Updates to slides

kyleabeauchamp · Feb 27, 2015 · 5a71205 · 5a71205
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diff --git a/base.html b/base.html
@@ -26,7 +26,8 @@
   <link rel="stylesheet" media="all" href="theme/css/custom.css">
   <link rel="stylesheet" media="only screen and (max-device-width: 480px)" href="theme/css/phone.css">
   <base target="_blank"> <!-- This amazingness opens all links in a new tab. -->
-  <script data-main="js/slides" src="js/require-1.0.8.min.js"></script>
+  <script data-main="js/slides", src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.14/require.min.js"></script>
+
 
   <!-- MathJax support  -->
   <script type="text/x-mathjax-config">
@@ -39,10 +40,20 @@
       displayMath: [ ['$$','$$'], ["\\[","\\]"] ],
       processEscapes: true
     },
+    TeX: {
+      extensions: ["color.js"]
+    },
     "HTML-CSS": { availableFonts: ["TeX"] }
   });
   </script>
-  <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+  <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+  <div style="display:hidden">
+  \[
+    \definecolor{data}{RGB}{18,110,213}
+    \definecolor{unknown}{RGB}{217,86,16}
+    \definecolor{learned}{RGB}{175,114,176}
+  \]
+  </div>
 
 </head>
 

diff --git a/index.html b/index.html
@@ -13,7 +13,7 @@
 <!DOCTYPE html>
 <html>
 <head>
-  <title> Conformational Dynamics in Mixtape</title>
+  <title> Conformational Dynamics in MSMBuilder3</title>
   <meta charset="utf-8">
   <meta http-equiv="X-UA-Compatible" content="chrome=1">
   <!--<meta name="viewport" content="width=device-width, initial-scale=1.0, minimum-scale=1.0">-->
@@ -26,7 +26,8 @@
   <link rel="stylesheet" media="all" href="theme/css/custom.css">
   <link rel="stylesheet" media="only screen and (max-device-width: 480px)" href="theme/css/phone.css">
   <base target="_blank"> <!-- This amazingness opens all links in a new tab. -->
-  <script data-main="js/slides" src="js/require-1.0.8.min.js"></script>
+  <script data-main="js/slides", src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.14/require.min.js"></script>
+
 
   <!-- MathJax support  -->
   <script type="text/x-mathjax-config">
@@ -39,10 +40,20 @@
       displayMath: [ ['$$','$$'], ["\\[","\\]"] ],
       processEscapes: true
     },
+    TeX: {
+      extensions: ["color.js"]
+    },
     "HTML-CSS": { availableFonts: ["TeX"] }
   });
   </script>
-  <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+  <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+  <div style="display:hidden">
+  \[
+    \definecolor{data}{RGB}{18,110,213}
+    \definecolor{unknown}{RGB}{217,86,16}
+    \definecolor{learned}{RGB}{175,114,176}
+  \]
+  </div>
 
 </head>
 
@@ -52,9 +63,9 @@
 <slide class="title-slide segue nobackground">
   <hgroup class="auto-fadein">
 
-    <h1> Conformational Dynamics in Mixtape</h1>
+    <h1> Conformational Dynamics in MSMBuilder3</h1>
     <h2></h2>
-    <p> Kyle A. Beauchamp<br/> September 3, 2014</p>
+    <p> Kyle A. Beauchamp<br/> Updated Feb. 27, 2015 (msmbuilder v3.1)</p>
   </hgroup>
 </slide>
 
@@ -140,7 +151,7 @@ <h3></h3>
 <slide  >
 
     <hgroup>
-      <h2>Mixtape: Philosophy</h2>
+      <h2>MSMBuilder: Philosophy</h2>
       <h3></h3>
     </hgroup>
     <article ><p>Let's build on <a href="http://scikit-learn.org/stable/">scikit-learn</a> idioms:</p>
@@ -162,14 +173,14 @@ <h3></h3>
     </hgroup>
     <article ><pre class="prettyprint" data-lang="python">
 
->>> import mixtape.cluster
->>> clusterer = mixtape.cluster.KMeans(n_clusters=4)
+>>> import msmbuilder.cluster
+>>> clusterer = msmbuilder.cluster.KMeans(n_clusters=4)
 
->>> import mixtape.tica
->>> tica = mixtape.tica.tICA(n_components=3)
+>>> import msmbuilder.decomposition
+>>> tica = msmbuilder.decomposition.tICA(n_components=3)
 
->>> import mixtape.markovstatemodel
->>> msm = mixtape.markovstatemodel.MarkovStateModel()
+>>> import msmbuilder.msm
+>>> msm = msmbuilder.msm.MarkovStateModel()
 
 </pre>
 
@@ -188,11 +199,11 @@ <h3></h3>
     </hgroup>
     <article ><pre class="prettyprint" data-lang="python">
 
->>> import mixtape.cluster
+>>> import msmbuilder.cluster
 
 >>> trajectories = [np.random.normal(size=(100, 3))]
 
->>> clusterer = mixtape.cluster.KMeans(n_clusters=4, n_init=10)
+>>> clusterer = msmbuilder.cluster.KMeans(n_clusters=4, n_init=10)
 >>> clusterer.fit(trajectories)
 
 >>> clusterer.cluster_centers_
@@ -217,11 +228,11 @@ <h3></h3>
     </hgroup>
     <article ><pre class="prettyprint" data-lang="python">
 
->>> import mixtape.markovstatemodel
+>>> import msmbuilder.msm
 
 >>> trajectories = [np.array([0, 0, 0, 1, 1, 1, 0, 0])]
 
