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:
Topic | Instructor | Video | Slides | ||||||
---|---|---|---|---|---|---|---|---|---|
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 |
Topic | Tutorial Videos / Online Tutorials | Prerequisit to | |
---|---|---|---|
R | R Workshop Material (Apr-Jun 2022) |
| |
Python | Introduction to Python |
|
...
Day 1: Welcome! Understanding Clinical Research Questions and Reproducible Science (July 5, 2021)
...
Day 2: Applied Ethics in Machine Learning and Mental Health (July 6, 2021)
...
Day 3: Fundamental Methods for Genomic and Single-Cell Transcriptome Analysis (July 7, 2021)
...
|
...
Day 5: Whole-Brain Modelling and Neuroimaging Connectomics (July 9, 2021)
...
Day 6: Bayesian Models of Learning and Integration of Neuroimaging Data (July 12, 2021)
...
Day 7: Digital Health and Population-Based Data Resources (July 13, 2021)
...
Day 8: Integrative Research Methods and Final Panel Discussion (July 14, 2021)
...
Instructors: Erin Dickie, Sean Hill, Sejal Patel, Victor Tang, Brett Jones
TA's: Kevin Kadak, Taha Morshedzadeh, Kevin Witczak
...
Time (EST)
...
Session
...
9:00-10:30
...
Lecture 1: Welcome and Orientation
...
Watch on Crowdcast
...
10:45-12:15
...
Lecture 2: Problems and opportunities in the diagnosis and treatment of major depression
...
Watch on Crowdcast
...
1:00-2:30pm
...
Workshop 1: Guiding principles for FAIR and open science
...
Watch on Crowdcast
...
2:45-4:15pm
...
Workshop 2: Tools for Reproducible Science
...
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
...
Time (EST)
...
Session
...
9:00-10:30
...
Lecture 1: Welcome and Orientation
...
Watch on Crowdcast
...
10:45-12:15
...
Lecture 2: Problems and opportunities in the diagnosis and treatment of major depression
...
Watch on Crowdcast
...
1:00-2:30pm
...
Workshop 1: Guiding principles for FAIR and open science
...
Watch on Crowdcast
...
2:45-4:15pm
...
Workshop 2: Tools for Reproducible Science
...
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
...
Time (EST)
...
Session
...
9:00-10:30
...
Lecture 1: Welcome and Orientation
...
Watch on Crowdcast
...
10:45-12:15
...
Lecture 2: Problems and opportunities in the diagnosis and treatment of major depression
...
Watch on Crowdcast
...
1:00-2:30pm
...
Workshop 1: Guiding principles for FAIR and open science
...
Watch on Crowdcast
...
2:45-4:15pm
...
Workshop 2: Tools for Reproducible Science
...
Watch on Crowdcast
...
Instructors: Daniel Buchman, Marta Maslej & Laura Sikstrom
All videos previously recorded July 6th, 2021 as part of the KCNI Summer School
...
Zoom Q&A
...
Session
...
Lecture 1: Introduction to AI Ethics
...
Watch on Crowdcast
...
Lecture 2: Fairness and Health Equity
...
Watch on Crowdcast
...
Workshop 1: Research Design, Data Collection, Model Construction and Validation
...
Watch on Crowdcast
...
Workshop 2: Analysis, Interpretation and Knowledge Exchange and/or Translation
...
Watch on Crowdcast
...
Instructors: Shreejoy Tripathy & Dan Felsky
TA's: Keon Arbabi, Sonny Chen, Micaela Consens, Amin Kharaghani
...
Time (EST)
...
Session
...
9:00-10:30
...
Lecture 1: Basics of genotype, central dogma, GWAS, and polygenic risk scores
...
Watch on Crowdcast
...
10:45-12:15
| |||
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
Session | Video | Materials | ||||||
---|---|---|---|---|---|---|---|---|
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 |
Topic | Video | Materials | |
---|---|---|---|
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
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) |
The workshop demostates how to work with the Synapse platform.
Expand | ||
---|---|---|
| ||
Workshop 1 will use push and pull data to the synapse platform for sharing biomedical datasets using the
|
Session | Instructor | Video | Materials |
---|---|---|---|
Lecture 1: Basics of genotype, central dogma, GWAS, and polygenic risk scores | 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 |
---|---|---|---|
Lecture 1 |
...
: Transcriptomics at the single-cell and bulk level level |
...
Watch on Crowdcast
Shreejoy Tripathy | YouTube (1: |
...
...
Watch on Crowdcast
Sonny Chen | YouTube (1:19:17) |
...
Workshop 2: Explore cellular changes in major depression using bulk and single-cell RNAseq data |
...
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
...
Session | Instructors | Video | Materials |
---|
...
Instructors: Etay Hay & Frank Mazza
...
Time (EST)
...
Session
...
Lecture 1: Simulating brain microcircuit activity in mental health |
...
Watch on Crowdcast
Etay Hay & Frank Mazza | YouTube (1:20:43) | slides |
...
Lecture 2: Simulating EEG from brain microcircuits in mental health |
...
Watch on Crowdcast
Etay Hay & Frank Mazza | YouTube (1:11:04) | slides |
...
Workshop 1: Simulating and analyzing spiking from neurons and microcircuits |
...
Watch on Crowdcast
Etay Hay & Frank Mazza | YouTube (1:39:51) |
...
Workshop 2: Simulating and analyzing EEG signals from brain microcircuits |
...
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
Session | Instructors | Video | Materials |
---|
...
Instructors: Erin Dickie & John Griffiths
TA's: Shreyas Harita, Jerrold Jeyachandra, Kevin Kadak
...
Time (EST)
...
Session
...
Lecture 1: Introduction to neuroimaging connectomics |
...
Watch on Crowdcast
Erin Dickie & John Griffiths | YouTube (1:47:22) | slides |
...
Workshop 1: Calculating Neuroimaging Connectomes |
...
Watch on Crowdcast
Erin Dickie & John Griffiths | YouTube (1:39:04) |
Session | Instructors | Video | Materials |
---|
...
Lecture 2: Intro to whole-brain modelling (Lecture) |
...
Watch on Crowdcast
John Griffiths | YouTube (1:24:44) |
...
Workshop 2: simulating whole-brain activity, EEG, evoked responses, brain stimulation |
...
John Griffiths | YouTube (1:16:10) |
All videos previously recorded July 9th, 2021 as part of the KCNI Summer School
...
Watch on Crowdcast
...
...
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
...
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
Session | Instructor | Video | Materials | |
---|---|---|---|---|
Lecture 1: Population |
...
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
...
-based resources and the BrainHealth Databank |
...
Watch on Crowdcast
...
Workshop 1: |
...
Watch on Crowdcast
...
2:45-4:15pm
...
Introduction to interactive methods |
...
Watch on Crowdcast
...
Daniel Felsky | YouTube (1:24:30) | |
Lecture 2: Types |
...
Instructors: Daniel Felsky & Abhi Pratap + All Instructor Panel
TA's: Mohamed Abdelhack, Amin Kharaghani, Marta Maslej, Milos Milic, Earvin Tio
...
Time (EST)
...
Session
...
9:00-10:30
...
of integrative research and Whole Person Modelling |
...
Watch on Crowdcast
Daniel Felsky | YouTube (1:28:14) | |
Workshop 2 |
...
10:45-12:15
...
: SNF / Subtyping |
...
Watch on Crowdcast
Daniel Felsky | YouTube (1: |
...
...
Group Panel Discussion
...
Watch on Crowdcast
...
2:45-4:15pm
...
Final Social Hour
...