Skip to content

M
mooc-rr-ressources
Commit 81f4189a authored by Arnaud Legrand's avatar Arnaud Legrand
Browse files
Options

Add images and update links

parent 506db734
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 6867 additions and 78 deletions
module4/slides/Makefile 0 → 100644
View file @ 81f4189a
C028AL_slides_module4-en-gz.pdf: slides_module4.pdf
mv $< $@
C028AL_slides_module4-fr-gz.pdf: diapos_module4.pdf
mv $< $@
%-gz.pdf: %.pdf
gzprez $<
%.pdf: %.tex
pdflatex --shell-escape $^
pdflatex --shell-escape $^
%.tex: %.org
emacs -batch --eval "(setq enable-local-eval t)" --eval "(setq enable-local-variables t)" $^ --funcall org-beamer-export-to-latex
# sed -i -e 's|includegraphics\(.*\)../assets/img/|includegraphics\1../assets/img/thumbnail/|' -e 's/\.png}/.jpg}/i' $@
module4/slides/diapos_module4.org
View file @ 81f4189a
...@@ -108,26 +108,20 @@ ...@@ -108,26 +108,20 @@
http://phdcomics.com/comics/archive/phd051017s.gif http://phdcomics.com/comics/archive/phd051017s.gif
** Graphe syndrome grippal: ** Graphe syndrome grippal:
#+begin_src shell :results output raw :exports both #+begin_src shell :results output raw :exports both
debtree python3-matplotlib > python3-matplotlib.dot debtree python3-matplotlib > img/python3-matplotlib.dot
sed -i -e 's/rankdir=LR/rankdir=RL/g' \ sed -i -e 's/rankdir=LR/rankdir=RL/g' \
-e 's/node \[shape=box\]/node [shape=box, color=black, fillcolor=gray, fontcolor=black, style=filled]/g' \ -e 's/node \[shape=box\]/node [shape=box, color=black, fillcolor=gray, fontcolor=black, style=filled]/g' \
python3-matplotlib.dot python3-matplotlib.dot
dot -Tpng python3-matplotlib.dot > python3-matplotlib.png dot -Tpng img/python3-matplotlib.dot > img/python3-matplotlib.png
echo file:python3-matplotlib.png echo file:img/python3-matplotlib.png
#+end_src
#+RESULTS:
file:python3-matplotlib.png
#+begin_src shell :results output :exports both
mv python3-matplotlib.png ../assets/img/
#+end_src #+end_src
#+RESULTS: #+RESULTS:
file:img/python3-matplotlib.png
* M4-S0: Vers une étude reproductible : la réalité du terrain * M4-S0: Vers une étude reproductible : la réalité du terrain
** L'enfer de la Recherche Reproductible ** L'enfer de la Recherche Reproductible
file:../assets/img/phd_sisyphe.png file:img/phd_sisyphe.png
*** Notes *** Notes
:PROPERTIES: :PROPERTIES:
...@@ -286,9 +280,9 @@ Rechercher des formats binaires pour : ...@@ -286,9 +280,9 @@ Rechercher des formats binaires pour :
Git(hub/lab/...) : pas bien adapté au stockage de données Git(hub/lab/...) : pas bien adapté au stockage de données
#+BEGIN_CENTER #+BEGIN_CENTER
#+ATTR_LATEX: :height 1cm :center nil #+ATTR_LATEX: :height 1cm :center nil
file:../assets/img/Zenodo-logo.jpg file:img/Zenodo-logo.jpg
#+ATTR_LATEX: :height 1cm :center nil #+ATTR_LATEX: :height 1cm :center nil
file:../assets/img/Figshare-logo.png file:img/Figshare-logo.png
#+END_CENTER #+END_CENTER
** Conclusions ** Conclusions
...@@ -306,16 +300,16 @@ file:../assets/img/Figshare-logo.png ...@@ -306,16 +300,16 @@ file:../assets/img/Figshare-logo.png
4. Conclusion 4. Conclusion
** Passage à l'échelle ** Passage à l'échelle
#+ATTR_LATEX: :width \linewidth #+ATTR_LATEX: :width \linewidth
file:../assets/img/il-marche-mon-programme.jpg file:img/il-marche-mon-programme.jpg
