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Krembil Centre for Neuroinformatics Summer School

Solving Problems in Mental Health using Multi-Scale Computational Neuroscience

Distribution Date: June 2022

Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health


Table of Contents
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Join us for the Krembil Centre For Neuroinformatics Open House!


Introductory Concepts (July 5, 2021)


Topic
InstructorVideoSlides

A Multiscale Approach to Brain Disorders
Expand
titleSean Hill

Sean Hill, Ph.D. Director, Krembil Centre for Neuroinformatics Senior Scientist, Centre for Addiction and Mental Health Professor, Departments of Psychiatry and Physiology, University of Toronto, Canada Titular Professor, École Polytechnique Fédérale de Lausanne, Switzerland krembilneuroinformatics.ca

Watch on Crowdcast
slides

Problems and opportunities in the diagnosis and treatment of major depression
Expand
titleVictor Tang & Brett Jones

Victor Tang MD MSc, Clinician-Scientist/Resident,Centre for Addiction and Mental Health, Twitter: @victormarktang

Brett Jones MD MSc, Clinician-Scientist/Resident, Centre for Addiction and Mental Health

Watch on Crowdcast
slides


Computing Fundamentals

For those who need more help with computing fundamentals - going into the later content. We recommend content available from the KCNI Scientific Computing Working Group.

TopicTutorial VideosOnline TutorialsPrerequisit to
R


Python

Those working with imaging data
Git/Github


Linux/Bash



Reproducible Science (including Docker and Binder) 

2022 Watch Party Time (EST)
Session
InstructorsVideoMaterials

1:00-2:30pm
Workshop 1: Guiding principles for FAIR and open science
Erin Dickie, Sejal Patel
Watch on Crowdcast
2:45-4:15pm		slides

Workshop 2: Tools for Reproducible Science
Erin Dickie, Sejal Patel
Watch on Crowdcast

github code

rstudio example BinderImage Added jupyter example BinderImage Added


Applied Ethics in Machine Learning and Mental Health 

2022 Watch Party Time
Topic
InstructorVideoMaterials

Lecture 1: Introduction to AI Ethics
Daniel Buchman
Watch on Crowdcast


Lecture 2:  Fairness and Health Equity
Marta Maslej & Laura Sikstrom
Watch on Crowdcast


Workshop 1: Research Design, Data Collection, Model Construction and Validation
Marta Maslej & Laura Sikstrom
Watch on Crowdcast


Workshop 2: Analysis, Interpretation and Knowledge Exchange and/or Translation
Marta Maslej & Laura Sikstrom
Watch on Crowdcast

All videos previously recorded July 6th, 2021 as part of the KCNI Summer School


Digital Health

Time (EST)
Session
InstrutorVideoMaterials

Lecture 1: Digital Health for Mental health

Watch on Crowdcast


Workshop 1: accessing reproducible datasets from Synapse as part of integrated workflow

Watch on Crowdcast


Fundamental Methods for Genomic Analysis

Instructor: Dan Felsky

Time (EST)
Session
9:00-10:30
InstructorVideoMaterials

Lecture 1: Basics of genotype, central dogma, GWAS, and polygenic risk scores
Dan Felsky
Watch on Crowdcast
1:00-2:30pm


Workshop 1: Intro to transcriptomic data types, including single-cell and bulk RNAseq
Dan Felsky
Watch on Crowdcast

All videos previously recorded July 7th, 2021 as part of the KCNI Summer School


Fundamental Methods for Single-Cell Transcriptome Analysis


Session
InstructorVideoMaterials
(July 7, 2021)
Instructors:  Shreejoy Tripathy & Dan Felsky
TA's:  Keon Arbabi, Sonny Chen, Micaela Consens, Amin Kharaghani

Recorded on July 7, 2021 as a part of the Centre for Addiction and Mental Health’s Krembil Centre for Neuroinformatics (KCNI) Summer School, (CAMH KCNI SS)

Time (EST)
Session
10:45-12:15

Lecture 1:  Transcriptomics at the single-cell and bulk level level
Shreejoy Tripathy
Watch on Crowdcast
1:00-2:30pm


Workshop 1: Intro to transcriptomic data types, including single-cell and bulk RNAseq
Dan Felsky
Watch on Crowdcast
2:45-4:15pm


Workshop 2: Explore cellular changes in major depression using bulk and single-cell RNAseq data
Dan Felsky
Watch on Crowdcast

All videos previously recorded July 7th, 2021 as part of the KCNI Summer School

TA's:  Keon Arbabi, Sonny Chen, Micaela Consens, Amin Kharaghani


Simulating Brain Microcircuit Activity and Signals in Mental

Health Instructors: Etay Hay & Frank Mazza

Health

Watch Party Time (EST)
Session
9:00-10:30
InstructorsVideoMaterials

Lecture 1: Simulating brain microcircuit activity in mental health

Watch on Crowdcast
10:45-12:15


Lecture 2: Simulating EEG from brain microcircuits in mental health

Watch on Crowdcast
1:00-2:30pm


Workshop 1: Simulating and analyzing spiking from neurons and microcircuits

Watch on Crowdcast
2:45-4:15pm


Workshop 2: Simulating and analyzing EEG signals from brain microcircuits

Watch on Crowdcast

All videos previously recorded July 8th, 2021 as part of the KCNI Summer School

Day 5: Whole-Brain Modelling and


Neuroimaging Connectomics

(July 9, 2021)

Instructors: Erin Dickie & John Griffiths
TA's: Shreyas Harita, Jerrold Jeyachandra, Kevin Kadak
Time (EST)
Session
9:00-10:30
InstructorsVideoMaterials

