-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.html
339 lines (285 loc) · 12.8 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>rOpenSci - UGA Quick Intro</title>
<meta name="description" content="Montreal QCBS Talk">
<meta name="author" content="Scott Chamberlain">
<meta name="apple-mobile-web-app-capable" content="yes" />
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
<link rel="stylesheet" href="css/reveal.min.css">
<link rel="stylesheet" href="css/theme/solarized.css" id="theme">
<!-- <link rel="stylesheet" href="http://netdna.bootstrapcdn.com/bootstrap/3.0.3/css/bootstrap.min.css"> -->
<link rel="stylesheet" href="http://netdna.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.css">
<link rel="stylesheet" href="lib/css/font-awesome-4.2.0/css/font-awesome.css">
<!-- For syntax highlighting -->
<link rel="stylesheet" href="lib/css/zenburn.css">
<!-- <link rel="stylesheet" href="lib/css/foundation.css"> -->
<!-- <link rel="stylesheet" href="lib/css/font-awesome.min.css"> -->
<!-- If the query includes 'print-pdf', use the PDF print sheet -->
<script>
document.write( '<link rel="stylesheet" href="css/print/' + ( window.location.search.match( /print-pdf/gi ) ? 'pdf' : 'paper' ) + '.css" type="text/css" media="print">' );
</script>
<!--[if lt IE 9]>
<script src="lib/js/html5shiv.js"></script>
<![endif]-->
<style type="text/css">
#rotate_text {
-webkit-transform: rotate(-90deg);
-moz-transform: rotate(-90deg);
transform: rotate(-90deg);
position: absolute;
vertical-align: middle;
filter:progid:DXImageTransform.Microsoft.BasicImage(rotation=3);
}
</style>
</head>
<body>
<div class="reveal">
<!-- Any section element inside of this container is displayed as a slide -->
<div class="slides">
<section id="repo">
<br><br><br>
<h1>bit.ly/uga14</h1>
</section>
<section id="front">
<br>
<h1>rOpenSci - Open tools for open science</h1>
</section>
<section id="notes">
<center><img src="img/notes_for_nature.png" width="1100"></center>
</section>
<section id="sensors">
<center><img src="img/sensors.png" width="1100"></center>
</section>
<section id="data_hard">
<h1 align="left">These data are hard to get</h1>
<h2><i class="fa fa-lock fa-5x" style="color:#b22d28"></i></h2>
</section>
<section id="weneed">
<center><h1 align="left">We need...</h2></center>
<br><br>
<center><div class="row">
<font color="green"><h2><i class="fa fa-unlock fa-5x"></i></font></h2></font>
</div></center>
</section>
<section id="why_open">
<h1> <font color="green"><i class="fa fa-unlock"></i></font> Why Open?</h1>
</section>
<section id="why_open_public">
<center>
<font color="green"> <i class="fa fa-unlock fa-3x"> Why Open?</i></font>
<br><br><br><br>
<h2>Most research publicly funded</h2>
<br><br>
<center><i class="fa fa-dollar fa-5x"></i>
</section>
<section id="why_open_pace">
<font color="green"> <i class="fa fa-unlock fa-3x"> Why Open?</i></font>
<br><br><br><br>
<h2>To increase the pace of science</h2>
<br><br>
<i class="fa fa-rocket fa-5x"></i>
</section>
<section id="why_open_citations">
<center>
<font color="green"> <i class="fa fa-unlock fa-3x"> Why Open?</i></font>
<br><br>
<h2> Sharing data increases citations</h2>
<center><img src="img/piwowar.png" width="700"></center>
<a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000308" style="float:right;">Piwowar et al. 2007</a>
</section>
<!-- <section id="reproducible">
<h1> Openness <font color="green"><i class="fa fa-unlock"></i></font> facilitates reproducibility <font color="blue"><i class="fa fa-spinner"> </i></font></h1>