** Des codes complexes... ** Des codes complexes...
#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb1.png}% #+LaTeX: \includegraphics<+>[height=6cm]{img/nb1.png}%
#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb2.png}% #+LaTeX: \includegraphics<+>[height=6cm]{img/nb2.png}%
#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb3.png}% #+LaTeX: \includegraphics<+>[height=6cm]{img/nb3.png}%
#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb4.png}% #+LaTeX: \includegraphics<+>[height=6cm]{img/nb4.png}%
#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/grippal_orgmode1.png}% #+LaTeX: \includegraphics<+>[height=6cm]{img/grippal_orgmode1.png}%
#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/grippal_orgmode2.png}% #+LaTeX: \includegraphics<+>[height=6cm]{img/grippal_orgmode2.png}%
#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb5.png}% #+LaTeX: \includegraphics<+>[height=6cm]{img/nb5.png}%
- Un vrai plat de spaghettis - Un vrai plat de spaghettis
- Pas de vision d'ensemble - Pas de vision d'ensemble
- Interaction entre plusieurs langages = danger - Interaction entre plusieurs langages = danger
...@@ -330,9 +324,9 @@ file:../assets/img/il-marche-mon-programme.jpg ...@@ -330,9 +324,9 @@ file:../assets/img/il-marche-mon-programme.jpg
** ... et difficiles à orchestrer ** ... et difficiles à orchestrer
#+LaTeX: \only<1>{\begin{overlayarea}{1.5\linewidth}{7cm} #+LaTeX: \only<1>{\begin{overlayarea}{1.5\linewidth}{7cm}
#+ATTR_LATEX: :height 7cm :center nil #+ATTR_LATEX: :height 7cm :center nil
file:../assets/img/SbmlParameterisation.png file:img/SbmlParameterisation.png
#+ATTR_LATEX: :height 7cm :center nil #+ATTR_LATEX: :height 7cm :center nil
file:../assets/img/SbmlModelling.png file:img/SbmlModelling.png
#+LaTeX: \end{overlayarea}}\pause #+LaTeX: \end{overlayarea}}\pause
Le *Workflow* : Le *Workflow* :
...@@ -462,7 +456,7 @@ python3-cycler (>= 0.10.0), python3:any (>= 3.3.2-2~), libc6 (>= ...@@ -462,7 +456,7 @@ python3-cycler (>= 0.10.0), python3:any (>= 3.3.2-2~), libc6 (>=
1.6.2-1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4) 1.6.2-1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4)
#+END_EXAMPLE #+END_EXAMPLE
#+LaTeX: \only<2>{\vspace{-3.5cm}\includegraphics<2>[width=\linewidth]{../assets/img/python3-matplotlib.png}}\vspace{10cm} #+LaTeX: \only<2>{\vspace{-3.5cm}\includegraphics<2>[width=\linewidth]{img/python3-matplotlib.png}}\vspace{10cm}
*** Notes *** Notes
:PROPERTIES: :PROPERTIES:
...@@ -694,7 +688,7 @@ SHA256: 8f5d3509d4f5451468c6de44fc8dfe391c3df4120079adc01ab5f13ff4194f5a ...@@ -694,7 +688,7 @@ SHA256: 8f5d3509d4f5451468c6de44fc8dfe391c3df4120079adc01ab5f13ff4194f5a
#+END_EXAMPLE #+END_EXAMPLE
** L'épreuve du temps ** L'épreuve du temps
file:../assets/img/soviet_space_shuttle.jpg file:img/soviet_space_shuttle.jpg
** Compatibilité ascendante ** Compatibilité ascendante
\small \small
- Python et tout son écosystème à évolution hyper rapide - Python et tout son écosystème à évolution hyper rapide
...@@ -712,9 +706,9 @@ python3 -c "print(10/3)" ...@@ -712,9 +706,9 @@ python3 -c "print(10/3)"
#+LaTeX: } #+LaTeX: }
\pause \pause
#+ATTR_LATEX: :height 3.2cm :center nil #+ATTR_LATEX: :height 3.2cm :center nil
file:../assets/img/plot_1.5.3.png file:img/plot_1.5.3.png
#+ATTR_LATEX: :height 3.2cm :center nil #+ATTR_LATEX: :height 3.2cm :center nil
file:../assets/img/plot_2.1.1.png file:img/plot_2.1.1.png
\pause \pause
- Cortical Thickness Measurements (PLOS ONE, - Cortical Thickness Measurements (PLOS ONE,
...@@ -760,7 +754,7 @@ file:../assets/img/plot_2.1.1.png ...@@ -760,7 +754,7 @@ file:../assets/img/plot_2.1.1.png
Popper: [[http://falsifiable.us/][http://falsifiable.us/]] Popper: [[http://falsifiable.us/][http://falsifiable.us/]]
#+ATTR_LATEX: :height 1.5cm :center nil #+ATTR_LATEX: :height 1.5cm :center nil
file:../assets/img/popper_logo_just_jug.png file:img/popper_logo_just_jug.png
*Autre possibilité* : *Autre possibilité* :
- Se restreindre à ce qui est maîtrisable (C par exemple) - Se restreindre à ce qui est maîtrisable (C par exemple)
...@@ -806,9 +800,9 @@ file:../assets/img/plot_2.1.1.png ...@@ -806,9 +800,9 @@ file:../assets/img/plot_2.1.1.png
- Github/Gitlab/... : stables, ouverts, \dots pérennes ? - Github/Gitlab/... : stables, ouverts, \dots pérennes ?
- +Google Code+, +Gitorious+, +Code Spaces+ - +Google Code+, +Gitorious+, +Code Spaces+
#+ATTR_LATEX: :height 1.3cm :center nil #+ATTR_LATEX: :height 1.3cm :center nil
file:../assets/img/swh-logo.png file:img/swh-logo.png
#+ATTR_LATEX: :height 1.3cm :center nil #+ATTR_LATEX: :height 1.3cm :center nil
file:../assets/img/LogoHAL.PNG file:img/LogoHAL.png
*Gestion des environnements* *Gestion des environnements*
- Pérénité de l'accès à dockerhub, nix repository, code ocean... ? - Pérénité de l'accès à dockerhub, nix repository, code ocean... ?
...@@ -822,9 +816,9 @@ file:../assets/img/plot_2.1.1.png ...@@ -822,9 +816,9 @@ file:../assets/img/plot_2.1.1.png
:BEAMER_ENV: note :BEAMER_ENV: note
:END: :END:
- Dans les exercices, faites y bien attention. - Dans les exercices, faites y bien attention.
