diff --git a/MNI_ecosystem.html b/MNI_ecosystem.html index 79997e4..0c270c1 100644 --- a/MNI_ecosystem.html +++ b/MNI_ecosystem.html @@ -35,45 +35,14 @@
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THE MNI Ecosystem

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Database management and processing ecosystem for data-sharing initiatives

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NOVEMBER 2017

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Samir Das
Director of Technology

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McGill Centre for Integrative Neuroscience
Montreal Neurological Institute

- - - - - - -
- - - - - -
- -
- - +

THE MNI Ecosystem

-

Database management and processing ecosystem for data-sharing initiatives

+

Data management and processing ecosystem for data-sharing initiatives

- -

NOVEMBER 2017

Samir Das
Director of Technology

McGill Centre for Integrative Neuroscience
Montreal Neurological Institute

@@ -90,38 +59,11 @@

- -

THE MNI Ecosystem

- -

Database management and processing ecosystem for data-sharing initiatives

- - -

NOVEMBER 2017

-

Samir Das
Director of Technology

-

McGill Centre for Integrative Neuroscience
Montreal Neurological Institute

- - - - - - - -
- - - - - -
-
+
- +
@@ -133,27 +75,22 @@

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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! -

-
+
+

What’s involved?

+

+ 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! +

+

LORIS-CBRAIN INTEGRATION

+

More on these next!

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WHAT IS LORIS?

 @@ -171,47 +108,51 @@

LORIS-CBRAIN INTEGRATION

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What is LORIS?

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What does LORIS do?


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Heterogenous data acquisition

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Multi-modal data acquisition
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Storage, processing & dissemination

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Storage, curation & dissemination
+ +
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LORIS Globally

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- -
-

What does LORIS do?

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+ +
+

What does LORIS
actually do?

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-

What does LORIS do?

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+ +

Data Entry
Data Management
Data Visualization
Data Querying

+

Try the
LORIS Demo

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+ +
+
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Extensible and modular design

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Extensible and
modular design

@@ -226,75 +167,33 @@

Extensible and modular design

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What does LORIS actually do?

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DATA ENTRY
DATA MANAGEMENT
DATA VISUALISATION
DATA QUERYING

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TRY ME!

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Heterogenous Data

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Candidate Profile, Instrument Builder, Feedback Module, Double Data Entry, Conflict Resolver

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Imaging Data

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1. Acquisition & Storage

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2. Visualisation: Imaging Browser, BrainBrowser

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3. Quality Control: Radiological Review Module, DCC MRI

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Data Querying

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  • Imaging Statistiscs

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  • Data Querying Tool (DQT)

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Cross-Modal Querying

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Cross-Modal Querying

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Real-Time Query Results

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Statistical Analysis

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Genomics Browser

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+

LORIS Globally

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@@ -315,12 +214,12 @@

Genomics Browser
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What does CBRAIN do?

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..enables distributed execution of software pipelines

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What does
CBRAIN do?

+

...enables distributed execution
of software pipelines
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..aggregates multiple distributed file systems into uniform view

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...aggregates multiple distributed
file systems into uniform view

@@ -329,15 +228,13 @@

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NOW

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611 users (199 international)
191 sites
29 countries -

+

611 users (199 international)
191 sites
29 countries

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CBRAIN Computing Resources

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51 tools, 1M+ files
6 Compute Canada clusters
24M CPU core hours

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CBRAIN Computing Resources

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51 tools, 1M+ files
6 Compute Canada clusters
24M CPU core hours

@@ -352,41 +249,54 @@

CBRAIN portal

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CIVET

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CIVET is one local imaging pipeline

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+
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NIAK is another

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http://niak.simexp-lab.org/
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+ +

CARMIN

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Common API for Research Medical Imaging Network

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Common API for Research Medical Imaging Network

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A common web API for remote pipeline execution

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NIAK

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http://niak.simexp-lab.org/

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+

Boutiques and Containerization

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-
+ +

From Data

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To

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to

Visualization

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BrainBrowser

..a set of web-based 3D visualization tools primarily used for viewing neurological data i.e. MRI scans.

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It allows for real-time manipulation and analysis of 3D neuroimaging data through any modern web browser. TRY ME!

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It allows for real-time manipulation and analysis of 3D data through any modern web browser.

+

TRY ME!

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BigBrain

 @@ -435,6 +344,12 @@

Volume Viewer on LORI

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+

What is BigBrain?

