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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>MNI Open Science</title>
<meta name="description" content="Open Science">
<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">
<!-- MNI ecosystem menu/summary-->
<section>
<!--<section>
<table class="reveal">
<tr>
<td width="60%" style="vertical-align: middle">
<a href="CBRAIN_indepth.html#/cbrain-indepth-destination"><img src = "images/cbrain-blue.png" style="border: 0; border-radius:30px;"></a>
</td>
<td width = "40%" style = "vertical-align: middle">
<a href="LORIS_indepth.html#/loris-indepth-destination"><img src = "images/loris-new-white.png" style="border: 0"></a>
</td>
</tr></table>
<h1> THE MNI ECOSYSTEM</h1>
<table class = "reveal">
<tr>
<td width = "25%" style = "vertical-align:middle">
<a href = "Brain_browser.html"><img src="images/BrainBrowser_SurfaceViewer.png"></a>
</td>
<td width = "25%" style = "vertical-align:middle">
<a href="Open_Science.html#/openscience-destination"><img src="images/Open_science.png"></a>
</td>
<td width = "25%" style = "vertical-align:middle">
<a href = "Big_brain.html"><img src="images/BigBrain.png"</a>
</td>
<td width = "25%" style = "vertical-align:middle">
<a href="Data_sharing.html#/data-sharing-destination"><img src="images/Data_sharing_cartoon.png"></a>
</td>
</tr></table>
</section>-->
<section data-background="images/mni_eco_info_5.jpg" data-background-size="100%">
</section>
<!-- MNI PAPER -->
<section data-transition="fade">
<a href="https://www.researchgate.net/publication/281780543_The_MNI_data-sharing_and_processing_ecosystem" target="_blank"><img src="images/MNI_ecosystem_paper.png"></a>
</section>
<section id="fragments">
<h2><font color="12a3d8">What’s involved?</font></h2>
<p>
<span class="fragment">Longitudinal Acquisition, Storage and Curation, </span>
<span class="fragment"><font color="f27c30">Interoperability, Reproducibility</font>, Transfer, Anonymization, </span>
<span class="fragment">Security, Privacy, Ethics, APIs, </span>
<span class="fragment">Validation, Quality Control, Protocol Checking, </span>
<span class="fragment">Preprocessing, Analysis, HPC, </span>
<span class="fragment">Provenance, Ontological Standarization, <font color="f27c30">Data Harmonization</font>, </span>
<span class="fragment">Upgrades, Maintenance, Bug Fixes, </span>
<span class="fragment">User Interface, Javascript, Bootstrap,</span>
<span class="fragment">Tracking, <font color="f27c30">Extensibility</font>, </span>
<span class="fragment">Data Management, Summary Statistics, </span>
<span class="fragment">Workflows, Development, Tool Integration, </span>
<span class="fragment"><font color="f27c30">Data Sharing</font>, Download, Multi-Modal Linking, <font color="f27c30">Querying</font>, </span>
<span class="fragment">Image Processing, Visualization, </span>
<span class="fragment">Networking, System Administration, </span>
<span class="fragment">Partnerships, Funding, HR</span>
<span class="fragment"><font color="f27c30">...No big deal!</font></span>
</p>
</section>
<section>
<h2><font color="12a3d8">LORIS-CBRAIN INTEGRATION</font></h2>
<p>Benefits <font color="f27c30">vs</font> Challenges</p>
<img src="images/Data_flow.jpg">
</section>
</section>
<section data-transition="convex" id="openscience-destination">
<section>
<h2>What is Open Science?</h2>
<table class="reveal">
<tr>
<td width="47%" style="vertical-align: middle">
<img src="images/Nature_open_science.png">
</td>
<td width="53%" style="vertical-align: middle">
<img src="images/Open_science.png">
</td></tr></table>
</section>
<section>
<img src="images/TOSI.png">
</section>
<section>
<h2><Demo</h2>
<img src="images/Open_science_paper.png">
</section>
<!-- Centralized versus De-centralized -->