# file:../assets/img/ArXiv-web.png" height=60 /> # file:img/ArXiv-web.png" height=60 />
# file:../assets/img/Zenodo-logo.jpg" height=60 /> # file:img/Zenodo-logo.jpg" height=60 />
# file:../assets/img/Figshare-logo.png" height=60 /> # file:img/Figshare-logo.png" height=60 />
* M4-S3: L'enfer du calcul * M4-S3: L'enfer du calcul
** Vers une étude reproductible : la réalité du terrain :noexport: ** Vers une étude reproductible : la réalité du terrain :noexport:
1. L'enfer des données 1. L'enfer des données
...@@ -844,7 +838,7 @@ file:../assets/img/plot_2.1.1.png ...@@ -844,7 +838,7 @@ file:../assets/img/plot_2.1.1.png
** L'arithmétique à virgule flottante ** L'arithmétique à virgule flottante
file:../assets/img/polynome1.svg file:img/polynome1.svg
#+begin_src python :results output :exports both #+begin_src python :results output :exports both
def polynome(x): def polynome(x):
return x**9 - 9.*x**8 + 36.*x**7 - 84.*x**6 + 126.*x**5 \ return x**9 - 9.*x**8 + 36.*x**7 - 84.*x**6 + 126.*x**5 \
...@@ -860,7 +854,7 @@ def polynome(x): ...@@ -860,7 +854,7 @@ def polynome(x):
** L'arithmétique à virgule flottante ** L'arithmétique à virgule flottante
file:../assets/img/polynome2.svg file:img/polynome2.svg
#+begin_src python :results output :exports both #+begin_src python :results output :exports both
def horner(x): def horner(x):
return x*(x*(x*(x*(x*(x*(x*(x*(x - 9.) + 36.) - 84.) + 126.) \ return x*(x*(x*(x*(x*(x*(x*(x*(x - 9.) + 36.) - 84.) + 126.) \
...@@ -878,7 +872,7 @@ def horner(x): ...@@ -878,7 +872,7 @@ def horner(x):
** L'arithmétique à virgule flottante ** L'arithmétique à virgule flottante
file:../assets/img/polynome3.svg file:img/polynome3.svg
#+begin_src python :results output :exports both #+begin_src python :results output :exports both
def simple(x): def simple(x):
return (x-1.)**9 return (x-1.)**9
...@@ -895,7 +889,7 @@ def simple(x): ...@@ -895,7 +889,7 @@ def simple(x):
** L'arithmétique à virgule flottante ** L'arithmétique à virgule flottante
file:../assets/img/polynome3-4.svg file:img/polynome3-4.svg
*** Notes *** Notes
:PROPERTIES: :PROPERTIES:
...@@ -905,7 +899,7 @@ file:../assets/img/polynome3-4.svg ...@@ -905,7 +899,7 @@ file:../assets/img/polynome3-4.svg
** L'arithmétique à virgule flottante ** L'arithmétique à virgule flottante
file:../assets/img/polynome4.svg file:img/polynome4.svg
*** Notes *** Notes
:PROPERTIES: :PROPERTIES:
...@@ -1009,7 +1003,7 @@ Pour un calcul reproductible, il y a deux approches: ...@@ -1009,7 +1003,7 @@ Pour un calcul reproductible, il y a deux approches:
** Calcul parallèle: exemple ** Calcul parallèle: exemple
file:../assets/img/gouttedo1.png file:img/gouttedo1.png
Source: Thèse de Rafife Nheili, Université de Perpignan, 2016 Source: Thèse de Rafife Nheili, Université de Perpignan, 2016
...@@ -1026,7 +1020,7 @@ Source: Thèse de Rafife Nheili, Université de Perpignan, 2016 ...@@ -1026,7 +1020,7 @@ Source: Thèse de Rafife Nheili, Université de Perpignan, 2016
** Calcul parallèle: exemple ** Calcul parallèle: exemple
file:../assets/img/gouttedo2.png file:img/gouttedo2.png
Source: Thèse de Rafife Nheili, Université de Perpignan, 2016 Source: Thèse de Rafife Nheili, Université de Perpignan, 2016
...@@ -1081,10 +1075,10 @@ Source: Thèse de Rafife Nheili, Université de Perpignan, 2016 ...@@ -1081,10 +1075,10 @@ Source: Thèse de Rafife Nheili, Université de Perpignan, 2016
** Générateur de nombres pseudo-aléatoires ** Générateur de nombres pseudo-aléatoires
#+LaTeX: \vspace{1cm} #+LaTeX: \vspace{1cm}
#+LaTeX: \only<+>{\includesvg[scale=.45]{../assets/img/nombres-aleatoires-1.svg}} #+LaTeX: \only<+>{\includesvg[scale=.45]{img/nombres-aleatoires-1.svg}}
#+LaTeX: \only<+>{\includesvg[scale=.45]{../assets/img/nombres-aleatoires-2.svg}} #+LaTeX: \only<+>{\includesvg[scale=.45]{img/nombres-aleatoires-2.svg}}
#+LaTeX: \only<+>{\includesvg[scale=.45]{../assets/img/nombres-aleatoires-3.svg}} #+LaTeX: \only<+>{\includesvg[scale=.45]{img/nombres-aleatoires-3.svg}}
#+LaTeX: \only<+>{\includesvg[scale=.45]{../assets/img/nombres-aleatoires-4.svg}} #+LaTeX: \only<+>{\includesvg[scale=.45]{img/nombres-aleatoires-4.svg}}
#+LaTeX: \vspace{10cm} #+LaTeX: \vspace{10cm}
*** Notes *** Notes
:PROPERTIES: :PROPERTIES:
......
