diff --git a/Data_sharing.html b/Data_sharing.html index 95e141d..9c61ad9 100644 --- a/Data_sharing.html +++ b/Data_sharing.html @@ -41,57 +41,46 @@
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DATA SHARING

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What is Data Sharing?

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Exchange of information

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Datasets

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Tools

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Standarization

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Databases

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Collaborations

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Conferences, hackathons

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Facebook, Google, Twitter, etc.

+ Read more here +
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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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LORIS-CBRAIN INTEGRATION

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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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What is Data Sharing?

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Exchange of information

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Datasets

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Tools

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Standarization

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Databases

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Collaborations

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Conferences, hackathons

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Facebook, Google, Twitter, etc.

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Image source: http://blog.veritythink.com/post/87880448269/creative-data-sharing-and-open-humanitarianism

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Data Sharing Issues

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Data Sharing Issues

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Privacy Concerns

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Best practices in Data Sharing

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Best practices in
Data Sharing

Committee on Best Practices in Data Analysis and Sharing (COBIDAS)
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COBIDAS - Key points

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COBIDAS - Key points

  1. Experimental Design
  2. Acquisition Reporting
    3. @@ -181,87 +171,122 @@

    COBIDAS - Key points

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Centralized or Distributed?

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Some Data Sharing solutions?

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Some Data
Sharing solutions?

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WHAT IS LORIS?

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Fear
Reduces waste/duplicationReduces waste Technical challenges
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“..is a modular and extensible web-based data and project management software that integrates all aspects of a multi-center neuroimaging research study. It is an OPEN SOURCE framework and database suitable for managing large datasets.”

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WHAT IS CBRAIN?

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“..is an OPEN SOURCE web-based collaborative High-Performance Computing (HPC) platform for neuroimaging research, connecting researchers to the tools required to handle large datasets.”

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LORIS-CBRAIN INTEGRATION

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Global Data Sharing Initiatives

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Public Data Repositories

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CBRAIN hooks

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BIDS

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NIDM

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Neurovault

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Braincode interoperability

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Interoperability with other competitors

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Best practices

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Global Data
Sharing Initiatives

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Public Data Repositories

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CBRAIN hooks

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BIDS

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NIDM

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Neurovault

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Braincode interoperability

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Interoperability with other competitors

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Best practices

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External Initiatives

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- INCF, - Open Science Framework, - NITRC, - Allen Institute, - NDAR, - Open fMRI, - Organization Human Brain Mapping, - Human Brain Project, - Compute Canada, - Maelstrom, - UK Biobank, - Edinburgh BRAINS ImageBank, - BRAIN, - ENIGMA, - Enhanced Nathan Kline Institute (1000 Functional Connectomes), - LONI, - GAAIN, - COINS, - XNAT, - BrainSpell, - VIP, - SPM, - BrainCode, - FSL, - FBIRN, - Synapse, - CIMA-Q, - NeuroDevNet, - GUSTO, - QPN, - The NeuroBureau, - - ABCD... -

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External Initiatives

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+ INCF, + Open Science Framework, + NITRC, + Allen Institute, + NDAR, + Open fMRI, + Organization Human Brain Mapping, + Human Brain Project, + Compute Canada, + Maelstrom, + UK Biobank, + Edinburgh BRAINS ImageBank, + BRAIN, + ENIGMA, + Enhanced Nathan Kline Institute (1000 Functional Connectomes), + LONI, + GAAIN, + COINS, + XNAT, + BrainSpell, + VIP, + SPM, + BrainCode, + FSL, + FBIRN, + Synapse, + CIMA-Q, + NeuroDevNet, + GUSTO, + QPN, + The NeuroBureau, + ABCD... +

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So - many - initiatives! +

So + many + initiatives!

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INCF - Los Angeles 2016

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BIDS

NeuroImaging Data Model

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Format for storing metadata, provenance, processing information

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Format for storing metadata,
provenance, processing information

DataLad

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Atlas template building

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Goal:

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To create standardized JSON metadata to describe atlases

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For either volumetric or surface atlases

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Pipelines (e.g.CIVET) can access more atlases for anatomical standardization

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Consolidated datasets

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Consolidated datasets

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- 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... -

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So - many - datasets! +

+ 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... +

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So + many + datasets!

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ADNI

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  • Cited 343 times

  • Data-use agreements

  • Used for countless analyses

  • Restrictive

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Quebec Parkinson Network

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Tools and Environments

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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... - -

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Tools and Environments

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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... +

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So - many - Tools! +

So + many + Tools!

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BrainBrowser

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Hackathons

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Hackathons

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LORIS - CBRAIN Data Flow

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As this graph shows, the amount of data collected from
neuroscientific studies will only continue to increase exponentially.

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Data Science is COMPLEX!

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LORIS - CBRAIN Data Flow

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LORIS - Key features

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LORIS Dashboard

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LORIS globally

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  • Cited 295 times
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  • Control data for NDAR
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  • Longitudinal study (8 years)
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  • 532 subjects
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  • 8000 distinct variables
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  • 37000 individual assessments
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  • T1, T2, PD, DTI, Spectroscopy
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  • ∼3TB of imaging data
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  • 2000 MRI acquisitions
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  • Autism infant brain development
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  • 3000+ scans
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  • 700+ subjects
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  • 7000 distinct variables
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  • T1, T2, DTI, BOLD
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CCNA

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  • $35 million

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  • CIHR funded

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  • Pan Canadian Consortium

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  • Acquisition in June, 2016

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  • 35 collections sites

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  • LORIS powered

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BigBrain

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OMEGA

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  • Open MEG Archive

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  • First open MEG repository

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  • 180 user accounts created

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  • Associated structural data

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CBRAIN

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Several default tools: -

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  • CIVET
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  • And many more...
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cbrain-support.mni@mcgill.ca

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CBRAIN projects

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CBRAIN tasks

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CIVET for neonates

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Open Science

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Cybersecurity

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What's in it for me?

diff --git a/images/BIDS.png b/images/BIDS.png index 5a95ca1..62187de 100644 Binary files a/images/BIDS.png and b/images/BIDS.png differ