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
Topic | Instructor | Video | Slides |
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Lecture 1: Welcome and Orientation
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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 |
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Workshop 1: Guiding principles for FAIR and open science
Watch on Crowdcast
Workshop 2: Tools for Reproducible Science
| YouTube (1:29:28) | slides |
Topic | Tutorial Videos |
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/ 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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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
2022 Watch Party Time (EST)
Session |
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Video | Materials |
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1:00-2:30pm
Workshop 1: Guiding principles for FAIR and open science -Erin Dickie, Sejal Patel
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Watch on Crowdcast
| Watch on Youtube | slides | |||||
Workshop 2: |
Tools for Reproducible Science -Erin Dickie, Sejal Patel
| Watch on |
YouTube |
Topic |
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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 |
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
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) |
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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Session | Instructor | Video | Materials |
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Time (EST)
Session
Lecture 1: Basics of genotype, central dogma, GWAS, and polygenic risk scores |
Watch on Crowdcast
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
Session | Instructor | Video | Materials |
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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|||
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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
Session | Instructors | Video | Materials |
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Instructors: Etay Hay & Frank Mazza
Watch Party Time (EST) | Session | 9:00-10:30|||
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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)
Session | Instructors | Video | Materials |
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Instructors: Erin Dickie & John Griffiths
TA's: Shreyas Harita, Jerrold Jeyachandra, Kevin Kadak
Time (EST) | Session | 9:00-10:30|||
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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) |
Session | Instructors | Video | Materials | |
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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
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
Session | Instructor | Video | Materials | |
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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
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10:45-12:15
Turorial 1: Hierarchical Gaussian Filter and Simulating Learners
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1:00-2:30pm
Lecture 2: Computational Modelling of EEG Data
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2:45-4:15pm
Tutorial 2: Single-trial EEG Modelling
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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
Time (EST) | Session | ||||||
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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 | ||||||
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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