From aca7db9d526b7583e36c578354b9ad07c980a33d Mon Sep 17 00:00:00 2001 From: Alex Knoll <37813606+knoll-alex@users.noreply.github.com> Date: Wed, 2 Oct 2019 14:08:36 -0400 Subject: [PATCH 1/3] Create Open_Science_New new file to work off for Samir's Open Science presentation --- Open_Science_New | 654 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 654 insertions(+) create mode 100644 Open_Science_New diff --git a/Open_Science_New b/Open_Science_New new file mode 100644 index 0000000..5b86598 --- /dev/null +++ b/Open_Science_New @@ -0,0 +1,654 @@ + + + + + + + MNI Open Science + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+ +
+ +

Open Science

+ +

Cuban Neuroscience Centre

+ + +

February 2019

+

Samir Das
Associate Director - Research Software Development

+

McGill Centre for Integrative Neuroscience
Montreal Neurological Institute

+ + + + + + + +
+ + + + + +
+
+ +
+ +
+ +
+ +
+
+ + + +
+

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! +

+
+ + +
+ +
+

What is Open Science?

+
+ + +
+ +
+ +
+ +
+ + +
+ +
+ +
+ +
+
+

Open Science Initiatives

+ + + +
+ + + +
+
+ + +
+
+ + +
+ +
+ + +
+

+ +

+ + +
+ +
+ + +
+ +
+ + +
+ + + + +
+ +

Richard Stallman
Visit to the MNI
May 2017

+ 		+ + +
+
+
+ + +
+
+

Data Publishing
+ - Not Data Sharing -

+
+ +
+ +
+ + +
+ +
+ + +
+ +
+
+ + +
+ +
+

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 video

 +
+
+ + +
+ + +
+

Interoperability

+
+ + +
+

Ontological Harmonization

+ +
+ + + +
+

API

+ +
+ +
+

File Formats

+ +
+ + +
+

Imaging and Genomics

+ + + + +
+ + + +
+
+ +
+ + +
+
+

Standardization

+ +
+ + +
+ + + + + +
+ + + + + + + +
+
+ + +
+ +
+ + +
+ +
+ +
+ + +
+
+

Improved Infrastructure

+

Databases, NoSQL, APIs, Version Control, Provenance Capture

 +
+ +
+

Connectivity and Data Access

+ +
+ +
+

HPCs

+ +
+ +
+

SQL versus NoSQL

+ +
+ + +
+ +

Git & Github

+ + + +
+ + + +
+
+ + +
+ +
+ + +
+ +
+
+ + + + + +
+

Centralized or Distributed?

+ +
+ + + +
+
+

Ethics Framework

+ +
+ + +
+

Privacy Concerns

+ + + + +
+ + + + + + + Adrian Thorogood BIC lecture - March 9, 2016 + +
+
+
+ + +
+ +

Hackathons

+ + + +
+ + +

Important value of hackathons to data sharing initiatives

+ +
+
+ + +
+
+
+ + +
+ +
+ + +
+

WHAT IS LORIS?

 + + + +
+ +

“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.”

+ 		+ +
+
+ +
+

Extensible and modular design

+ + + + + + +
+ + + + + +
+
+ +
+ +
+ +
+

Cross-Modal Querying

+
+ +
+

Real-Time Query Results

+
+ +
+

WHAT IS CBRAIN?

 + + + + + + +
+ + + +


“..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.”

+
+
+ +
+ +
+ +
+

..aggregates multiple distributed file systems into uniform view

+
+ + +
+ +
+ + +
+ +
+
+ + +
+
+

BrainBrowser

 +

..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. TRY ME!

+ + +
+ + +
+
+ + +
+

Volume Viewer on LORIS

+
+
+ + +
+ + +
+ +
+ + +
+

Tannenbaum Open Science Initiative

+ +
+ + +
+ +
+ +
+

Human Brain Mapping

+
How It's Made
+ +
+ +
+

BigBrain - high resolution reference brain

+

Multimodal integration into an anatomically realistic standard space

+

Years of development

+

20 micron resolution

+

7404 histological slices

+

1 Terabyte dataset

+

Click to launch the Neuroglancer Viewer!

+
+ + +
+ +

CCNA

+ + + +
+ + +

+

    +
  • $35 million

    • +
  • CIHR funded

    • +
  • Pan Canadian Consortium

    • +
  • Acquisition in June, 2016

    • +
  • 35 collections sites

    • +
  • LORIS powered

    • +
+

+
+
+ + +
+ +
+ + +
+ +
+ + +
+ +
+ + +
+ +
+ +
+ +

ABIDE

+ + + +
+ + + +
+
+ +
+ + + + +
+ +
+ + +
+ + + + +
+ + + +

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.