module4/slides/img/nb4.png 0 → 100644
View file @ 81f4189a
This diff is collapsed.
module4/slides/img/nb5.png 0 → 100644
View file @ 81f4189a
This diff is collapsed.
module4/slides/img/nombres-aleatoires-1.svg 0 → 100644
View file @ 81f4189a
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Created with Inkscape (http://www.inkscape.org/) -->
<svg
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:cc="http://creativecommons.org/ns#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:svg="http://www.w3.org/2000/svg"
xmlns="http://www.w3.org/2000/svg"
xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
width="199.75809mm"
height="56.37635mm"
viewBox="0 0 199.75809 56.37635"
version="1.1"
id="svg3797"
inkscape:version="0.92.2 (5c3e80d, 2017-08-06)"
sodipodi:docname="nombres-aleatoires-1.svg">
<defs
id="defs3791">
<marker
inkscape:isstock="true"
style="overflow:visible"
id="marker6467"
refX="0"
refY="0"
orient="auto"
inkscape:stockid="Arrow2Mend">
<path
transform="scale(-0.6)"
d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z"
style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:0.625;stroke-linejoin:round;stroke-opacity:1"
id="path6465"
inkscape:connector-curvature="0" />
</marker>
<marker
inkscape:stockid="Arrow2Mend"
orient="auto"
refY="0"
refX="0"
id="marker5388"
style="overflow:visible"
inkscape:isstock="true">
<path
id="path5386"
style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:0.625;stroke-linejoin:round;stroke-opacity:1"
d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z"
transform="scale(-0.6)"
inkscape:connector-curvature="0" />
</marker>
<marker
inkscape:stockid="Arrow2Send"
orient="auto"
refY="0"
refX="0"
id="Arrow2Send"
style="overflow:visible"
inkscape:isstock="true">
<path
id="path4771"
style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:0.625;stroke-linejoin:round;stroke-opacity:1"
d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z"
transform="matrix(-0.3,0,0,-0.3,0.69,0)"
inkscape:connector-curvature="0" />
</marker>
<marker
inkscape:stockid="Arrow2Mend"
orient="auto"
refY="0"
refX="0"
id="Arrow2Mend"
style="overflow:visible"
inkscape:isstock="true">
<path
id="path4765"
style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:0.625;stroke-linejoin:round;stroke-opacity:1"
d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z"
transform="scale(-0.6)"
inkscape:connector-curvature="0" />
</marker>
<marker
inkscape:stockid="Arrow1Mend"
orient="auto"
refY="0"
refX="0"
id="Arrow1Mend"
style="overflow:visible"
inkscape:isstock="true">
<path
id="path4747"
d="M 0,0 5,-5 -12.5,0 5,5 Z"
style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.00000003pt;stroke-opacity:1"
transform="matrix(-0.4,0,0,-0.4,-4,0)"
inkscape:connector-curvature="0" />
</marker>
<marker
inkscape:stockid="Arrow2Lend"
orient="auto"
refY="0"
refX="0"
id="Arrow2Lend"
style="overflow:visible"
inkscape:isstock="true">
<path
id="path4759"
style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:0.625;stroke-linejoin:round;stroke-opacity:1"
d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z"
transform="matrix(-1.1,0,0,-1.1,-1.1,0)"
inkscape:connector-curvature="0" />
</marker>
</defs>
<sodipodi:namedview
id="base"
pagecolor="#ffffff"
bordercolor="#666666"
borderopacity="1.0"
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
inkscape:zoom="0.94"
inkscape:cx="152.54525"
inkscape:cy="36.537983"
inkscape:document-units="mm"
inkscape:current-layer="g4184"
showgrid="false"
inkscape:window-width="1680"
inkscape:window-height="986"
inkscape:window-x="0"
inkscape:window-y="27"
inkscape:window-maximized="1"
fit-margin-top="1"
fit-margin-left="1"
fit-margin-bottom="1"
fit-margin-right="1" />
<metadata
id="metadata3794">
<rdf:RDF>
<cc:Work
rdf:about="">
<dc:format>image/svg+xml</dc:format>
<dc:type
rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
<dc:title></dc:title>
</cc:Work>
</rdf:RDF>
</metadata>
<g
inkscape:label="Layer 1"
inkscape:groupmode="layer"
id="layer1"
transform="translate(-9.4595477,-34.571133)">
<g
transform="matrix(0.28222223,0,0,0.28222223,7.592776,-17.518982)"
id="g4184">
<g
id="g3855"
transform="translate(-54.374999)">
<rect
style="opacity:1;fill:#edb2b2;fill-opacity:1;stroke:#000000;stroke-width:0.71042091;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
id="rect4156"
width="121.60297"
height="60.711681"
x="64.888062"
y="188.46979" />
<text
id="text4142"
y="230.61029"
x="77.847748"
style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;line-height:0%;font-family:Helvetica;-inkscape-font-specification:'Helvetica, Normal';text-align:start;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
xml:space="preserve"><tspan
style="font-size:30px;line-height:1"
y="230.61029"
x="77.847748"
id="tspan4144"
sodipodi:role="line">graine</tspan></text>
</g>
</g>
</g>
</svg>
module4/slides/img/nombres-aleatoires-2.svg 0 → 100644
View file @ 81f4189a
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Created with Inkscape (http://www.inkscape.org/) -->
<svg
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:cc="http://creativecommons.org/ns#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:svg="http://www.w3.org/2000/svg"
xmlns="http://www.w3.org/2000/svg"
xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
width="199.75809mm"
height="56.37635mm"
viewBox="0 0 199.75809 56.37635"
version="1.1"
id="svg3797"
inkscape:version="0.92.2 (5c3e80d, 2017-08-06)"
sodipodi:docname="nombres-aleatoires-2.svg">
<defs
id="defs3791">