<section data-transition="concave">
<h2>Centralized or Distributed?</h2>
<img src="images/Networks.png" width="80%">
</section>
<!-- Free as in beer-->
<section data-transition="zoom">
<a href="https://www.ohbmbrainmappingblog.com/blog/free-beer-and-free-speech-a-conversation-with-samir-das-and-pierre-bellec" target="_blank"><img src="images/Free_beer.png"></a>
</section>
<!-- Stallman -->
<section data-transition="concave">
<table class="reveal">
<tr>
<td width="50%" style="vertical-align:middle">
<img src="images/Stallman.png">
<p align="center">Richard Stallman <br>Visit to the MNI<br> May 2017</p>
</td>
<td width="50%" style="vertical-align:middle">
<img <img src="images/fsf_screenshot.png">
<img src="images/Stallman_Samir.png">
</td>
</tr></table>
</section>
</section>
<!-- Why the MNI made this move? (2 slides) -->
<section data-transition="concave">
<!-- Why the MNI made this move? (2 slides) -->
<section>
<h2>Why did the MNI move towards Open Science?</h2>
<span class="fragment"><a href="https://www.mcgill.ca/neuro/open-science-0" target="_blank"><p><small>https://www.mcgill.ca/neuro/open-science-0</small></p></a></span>
</section>
<section>
<p>Increased exposure</p>
<p>Greater collaborations</p>
<p>More citations</p>
<p>Less money spent of patents</p>
<p>New funding opportunities</p>
<p>Improved reproducibility</p>
<p><font color="yellow">Enable scientific discovery</font></p>
<p><font color="yellow">It's the future!</font></p>
<a href="https://www.youtube.com/watch?v=Wtp7R97jz5k" target="_blank"><p><small><font color="orange">Aled Edwards video</font></small></p></a>
</section>
<section data-transition="concave">
<h2>Open Science Functionality</h2>
<table>
<thead>
<tr>
<th><font color="yellow">Acquisition & Storage</font></th>
<th><font color="yellow">Dissemination & Analysis</font></th>
</tr>
</thead>
<tbody>
<tr>
<td><small>Organized/Accessible data</small></td>
<td><small>Centralized repository</small></td>
</tr>
<tr>
<td><small>Long term storage</small></td>
<td><small>Provenance Capture</small></td>
</tr>
<tr>
<td><small>Quality Control mechanisms</small></td>
<td><small>API for interoperability</small></td>
</tr>
<tr>
<td><small>Web visualization</small></td>
<td><small>Consent is factored in</small></td>
</tr>
<tr>
<td><small>Tablet/Mobile Friendly</small></td>
<td><small>User account access control</small></td>
</tr>
<tr>
<td><small>Anonymized automatically</small></td>
<td><small>Completely de-identified</small></td>
</tr>
<tr>
<td><small>Cross-modal linking</small></td>
<td><small>Cross-study correlation</small></td>
</tr>
<tr>
<td><small>Online Data Querying</small></td>
<td><small>Access to high performance computing</small></td>
</tr>
</tbody>
</table>
</section>
</section>
<!--Changes needed to make reality -->
<section>
<section>
<h2 style="margin:100px 0px 0px 0px;">What changes are necessary to make this a reality?</h2>
<p><font color="12a3d8"><span class="fragment">Improved Infrastructure</span><br>
<span class="fragment">Standardization</span><br>
<span class="fragment">Datasets</span><br>
<span class="fragment">Tools & Environments</span></font></p>
</section>
</section>
<!-- Infrastructure (8 Slides)-->
<section data-transition="convex">
<section>
<h2>Improved Infrastructure</h2>
<span class="fragment"><p><font color="f27c30">Databases, NoSQL, APIs, Version Control, Provenance Capture</p></font></span>
</section>
<section>
<h2>NoSQL</h2>
<img src="images/NoSQL_database.jpg">
</section>
<section>
<h2>LORIS API</h2>
<p align="center"><font color="12a3d8">Instrument Format</font></p>
<img width="80%" src="images/LORIS_api.png">
</section>
<!-- Git Annex -->
<section data-transition="fade">
<img src="images/Git_annex.png">
</section>
<!-- NeuroImgaging Data Model (NiDM)-->
<section data-transition="fade">
