update 2015_04_29_Improve_methodology_retraite_AGTI

.gitignore

@@ -3,3 +3,4 @@
 *.avi
 *.mpeg
 *.xvid
+*.pdf

2015_04_29_Improve_methodology_retraite_AGTI/.ipynb_checkpoints/2015_04_29_Improve_methodology_retraite_AGTI-checkpoint.ipynb

 %% Cell type:markdown id: tags:
 
+# PREPARE RISE PRESENTATION
+
+%% Cell type:code id: tags:
+
+``` python
+from IPython.html.services.config import ConfigManager
+from IPython.utils.path import locate_profile
+cm = ConfigManager(profile_dir=locate_profile(get_ipython().profile))
+cm.update('livereveal', {
+              'theme': 'solarized',
+              'transition': 'linear',
+              'start_slideshow_at': 'selected'})
+
+# transition = default/cube/page/concave/zoom/linear/none
+# theme = beige/blood/default/moon/night/serif/simple/sky/solarized
+# start_slideshow_at = selected/beginning
+```
+
+%%%% Output: execute_result
+
+    {'start_slideshow_at': 'selected',
+     'theme': 'solarized',
+     'transition': 'linear'}
+
+%% Cell type:code id: tags:
+
+``` python
+from IPython.display import HTML, Image, SVG, YouTubeVideo
+```
+
+%% Cell type:markdown id: tags:
+
+# PRESENTATION STARTS BELOW
+
+%% Cell type:markdown id: tags:
+
 #Can we improve our methodology ?
 
-### Adrien Leger
-### Emilie Lecomte
-### Jean-Baptiste Dupont
-### Célia Couzinié
+%% Cell type:markdown id: tags:
+
+**Sure we can!**
+
+%% Cell type:markdown id: tags:
+
+#Why we have to improve our methodologies, analyses and reporting
 
-![](http://static.blog.mendeley.com/wp-content/uploads/2012/08/Reproducibility-Initiative_resized.png)
+**Emilie Lecomte / Jean-Baptiste Dupont / Célia Couzinié / Adrien Leger**
+
+**Retraite AGT / 29 Avril 2015**
 
 %% Cell type:markdown id: tags:
 
-#Reproducibility crisis in science
+#Believe it or not but Science is in a reproducibility crisis
+
+Florian Prinz et al (2011), *How much can we rely on published data on potential drug targets?* Nature Reviews Drug Discovery 10, 712
 
-Believe it or not: how much can we rely on published data on potential drug targets?
+Editorial board (2012). *Must try harder*. Nature 483: 509–509.
 
-Florian Prinz, Thomas Schlange & Khusru Asadullah
+Landis et al. (2012). *A call for transparent reporting to optimize the predictive value of preclinical research.* Nature 490: 187–191.
+
+
+%% Cell type:markdown id: tags:
 
-Nature Reviews Drug Discovery 10, 712 (September 2011)
+### I have numbers...
 
 %% Cell type:markdown id: tags:
 
 ![](http://www.nature.com.gate2.inist.fr/nrd/journal/v10/n9/images/nrd3439-c1-f1.jpg)
 
-%% Cell type:code id: tags:
+%% Cell type:markdown id: tags:
 
