forked from samirdas/samirdas.github.io
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Big_data.html
519 lines (444 loc) · 16.4 KB
/
Big_data.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
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Bringing big data to the NICU</title>
<meta name="description" content="A framework for easily creating beautiful presentations using HTML">
<meta name="author" content="Hakim El Hattab">
<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, minimal-ui">
<!-- The important Javascript libraries -->
<link rel="stylesheet" href="css/reveal.css">
<link rel="stylesheet" href="css/theme/black.css" id="theme">
<!-- Code syntax highlighting -->
<link rel="stylesheet" href="lib/css/zenburn.css">
<!-- Printing and PDF exports -->
<script>
var link = document.createElement( 'link' );
link.rel = 'stylesheet';
link.type = 'text/css';
link.href = window.location.search.match( /print-pdf/gi ) ? 'css/print/pdf.css' : 'css/print/paper.css';
document.getElementsByTagName( 'head' )[0].appendChild( link );
</script>
<!--[if lt IE 9]>
<script src="lib/js/html5shiv.js"></script>
<![endif]-->
</head>
<body>
<div class="reveal">
<!-- Any section element inside of this container is displayed as a slide -->
<div class="slides">
<!-- Big Data -->
<section>
<section>
<h2>Bringing big data to the NICU</h2>
<table class="reveal">
<tr>
<td width="50%" style="vertical-align: middle">
<p><font color='yellow'>Canadian Neonatal Brain Platform Symposium 2017<br><small> Sainte Justine - September 26, 2017</small></font></p>
<p><small>Samir Das - Software Manager<br>
McGill Centre for Integrative Neuroscience </small></p>
<img src="images/Neuro.png">
<img src="images/MCIN.png">
<img src="images/Ludmer.png">
<td>
<img src="images/Biological_psych.png">
</td></tr>
<tr>
</tr>
</table>
</section>
<section data-transition="convex">
<img src="images/Spock.png">
</section>
</section>
<!-- Big Data Curve-->
<section data-transition="zoom">
<img src="images/Big_data.jpg">
</section>
<!-- Big Data Curve-->
<section data-transition="zoom">
<img src="images/Big_data.png">
</section>
<!-- Types of data-->
<section data-transition="zoom">
<img src="images/Neuroinformatics_scope.jpg">
</section>
<!-- Cross Modal Data-->
<section data-transition="zoom">
<img src="images/Cross_modal.png">
</section>
<!-- Big data projects-->
<section data-transition="zoom">
<img src="images/HBP.png">
</section>
<!-- What is Data Sharing? -->
<section data-background="images/Data_sharing_cartoon.png">
<h2><font color="black">What is Data Sharing?</font></h2>
<p class="fragment roll-in"><font color="purple">Exchange of information</font></p>
<p class="fragment roll-in"><font color="black">Datasets</font></p>
<p class="fragment roll-in"><font color="black">Tools</font></p>
<p class="fragment roll-in"><font color="black">Standardization</font></p>
<p class="fragment roll-in"><font color="black">Databases</font></p>
<p class="fragment roll-in"><font color="black">Collaborations</font></p>
<p class="fragment roll-in"><font color="black">Conferences, hackathons</font></p>
<p class="fragment roll-in"><font color="black">Facebook, Google, Twitter, etc.</font></p>
<br>
<p><font size="1" color="black">Image source: http://blog.veritythink.com/post/87880448269/creative-data-sharing-and-open-humanitarianism</font></p>
</section>
<section data-transition="concave">
<!-- Why is Data Sharing Important? -->
<section data-transition="concave">
<h2>Data Sharing Considerations</h2>
<table>
<thead>
<tr>
<th><font color="yellow">Benefits </font></th>
<th><font color="yellow">Hurdles </font></th>
</tr>
</thead>
<tbody>
<tr>
<td>Increased validation</td>
<td>Obtaining ethics</td>
</tr>
<tr>
<td>Reduces waste/duplication</td>
<td>Technical challenges</td>
</tr>
<tr>
<td>Increased exposure</td>
<td>Privacy concerns</td>
</tr>
<tr>
<td>Access to larger datasets</td>
<td>Data Harmonization</td>
</tr>
<tr>
<td>Access to rare data</td>
<td>Interoperability</td>
</tr>
<tr>
<td>Less attrition</td>
<td>Reproducibility</td>
</tr>
<tr>
<td>Saving Tax $$</td>
<td>Public dataset not identical</td>
</tr>
</tbody>
</table>
</section>
<!-- Problem Case -->
<section data-transition="convex">
<h2>Privacy Concerns</h2>
<table class="reveal">
<tr>
<td width="40%" style="vertical-align: middle">
