“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.”
“..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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..aggregates multiple distributed file systems into uniform view
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 Special thanks to Alan Evans for making all of this possible.
“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.”
“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.”
“..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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-
-
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-
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..aggregates multiple distributed file systems into uniform view
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 Special thanks to Alan Evans for making all of this possible.
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 is expected to increase exponentially.
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+
Data science is COMPLEX!
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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, CEO
+
Structural Genomics Consortium
+
TED Talk: The Need for Biomedical Philanthropy
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Data Publishing
+ - Not Data Sharing -
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Open Science Initiatives
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MNI Initiatives
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The Neuro (Montreal Neurological Institute-Hospital) integrates patient care with Open Science research and training, key to advancing science and medicine.
+
Continue scrolling down to explore some of MNI's Open Science initiatives.
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MNI's LORIS and CBRAIN platforms (more on these later) have been tasked with the technical challenges specific to the institutional-level implementation of open data sharing.
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Richard Stallman Visit to the MNI May 2017
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Healthy Brains, Healthy Lives (HBHL) Initiatives
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HBHL seeks to improve the lives of Canadians by advancing our understanding of how the individual brain functions in health and disease, throughout our lives.
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+
Canadian Open Science Neuroscience Platform (CONP) Initiatives
+
+
The Canadian Open Neuroscience Platform (CONP) aims to bring together many of the country’s leading scientists in basic and clinical neuroscience to form an interactive network of collaborations in brain research, interdisciplinary student training, international partnerships, clinical translation and open publishing.
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Organization for Human Brain Mapping (OHBM) Iniatives
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OHBM is an international society dedicated to using neuroimaging to discover the organization of the human brain.
+
Continue scrolling down to explore some of OHBM's Open Science initiatives.
Samir Das Associate Director - Research Software Development
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McGill Centre for Integrative Neuroscience Montreal Neurological Institute
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+
McGill Centre for Integrative Neuroscience Montreal Neurological Institute
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@@ -65,20 +65,20 @@
What is Open Science?
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As this graph shows, the amount of data collected from neuroscientific studies is expected to increase exponentially.
As this graph shows, the amount of data collected from neuroscientific studies will only continue to increase exponentially.
@@ -87,7 +87,7 @@
What is Open Science?
Data science is COMPLEX!
-
+
Benefits of Open Science
@@ -99,37 +99,37 @@
Benefits of Open Science
Improved reproducibility
Enable scientific discovery
...It's the future!
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Aled Edwards, CEO
Structural Genomics Consortium
TED Talk: The Need for Biomedical Philanthropy
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Data Publishing
- Not Data Sharing -
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Open Science Initiatives
@@ -140,9 +140,9 @@
Open Science Initiatives
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MNI Initiatives
The Neuro (Montreal Neurological Institute-Hospital) integrates patient care with Open Science research and training, key to advancing science and medicine.
Continue scrolling down to explore some of MNI's Open Science initiatives.
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MNI's LORIS and CBRAIN platforms (more on these later) have been tasked with the technical challenges specific to the institutional-level implementation of open data sharing.
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MNI Initiatives
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Healthy Brains, Healthy Lives (HBHL) Initiatives
HBHL seeks to improve the lives of Canadians by advancing our understanding of how the individual brain functions in health and disease, throughout our lives.
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+
Canadian Open Science Neuroscience Platform (CONP) Initiatives
-
The Canadian Open Neuroscience Platform (CONP) aims to bring together many of the country’s leading scientists in basic and clinical neuroscience to form an interactive network of collaborations in brain research, interdisciplinary student training, international partnerships, clinical translation and open publishing.
+
The Canadian Open Neuroscience Platform (CONP) aims to bring together many of the country’s leading scientists in basic and clinical neuroscience to form an interactive network of collaborations in brain research, interdisciplinary student training, international partnerships, clinical translation and open publishing.
+ Continue scrolling down to explore some of CONP's Open Science initiatives.
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Tannenbaum Open Science Initiative
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@@ -202,17 +221,275 @@
Organization for Human Brain Mapping (OHBM) Iniatives
OHBM is an international society dedicated to using neuroimaging to discover the organization of the human brain.
Continue scrolling down to explore some of OHBM's Open Science initiatives.
“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.”
“..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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..aggregates multiple distributed file systems into uniform view
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Hackathons
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Important value of hackathons to data sharing initiatives
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From 80739e3f84cf842162d45df764b02106b4ab86f0 Mon Sep 17 00:00:00 2001
From: Alex Knoll <37813606+knoll-alex@users.noreply.github.com>
Date: Tue, 8 Oct 2019 20:07:23 -0400
Subject: [PATCH 07/16] Final version ready for Oct 9 call
---
Open_Science_New.html | 107 ++++++++++++++++++++++++++++++++----------
1 file changed, 81 insertions(+), 26 deletions(-)
diff --git a/Open_Science_New.html b/Open_Science_New.html
index 967f5a5..1abc83f 100644
--- a/Open_Science_New.html
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MNI Open Science
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What is Open Science?
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Data science is COMPLEX!
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Data Science is COMPLEX!
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Structural Genomics Consortium
Data Publishing
- Not Data Sharing -
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This is an important differentiation. Data publishing calls for extensive reviewing and quality control processes.
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This intiative was officially launched as
+ "Plan S" by Brussels-based Science Europe in September of 2018.
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Because of Open Science, best practices are important to follow. If data uploads follow guidelines, usability is increased.
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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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Open Science Initiatives
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Open Science Initiatives
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In the following columns, we'll look at some current initiatives.
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MNI Initiatives
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MNI Initiatives
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This presentation provides further details
+ on our initiatives at the MNI.
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Healthy Brains, Healthy Lives (HBHL) Initiatives
HBHL seeks to improve the lives of Canadians by advancing our understanding of how the individual brain functions in health and disease, throughout our lives.
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Canadian Open Science Neuroscience Platform (CONP) Initiatives
@@ -213,7 +242,7 @@
Tannenbaum Open Science Initiative
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Organization for Human Brain Mapping (OHBM) Iniatives
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Organization for Human Brain Mapping (OHBM) Iniatives
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Let's align systems and data standards!
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Standardization
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Improved Infrastructure
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Databases, NoSQL, APIs, Version Control, Provenance Capture
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Improved Infrastructure
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Connectivity and Data Access
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HPCs
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High Productivity Computing Systems (HPCs)
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SQL versus NoSQL
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Git & Github
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Version Control!
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Git & Github
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Git & Github
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Version Control!
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Version Control!
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Ethics Framework
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Ethics Framework
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A systematic way of recording data use conditions that are based on consent permissions as found in the datasets of the main public genome archives
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!
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LORIS team on left Special thanks to Alan Evans for making all of this possible.
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+ Adrian Thorogood BIC lecture - March 9, 2016
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