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
Please register at: https://www.crowdcast.io/e/kcni-summer-school-2021
Our Learning Modules:
Introductory Concepts
A collection of lectures on overaching concepts in Neuroinformatics Research.
Topic | Instructor | Video | Slides | ||||||
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A Multiscale Approach to Brain Disorders |
| YouTube (1:09:33) | slides | ||||||
Problems and opportunities in the diagnosis and treatment of major depression |
| YouTube (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 Tutorials | Prerequisit to | |
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| R | R Workshop Material (Apr-Jun 2022) |
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| Python | Introduction to Python |
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Day 1: Welcome! Understanding Clinical Research Questions and Reproducible Science (July 5, 2021)
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Day 2: Applied Ethics in Machine Learning and Mental Health (July 6, 2021)
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Day 3: Fundamental Methods for Genomic and Single-Cell Transcriptome Analysis (July 7, 2021)
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Day 5: Whole-Brain Modelling and Neuroimaging Connectomics (July 9, 2021)
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Day 6: Bayesian Models of Learning and Integration of Neuroimaging Data (July 12, 2021)
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Day 7: Digital Health and Population-Based Data Resources (July 13, 2021)
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Day 8: Integrative Research Methods and Final Panel Discussion (July 14, 2021)
Learning Modules
Computing Fundamentals
Reproducible Science
Day 1: Welcome! Understanding Clinical Research Questions and Reproducible Science (July 5, 2021)
Instructors: Erin Dickie, Sean Hill, Sejal Patel, Victor Tang, Brett Jones
TA's: Kevin Kadak, Taha Morshedzadeh, Kevin Witczak
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Time (EST)
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Session
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9:00-10:30
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Lecture 1: Welcome and Orientation
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Watch on Crowdcast
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10:45-12:15
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Lecture 2: Problems and opportunities in the diagnosis and treatment of major depression
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Watch on Crowdcast
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1:00-2:30pm
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Workshop 1: Guiding principles for FAIR and open science
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Watch on Crowdcast
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2:45-4:15pm
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Workshop 2: Tools for Reproducible Science
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Watch on Crowdcast
Problems and opportunities in the diagnosis and treatment of major depression
(July 5, 2021)
Instructors: Victor Tang, Brett Jones
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Time (EST)
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Session
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9:00-10:30
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Lecture 1: Welcome and Orientation
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Watch on Crowdcast
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10:45-12:15
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Lecture 2: Problems and opportunities in the diagnosis and treatment of major depression
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Watch on Crowdcast
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1:00-2:30pm
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Workshop 1: Guiding principles for FAIR and open science
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Watch on Crowdcast
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2:45-4:15pm
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Workshop 2: Tools for Reproducible Science
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Watch on Crowdcast
Day 1: Welcome! Understanding Clinical Research Questions and Reproducible Science (July 5, 2021)
Instructors: Erin Dickie, Sean Hill, Sejal Patel, Victor Tang, Brett Jones
TA's: Kevin Kadak, Taha Morshedzadeh, Kevin Witczak
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Time (EST)
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Session
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9:00-10:30
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Lecture 1: Welcome and Orientation
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Watch on Crowdcast
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10:45-12:15
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Lecture 2: Problems and opportunities in the diagnosis and treatment of major depression
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Watch on Crowdcast
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1:00-2:30pm
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Workshop 1: Guiding principles for FAIR and open science
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Watch on Crowdcast
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2:45-4:15pm
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Workshop 2: Tools for Reproducible Science
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Watch on Crowdcast
Applied Ethics in Machine Learning and Mental Health
Instructors: Daniel Buchman, Marta Maslej & Laura Sikstrom
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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)
Session | Video | Materials | ||||||
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Workshop 1: Guiding principles for FAIR and open science -Erin Dickie, Sejal Patel
| Watch on Youtube | slides | ||||||
Workshop 2: Tools for Reproducible Science -Erin Dickie, Sejal Patel
| Watch on YouTube | |||||||
Applied Ethics in Machine Learning and Mental Health
Topic | Video | Materials | |
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Lecture 1: Introduction to AI Ethics -Daniel Buchman | Watch on YouTube (1:22:07) | slides | |
Lecture 2: Fairness and Health Equity -Laura Sikstrom | Watch on Youtube (1:06:36) | slides | |
Workshop 1: Research Design, Data Collection, Model Construction and Validation -Part 2: Intersectional Bias AssessmentMarta Maslej & Laura Sikstrom | Watch on 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 |
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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) |
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Zoom Q&A
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Session
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Lecture 1: Introduction to AI Ethics
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Watch on Crowdcast
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Lecture 2: Fairness and Health Equity
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Watch on Crowdcast
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Workshop 1: Research Design, Data Collection, Model Construction and Validation
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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
Presented by Dr Dan, Felsky - Independent Scientist and Head of Whole Person Modelling at KCNI, Assistant Professor in the Department of Psychiatry, University of Toronto. Assistant Professor at the Dalla Lana School of Public Health, University of Toronto.
- Dr Felsky has a PhD in neuroimaging and genetics of Alzheimer’s disease at U of T, Postdocs in computational neuroimmunology and bioinformatics at Broad Institute, Harvard Medical School & Columbia University.