<table class="reveal">
<h2>NeuroImaging Data Model</h2>
<tr>
<td width="55%" style="vertical-align: middle">
<img src="images/Nidm.png">
</td>
<td width="45%" style="vertical-align: middle">
<img src="images/NIDM_paper.png">
</td>
</tr></table>
</section>
</section>
<!-- Standarization -->
<section data-transition="convex">
<!-- Databases, APIS, BIDS, HPCs, CBRAIN, Boutiques, etc... -->
<section>
<h2 style="margin: 0px -200px 0px -200px;">Standardization & Interoperability</h2>
</section>
<!-- BIDS -->
<section data-transition="fade" data-background="images/BIDS.png">
<a href="http://bids.neuroimaging.io/" target="_blank"><p style="margin:-280px 0px 0px 0px;"><small>http://bids.neuroimaging.io/</small></p></a>
</section>
<!-- BIDS -->
<section data-transition="fade">
<table class="reveal">
<h2>BIDS Format</h2>
<tr>
<td width="42%" style="vertical-align: middle">
<img src="images/BIDS_paper.png">
</td>
<td width="58%" style="vertical-align: middle">
<img src="images/BIDS_structure.png">
</td>
</tr></table>
</section>
<!-- Boutiques -->
<section data-transition="fade">
<table class="reveal">
<h2>Boutiques</h2>
<tr>
<td width="50%" style="vertical-align: top">
<img src="images/Boutiques_web.png">
<p align="center">What is a <a href="https://www.docker.com/what-container" target="_blank">container?</a></p>
</td>
<td width="50%" style="vertical-align: middle">
<img src="images/Boutiques_paper.png">
</td>
</tr></table>
</section>
<!-- APIs -->
<section data-background="images/api_background.jpg">
<h2 style="margin: 0px -200px 0px -200px;text-shadow:
-1px -1px 0 #000,
1px -1px 0 #000,
-1px 1px 0 #000,
1px 1px 0 #000;"><font color="yellow">API Building & Standardization</font></h2>
</section>
<!-- Working group for atlas building template-->
<section data-transition="fade">
<h2>Atlas template building</h2>
<table class="reveal">
<tr>
<td width="45%" style="vertical-align: middle">
<img src="images/Mesh_image.png">
</td>
<td width="55%" style="vertical-align: middle">
<p><font color="yellow">Goal:</font></p>
<p>To create standardized JSON metadata to describe atlases</p>
<p>For either volumetric or surface atlases</p>
<p>Pipelines can access more atlases for anatomical standardization</p>
</td>
</tr></table>
</section>
</section>
<!-- Easily available data (9 Slides)-->
<section data-transition="convex">
<section>
<h2>Consolidated datasets</h2>
<p>
<span class="fragment"><a href="http://adni.loni.usc.edu" target="_blank">ADNI, </a>
<a href="http://www.loni.usc.edu/ICBM/" target="_blank">ICBM, </a>
<a href="http://pediatricmri.nih.gov/nihpd/info/index.html" target="_blank">NIHPD, </a>
<a href="http://mouse.brain-map.org" target="_blank">Allen Mouse Brain, </a>
<a href="https://ndar.nih.gov/edit_collection.html?id=19" target="_blank">IBIS, </a>
<a href="http://www.generationr.nl/researchers.html" target="_blank">Generation-R, </a>
<a href="http://fcon_1000.projects.nitrc.org/indi/abide/" target="_blank">ABIDE, </a>
<a href="http://preprocessed-connectomes-project.org/abide/" target="_blank">ABIDE Preprocessed, </a>
<a href="http://fcon_1000.projects.nitrc.org/indi/adhd200/index.html" target="_blank">ADHD 200, </a>
<a href="http://neurobureau.projects.nitrc.org/ADHD200/Introduction.html" target="_blank">ADHD Preprocessed, </a>
<a href="http://www.humanconnectomeproject.org" target="_blank">Human Connectome Project, </a>
<a href="https://omega.bic.mni.mcgill.ca/main.php" target="_blank">OMEGA, </a>
<a href="http://www.ukbiobank.ac.uk" target="_blank">UK Biobank, </a></span>
<span class="fragment"><a href="" target="_blank">Edinburgh Biobank, </a>
<a href="https://bigbrain.loris.ca/main.php" target="_blank">BigBrain, </a>
<a href="http://www.talairach.org" target="_blank">Talairach, </a>