+
+ +
+ + +
+ +
+ + + + + + + + From c4c34bb51ea31c35aa10744f39c48d5452291734 Mon Sep 17 00:00:00 2001 From: Alex Knoll <37813606+knoll-alex@users.noreply.github.com> Date: Wed, 27 Nov 2019 22:05:13 -0500 Subject: [PATCH 2/3] updated readme --> style guide --- README.md | 24 +++++++++++++++++++++--- 1 file changed, 21 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 17a8df3..1ccdcb6 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,22 @@ -loris.github.io -=============== +# Style Guide for Reveal Presentations -General LORIS presentation +Here are some quick tips to use as reference when building/updating LORIS-related presentations in Reveal.js + +### Architecture + +Using Reveal.js, these presentations are organized into columns and rows. You shouldn't have more than 10 rows per column—even that is pushing it. Organize columns in a logical way that tells "a story" to the reader. While designed to be presented, these are also accessible online by anyone that wants to learn more. Therefore, slides should work together in a way that the context and intnded purpose is always clear. + +### Colours + +LORIS orange: #f27c30 +CBRAIN blue: #12a3d8 + +Otherwise, stick to white or black font + +### Hyperlinks + +Try to link as many images and headings as possible, where applicable. Make sure to use the `target=”_blank”` function to ensure hyperlinks open up in a new browser tab. + +### Images + +Ensure images are always big enough to see clearly. If images include text, you should be able to read the text. From 6844f615b91cab7e16f0ffa8e92320f0d31061cd Mon Sep 17 00:00:00 2001 From: Alex Knoll <37813606+knoll-alex@users.noreply.github.com> Date: Wed, 27 Nov 2019 22:17:57 -0500 Subject: [PATCH 3/3] Delete Open_Science_New --- Open_Science_New | 654 ----------------------------------------------- 1 file changed, 654 deletions(-) delete mode 100644 Open_Science_New diff --git a/Open_Science_New b/Open_Science_New deleted file mode 100644 index 5b86598..0000000 --- a/Open_Science_New +++ /dev/null @@ -1,654 +0,0 @@ - - - - - - - MNI Open Science - - - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
- -
- -

Open Science

- -

Cuban Neuroscience Centre

- - -

February 2019

-

Samir Das
Associate Director - Research Software Development

-

McGill Centre for Integrative Neuroscience
Montreal Neurological Institute

- - - - - - - -
- - - - - -
-
- -
- -
- -
- -
-
- - - -
-

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! -

-
- - -
- -
-

What is Open Science?

-
- - -
- -
- -
- -
- - -
- -
- -
- -
-
-

Open Science Initiatives

- - - -
- - - -
-
- - -
-
- - -
- -
- - -
-

- -

- - -
- -
- - -
- -
- - -
- - - - -
- -

Richard Stallman
Visit to the MNI
May 2017

- 		- - -
-
-
- - -
-
-

Data Publishing
- - Not Data Sharing -

-
- -
- -
- - -
- -
- - -
- -
-
- - -
- -
-

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 video

 -
-
- - -
- - -
-

Interoperability

-
- - -
-

Ontological Harmonization

- -
- - - -
-

API

- -
- -
-

File Formats

- -
- - -
-

Imaging and Genomics

- - - - -
- - - -
-
- -
- - -
-
-

Standardization

- -
- - -
- - - - - -
- - - - - - - -
-
- - -
- -
- - -
- -
- -
- - -
-
-

Improved Infrastructure

-

Databases, NoSQL, APIs, Version Control, Provenance Capture

 -
- -
-

Connectivity and Data Access

- -
- -
-

HPCs

- -
- -
-

SQL versus NoSQL

- -
- - -
- -

Git & Github

- - - -
- - - -
-
- - -
- -
- - -
- -
-
- - - - - -
-

Centralized or Distributed?

- -
- - - -
-
-

Ethics Framework

- -
- - -
-

Privacy Concerns

- - - - -
- - - - - - - Adrian Thorogood BIC lecture - March 9, 2016 - -
-
-
- - -
- -

Hackathons

- - - -
- - -

Important value of hackathons to data sharing initiatives

- -
-
- - -
-
-
- - -
- -
- - -
-

WHAT IS LORIS?

 - - - -
- -

“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.”

- 		- -
-
- -
-

Extensible and modular design

- - - - - - -
- - - - - -
-
- -
- -
- -
-

Cross-Modal Querying

-
- -
-

Real-Time Query Results

-
- -
-

WHAT IS CBRAIN?

 - - - - - - -
- - - -


“..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.”

-
-
- -
- -
- -
-

..aggregates multiple distributed file systems into uniform view

-
- - -
- -
- - -
- -
-
- - -
-
-

BrainBrowser

 -

..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. TRY ME!

- - -
- - -
-
- - -
-

Volume Viewer on LORIS

-
-
- - -
- - -
- -
- - -
-

Tannenbaum Open Science Initiative

- -
- - -
- -
- -
-

Human Brain Mapping

-
How It's Made
- -
- -
-

BigBrain - high resolution reference brain

-

Multimodal integration into an anatomically realistic standard space

-

Years of development

-

20 micron resolution

-

7404 histological slices

-

1 Terabyte dataset

-

Click to launch the Neuroglancer Viewer!

-
- - -
- -

CCNA

- - - -
- - -

-

    -
  • $35 million

    • -
  • CIHR funded

    • -
  • Pan Canadian Consortium

    • -
  • Acquisition in June, 2016

    • -
  • 35 collections sites

    • -
  • LORIS powered

    • -
-

-
-
- - -
- -
- - -
- -
- - -
- -
- - -
- -
- -
- -

ABIDE

- - - -
- - - -
-
- -
- - - - -
- -
- - -
- - - - -
- - - -

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.

-
- -
- - -
- -
- - - - - - - -