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
Introductory Concepts
A collection of lectures on overaching concepts in Neuroinformatics Research.
Join us for the Krembil Centre For Neuroinformatics Open House!
Topic | Instructor | Video | Slides | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
A Multiscale Approach to Brain Disorders |
| Watch on CrowdcastYouTube (1:09:33) | slides | ||||||||
Problems and opportunities in the diagnosis and treatment of major depression |
| Watch on CrowdcastYouTube (1:29:28) | 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.
| Topic | Tutorial Videos | Online/ Online Tutorials | Prerequisit to | ||
|---|---|---|---|---|---|
| R | R Workshop Material (Apr-Jun 2022) |
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| Python | Introduction to Python |
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| Git/Github | Introduction to Git and GitLab | ||||
| Linux/Bash | Introduction to Linux and Bash (Youtube) | ||||
many recordings available via from last falls series. 2021 Fall - SCWG Workshop Recordings
Reproducible Science (including Git, Docker and Binder)
2022 Watch Party Time (EST) | Session | InstructorsVideo | Materials | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
Workshop 1: Guiding principles for FAIR and open science -Erin Dickie, Sejal Patel
| Watch onCrowdcastYoutube | slides2:45-4:15pm | ||||||||
Workshop 2: | Tools Tools for Reproducible Science -Erin Dickie, Sejal Patel
| Watch onCrowdcastYouTube | ||||||||
Applied Ethics in Machine Learning and Mental Health
| 2022 Watch Party Time | Topic | Instructor | Video | Materials | ||
|---|---|---|---|---|---|---|
Lecture 1: | Introduction Introduction to AI Ethics -Daniel Buchman | Watch onCrowdcastYouTube (1:22:07) | slides | |||
Lecture 2: Fairness and Health Equity - | Marta Maslej & Laura Sikstrom | Watch onCrowdcastYoutube (1:06:36) | slides | |||
Workshop 1: Research Design, Data Collection, Model Construction and Validation -Part 2: Intersectional Bias AssessmentMarta Maslej & Laura Sikstrom | Watch onCrowdcast | Workshop 2: Analysis, Interpretation and Knowledge Exchange and/or Translation | Marta Maslej & Laura Sikstrom | Youtube (52:27) | ||
All videos previously recorded July 6th, 2021 as part of the KCNI Summer School
Digital Health for Mental Health
Dr. Abhishek (Abhi) Pratap
Independent Scientist & Lead of the Augmented Intelligence and Digital Tech for Mental Health (AID 4 Mental Heath) Lab,
The Krembil Centre for Neuroinformatics, Campbell Family Mental Health Research Institute, CAMH
Computing environment: Python (jupyter)
Session | Instructor | Video | Materials |
|---|---|---|---|
Lecture 1: Digital Health for Mental health | Abhi Pratap | Youtube (1:20:28) | |
Workshop 1: accessing reproducible datasets from Synapse as part of integrated workflow | Abhi Pratap | YouTube (1:15:12) | Watch on Crowdcast |
The workshop demostates how to work with the Synapse platform.
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Workshop 1 will use push and pull data to the synapse platform for sharing biomedical datasets using the
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Fundamental Methods for Genomic Analysis
Session | Instructor | Video | Materials |
|---|
Time (EST) | Session | 9:00-10:30|||
|---|---|---|---|---|
Lecture 1: Basics of genotype, central dogma, GWAS, and polygenic risk scores | Watch on Crowdcast | Dan Felsky | YouTube (1:00-2:30pm28:17) | |
Workshop 1:Intro to transcriptomic data types, including single-cell and bulk RNAseqManaging genotype data using PLINK | Dan Felsky | YouTube (1:27:18) | code (GitHub) | |
| Workshop 2: Calculation of polygenic risk scores in PRSice | Dan Felsky | YouTube (1:53:34) | code (GitHub) | |
| Considering population stratification and admixture in modern GWAS; concepts and tools | Dan Felsky | Register for the live webinar | Watch on Crowdcast |
All videos previously recorded July July 7th, 2021 as part of the KCNI Summer School
Fundamental Methods for Single-Cell Transcriptome Analysis
Session | Instructor | Video | Materials |
|---|
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 | Watch on Crowdcast | Shreejoy Tripathy | YouTube (1:00-2:30pm29:08) | slides |
Workshop 1: Intro to transcriptomic data types, including single-cell and bulk RNAseq | Watch on Crowdcast | Sonny Chen | YouTube (1:19:17) | 2:45-4:15pm |
Workshop 2: Explore cellular changes in major depression using bulk and single-cell RNAseq data | Keon Arbabi | YouTube (1:15:14) | 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
Register for Virtual Q&A - June 23, 2022 3:30pm EST
Presented by Etay Hay and Brain Circuit Modelling Group
Session | Instructors | Video | Materials |
|---|