<a href="http://fcon_1000.projects.nitrc.org/indi/enhanced/" target="_blank">1000 Functional Connectomes, </a>
<a href="http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27" target="_blank">Colin 27, </a>
<a href="http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305" target="_blank">MNI 305, </a>
<a href="http://journal.frontiersin.org/article/10.3389/fnagi.2014.00149/full" target="_blank">1000 Brains, </a>
<a href="http://qnl.bu.edu/obart/explore/AAL/" target="_blank">AAL, </a>
<a href="" target="_blank">ANIMAL, </a>
<a href="" target="_blank">MAVAN, </a>
<a href="http://www.preventad.com" target="_blank">PreventAD, </a>
<a href="http://pingstudy.ucsd.edu" target="_blank">PING, </a>
<a href="http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin" target="_blank">MNI 152, </a>
<a href="http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305" target="_blank">MNI 305, </a></span>
<span class="fragment"><a href="http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/" target="_blank">FSL... </a></span>
</p>
<p><b><font color="green"><span class="fragment">Not </span></font>
<font color="yellow"><span class="fragment">enough </span></font></b>
<font color="red"><span class="fragment">datasets! </span></font>
</p>
</section>
<!-- BigBrain -->
<section data-transition="fade">
<table class="reveal">
<h2>BigBrain</h2>
<tr>
<td width="55%" style="vertical-align: middle">
<img src="images/BigBrain.png">
</td>
<td width="45%" style="vertical-align: middle">
<img src="images/BigBrain_paper.png">
</td>
</tr></table>
</section>
<section>
<img src="images/bigbrain_data.png">
</section>
<!-- ADNI -->
<section data-transition="zoom">
<h2>ADNI</h2>
<table class="reveal">
<tr>
<td style="vertical-align: middle">
<img src="images/ADNI_paper.png">
</td>
<td style="vertical-align: top">
<p>
<ul>
<li>Cited 343 times</li><br>
<li>Data-use agreements</li><br>
<li>Used for countless analyses</li><br>
<li>Restrictive</li><br>
</ul>
</p>
</td>
</tr></table>
</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>
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</section>
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<h2>CCNA</h2>
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<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>
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</section>
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<h2>ABIDE</h2>
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</td>
<td width="55%" style="vertical-align: middle">
<img src="images/ABIDE_preprocessed.png">
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</section>
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<h2>Quebec Parkinson Network</h2>
<img src="images/QPN.png" width="80%">
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<h2><a href="https://omega.bic.mni.mcgill.ca">OMEGA</a></h2>
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<p><small>
<ul>
<li>Open MEG Archive</li><br>
<li>First open MEG repository</li><br>
<li>180 user accounts created</li><br>
<li>Associated structural data</li><br>
<li>500+ reads on academia.edu</li><br>
</ul>
</small></p>
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</section>
</section>
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<h2>Tools and Environments</h2>
<p>
<span class="fragment"><a href="https://www.incf.org" target="_blank">Neurovault, </a>
<a href="https://osf.io" target="_blank">NeuroSynth, </a>
<a href="https://www.nitrc.org" target="_blank">CIVET, </a>
<a href="http://alleninstitute.org" target="_blank">VIP, </a>
<a href="https://ndar.nih.gov" target="_blank">Boutiques, </a>
<a href="https://openfmri.org" target="_blank">Git-Annex, </a>
<a href="http://www.humanbrainmapping.org" target="_blank">SOLID, </a>
