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
Join us for the Krembil Centre For Neuroinformatics Open House!
Krembil Centre for Neuroinformatics Virtual Open House
The Krembil Centre for Neuroinformatics is excited to host its Annual Open House on Friday, June 24 starting at 10am.
Come meet the KCNI team and learn about the latest developments virtually, or even better, in person!
Register for in-person or virtual here.
Introductory Concepts
A collection of lectures on overaching concepts in Neuroinformatics Research.
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 |
|---|---|---|---|
| R | (see recording within tutorials page) | R Workshop Material (Apr-Jun 2022) | |
| Python | Introduction to Python | Those working with imaging data | |
| Git/Github | Introduction to Git and GitLab | ||
| Linux/Bash | Youtube | Introduction to Linux and Bash |
many recordings available via from last falls series. SCWG Workshop Recordings - Nov 2021 Series
Reproducible Science (including Git, Docker and Binder)
Register for Virtual Q&A - June 10, 2022 1:00pm EST
2022 Watch Party Time(EST) | Session | Instructors | Video | Materials |
|---|---|---|---|---|
| 9:30-11:00am | Workshop 1: Guiding principles for FAIR and open science | Erin Dickie, Sejal Patel | Watch on Crowdcast | slides |
| 11:00-12:30pm | Workshop 2: Tools for Reproducible Science | Erin Dickie, Sejal Patel | Watch on Crowdcast | rstudio example |
Register for the Virtual Q&A
3:30pm EST
Applied Ethics in Machine Learning and Mental Health
Register for the Virtual Q&A 3:30pm EST
2022 Watch Party Time EST | Topic | Instructor | Video | Materials |
|---|---|---|---|---|
| 9:00-10:30am | Lecture 1: Introduction to AI Ethics | Daniel Buchman | Watch on Crowdcast | |
| 10:30-12:00pm | Lecture 2: Fairness and Health Equity | Marta Maslej & Laura Sikstrom | Watch on Crowdcast | slides |
| 12:30-2:00pm | Workshop 1: Research Design, Data Collection, Model Construction and Validation | Marta Maslej & Laura Sikstrom | Watch on Crowdcast | |
| 2:00-3:30pm | 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 for Mental Health
Presented by Abhi Pratap
Register for Virtual Q&A - June 20, 2022 1:00pm EST
Watch PartyTime (EST) | Session | Instructor | Video | Materials |
|---|---|---|---|---|
| 9:30-11:00am | Lecture 1: Digital Health for Mental health | Abhi Pratap | Watch on Crowdcast | |
| 11:00-12:30pm | Workshop 1: accessing reproducible datasets from Synapse as part of integrated workflow | Abhi Pratap | Watch on Crowdcast |
The workshop demostates how to work with the Synapse platform.
Fundamental Methods for Genomic Analysis
Time (EST) | Session | Instructor | Video | Materials |
|---|---|---|---|---|
Lecture 1: Basics of genotype, central dogma, GWAS, and polygenic risk scores | Dan Felsky | Watch on Crowdcast | ||
Workshop 1: Managing genotype data using PLINK | Dan Felsky | Watch on Crowdcast | code (GitHub) | |
| Workshop 2: Calculation of polygenic risk scores in PRSice | Dan Felsky | Watch on Crowdcast | code (GitHub) |
All videos previously recorded July 7th, 2021 as part of the KCNI Summer School
Fundamental Methods for Single-Cell Transcriptome Analysis
Session | Instructor | Video | Materials | |
|---|---|---|---|---|
Lecture 1: Transcriptomics at the single-cell and bulk level level | Shreejoy Tripathy | Watch on Crowdcast | slides | |
Workshop 1: Intro to transcriptomic data types, including single-cell and bulk RNAseq | Dan Felsky | Watch on Crowdcast | ||
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
Watch Party Time (EST) | Session | Instructors | Video | Materials |
|---|---|---|---|---|
Lecture 1: Simulating brain microcircuit activity in mental health | Etay Hay & Frank Mazza | Watch on Crowdcast | slides | |
Lecture 2: Simulating EEG from brain microcircuits in mental health | Etay Hay & Frank Mazza | Watch on Crowdcast | slides | |
Workshop 1: Simulating and analyzing spiking from neurons and microcircuits | Etay Hay & Frank Mazza | Watch on Crowdcast | ||
Workshop 2: Simulating and analyzing EEG signals from brain microcircuits | Etay Hay & Frank Mazza | Watch on Crowdcast |
All videos previously recorded July 8th, 2021 as part of the KCNI Summer School
Neuroimaging Connectomics
Time (EST) | Session | Instructors | Video | Materials |
|---|---|---|---|---|
Lecture 1: Introduction to neuroimaging connectomics | Erin Dickie & John Griffiths | Watch on Crowdcast | slides | |
Workshop 1: Calculating Neuroimaging Connectomes | Erin Dickie & John Griffiths | Watch on Crowdcast |
Whole-Brain Modelling
Time (EST) | Session | Instructors | Video | Materials |
|---|---|---|---|---|
Lecture 2: Intro to whole-brain modelling (Lecture) | John Griffiths | Watch on Crowdcast | ||
Workshop 2: simulating whole-brain activity, EEG, evoked responses, brain stimulation | John Griffiths | Watch on Crowdcast |
All videos previously recorded July 9th, 2021 as part of the KCNI Summer School
Bayesian Models of Learning and Integration of Neuroimaging Data
Coding Language: MATLAB more setup info
Time (EST) | Session | Instructor | Video | Materials |
|---|---|---|---|---|
Lecture 1: Bayesian Models of Learning | Andreea Diaconescu | Watch on Crowdcast | slides | |
Turorial 1: Hierarchical Gaussian Filter and Simulating Learners | Andreea Diaconescu | Watch on Crowdcast | code (github) | |
Lecture 2: Computational Modelling of EEG Data | Andreea Diaconescu | Watch on Crowdcast | slides | |
Tutorial 2: Single-trial EEG Modelling | Andreea Diaconescu | Watch on Crowdcast | code (github) |
TA's: Colleen Charlton, Daniel Hauke, Peter Bedford, Povilas Karvelis
Population-Based Data Resources & Integrative Research Methods
Session | Instructor | Video | Materials | |
|---|---|---|---|---|
Lecture 1: Population-based resources and the BrainHealth Databank | Joanna Yu | Watch on Crowdcast | slides | |
Workshop 1: Introduction to interactive methods | Daniel Felsky | Watch on Crowdcast | ||
Lecture 2: Types of integrative research and Whole Person Modelling | Daniel Felsky | Watch on Crowdcast | ||
Workshop 2: SNF / Subtyping | Daniel Felsky | Watch on Crowdcast |