<marker
inkscape:isstock="true"
style="overflow:visible"
id="marker6467"
refX="0"
refY="0"
orient="auto"
inkscape:stockid="Arrow2Mend">
<path
transform="scale(-0.6)"
d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z"
style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:0.625;stroke-linejoin:round;stroke-opacity:1"
id="path6465"
inkscape:connector-curvature="0" />
</marker>
<marker
inkscape:stockid="Arrow2Mend"
orient="auto"
refY="0"
refX="0"
id="marker5388"
style="overflow:visible"
inkscape:isstock="true">
<path
id="path5386"
style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:0.625;stroke-linejoin:round;stroke-opacity:1"
d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z"
transform="scale(-0.6)"
inkscape:connector-curvature="0" />
</marker>
<marker
inkscape:stockid="Arrow2Mend"
orient="auto"
refY="0"
refX="0"
id="marker5196"
style="overflow:visible"
inkscape:isstock="true"
inkscape:collect="always">
<path
id="path5194"
style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:0.625;stroke-linejoin:round;stroke-opacity:1"
d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z"
transform="scale(-0.6)"
inkscape:connector-curvature="0" />
</marker>
<marker
inkscape:stockid="Arrow2Send"
orient="auto"
refY="0"
refX="0"
id="Arrow2Send"
style="overflow:visible"
inkscape:isstock="true">
<path
id="path4771"
style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:0.625;stroke-linejoin:round;stroke-opacity:1"
d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z"
transform="matrix(-0.3,0,0,-0.3,0.69,0)"
inkscape:connector-curvature="0" />
</marker>
<marker
inkscape:stockid="Arrow2Mend"
orient="auto"
refY="0"
refX="0"
id="Arrow2Mend"
style="overflow:visible"
inkscape:isstock="true">
<path
id="path4765"
style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:0.625;stroke-linejoin:round;stroke-opacity:1"
d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z"
transform="scale(-0.6)"
inkscape:connector-curvature="0" />
</marker>
<marker
inkscape:stockid="Arrow1Mend"
orient="auto"
refY="0"
refX="0"
id="Arrow1Mend"
style="overflow:visible"
inkscape:isstock="true">
<path
id="path4747"
d="M 0,0 5,-5 -12.5,0 5,5 Z"
style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:1.00000003pt;stroke-opacity:1"
transform="matrix(-0.4,0,0,-0.4,-4,0)"
inkscape:connector-curvature="0" />
</marker>
<marker
inkscape:stockid="Arrow2Lend"
orient="auto"
refY="0"
refX="0"
id="Arrow2Lend"
style="overflow:visible"
inkscape:isstock="true">
<path
id="path4759"
style="fill:#000000;fill-opacity:1;fill-rule:evenodd;stroke:#000000;stroke-width:0.625;stroke-linejoin:round;stroke-opacity:1"
d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z"
transform="matrix(-1.1,0,0,-1.1,-1.1,0)"
inkscape:connector-curvature="0" />
</marker>
</defs>
<sodipodi:namedview
id="base"
pagecolor="#ffffff"
bordercolor="#666666"
borderopacity="1.0"
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
inkscape:zoom="0.94"
inkscape:cx="152.54525"
inkscape:cy="36.537983"
inkscape:document-units="mm"
inkscape:current-layer="g4184"
showgrid="false"
inkscape:window-width="1680"
inkscape:window-height="986"
inkscape:window-x="0"
inkscape:window-y="27"
inkscape:window-maximized="1"
fit-margin-top="1"
fit-margin-left="1"
fit-margin-bottom="1"
fit-margin-right="1" />
<metadata
id="metadata3794">
<rdf:RDF>
<cc:Work
rdf:about="">
<dc:format>image/svg+xml</dc:format>
<dc:type
rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
<dc:title></dc:title>
</cc:Work>
</rdf:RDF>
</metadata>
<g
inkscape:label="Layer 1"
inkscape:groupmode="layer"
id="layer1"
transform="translate(-9.4595477,-34.571133)">
<g
transform="matrix(0.28222223,0,0,0.28222223,7.592776,-17.518982)"
id="g4184">
<g
id="g3855"
transform="translate(-54.374999)">
<rect
style="opacity:1;fill:#edb2b2;fill-opacity:1;stroke:#000000;stroke-width:0.71042091;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
id="rect4156"
width="121.60297"
height="60.711681"
x="64.888062"
y="188.46979" />
<text
id="text4142"
y="230.61029"
x="77.847748"
style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;line-height:0%;font-family:Helvetica;-inkscape-font-specification:'Helvetica, Normal';text-align:start;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
xml:space="preserve"><tspan
style="font-size:30px;line-height:1"
y="230.61029"
x="77.847748"
id="tspan4144"
sodipodi:role="line">graine</tspan></text>
</g>
<g
id="g3860"
transform="translate(-23.750037)">
<rect
y="188.46979"
x="220.51308"
height="60.711681"
width="121.60297"
id="rect3816"
style="opacity:1;fill:#edb2b2;fill-opacity:1;stroke:#000000;stroke-width:0.71042091;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1" />
<text
xml:space="preserve"
style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;line-height:0%;font-family:Helvetica;-inkscape-font-specification:'Helvetica, Normal';text-align:start;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
x="236.95909"
y="230.61029"
id="text3820"><tspan
sodipodi:role="line"
id="tspan3818"
x="236.95909"
y="230.61029"
style="font-size:30px;line-height:1">état 1</tspan></text>
</g>
<path
style="fill:none;stroke:#000000;stroke-width:3.77362204;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1;marker-end:url(#marker5196)"
d="m 137.77731,218.82563 c 50.86436,0 50.86436,0 50.86436,0"
id="path3931"
inkscape:connector-curvature="0" />
</g>
</g>
</svg>
module4/slides/img/nombres-aleatoires-3.svg 0 → 100644
View file @ 81f4189a
This diff is collapsed.