Lecture 1: Introduction to neuroimaging connectomics
Erin Dickie & John Griffiths
Watch on Crowdcast
10:45-12:15


Workshop 1: Calculating Neuroimaging Connectomes
Erin Dickie & John Griffiths
Watch on Crowdcast

All videos previously recorded July 9th, 2021 as part of the KCNI Summer School



Whole-Brain Modelling

Time (EST)
Session
InstructorsVideoMaterials
1:00-2:30pm

Lecture 2: Intro to whole-brain modelling (Lecture)
John Griffiths
Watch on Crowdcast
2:45-4:15pm


Workshop 2: simulating whole-brain activity, EEG, evoked responses, brain stimulation
John Griffiths
Watch on Crowdcast
Day 6: Bayesian

All videos previously recorded July 9th, 2021 as part of the KCNI Summer School


Bayesian Models of Learning and Integration of Neuroimaging Data

(July 12, 2021)

Instructors: Andreea Diaconescu
TA's: Colleen Charlton, Daniel Hauke, Peter Bedford, Povilas Karvelis
Time (EST)
Session
9:00-10:30
InstructorVideoMaterials

Lecture 1: Bayesian Models of Learning

Watch on Crowdcast
10:45-12:15


Turorial 1:  Hierarchical Gaussian Filter and Simulating Learners

Watch on Crowdcast
1:00-2:30pm


Lecture 2: Computational Modelling of EEG Data

Watch on Crowdcast
2:45-4:15pm


Tutorial 2: Single-trial EEG Modelling

Watch on Crowdcast
AnchorDigital HealthDigital HealthDigital Health and Population-Based Data Resources (July 13, 2021)
Instructors: Daniel Felsky, Abhi Pratap & Joanna Yu

All videos previously recorded July 12th, 2021 as part of the KCNI Summer School
TA's:
Mohamed Abdelhack, Grace Jacobs, Amin Kharaghani, Marta Maslej, Milos Milic, Earvin Tio
 Colleen Charlton, Daniel Hauke, Peter Bedford, Povilas Karvelis



Population-Based Data Resources & Integrative Research Methods

Lecture 2: Population1:00-2:30pm accessing reproducible datasets from Synapse as part of integrated workflowWorkshop 2: Introduction

Session
InstructorVideoMaterials

Lecture 1: Population
Time (EST)
Session
9:00-10:30
Lecture 1: Digital Health for Mental health
Expand
titledetails

Presented by Abhi Pratap 

Watch on Crowdcast
10:45-12:15
-based resources and the BrainHealth Databank
Watch on Crowdcast
Joanna Yu



Workshop 1:
Watch on Crowdcast
2:45-4:15pm
Introduction to interactive methods
Watch on Crowdcast

Integrative Research Methods and Final Panel Discussion (July 14, 2021)

Instructors: Daniel Felsky & Abhi Pratap + All Instructor Panel
TA's: Mohamed Abdelhack, Amin Kharaghani, Marta Maslej, Milos Milic, Earvin Tio
1:00-2:30pm
Daniel Felsky



Lecture 2: Types
Time (EST)
Session
Lecture 2: Population-based resources and the BrainHealth Databank
Workshop 2: Introduction to interactive methods
9:00-10:30
Lecture 1: Types
of integrative research and Whole Person Modelling
Daniel Felsky
Watch on Crowdcast


10:45-12:15
Workshop
Workshop 2: SNF / Subtyping
Watch on Crowdcast
Daniel Felsky
Watch on Crowdcast
2:45-4:15pm

Additional Lecture Content (no zoom Q&A event)

"A Multiscale Approach to Brain Disorders” - presented by Sean Hill, 

Expand
titledetails..

Presented by: Sean Hill, Ph.D. Director, Krembil Centre for Neuroinformatics Senior Scientist, Centre for Addiction and Mental Health Professor, Departments of Psychiatry and Physiology, University of Toronto, Canada Titular Professor, École Polytechnique Fédérale de Lausanne, Switzerland krembilneuroinformatics.ca

Recorded on July 5, 2021 as a part of the Centre for Addiction and Mental Health’s Krembil Centre for Neuroinformatics (KCNI) Summer School, (CAMH KCNI SS)

Slides available from:  https://github.com/krembilneuroinformatics/kcni-school-lessons/blob/8ef714f18125ff7f905ef61c97a995bc18e705a2/day1/KCNISS_day1_1_Hill-compressed.pdf

KCNI Summer School schedule and materials at:  https://github.com/krembilneuroinformatics/kcni-school-lessons

© Centre for Addiction and Mental Health, all rights reserved.

Lecture:  “A Multiscale Approach to Brain Disorders”

Presented by: Sean Hill, Ph.D. Director, Krembil Centre for Neuroinformatics Senior Scientist, Centre for Addiction and Mental Health Professor, Departments of Psychiatry and Physiology, University of Toronto, Canada Titular Professor, École Polytechnique Fédérale de Lausanne, Switzerland krembilneuroinformatics.ca

Recorded on July 5, 2021 as a part of the Centre for Addiction and Mental Health’s Krembil Centre for Neuroinformatics (KCNI) Summer School, (CAMH KCNI SS)

Slides available from:  https://github.com/krembilneuroinformatics/kcni-school-lessons/blob/8ef714f18125ff7f905ef61c97a995bc18e705a2/day1/KCNISS_day1_1_Hill-compressed.pdf

KCNI Summer School schedule and materials at:  https://github.com/krembilneuroinformatics/kcni-school-lessons

© Centre for Addiction and Mental Health, all rights reserved.

Problems and opportunities in the diagnosis and treatment of major depression. Speakers: Victor Tang, Brett Jones, Recorded July 5, 2021

2020 Summer School Overview