-``` python
-```
+###More numbers ...
+
+%% Cell type:markdown id: tags:
+
+bla bla
+
+%% Cell type:markdown id: tags:
+
+###And Nature group created the open acces collection
+
+### "[Challenges in irreproducible research](http://www.nature.com.gate2.inist.fr/nature/focus/reproducibility/index.html)"
+
+![Design](files/fig/nature.png)
+
+%% Cell type:markdown id: tags:
+
+#What are the consequences ?
+
+%% Cell type:markdown id: tags:
+
+* Biotech failure
+* ...
+
+%% Cell type:markdown id: tags:
+
+###Biotech and Big Pharma loose confidence in academics
+
+![](http://www.addconsortium.org/EVENTS/EV1000165.jpg)
+
+%% Cell type:markdown id: tags:
+
+#What caused the reproducibility crisis?
+
+%% Cell type:markdown id: tags:
+
+### Scientific fraud
+
+** Real issue but concerns only an small proportion of irreproductible studies**
+
+![](http://languagelog.ldc.upenn.edu/myl/NoahsPublisher.gif)
+
+%% Cell type:markdown id: tags:
+
+### Unrelated data panels / missing references / incorrect controls
+
+=> big classic
+
+%% Cell type:markdown id: tags:
+
+###  Pseudo replicates
+Failure to understand the difference between technical and biological replicates =
+
+%% Cell type:markdown id: tags:
+
+### Underpowered studies = Small effect sizes
+
+There may be an significant difference between 2 experimental groups but the study is underpowered and the conclusion indicate an absence of difference ...
+
+Example Garcia 1 dog...
+
+%% Cell type:markdown id: tags:
+
+### Data handling
+
+* Interim data analysis
+* Ad hoc exclusion of data
+
+%% Cell type:markdown id: tags:
+
+### Misusage and Over-interpretation of statistical tests
+
+Nuzzo, R (2014). *Scientific method: Statistical errors*. Nature 506: 150–152.
+
+![](http://www.nature.com.gate2.inist.fr/polopoly_fs/7.15481.1392118822!/image/pvalue_art.jpg_gen/derivatives/landscape_630/pvalue_art.jpg)
+
+%% Cell type:markdown id: tags:
+
+### Inaccurate and incomplete reporting of methods
+
+Impossibility to reproduce results example = experiment acinar Ed
+
+**=> Report the methodology extensively, Provide raw tables in sup data in addition to graphics**
+
+%% Cell type:markdown id: tags:
+
+#How do we fix it?
+
+%% Cell type:markdown id: tags:
+
+ ### Formal training in statistics and study design of project leader
+ ### Or
+ ###work with consultants in methodology design and statistics
+
+%% Cell type:markdown id: tags:
+
+**Pas le temps! Pas l'argent! ...**
+
+ ![](http://38.media.tumblr.com/df91e5cf7e1bfe9f8568b8e1a5a471f3/tumblr_nld3boY3Il1s8pd5uo1_500.gif)
+
+%% Cell type:markdown id: tags:
+
+**Study have to be designed before starting new projects**
+**Exclusion criteria for all experimental protocols**
+**
+
+%% Cell type:markdown id: tags:
+
+### Small sample effects
+
+* Randomisation of animals
+
+* For advanced preclinical studies = Reduce the number of experiental conditions
+
+* Be more stringent in statistical tests = don't choose a statistical test because it looks better with your data
+
+%% Cell type:markdown id: tags:
+
+Standardization
+Blinding
+
+%% Cell type:markdown id: tags:
+
+![](http://38.media.tumblr.com/d165f749635c27b7500f8adf2f37628a/tumblr_nl8zsrgLWw1s8pd5uo1_400.gif)

2015_04_29_Improve_methodology_retraite_AGTI/2015_04_29_Improve_methodology_retraite_AGTI.ipynb

 %% Cell type:markdown id: tags:
 
+# PREPARE RISE PRESENTATION
+
+%% Cell type:code id: tags:
+
+``` python
+from IPython.html.services.config import ConfigManager
+from IPython.utils.path import locate_profile
+cm = ConfigManager(profile_dir=locate_profile(get_ipython().profile))
+cm.update('livereveal', {
+              'theme': 'solarized',
+              'transition': 'linear',
+              'start_slideshow_at': 'selected'})
+
+# transition = default/cube/page/concave/zoom/linear/none
+# theme = beige/blood/default/moon/night/serif/simple/sky/solarized
+# start_slideshow_at = selected/beginning
+```
+
+%%%% Output: execute_result
+
+    {'start_slideshow_at': 'selected',
+     'theme': 'solarized',
+     'transition': 'linear'}
+
+%% Cell type:code id: tags:
+
+``` python
+from IPython.display import HTML, Image, SVG, YouTubeVideo
+```
+
+%% Cell type:markdown id: tags:
+
+# PRESENTATION STARTS BELOW
+
+%% Cell type:markdown id: tags:
+
 #Can we improve our methodology ?
 
-### Adrien Leger
-### Emilie Lecomte
-### Jean-Baptiste Dupont
-### Célia Couzinié
+%% Cell type:markdown id: tags:
+
+**Sure we can!**
+
+%% Cell type:markdown id: tags:
+
+#Why we have to improve our methodologies, analyses and reporting
 
-![](http://static.blog.mendeley.com/wp-content/uploads/2012/08/Reproducibility-Initiative_resized.png)
+**Emilie Lecomte / Jean-Baptiste Dupont / Célia Couzinié / Adrien Leger**
+
+**Retraite AGT / 29 Avril 2015**
 
 %% Cell type:markdown id: tags:
 
-#Reproducibility crisis in science
+#Believe it or not but Science is in a reproducibility crisis
+
+Florian Prinz et al (2011), *How much can we rely on published data on potential drug targets?* Nature Reviews Drug Discovery 10, 712
 
-Believe it or not: how much can we rely on published data on potential drug targets?
+Editorial board (2012). *Must try harder*. Nature 483: 509–509.
 