module4/slides/img/nombres-aleatoires-4.svg 0 → 100644
View file @ 81f4189a
This diff is collapsed.
module4/slides/img/polynome1.svg 0 → 100644
View file @ 81f4189a
This diff is collapsed.
module4/slides/img/polynome2.svg 0 → 100644
View file @ 81f4189a
This diff is collapsed.
module4/slides/img/polynome3-4.svg 0 → 100644
View file @ 81f4189a
This diff is collapsed.
module4/slides/img/polynome3.svg 0 → 100644
View file @ 81f4189a
This diff is collapsed.
module4/slides/img/polynome4.svg 0 → 100644
View file @ 81f4189a
This diff is collapsed.
module4/slides/img/python3-matplotlib.png 0 → 100644
View file @ 81f4189a
This diff is collapsed.
module4/slides/slides_module4.org
View file @ 81f4189a
...@@ -127,7 +127,7 @@ ...@@ -127,7 +127,7 @@
* M4-S0: The Rough Road to Real-Life Reproducible Research * M4-S0: The Rough Road to Real-Life Reproducible Research
** Reproducible Research Hell ** Reproducible Research Hell
file:../assets/img/phd_sisyphe.png file:img/phd_sisyphe.png
*** Notes *** Notes
:PROPERTIES: :PROPERTIES:
...@@ -285,9 +285,9 @@ Wanted: binary formats for ...@@ -285,9 +285,9 @@ Wanted: binary formats for
Git (hub, lab, ...): not well suited for data storage Git (hub, lab, ...): not well suited for data storage
#+BEGIN_CENTER #+BEGIN_CENTER
#+ATTR_LATEX: :height 1cm :center nil #+ATTR_LATEX: :height 1cm :center nil
file:../assets/img/Zenodo-logo.jpg file:img/Zenodo-logo.jpg
#+ATTR_LATEX: :height 1cm :center nil #+ATTR_LATEX: :height 1cm :center nil
file:../assets/img/Figshare-logo.png file:img/Figshare-logo.png
#+END_CENTER #+END_CENTER
** Conclusions ** Conclusions
...@@ -305,16 +305,16 @@ file:../assets/img/Figshare-logo.png ...@@ -305,16 +305,16 @@ file:../assets/img/Figshare-logo.png
4. Conclusion 4. Conclusion
** Scaling up ** Scaling up
#+ATTR_LATEX: :width \linewidth #+ATTR_LATEX: :width \linewidth
file:../assets/img/il-marche-mon-programme.jpg file:img/il-marche-mon-programme.jpg