Instructors: Etay Hay & Frank Mazza
Watch Party Time (EST) | Session | 9:00-10:30|||
|---|---|---|---|---|
Lecture 1: Simulating brain microcircuit activity in mental health | Watch on Crowdcast | Etay Hay & Frank Mazza | YouTube (1:20:43) | slides10:45-12:15 |
Lecture 2: Simulating EEG from brain microcircuits in mental health | Watch on Crowdcast | Etay Hay & Frank Mazza | YouTube (1:11:04) | slides1:00-2:30pm |
Workshop 1: Simulating and analyzing spiking from neurons and microcircuits | Watch on Crowdcast | Etay Hay & Frank Mazza | YouTube (1:39:51) | 2:45-4:15pm |
Workshop 2: Simulating and analyzing EEG signals from brain microcircuits | Etay Hay & Frank Mazza | YouTube (1:30:41) | 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)
Neuroimaging Connectomics
Presented by:
John Griffiths Ph.D - Lead - Whole Brain Modeling Group, Krembil Centre for Neuroinformatics - CAMH, Assistant Professor, University of Toronto Depts. Psychiatry & Medical Sciences, Twitter: @neurodidact, Github: @JohnGriffiths, @GriffithsLab, Website: grifflab.com
Erin Dickie Ph.D - Education and Knowledge Lead - KCNI, Scientist - Kimel Family Translational Imaging-Genetics Lab, Twitter: @ErinWDickie ,Github: @edickie
Session | Instructors | Video | Materials |
|---|
Instructors: Erin Dickie & John Griffiths
TA's: Shreyas Harita, Jerrold Jeyachandra, Kevin Kadak
Time (EST) | Session | 9:00-10:30||||
|---|---|---|---|---|---|
Lecture 1: Introduction to neuroimaging connectomics | Watch on Crowdcast | Erin Dickie & John Griffiths | YouTube (1:47:22) | slides10:45-12:15 | |
Workshop 1: Calculating Neuroimaging Connectomes | Watch on Crowdcast | 1:00-2:30pmErin Dickie & John Griffiths | YouTube (1:39:04) |
Whole-Brain Modelling
Presented by:
John Griffiths Ph.D - Lead - Whole Brain Modeling Group, Krembil Centre for Neuroinformatics - CAMH, Assistant Professor, University of Toronto Depts. Psychiatry & Medical Sciences, Twitter: @neurodidact, Github: @JohnGriffiths, @GriffithsLab, Website: grifflab.com
Session | Instructors | Video | Materials | |
|---|---|---|---|---|
Lecture 2: Intro to whole-brain modelling (Lecture) | Watch on Crowdcast | John Griffiths | YouTube (1:24:44)2:45-4:15pm | |
Workshop 2: simulating whole-brain activity, EEG, evoked responses, brain stimulation | Watch on Crowdcast |
John Griffiths | YouTube (1:16:10) |
All videos previously recorded July 9th, 2021 as part of the KCNI Summer School
Bayesian Models of Learning and Integration of Neuroimaging Data
Presented by Andreea Diaconescu and the Cognitive Network Modelling (CogNeMo) Group
Coding Language: MATLAB more setup info
Session | Instructor | Video | Materials |
|---|---|---|---|
Lecture 1: Modelling Cognition using Bayesian Inference | Andreea Diaconescu | YouTube (1:28:14) | slides |
Workshop 1: Modelling Abnormal Beliefs | Daniel Hauke | YouTube (1:15:04) | code (github) |
Lecture 2: Integration of Neuroimaging: Dynamic Causal Modelling for fMRI and EEG Data | Andreea Diaconescu, Colleen Charlton | YouTube (1:32:42) | slides |
Workshop 2: Dynamic Causal Modelling for fMRI: Extensions and Simulations | Peter Bedford, Povilas Karvelis | YouTube (1:22:21) | code (github) |
All videos previously recorded July 12th, 2021 as part of the KCNI Summer School
TA's: Colleen Charlton, Daniel Hauke, Peter Bedford, Povilas Karvelis
Population-Based Data Resources & Integrative Research Methods
Session | Instructor | Video | Materials | |
|---|---|---|---|---|
Lecture 1: Population |
Instructors: Andreea Diaconescu
TA's: Colleen Charlton, Daniel Hauke, Peter Bedford, Povilas Karvelis
Time (EST)
Session
9:00-10:30
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
Instructors: Daniel Felsky, Abhi Pratap & Joanna Yu
TA's: Mohamed Abdelhack, Grace Jacobs, Amin Kharaghani, Marta Maslej, Milos Milic, Earvin Tio
Time (EST) | Session | ||||||
|---|---|---|---|---|---|---|---|
9:00-10:30 | Lecture 1: Digital Health for Mental health
| Watch on Crowdcast | |||||
10:45-12:15 | Lecture 2: Population-based resources and the BrainHealth Databank | Watch on Crowdcast | 1:00-2:30pmJoanna Yu | YouTube | slides | ||
Workshop 1: | accessing reproducible datasets from Synapse as part of integrated workflowWatch on Crowdcast | 2:45-4:15pm | Workshop 2: Introduction 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
Daniel Felsky | YouTube (1:24:30) | |||||||
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 | Watch on Crowdcast | 10:45-12:15 | Daniel Felsky | YouTube (1:28:14) | |
Workshop 2Workshop: SNF / Subtyping | Watch on Crowdcast | Daniel Felsky | YouTube (1:00-2:30pm | 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,
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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