Session | Instructor | Video | Materials |
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Workshop 2: Analysis, Interpretation and Knowledge Exchange and/or Translation
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Watch on Crowdcast
Day 3: Fundamental Methods for Genomic and Single-Cell Transcriptome Analysis (July 7, 2021)
Instructors: Shreejoy Tripathy & Dan Felsky
TA's: Keon Arbabi, Sonny Chen, Micaela Consens, Amin Kharaghani
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Time (EST)
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Session
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Lecture 1: Basics of genotype, central dogma, GWAS, and polygenic risk scores |
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Watch on Crowdcast
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10:45-12:15
| Dan Felsky | YouTube (1:28:17) | ||
Workshop 1: Managing 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 |
All videos previously recorded July July 7th, 2021 as part of the KCNI Summer School
Fundamental Methods for Single-Cell Transcriptome Analysis
Presented by Shreejoy Tripathy & the Computational Genomics Lab
- Independent Scientist and Head of Computational Genomics at KCNI, Assistant Professor in the Department of Psychiatry, University of Toronto., Assistant Professor in the Department of Physiology, University of Toronto
- PhD in Computational Neuroscience from Carnegie Mellon and Post-doc in neuroinformatics and bioinformatics at University of British Columbia.
Session | Instructor | Video | Materials |
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Lecture 1 |
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: Transcriptomics at the single-cell and bulk level level |
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Watch on Crowdcast
| Shreejoy Tripathy | YouTube (1: |
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Watch on Crowdcast
| Sonny Chen | YouTube (1:19:17) |
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Workshop 2: Explore cellular changes in major depression using bulk and single-cell RNAseq data |
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Watch on Crowdcast
| Keon Arbabi | YouTube (1:15:14) |
All videos previously recorded July 7th, 2021 as part of the KCNI Summer School
TA's: Keon Arbabi, Sonny Chen, Micaela Consens, Amin Kharaghani
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Session | Instructors | Video | Materials |
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Instructors: Etay Hay & Frank Mazza
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Time (EST)
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Session
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Lecture 1: Simulating brain microcircuit activity in mental health |
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Watch on Crowdcast
| Etay Hay & Frank Mazza | YouTube (1:20:43) | slides |
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Lecture 2: Simulating EEG from brain microcircuits in mental health |
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Watch on Crowdcast
| Etay Hay & Frank Mazza | YouTube (1:11:04) | slides |
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Workshop 1: Simulating and analyzing spiking from neurons and microcircuits |
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Watch on Crowdcast
| Etay Hay & Frank Mazza | YouTube (1:39:51) |
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Workshop 2: Simulating and analyzing EEG signals from brain microcircuits |
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Watch on Crowdcast
| Etay Hay & Frank Mazza | YouTube (1:30:41) |
All videos previously recorded July 8th, 2021 as part of the KCNI Summer School
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 |
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Day 5: Whole-Brain Modelling and Neuroimaging Connectomics (July 9, 2021)
Instructors: Erin Dickie & John Griffiths
TA's: Shreyas Harita, Jerrold Jeyachandra, Kevin Kadak
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Time (EST)
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Session
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Lecture 1: Introduction to neuroimaging connectomics |
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Watch on Crowdcast
Erin Dickie & John Griffiths | YouTube (1:47:22) | slides |
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Workshop 1: Calculating Neuroimaging Connectomes |
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Watch on Crowdcast
Erin 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 |
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Lecture 2: Intro to whole-brain modelling (Lecture) |
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Watch on Crowdcast
John Griffiths | YouTube (1:24:44) |
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Workshop 2: simulating whole-brain activity, EEG, evoked responses, brain stimulation |
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Watch on Crowdcast
John Griffiths | YouTube (1:16:10) |
All videos previously recorded July 9th, 2021 as part of the KCNI Summer School
Bayesian
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Session | Instructor | Video | Materials |
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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 | |
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Lecture 1: Population |
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Instructors: Andreea Diaconescu
TA's: Colleen Charlton, Daniel Hauke, Peter Bedford, Povilas Karvelis
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Time (EST)
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Session
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9:00-10:30
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Lecture 1: Bayesian Models of Learning
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Watch on Crowdcast
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10:45-12:15
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Turorial 1: Hierarchical Gaussian Filter and Simulating Learners
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Watch on Crowdcast
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1:00-2:30pm
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Lecture 2: Computational Modelling of EEG Data
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Watch on Crowdcast
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2:45-4:15pm
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Tutorial 2: Single-trial EEG Modelling
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Watch on Crowdcast
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Instructors: Daniel Felsky, Abhi Pratap & Joanna Yu
TA's: Mohamed Abdelhack, Grace Jacobs, Amin Kharaghani, Marta Maslej, Milos Milic, Earvin Tio
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Time (EST)
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Session
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9:00-10:30
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Lecture 1: Digital Health for Mental health
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Watch on Crowdcast
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10:45-12:15
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-based resources and the BrainHealth Databank |
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Watch on Crowdcast
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Workshop 1: |
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Watch on Crowdcast
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2:45-4:15pm
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Introduction to interactive methods |
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Watch on Crowdcast
Day 8: 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
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Time (EST)
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Session
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9:00-10:30
Daniel Felsky | YouTube (1:24:30) | |
Lecture 2: Types |
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of integrative research and Whole Person Modelling |
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Watch on Crowdcast
Daniel Felsky | YouTube (1:28:14) | |
Workshop 2 |
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10:45-12:15
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: SNF / Subtyping |
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Watch on Crowdcast
Daniel Felsky | YouTube (1: |
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Group Panel Discussion
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Watch on Crowdcast
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2:45-4:15pm
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Final Social Hour
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.
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