</section>
<section id="why_reproducible_selfish">
<font color="blue"><i class="fa fa-spinner fa-3x"> Why Reproducible?</i> </font>
<br><br><br><br>
<h2>For yourself!</h2>
<br><br>
<i class="fa fa-user fa-5x"></i>
</section>
<section id="why_reproducible_mistakes">
<font color="blue"><i class="fa fa-spinner fa-3x"> Why Reproducible?</i> </font>
<br><br><br>
<h2>To avoid mistakes</h2>
<br><br>
<table cellpadding="40" cellspacing="40">
<tr>
<td> </td>
<td> <center><p>Reinhart-Rogoff<img src="img/excel.png" width="500"></center>
<a href="http://www.nytimes.com/2013/04/19/opinion/krugman-the-excel-depression.html?_r=0" style="float:left;">excel</a></td>
<td> </td>
<td> <center><p>Chronic fatigue syndrome-XMRV<img src="img/judy.jpg" width="300"></center>
<a href="http://retractionwatch.com/2011/12/22/chronic-fatigue-syndrome-xmrv-paper-retracted-by-science-completely-this-time/" style="float:left;">cfs</a></td>
</tr>
</table>
</section> -->
<!-- <section id="easier">
<font size="52"><h1 align="left">Or maybe you just want science to be easier</h1></font>
</section> -->
<section id="whats_needed">
<font size="52"><h1 align="left">What tools do we need? <br><br>What's missing?</h1></font>
</section>
<section id="reproducible_workflow">
<font size="52"><h1 align="left"><i class="fa fa-arrow-circle-right"></i> A reproducible workflow</h1></font>
</section>
<!-- <section id="not_these">
<center><h2>Not these!</h2></center>
<img src="img/closedtools.png" width="1000">
</section>
<section id="these">
<center><h2>These!</h2></center>
<img src="img/opentools.png" width="1000">
</section>
<section id="learning_curve">
<center><h2>There's a learning curve, but...</h2></center>
<img src="img/tasks.jpg" width="1000">
<a href="http://www.globalnerdy.com/2012/04/24/geeks-and-repetitive-tasks/">link</a>
</section> -->
<section id="workflows">
<center><h2> Workflows side by side</h2></center>
<table cellpadding="40" cellspacing="20">
<tr>
<td> </td>
<td width="50%"> <p>Our workflow now
<ul>
<font size="6">
<li>Browser</li>
<li>Excel</li>
<li>SAS</li>
<li>SigmaPlot</li>
<li>Word</li>
<li>Endnote</li>
</font>
</ul> </td>
<td> </td>
<td width="50%"> <p>What it could be
<ul>
<li>R (or Python)</li>
<li>+ a few open source things (<a href="http://daringfireball.net/projects/markdown/">Markdown</a>, or <a href="http://www.latex-project.org/">LaTeX</a> )</li></ul></td>
<td> </td>
</tr>
<tr>
<td> </td>
<td><p> <i class="fa fa-money"></i> Cost = $$$$$$$<br>
<p> <i class="fa fa-unlock"></i> Open? = Nope
<p> <i class="fa fa-spinner"></i> Reproducible? = Nope</td>
<td> </td>
<td><p> <i class="fa fa-money"></i> Cost = 0<br>
<p> <i class="fa fa-unlock"></i> Open? = Yes!
<p> <i class="fa fa-spinner"></i> Reproducible? = Yep</td>
</tr>
</table>
</section>
<!-- <section id="perfect">
<center><h2>A perfect marriage</h2></center>
<br><br>
<center>
<font color="red" size="12"><i class="fa fa-spinner fa-5x"> </i></font>
<font color="green" size="12"> <i class="fa fa-unlock fa-5x"> </i></font>
<font color="blue" size="12" class="fragment"><i class="fa fa-cloud fa-5x"> </i></font>
</center>
</section>
<section id="dataweb">
<h2>Data is increasingly on the web <font color="blue"><i class="fa fa-cloud"></i></font></h2>
<img src="img/data.png" width="1000">
</section>
<section id="apis">
<h2> <font color="red">Reproducibly</font> plug data from the web into your science</h2>
<br><br>
<p style="float:left;">API: Application Programming Interface - APIs are the highways connecting providers to users.