-Florian Prinz, Thomas Schlange & Khusru Asadullah
+Landis et al. (2012). *A call for transparent reporting to optimize the predictive value of preclinical research.* Nature 490: 187–191.
+
+
+%% Cell type:markdown id: tags:
 
-Nature Reviews Drug Discovery 10, 712 (September 2011)
+### I have numbers...
 
 %% Cell type:markdown id: tags:
 
 ![](http://www.nature.com.gate2.inist.fr/nrd/journal/v10/n9/images/nrd3439-c1-f1.jpg)
 
-%% Cell type:code id: tags:
+%% Cell type:markdown id: tags:
 
-``` python
-```
+###More numbers ...
+
+%% Cell type:markdown id: tags:
+
+bla bla
+
+%% Cell type:markdown id: tags:
+
+###And Nature group created the open acces collection
+
+### "[Challenges in irreproducible research](http://www.nature.com.gate2.inist.fr/nature/focus/reproducibility/index.html)"
+
+![Design](files/fig/nature.png)
+
+%% Cell type:markdown id: tags:
+
+#What are the consequences ?
+
+%% Cell type:markdown id: tags:
+
+* Biotech failure
+* ...
+
+%% Cell type:markdown id: tags:
+
+###Biotech and Big Pharma loose confidence in academics
+
+![](http://www.addconsortium.org/EVENTS/EV1000165.jpg)
+
+%% Cell type:markdown id: tags:
+
+#What caused the reproducibility crisis?
+
+%% Cell type:markdown id: tags:
+
+### Scientific fraud
+
+** Real issue but concerns only an small proportion of irreproductible studies**
+
+![](http://languagelog.ldc.upenn.edu/myl/NoahsPublisher.gif)
+
+%% Cell type:markdown id: tags:
+
+### Unrelated data panels / missing references / incorrect controls
+
+=> big classic
+
+%% Cell type:markdown id: tags:
+
+###  Pseudo replicates
+Failure to understand the difference between technical and biological replicates =
+
+%% Cell type:markdown id: tags:
+
+### Underpowered studies = Small effect sizes
+
+There may be an significant difference between 2 experimental groups but the study is underpowered and the conclusion indicate an absence of difference ...
+
+Example Garcia 1 dog...
+
+%% Cell type:markdown id: tags:
+
+### Data handling
+
+* Interim data analysis
+* Ad hoc exclusion of data
+
+%% Cell type:markdown id: tags:
+
+### Misusage and Over-interpretation of statistical tests
+
+Nuzzo, R (2014). *Scientific method: Statistical errors*. Nature 506: 150–152.
+
+![](http://www.nature.com.gate2.inist.fr/polopoly_fs/7.15481.1392118822!/image/pvalue_art.jpg_gen/derivatives/landscape_630/pvalue_art.jpg)
+
+%% Cell type:markdown id: tags:
+
+### Inaccurate and incomplete reporting of methods
+
+Impossibility to reproduce results example = experiment acinar Ed
+
+**=> Report the methodology extensively, Provide raw tables in sup data in addition to graphics**
+
+%% Cell type:markdown id: tags:
+
+#How do we fix it?
+
+%% Cell type:markdown id: tags:
+
+ ### Formal training in statistics and study design of project leader
+ ### Or
+ ###work with consultants in methodology design and statistics
+
+%% Cell type:markdown id: tags:
+
+**Pas le temps! Pas l'argent! ...**
+
+ ![](http://38.media.tumblr.com/df91e5cf7e1bfe9f8568b8e1a5a471f3/tumblr_nld3boY3Il1s8pd5uo1_500.gif)
+
+%% Cell type:markdown id: tags:
+
+**Study have to be designed before starting new projects**
+**Exclusion criteria for all experimental protocols**
+**
+
+%% Cell type:markdown id: tags:
+
+### Small sample effects
+
+* Randomisation of animals
+
+* For advanced preclinical studies = Reduce the number of experiental conditions
+
+* Be more stringent in statistical tests = don't choose a statistical test because it looks better with your data
+
+%% Cell type:markdown id: tags:
+
+Standardization
+Blinding
+
+%% Cell type:markdown id: tags:
+
+![](http://38.media.tumblr.com/d165f749635c27b7500f8adf2f37628a/tumblr_nl8zsrgLWw1s8pd5uo1_400.gif)

2015_04_29_Improve_methodology_retraite_AGTI/custom.css

-/*Some css fixes to use night theme with IPython slides*/
-body {
-background-color: #111111;
-}
-.reveal p {
-color: white;
-}
-.reveal ul, ol {
-color: white;
-}
-div.output_area pre {
-color: white;
-}
-div.output_stderr {
-background: #F00;
-}
-.reveal table th, .reveal table td {
-color: white;
-}