** Complex code... ** Complex code...
#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb1.png}% #+LaTeX: \includegraphics<+>[height=6cm]{img/nb1.png}%
#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb2.png}% #+LaTeX: \includegraphics<+>[height=6cm]{img/nb2.png}%
#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb3.png}% #+LaTeX: \includegraphics<+>[height=6cm]{img/nb3.png}%
#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb4.png}% #+LaTeX: \includegraphics<+>[height=6cm]{img/nb4.png}%
#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/grippal_orgmode1.png}% #+LaTeX: \includegraphics<+>[height=6cm]{img/grippal_orgmode1.png}%
#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/grippal_orgmode2.png}% #+LaTeX: \includegraphics<+>[height=6cm]{img/grippal_orgmode2.png}%
#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb5.png}% #+LaTeX: \includegraphics<+>[height=6cm]{img/nb5.png}%
- A real spaghetti bowl - A real spaghetti bowl
- No global view - No global view
- Interaction between multiple languages = danger - Interaction between multiple languages = danger
...@@ -329,9 +329,9 @@ file:../assets/img/il-marche-mon-programme.jpg ...@@ -329,9 +329,9 @@ file:../assets/img/il-marche-mon-programme.jpg
** ... that is difficult to orchestrate ** ... that is difficult to orchestrate
#+LaTeX: \only<1>{\begin{overlayarea}{1.5\linewidth}{7cm} #+LaTeX: \only<1>{\begin{overlayarea}{1.5\linewidth}{7cm}
#+ATTR_LATEX: :height 7cm :center nil #+ATTR_LATEX: :height 7cm :center nil
file:../assets/img/SbmlParameterisation.png file:img/SbmlParameterisation.png
#+ATTR_LATEX: :height 7cm :center nil #+ATTR_LATEX: :height 7cm :center nil
file:../assets/img/SbmlModelling.png file:img/SbmlModelling.png
#+LaTeX: \end{overlayarea}}\pause #+LaTeX: \end{overlayarea}}\pause
*Workflows*: *Workflows*:
...@@ -459,7 +459,7 @@ python3-cycler (>= 0.10.0), python3:any (>= 3.3.2-2~), libc6 (>= ...@@ -459,7 +459,7 @@ python3-cycler (>= 0.10.0), python3:any (>= 3.3.2-2~), libc6 (>=
1.6.2-1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4) 1.6.2-1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4)
#+END_EXAMPLE #+END_EXAMPLE
#+LaTeX: \only<2>{\vspace{-3.5cm}\includegraphics<2>[width=\linewidth]{../assets/img/python3-matplotlib.png}}\vspace{10cm} #+LaTeX: \only<2>{\vspace{-3.5cm}\includegraphics<2>[width=\linewidth]{img/python3-matplotlib.png}}\vspace{10cm}
*** Notes *** Notes
:PROPERTIES: :PROPERTIES:
...@@ -690,7 +690,7 @@ SHA256: 8f5d3509d4f5451468c6de44fc8dfe391c3df4120079adc01ab5f13ff4194f5a ...@@ -690,7 +690,7 @@ SHA256: 8f5d3509d4f5451468c6de44fc8dfe391c3df4120079adc01ab5f13ff4194f5a
#+END_EXAMPLE #+END_EXAMPLE
** The test of time ** The test of time
file:../assets/img/soviet_space_shuttle.jpg file:img/soviet_space_shuttle.jpg
** Backwards compatibility ** Backwards compatibility
\small \small
- Python and its rapidly evolving environment - Python and its rapidly evolving environment
...@@ -708,9 +708,9 @@ python3 -c "print(10/3)" ...@@ -708,9 +708,9 @@ python3 -c "print(10/3)"
#+LaTeX: } #+LaTeX: }
\pause \pause
#+ATTR_LATEX: :height 3.2cm :center nil #+ATTR_LATEX: :height 3.2cm :center nil
file:../assets/img/plot_1.5.3.png file:img/plot_1.5.3.png
#+ATTR_LATEX: :height 3.2cm :center nil #+ATTR_LATEX: :height 3.2cm :center nil
file:../assets/img/plot_2.1.1.png file:img/plot_2.1.1.png
\pause \pause
- Cortical Thickness Measurements (PLOS ONE, - Cortical Thickness Measurements (PLOS ONE,
...@@ -754,7 +754,7 @@ file:../assets/img/plot_2.1.1.png ...@@ -754,7 +754,7 @@ file:../assets/img/plot_2.1.1.png
Popper: [[http://falsifiable.us/][http://falsifiable.us/]] Popper: [[http://falsifiable.us/][http://falsifiable.us/]]
#+ATTR_LATEX: :height 1.5cm :center nil #+ATTR_LATEX: :height 1.5cm :center nil
file:../assets/img/popper_logo_just_jug.png file:img/popper_logo_just_jug.png
*Another option*: *Another option*:
- Limit onself to what is manageable (C for example) - Limit onself to what is manageable (C for example)
...@@ -800,9 +800,9 @@ file:../assets/img/plot_2.1.1.png ...@@ -800,9 +800,9 @@ file:../assets/img/plot_2.1.1.png
- Git (hub, lab, ...) : stable, open, \dots durable ? - Git (hub, lab, ...) : stable, open, \dots durable ?
- +Google Code+, +Gitorious+, +Code Spaces+ - +Google Code+, +Gitorious+, +Code Spaces+
#+ATTR_LATEX: :height 1.3cm :center nil #+ATTR_LATEX: :height 1.3cm :center nil
file:../assets/img/swh-logo.png file:img/swh-logo.png
#+ATTR_LATEX: :height 1.3cm :center nil #+ATTR_LATEX: :height 1.3cm :center nil
file:../assets/img/LogoHAL.PNG file:img/LogoHAL.PNG
*Environment management* *Environment management*
- Longevity of access to Docker Hub, Nix repository, Code Ocean, ... ? - Longevity of access to Docker Hub, Nix repository, Code Ocean, ... ?
...@@ -815,9 +815,9 @@ file:../assets/img/plot_2.1.1.png ...@@ -815,9 +815,9 @@ file:../assets/img/plot_2.1.1.png
:BEAMER_ENV: note :BEAMER_ENV: note
:END: :END:
- Dans les exercices, faites y bien attention. - Dans les exercices, faites y bien attention.