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The BigBrain dataset is the result of a collaborative effort between the teams of Dr. Katrin Amunts and Dr. Karl Zilles (Forschungszentrum Jülich), and Dr. Alan Evans (Montreal Neurological Institute)

+

Available freely at https://bigbrain.loris.ca

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BigBrain - high resolution reference brain

@@ -445,40 +360,48 @@

Volume Viewer on LORI

1 Terabyte dataset

Click to launch the Neuroglancer Viewer!

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What is BigBrain?

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The BigBrain dataset is the result of a collaborative effort between the teams of Dr. Katrin Amunts and Dr. Karl Zilles (Forschungszentrum Jülich), and Dr. Alan Evans (Montreal Neurological Institute)

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Available freely at https://bigbrain.loris.ca

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Visualization with Atelier 3D

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Visualization with
Atelier 3D

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PIVT (New)

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Display

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Moving Neurogimaging to the web

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Easy integration into CBRAIN and LORIS

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Pixpipe

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Big Brain and Neuroglancer

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Feedback

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PIVT

+

Platform-Independent Visualization Tool

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Custom Javascript libraries for
+ moving Neurogimaging to the web.

+ Easy integration into LORIS, CBRAIN,
and other platforms

- +

Visualizing Series data for Electrophysiology and EEG
+ Javascript libraries in modular React components

+ +

The MNI Open iEEG Atlas in LORIS

- +
+ +
+ +

MCIN acts as the Data Coordinating Centre (DCC)
for the following ongoing studies:

+
+ +
+

HBHL

+

Healthy Brains, Healthy Lives

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An interdisciplinary program at McGill University leveraging neuroinformatic technologies to transform terminal or life-long afflications to treatable or even curable conditions

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+
@@ -548,51 +471,6 @@

PIVT (New)

Quebec Parkinson Network

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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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  • 500+ reads on academia.edu

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ADNI

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  • Cited 343 times

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  • Data-use agreements

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  • Used for countless analyses

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  • Restrictive

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@@ -603,112 +481,35 @@

ADNI

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Healthy Brains for Healthy Lives (HBHL)

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An interdisciplinary program at McGill University leveraging neuroinformatic technologies to transform terminal or life-long afflications to treatable or even curable conditions

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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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Standardization

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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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Exchange of information

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Datasets

+

Tools

+

Standardization

+

Databases

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Collaborations

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Conferences, Hackathons

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Facebook, Google, Twitter, etc.


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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Benefits Hurdles
More citationsFear
Reduces waste/duplicationTechnical challenges
Increased exposurePrivacy concerns
Access to larger datasetsData Harmonization
Access to rare dataInteroperability
Less attritionReproducibility
Increased validationObtaining ethics
Saving Tax $$/more fundingPublic dataset not identical
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Global Data Sharing Initiatives

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Global Data
Sharing Initiatives

+ -
Committee on Best Practices in Data Analysis and Sharing (COBIDAS) - -
@@ -724,42 +525,38 @@

Global Data Sharing Initiatives

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- +
+ +

= System parts working together successfully

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Collaboration with global data sharing groups

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Collaboration with global
data sharing groups

- INCF, - Open Science Framework, - NITRC, - Allen Institute, - NDAR, - HAWG (Atlas Building Group), - Organization Human Brain Mapping, - Human Brain Project, - Compute Canada, - Maelstrom, - - Edinburgh BRAINS ImageBank, - COINS, - XNAT, - - VIP, - BrainCode, - BIDS, - NIDM, - NeuroDevNet, - GUSTO, - QPN, - Boutiques, - VIP - - + INCF, + Open Science Framework, + NITRC, + Allen Institute, + NDAR, + HAWG (Atlas Building Group), + Organization Human Brain Mapping, + Human Brain Project, + Compute Canada, + Maelstrom, + Edinburgh BRAINS ImageBank, + COINS, + XNAT, + VIP, + BrainCode, + BIDS, + NIDM, + NeuroDevNet, + GUSTO, + QPN, + Boutiques, + VIP

@@ -793,24 +590,24 @@

Hackathon Accomplishments

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Open Science

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Open Science

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Cybersecurity

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Open Science Functionality

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Open Science Functionality

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Open Science Functionality

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LORIS Biobank instance

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LORIS Imaging instance

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National Network

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Future Direction

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  • Phase 2 LORIS/CBRAIN connectivity
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  • Enhanced API
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  • Additional modalities (eg. MEG/EEG)
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  • Institutional requirements
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  • Enhanced visualization
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  • Numerous new modules
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  • Biobanking Tracking
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  • Interoperability!
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  • Pipeline reproducibility
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  • Cloud technology
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  • Flexibility in storage, sharing, and remote processing!
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+
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