<img src="images/Data_breach_title.png">
<img src="images/Data_breach_consent.png">
<img src="images/Data_breach.png">
</td>
<td width="60%" style="vertical-align: middle">
<a href="https://tech.vijayp.ca/of-taxis-and-rainbows-f6bc289679a1#.jbat052vf"><img src="images/Data_breach_NYC_taxi.png"></a>
<small><a href="https://www.mcgill.ca/bic/channels/event/feindel-brain-imaging-lecture-series-adrian-thorogood-embracing-open-science-best-practices-258420" target="_blank">Adrian Thorogood BIC lecture - March 9, 2016</a></small>
<img src="images/Data_breach_magazine.png">
</td>
</tr></table>
</section>
</section>
<!-- COBIDAS -->
<section data-transition="concave">
<h2>Best practices in Data Sharing</h2>
<table class="reveal">
<tr>
<td width="50%" style="vertical-align: middle">
<img src="images/COBIDAS_Nature.png">
</td>
<td width="50%" style="vertical-align: middle">
<img src="images/COBIDAS.png">
</td>
</tr></table>
</section>
<!-- Data sharing solutions -->
<section data-transition="convex">
<h2>Some Data Sharing solutions?</h2>
<img src="images/Solutions.png">
</section>
<!-- External Initiatives -->
<section>
<!-- BIDS -->
<section data-transition="fade">
<table class="reveal">
<h2>BIDS</h2>
<tr>
<td width="75%" style="vertical-align: middle">
<img src="images/BIDS.png">
</td>
<td width="25%" style="vertical-align: middle">
<p>Common Ontology for Imaging Data</p>
</td>
</tr></table>
</section>
<!-- NeuroImgaging Data Model (NiDM)-->
<section data-transition="fade">
<h2>NeuroImaging Data Model</h2>
<img src="images/Nidm.png">
<p>Format for storing metadata, provenance, processing information</p>
</section>
<!--Neurovault-->
<section data-transition="fade">
<table class="reveal">
<tr>
<td width="50%" style="vertical-align: middle">
<img src="images/Neurovault.png">
</td>
<td width="50%" style="vertical-align: middle">
<img src="images/Neurovault_example.png">
</td>
</tr></table>
</section>
<!--DataLad-->
<section data-transition="fade">
<h2>DataLad</h2>
<img src="images/Datalad.png">
</section>
</section>
<!-- Some of our solutions-->
<section data-transition="fade">
<img src="images/MNI_ecosystem_paper.png">
</section>
<section data-transition="fade">
<h2>LORIS - CBRAIN Data Flow</h2>
<img src="images/Data_flow.jpg">
</section>
<!-- LORIS -->
<section data-transition="fade">
<!-- LORIS Key features -->
<section data-transition="zoom">
<h2>LORIS - Key features</h2>
<img src="images/Key_features.png">
</section>
<!-- LORIS Dashboard -->
<section data-transition="zoom">
<h2>LORIS Dashboard</h2>
<img src="images/LORIS_dashboard.png">
</section>
<!-- LORIS globally -->
<section data-background="images/LORIS_global.png">
<h1><font color ="blue">LORIS globally</font></h1>
</section>
<!-- NIHPD -->
<section data-transition="convex">
<img src="images/NIHPD_logo.jpg">
<table class="reveal">
<tr>
<td width="45%" style="vertical-align: middle">
<img src="images/NIHPD_paper.png">
</td>
<td width="30%" style="vertical-align: middle">
<img src="images/MRI_images_several.jpg">
</td>
<td width="30%" style="vertical-align: top">
<ul><small>
<li>Cited 295 times</li>
<li>Control data for NDAR</li>
<li>Longitudinal study (8 years)</li>
<li>532 subjects</li>
<li>8000 distinct variables</li>
<li>37000 individual assessments</li>
<li>T1, T2, PD, DTI, Spectroscopy</li>
<li>∼3TB of imaging data</li>
<li>2000 MRI acquisitions</li>
</small></ul>
</td>
</tr></table>
</section>
<!-- IBIS -->
<section data-transition="convex">
<img src="images/IBIS.png">
<table class="reveal">
<tr>
<td width="45%" style="vertical-align: middle">
<img src="images/IBIS_paper.png">
</td>
<td width="30%" style="vertical-align: middle">
<img src="images/IBIS_image.png">
</td>
<td width="30%" style="vertical-align: top">
<p><small>
<ul>
<li>Autism infant brain development</li>
<li>3000+ scans</li>
<li>700+ subjects</li>
<li>7000 distinct variables</li>
<li>150,000+ individual assessments</li>
<li>T1, T2, DTI, BOLD</li>
<li>∼5 TBs imaging data</li>
<li>Genetic/biospecimen data</li>
</ul>
</small></p>
</td>
</tr></table>
</section>
<!-- CCNA -->
<section data-transition="concave">
<table class="reveal">
<h2>CCNA</h2>
<tr>
<td width="70%" style="vertical-align: top">
<img src="images/CCNA.png">
</td>
<td width="30%" style="vertical-align: top">
<p><small>
<ul>
<li>$35 million</li><br>
<li>CIHR funded</li><br>