->>> msm = mixtape.markovstatemodel.MarkovStateModel()
+>>> msm = msmbuilder.msm.MarkovStateModel()
 >>> msm.fit(trajectories)
 
 >>> msm.transmat_
@@ -243,11 +254,11 @@ <h3></h3>
     </hgroup>
     <article ><pre class="prettyprint" data-lang="python">
 
->>> import mixtape.cluster
+>>> import msmbuilder.cluster
 
 >>> trajectories = [np.random.normal(size=(100, 3))]
 
->>> clusterer = mixtape.cluster.KMeans(n_clusters=4, n_init=10)
+>>> clusterer = msmbuilder.cluster.KMeans(n_clusters=4, n_init=10)
 >>> clusterer.fit(trajectories)
 >>> Y = clusterer.transform(trajectories)
 
@@ -271,13 +282,13 @@ <h3></h3>
     </hgroup>
     <article ><pre class="prettyprint" data-lang="python">
 
->>> import mixtape.cluster, mixtape.markovstatemodel
+>>> import msmbuilder.cluster, msmbuilder.msm
 >>> from sklearn.pipeline import Pipeline
 
 >>> trajectories = [np.random.normal(size=(100, 3))]
 
->>> clusterer = mixtape.cluster.KMeans(n_clusters=2, n_init=10)
->>> msm = mixtape.markovstatemodel.MarkovStateModel()
+>>> clusterer = msmbuilder.cluster.KMeans(n_clusters=2, n_init=10)
+>>> msm = msmbuilder.msm.MarkovStateModel()
 >>> pipeline = Pipeline([("clusterer", clusterer), ("msm", msm)])
 
 >>> pipeline.fit(trajectories)
@@ -305,8 +316,8 @@ <h3></h3>
 
 <pre class="prettyprint" style="width:75%" data-lang="python">
 
->>> from mixtape.featurizer import DihedralFeaturizer
->>> from mixtape.datasets import fetch_alanine_dipeptide
+>>> from msmbuilder.featurizer import DihedralFeaturizer
+>>> from msmbuilder.example_datasets import fetch_alanine_dipeptide
 >>> from matplotlib.pyplot import hexbin, plot
 
 >>> trajectories = fetch_alanine_dipeptide()["trajectories"]
@@ -349,10 +360,10 @@ <h3></h3>
     <article ><pre class="prettyprint" data-lang="python">
 
 >>> import mdtraj as md
->>> from mixtape.featurizer import DihedralFeaturizer
->>> from mixtape.datasets import fetch_alanine_dipeptide
->>> from mixtape.cluster import KCenters
->>> from mixtape.markovstatemodel import MarkovStateModel
+>>> from msmbuilder.featurizer import DihedralFeaturizer
+>>> from msmbuilder.example_datasets import fetch_alanine_dipeptide
+>>> from msmbuilder.cluster import KCenters
+>>> from msmbuilder.msm import MarkovStateModel
 >>> from sklearn.pipeline import Pipeline
 
 >>> trajectories = fetch_alanine_dipeptide()["trajectories"]
@@ -412,27 +423,14 @@ <h3></h3>
 
 </slide>
 
-<slide  >
-
-    <hgroup>
-      <h2>Model Scoring with GMRQ</h2>
-      <h3>We can improve a lot over KMeans.</h3>
-    </hgroup>
-    <article ><p><center>
-<img height=355 src=figures/SETD2_kcenters.png />
-<img height=355 src=figures/SETD2_tICA_KMeans.png />
-</center></p></article>
-
-</slide>
-
 
 <slide class="thank-you-slide segue nobackground">
   <!-- <aside class="gdbar right"><img src="images/google_developers_icon_128.png"></aside> -->
   <article class="flexbox vleft auto-fadein">
-    <h2> Thanks!</h2>
-    <p> Contributors: Robert M., Kyle B., Bharath R., Matt H., Steve K., Gert K., Muneeb S.</p>
+    <h2></h2>
+    <p></p>
   </article>
-  <p data-config-contact class="auto-fadein"> <span>www</span> <a href="http://msmbuilder-mixtape.s3-website-us-west-1.amazonaws.com/latest/index.html">mixtape docs</a><br/> <span>github</span> <a href="https://github.com/rmcgibbo/mixtape">mixtape</a></p>
+  <p data-config-contact class="auto-fadein"></p>
   </p>
 </slide>
 

diff --git a/js/slides.js b/js/slides.js
@@ -1,6 +1,23 @@
-require(['order!modernizr.custom.45394',
-         'order!prettify/prettify', 'order!hammer', 'order!slide-controller',
-         'order!slide-deck'], function(someModule) {
+requirejs.config({
+    baseUrl: "js/",
+    paths: {
+	modernizer: "modernizr.custom.45394",
+	prettify: "https://cdnjs.cloudflare.com/ajax/libs/prettify/r298/prettify.min",
+	underscore: "https://cdnjs.cloudflare.com/ajax/libs/underscore.js/1.7.0/underscore-min",
+	hammer: "https://cdnjs.cloudflare.com/ajax/libs/hammer.js/0.6.4/hammer.min"
+    },
+    shim:  {
+	'slide-deck' : {
+	    deps: ['modernizer', 'hammer', 'underscore'],
+	    exports: 'SlideDeck',
+	},
+	'modernizer' : 'Modernizr',
+	'hammer': {exports: 'Hammer'},
+    }	
+});
+
+require(['modernizer', 'prettify', 'hammer', 'slide-controller',
+	 'slide-deck'],function(someModule) {
 
 var initElasticity = function() {    
     var resize = function() {