<a href="https://www.humanbrainproject.eu" target="_blank">BIDS, </a>
<a href="https://www.computecanada.ca" target="_blank">NiDM, </a>
<a href="https://www.maelstrom-research.org" target="_blank">DiCAT, </a>
<a href="http://www.ukbiobank.ac.uk" target="_blank">DCMTK, </a>
<a href="http://nipy.org/nipype/" target="_blank">NiPype, </a>
<a href="http://www.braininitiative.nih.gov" target="_blank">ITK, </a>
<a href="http://enigma.ini.usc.edu" target="_blank">Freesurfer, </a></span>
<span class="fragment"><a href="http://fcon_1000.projects.nitrc.org/indi/enhanced/" target="_blank">SPM, </a>
<a href="http://www.loni.usc.edu" target="_blank">FSL, </a>
<a href="http://" target="_blank">Mobile MRI, </a>
<a href="http://coins.mrn.org" target="_blank">1000 Brains, </a>
<a href="http://www.xnat.org" target="_blank">AAL, </a>
<a href="https://www.braincode.ca" target="_blank">BrainCode, </a>
<a href="https://github.com" target="_blank">GitHub, </a>
<a href="https://aws.amazon.com" target="_blank">Amazon Cloud, </a>
<a href="http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/" target="_blank">FSL, </a>
<a href="https://ida.loni.usc.edu" target="_blank">IDA, </a>
<a href="http://brainvisa.info" target="_blank">BrainVisa, </a>
<a href="https://cmind.research.cchmc.org" target="_blank">DICOM Confidential, </a>
<a href="https://cmind.research.cchmc.org" target="_blank">DockerHub, </a>
<a href="http://www.opengatecollaboration.org" target="_blank">Gate, </a>
<a href="https://cmind.research.cchmc.org" target="_blank">CMIND... </a></span>
</p>
<p><b><font color="green"><span class="fragment">Too </span></font>
<font color="yellow"><span class="fragment">many </span></font></b>
<font color="red"><span class="fragment">Tools! </span></font>
</section>
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<h2>Neurovault Example</h2>
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<section>
<a href = "https://brainbrowser.cbrain.mcgill.ca" target="_blank"><h2>BrainBrowser</h2></a>
<p>..a set of web-based <font color="f27c30"><b>3D visualization tools</b></font> primarily used for viewing <font color="12a3d8">neurological data</font> i.e. <font color="12a3d8">MRI scans</font>.</p>
<p><small>It allows for real-time <font color="f27c30">manipulation</font> and <font color="f27c30">analysis</font> of 3D neuroimaging data through any modern web browser. <a href = "https://brainbrowser.cbrain.mcgill.ca/" target="_blank">TRY ME!</a></small></p>
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</section>
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<h1 style="text-shadow:-1px -1px 0 #000,1px -1px 0 #000,-1px 1px 0 #000,1px 1px 0 #000;"><font color="indigo">Data Publishing<br>
- Not Data Sharing -</font></h1>
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<h2>Data Publishing Geeksquad for Persistent DOIs</h2>
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<h2><a href="">Hackathons</a></h2>
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<p> Important value of hackathons to data sharing initiatives</p>
<img src="images/Brainhack.png">
</td>
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</section>
</section>
<!-- Open Science Beers at Else's -->
<section>
<h2> Open Science Beers </h2>
<p> Beers at Else's - Wednesday's at 4:44pm</p>
<img src="images/beer_oclock.png">
</section>
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<td width="40%" style="vertical-align: middle">
<p>Thank you!<small><font color="blue" size="4">Acknowledgements:</font><font color="black" size="2"> 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"><br>Special thanks to Alan Evans for making all of this possible.</font></p>
</td>
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</section>
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