxtrotcallback=true][Oncology]]: "/half of published studies, even in prestigious journals,
- [[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/"
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
- [[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
findings/, /only one-third of published psychology research was found
- [[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/
- [[https://en.wikipedia.org/wiki/Growth_in_a_Time_of_Debt][Reinhart et Rogoff]]: /Growth in a Time of Debt/
- [[https://en.wikipedia.org/wiki/Growth_in_a_Time_of_Debt][Reinhart et Rogoff]]: /Growth in a Time of Debt/
- Herndon, Ash et Pollin
- Herndon, Ash et Pollin
- Wray: combining data across centuries, exchange rate regimes,
- Wray: combining data across centuries, exchange rate regimes,
** Les IRM fonctionnelles
* 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
- 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
- 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/)
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
- 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
l'article d'origine]], c'est plutôt de l'ordre de /3 600 études qui
- [[http://www.nature.com/nrd/journal/v10/n9/full/nrd3439-c1.html?foxtrotcallback=true][Oncologie]]: "/half of published studies, even in prestigious journals,
- [[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/"
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
- [[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
findings/, /only one-third of published psychology research was found
to be reliable/"
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/.
- [[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.
- [[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.