<li>Pan Canadian Consortium</li><br>
<li>Acquisition in June, 2016</li><br>
<li>35 collections sites</li><br>
<li>LORIS powered</li><br>
</ul>
</small></p>
</td>
</tr></table>
</section>
<!-- BigBrain example -->
<section data-transition="fade">
<table class="reveal">
<h2>BigBrain</h2>
<tr>
<td width="50%" style="vertical-align: middle">
<img src="images/BigBrain.png">
</td>
<td width="50%" style="vertical-align: middle">
<img src="images/BigBrain_paper.png">
</td>
</tr></table>
</section>
</section>
<!-- CBRAIN -->
<section>
<section>
<table class="reveal">
<h2><a href="http://www.cbrain.ca">CBRAIN</a></h2>
<tr>
<td width="35%" style="vertical-align: top">
<p><small><font color="yellow">Several default tools:</font>
<ul>
<li>CIVET</li>
<li>CivetCombiner</li>
<li>CivetQC</li>
<li>Freesurfer</li>
<li>SPM-batch</li>
<li>NIAK</li>
<li>FSL (bedpostx, bet, fast, feat, first flirt, melodic, probtrackx)</li>
<li>Numerous converters</li>
<li>And many more...</li>
</ul>
<p><a href="mailto:[email protected]">[email protected]</a></p>
</td>
<td width="65%" style="vertical-align: middle">
<img src="images/CBRAIN_paper.png">
</td>
</tr></table>
</section>
<section>
<h2>CBRAIN projects</h2>
<img src="images/CBRAIN_mainpage.png">
</section>
<section>
<h2>CBRAIN tasks</h2>
<img src="images/CBRAIN_tasks.png">
</section>
<section>
<img src="images/CBRAIN_distribution.png">
</section>
<section>
<img src="images/CBRAIN_hours.png">
</section>
<section>
<img src="images/CBRAIN_schema.png">
</section>
<section>
<h2>CIVET for neonates</h2>
<table class="reveal">
<tr>
<td width="70%" style="vertical-align: middle">
<img src="images/CIVET_processing_steps.png">
</td>
<td>
<img src="images/CIVET_cortical_thickness.png">
<img src="images/CIVET.png">
</td>
</tr></table>
</section>
</section>
<!-- MNI Open Science -->
<section data-transition="convex">
<section>
<h2>Open Science</h2>
<table class="reveal">
<tr>
<td width="50%" style="vertical-align: middle">
<img src="images/Nature_open_science.png">
</td>
<td>
<img src="images/Open_science.png">
</td></tr></table>
</section>
<section>
<img src="images/Open_science_paper.png">
</section>
<section>
<h2>Cyberinfrastructure</h2>
<img src="images/Cyberinfrastructure.png">
</section>
<section>
<h2>Cybersecurity</h2>
<img src="images/Cybersecurity.png">
</section>
<section>
<img src="images/HBHL.png">
</section>
</section>
<!-- Acknowledgemnts -->
<section data-transition="slide" data-background="#87CEEB" data-background-transition="zoom">
<table class="reveal">
<tr>
<td width="70%" style="vertical-align: top">
<img src="images/LORIS_team.png">
</td>
<td width="30%" style="vertical-align: middle">
<p>Thank you!<small><font color="blue" size="4">Acknowledgements:</font><font color="black" size="2"> Alan Evans, Alex Zijdenbos, Dario Vins, Jonathan Harlap, Matt Charlet, Andrew Corderey, Sebastian Muehlboeck, Reza Adalat, Louis Collins, Vladimir Fonov, Marc Rousseau, Mia Petkova, Rathi Gnanasekaran, David Brownlee, Tarek Sherif, Pierre Rioux, Nic Kassis, Leigh MacIntyre, Claude Lepage, Ilana Leppert, Natasha Beck, Tristan Glatard, Bert Vincent, Lindsay Lewis, Najma Mahani, Elodie Portales-Casamar, Alden Woodward, Sylvain Milot, Jean Francois Malouin, Sylvain Baillet, Daniel Kroetz, Martin Weiss, Mathieu Desrosier, Jason Karamchandani, Amit Bar-Or, Ted Fon, John Brietner, Derek Lo, Patrick Bermudez, Chris Steele, Pamela Patterson and one of my favourites: Pierre Bellec!</font></small></p>
<p><font color="blue" size="4">LORIS team on left</font> <font size="2" color="black">(special thanks to Christine Rogers for listening to me.)</font></p>
</td>
</tr></table>
</section>
</div>
</div>
<script src="lib/js/head.min.js"></script>
<script src="js/reveal.js"></script>
<script>
// Full list of configuration options available at:
// https://github.com/hakimel/reveal.js#configuration
Reveal.initialize({
controls: true,
progress: true,
history: true,
center: true,
transition: 'slide', // none/fade/slide/convex/concave/zoom
// Optional reveal.js plugins
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, condition: function() { return !!document.querySelector( 'pre code' ); }, callback: function() { hljs.initHighlightingOnLoad(); } },
{ src: 'plugin/zoom-js/zoom.js', async: true },
{ src: 'plugin/notes/notes.js', async: true }
]
});
</script>
</body>
</html>