# file:../assets/img/ArXiv-web.png" height=60 /> # file:img/ArXiv-web.png" height=60 />
# file:../assets/img/Zenodo-logo.jpg" height=60 /> # file:img/Zenodo-logo.jpg" height=60 />
# file:../assets/img/Figshare-logo.png" height=60 /> # file:img/Figshare-logo.png" height=60 />
* M4-S3: Numerics Hell * M4-S3: Numerics Hell
** The Rough Road to Real-Life Reproducible Research :noexport: ** The Rough Road to Real-Life Reproducible Research :noexport:
1. Data Hell 1. Data Hell
...@@ -826,7 +826,7 @@ file:../assets/img/plot_2.1.1.png ...@@ -826,7 +826,7 @@ file:../assets/img/plot_2.1.1.png
4. Conclusion 4. Conclusion
** Floating-point arithmetic ** Floating-point arithmetic
file:../assets/img/polynome1.svg file:img/polynome1.svg
#+begin_src python :results output :exports both #+begin_src python :results output :exports both
def polynome(x): def polynome(x):
return x**9 - 9.*x**8 + 36.*x**7 - 84.*x**6 + 126.*x**5 \ return x**9 - 9.*x**8 + 36.*x**7 - 84.*x**6 + 126.*x**5 \
...@@ -842,7 +842,7 @@ def polynome(x): ...@@ -842,7 +842,7 @@ def polynome(x):
** Floating-point arithmetic ** Floating-point arithmetic
file:../assets/img/polynome2.svg file:img/polynome2.svg
#+begin_src python :results output :exports both #+begin_src python :results output :exports both
def horner(x): def horner(x):
return x*(x*(x*(x*(x*(x*(x*(x*(x - 9.) + 36.) - 84.) + 126.) \ return x*(x*(x*(x*(x*(x*(x*(x*(x - 9.) + 36.) - 84.) + 126.) \
...@@ -860,7 +860,7 @@ def horner(x): ...@@ -860,7 +860,7 @@ def horner(x):
** Floating-point arithmetic ** Floating-point arithmetic
file:../assets/img/polynome3.svg file:img/polynome3.svg
#+begin_src python :results output :exports both #+begin_src python :results output :exports both
def simple(x): def simple(x):
return (x-1.)**9 return (x-1.)**9
...@@ -877,7 +877,7 @@ def simple(x): ...@@ -877,7 +877,7 @@ def simple(x):
** Floating-point arithmetic ** Floating-point arithmetic
file:../assets/img/polynome3-4.svg file:img/polynome3-4.svg
*** Notes *** Notes
:PROPERTIES: :PROPERTIES:
...@@ -887,7 +887,7 @@ file:../assets/img/polynome3-4.svg ...@@ -887,7 +887,7 @@ file:../assets/img/polynome3-4.svg
** Floating-point arithmetic ** Floating-point arithmetic
file:../assets/img/polynome4.svg file:img/polynome4.svg
*** Notes *** Notes
:PROPERTIES: :PROPERTIES:
...@@ -989,7 +989,7 @@ Two options for computing reproducibly: ...@@ -989,7 +989,7 @@ Two options for computing reproducibly:
** Parallel computation: example ** Parallel computation: example
file:../assets/img/gouttedo1.png file:img/gouttedo1.png
Source: Rafife Nheili, PhD. Thesis, University of Perpignan, 2016 Source: Rafife Nheili, PhD. Thesis, University of Perpignan, 2016
...@@ -1006,7 +1006,7 @@ Source: Rafife Nheili, PhD. Thesis, University of Perpignan, 2016 ...@@ -1006,7 +1006,7 @@ Source: Rafife Nheili, PhD. Thesis, University of Perpignan, 2016
** Parallel computation: example ** Parallel computation: example
file:../assets/img/gouttedo2.png file:img/gouttedo2.png
Source: Rafife Nheili, PhD. Thesis, University of Perpignan, 2016 Source: Rafife Nheili, PhD. Thesis, University of Perpignan, 2016
...@@ -1061,10 +1061,10 @@ Source: Rafife Nheili, PhD. Thesis, University of Perpignan, 2016 ...@@ -1061,10 +1061,10 @@ Source: Rafife Nheili, PhD. Thesis, University of Perpignan, 2016
** Pseudo-random number generators ** Pseudo-random number generators
#+LaTeX: \vspace{1cm} #+LaTeX: \vspace{1cm}
#+LaTeX: \only<+>{\includesvg[scale=.45]{../assets/img/nombres-aleatoires-1.svg}} #+LaTeX: \only<+>{\includesvg[scale=.45]{img/nombres-aleatoires-1.svg}}
#+LaTeX: \only<+>{\includesvg[scale=.45]{../assets/img/nombres-aleatoires-2.svg}} #+LaTeX: \only<+>{\includesvg[scale=.45]{img/nombres-aleatoires-2.svg}}
#+LaTeX: \only<+>{\includesvg[scale=.45]{../assets/img/nombres-aleatoires-3.svg}} #+LaTeX: \only<+>{\includesvg[scale=.45]{img/nombres-aleatoires-3.svg}}
#+LaTeX: \only<+>{\includesvg[scale=.45]{../assets/img/nombres-aleatoires-4.svg}} #+LaTeX: \only<+>{\includesvg[scale=.45]{img/nombres-aleatoires-4.svg}}
#+LaTeX: \vspace{10cm} #+LaTeX: \vspace{10cm}
*** Notes *** Notes
:PROPERTIES: :PROPERTIES:
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment