Open Science at the MNI
November 28th, 2017
Samir Das - Associate Director of Software Development
McGill Centre for Integrative Neuroscience
Montreal Neurological Institute
samir.das@mcgill.ca
Exchange of information
Datasets
Tools
Standardization
Databases
Collaborations
Conferences, Hackathons
Facebook, Google, Twitter, etc.
Image source: http://blog.veritythink.com/post/87880448269/creative-data-sharing-and-open-humanitarianism
Committee on Best Practices in Data Analysis and Sharing (COBIDAS) |
Richard Stallman |
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
Databases, NoSQL, APIs, Version Control, Provenance Capture
Instrument Format
Makes use of Containers |
Goal: To create standardized JSON metadata to describe atlases For either volumetric or surface atlases Pipelines can access more atlases for anatomical standardization |
ADNI, ICBM, NIHPD, Allen Mouse Brain, IBIS, Generation-R, ABIDE, ABIDE Preprocessed, ADHD 200, ADHD Preprocessed, Human Connectome Project, OMEGA, UK Biobank, Edinburgh Biobank, BigBrain, Talairach, 1000 Functional Connectomes, Colin 27, MNI 305, 1000 Brains, AAL, ANIMAL, MAVAN, PreventAD, PING, MNI 152, MNI 305, FSL...
Not enough datasets!
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Neurovault, NeuroSynth, CIVET, VIP, Boutiques, Git-Annex, SOLID, BIDS, NiDM, DiCAT, DCMTK, NiPype, ITK, Freesurfer, SPM, FSL, Mobile MRI, 1000 Brains, AAL, BrainCode, GitHub, Amazon Cloud, FSL, IDA, BrainVisa, DICOM Confidential, DockerHub, Gate, CMIND...
Too many Tools!
..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.
Important value of hackathons to data sharing initiatives |
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 bureaucracies ...No big deal!
Several default tools:
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611 users; 199 international
191 sites
299 countries
Future unknowns | Fear of getting scooped |
Waste/duplication | Technical challenges |
Decreased exposure | Privacy concerns |
Changing the Publishing Culture | Data Harmonization |
Licensing and legal aspects | Interoperability |
More attrition | Reproducibility |
Sustainibility | Obtaining ethics |
Funding | Scalability |
Adrian Thorogood BIC lecture - March 9, 2016 |
Beers at Else's - Wednesday's at 4:44pm
Thank you!Acknowledgements: 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! LORIS team on left |