Open Science
+ +Samir Das
Associate Director - Research Software Development
McGill Centre for Integrative Neuroscience
Montreal Neurological Institute
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What is Open Science?
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+ As this graph shows, the amount of data collected from
neuroscientific studies will only continue to increase exponentially.
Data Science is COMPLEX!
+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, CEO
+Structural Genomics Consortium
+TED Talk: The Need for Biomedical Philanthropy
+ +Data Publishing
+ - Not Data Sharing -
+ This is an important differentiation. Data publishing calls for extensive reviewing and quality control processes.
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+ Best practices and standards are important in Open Science for usability and reproducability. + |
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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, Provenance, Ontological Standarization,
Data Harmonization, Upgrades, Maintenance, Bug Fixes, User Interface, Javascript, Bootstrap, Tracking, Extensibility, Data Management, Summary Statistics, Workflows, Development, Tool Integration, Data Sharing, Download, Multi-Modal Linking, Querying, Image Processing, Visualization, Networking, System Administration, Partnerships, Funding, HR ...No big deal!
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Let's look at some current
Open Science initiatives.
MNI
+Montreal Neurological Institute-Hospital
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+ "The Neuro" integrates patient care with Open Science research.
+Explore some of MNI's initiatives below.
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+ MCIN's LORIS and CBRAIN platforms (more on these later) have demonstrated the technical capacity to address the challenges of open science at an institutional level
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+ Richard Stallman |
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+ Click to view this presentation for further details + on our initiatives at the MNI.
+HBHL
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+ Exploring our brains' role in health and disease throughout our lives.
+What is HBHL?
+A high-priority, trans-disciplinary initiative focussing on areas of neuroscience that hold the greatest promise for delivering implementable, clinically effective outcomes in brain and mental health.
+Supported by Canada First Research Excellence Fund (CFREF) and based at McGill University.
+Scientific Director: Alan Evans.
CONP
+Canadian Open Neuroscience Platform
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+ A national platform for open sharing of neuroscience research data.
+Explore some of CONP's initiatives below
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+ Tannenbaum
Open Science
Initiative
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+ OHBM
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+ Explore some of OHBM's initiatives below.
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+ Interoperability
+Systems should allow the exchange
of data in standardized ways
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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+ = compatibility across data definitions and formats
+Aligning data formats, metadata standards, streamlined computational
workflows, and brain atlases will streamline open data access
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BIDS in LORIS Electrophysiology Browser
+Download BIDS format data and metadata
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+ Improving Infrastructure
+Connectivity and
Data Access
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+ High Performance Computing Systems (HPC)
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+ SQL versus NoSQL
+Traditional vs. Scalable Data Querying
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+ Version Control
+Open tools for streamlining workflows and storing code, datasets, and more
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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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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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What does LORIS do?
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+ LORIS Around the World!
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+ Extensible and modular design
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Multi-modal and BIDS-compliant features
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+ Cross-Modal Querying
+Real-Time Query Results
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+ Released in 2019: +LORIS best practices and operational procedures for data privacy and security + |
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What is CBRAIN?
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+ ..aggregates multiple distributed
file systems into uniform view
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+ Vital environments for collaboration and exchange of ideas, tools, and solutions for data sharing initiatives +
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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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