Open Science
+ +Cuban Neuroscience Centre
+ + +February 2019
+Samir Das
Associate Director - Research Software Development
McGill Centre for Integrative Neuroscience
Montreal Neurological Institute
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+ What’s involved?
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+ Longitudinal Acquisition, Storage and Curation, Interoperability, Reproducibility, Transfer, Anonymization, Security, Privacy, Ethics, APIs, Validation, Quality Control, Protocol Checking, Preprocessing, Analysis, HPC,
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+ Provenance, Ontological Standarization,
Data Harmonization, Upgrades, Maintenance, Bug Fixes, User Interface, Javascript, Bootstrap, Tracking, Extensibility, Data Management, Summary Statistics, Workflows,
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+ Development, Tool Integration, Data Sharing, Download, Multi-Modal Linking, Querying, Image Processing, Visualization, Networking, System Administration, Partnerships, Funding, HR
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+ ...No big deal!
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What is Open Science?
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+ Open Science Initiatives
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+ Richard Stallman |
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Data Publishing
+ - Not Data Sharing -
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+ Benefits of Open Science
+Increased exposure
+Greater collaborations
+More citations
+Less money spent of patents
+New funding opportunities
+Improved reproducibility
+ +Enable scientific discovery
+It's the future!
+Aled Edwards video
+Interoperability
+Ontological Harmonization
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+ API
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+ File Formats
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+ Imaging and Genomics
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Standardization
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+ Improved Infrastructure
+Databases, NoSQL, APIs, Version Control, Provenance Capture
+Connectivity and Data Access
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+ HPCs
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+ SQL versus NoSQL
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+ Centralized or Distributed?
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+ Ethics Framework
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+ Privacy Concerns
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+ Adrian Thorogood BIC lecture - March 9, 2016
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+ Important value of hackathons to data sharing initiatives +
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+ WHAT IS LORIS?
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+ “LORIS is a modular and extensible web-based data management system that integrates all aspects of a multi-center study: from heterogeneous data acquisition (imaging, clinical, behavior, genetics) to storage, processing and ultimately dissemination.” + |
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Extensible and modular design
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+ Cross-Modal Querying
+Real-Time Query Results
+WHAT IS CBRAIN?
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+ ..aggregates multiple distributed file systems into uniform view
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+ BrainBrowser
+..a set of web-based 3D visualization tools primarily used for viewing neurological data i.e. MRI scans.
+It allows for real-time manipulation and analysis of 3D neuroimaging data through any modern web browser. TRY ME!
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+ Volume Viewer on LORIS
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+ Tannenbaum Open Science Initiative
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+ Human Brain Mapping
+How It's Made
+ +BigBrain - high resolution reference brain
+Multimodal integration into an anatomically realistic standard space
+Years of development
+20 micron resolution
+7404 histological slices
+1 Terabyte dataset
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+ Thank you!Acknowledgements: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, 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! +LORIS team on left |
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