<br><br><br><br>
<h2><i class="fa fa-link fa-3x"></i> </h2>
</section> -->
<section id="ropensci">
<br><br><br>
<center><img src="img/ropensci_main.png"></center>
<br><br>
<center><img src="img/sloan_logo2.png"></center>
</section>
<!-- <section id="ropensci_team">
<h2>How rOpenSci got started</h2>
<div>
<img src="img/core_team.png">
</div><br>
<h3>formed from ad-hoc conversation over Twitter. Now a <a href="http://ropensci.org/community/#community" title="rOpenSci Community" target="_blank">worldwide community of researchers</a>.</h3>
</section> -->
<section id="workflow">
<br><br><br>
<center>
<h2>Data acquisition <i class="fa fa-cloud-download"></i> <i class="fa fa-plus"></i> <br><br> data manipulation/analysis/viz <i class="fa fa-bar-chart"></i> <i class="fa fa-plus"></i> <br><br> writing <i class="fa fa-pencil"></i> <i class="fa fa-plus"></i> <br><br> publish <i class="fa fa-cloud-upload"></i></h2>
</center>
</section>
<section id="workflow_acquisition">
<br><br><br>
<center>
<h2><font color="blue"><strong>Data acquisition</strong> <i class="fa fa-cloud-download"></i></font> <i class="fa fa-plus"></i> <br><br> data manipulation/analysis/viz <i class="fa fa-bar-chart"></i> <i class="fa fa-plus"></i> <br><br> writing <i class="fa fa-pencil"></i> <i class="fa fa-plus"></i> <br><br> publish <i class="fa fa-cloud-upload"></i></h2>
</center>
</section>
<section id="workflow_manip">
<br><br><br>
<center>
<h2>Data acquisition <i class="fa fa-cloud-download"></i> <i class="fa fa-plus"></i> <br><br> <font color="blue"><strong>data manipulation/analysis/viz</strong> <i class="fa fa-bar-chart"></i></font> <i class="fa fa-plus"></i> <br><br> writing <i class="fa fa-pencil"></i> <i class="fa fa-plus"></i> <br><br> publish <i class="fa fa-cloud-upload"></i></h2>
</center>
</section>
<section id="workflow_writing">
<br><br><br>
<center>
<h2>Data acquisition <i class="fa fa-cloud-download"></i> <i class="fa fa-plus"></i> <br><br> data manipulation/analysis/viz <i class="fa fa-bar-chart"></i> <i class="fa fa-plus"></i> <br><br> <font color="blue"><strong>writing</strong> <i class="fa fa-pencil"></i></font> <i class="fa fa-plus"></i> <br><br> publish <i class="fa fa-cloud-upload"></i></h2>
</center>
</section>
<section id="workflow_publish">
<br><br><br>
<center>
<h2>Data acquisition <i class="fa fa-cloud-download"></i> <i class="fa fa-plus"></i> <br><br> data manipulation/analysis/viz <i class="fa fa-bar-chart"></i> <i class="fa fa-plus"></i> <br><br> writing <i class="fa fa-pencil"></i> <i class="fa fa-plus"></i> <br><br> <font color="blue"><strong>publish</strong> <i class="fa fa-cloud-upload"></i></font></h2>
</center>
</section>
<section id="last">
<br>
<h3>rOpenSci on the web: <a href="http://ropensci.org/">http://ropensci.org/</a> </h3>
<br><br>
<h3> This talk on the interwebs: <a href="http://recology.info/talks/uga">http://recology.info/talks/uga</a> </h3>
<br><br><br><br><br><br>
<h3>Made w/ <a href="https://github.com/hakimel/reveal.js">reveal.js</a></h3>
<br>
<h3>Icons by: <a href="http://fortawesome.github.io/Font-Awesome/">FontAwesome v4.2.0</a></h3>
</section>
</div>
<!-- End slides -->
</div>
<script src="lib/js/head.min.js"></script>
<script src="js/reveal.min.js"></script>
<script>
// Full list of configuration options available here:
// https://github.com/hakimel/reveal.js#configuration
Reveal.initialize({
controls: false,
progress: true,
history: true,
center: false,
slideNumber: true,
keyboard: true,
touch: true,
fragments: true,
width: 1400,
height: 900,
theme: Reveal.getQueryHash().theme, // available themes are in /css/theme
transition: Reveal.getQueryHash().transition || 'none', // default/cube/page/concave/zoom/linear/fade/none
// Parallax scrolling
// parallaxBackgroundImage: 'https://s3.amazonaws.com/hakim-static/reveal-js/reveal-parallax-1.jpg',
// parallaxBackgroundSize: '2100px 900px',
// Optional libraries used to extend on reveal.js
dependencies: [
{ src: 'lib/js/classList.js', condition: function() { return !document.body.classList; } },
{ src: 'plugin/markdown/marked.js', condition: function() { return !!document.querySelector( '[data-markdown]' ); } },
{ src: 'plugin/markdown/markdown.js', condition: function() { return !!document.querySelector( '[data-markdown]' ); } },
{ src: 'plugin/highlight/highlight.js', async: true, callback: function() { hljs.initHighlightingOnLoad(); } },
{ src: 'plugin/zoom-js/zoom.js', async: true, condition: function() { return !!document.body.classList; } },
{ src: 'plugin/notes/notes.js', async: true, condition: function() { return !!document.body.classList; } }
]
});
</script>
</body>
</html>