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

KCNI Open House 2022_Poster.png

Join us for the Krembil Centre For Neuroinformatics 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.


Topic

Instructor

VideoSlides

A Multiscale Approach to Brain Disorders

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

YouTube (1:09:33)
slides

Problems and opportunities in the diagnosis and treatment of major depression

Victor Tang MD MSc, Clinician-Scientist/Resident,Centre for Addiction and Mental Health, Twitter: @victormarktang

Brett Jones MD MSc, Clinician-Scientist/Resident, Centre for Addiction and Mental Health

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.

TopicTutorial Videos / Online TutorialsPrerequisit to
RR Workshop Material (Apr-Jun 2022)
  • Fundamental Methods for Genomic Analysis
  • Fundamental Methods for Single-Cell Transcriptome Analysis
PythonIntroduction to Python
  • Simulating Brain Microcircuit Activity and Signals in Mental Health
  • Neuroimaging Connectomics
  • Whole Brain Modeling
Git/GithubIntroduction to Git and GitLab
Linux/BashIntroduction to Linux and Bash (Youtube)

many recordings available via from last falls series. SCWG Workshop Recordings - Nov 2021 Series


2022 Watch Party Time
  (EST)
Session
VideoMaterials
9:30-11:00am
Workshop 1: Guiding principles for FAIR and open science - 
Erin Dickie, Sejal Patel

Why reproducible science?

The things you need to know to get through this course:

Versioning and publishing code (github)

Versioning and publishing software (docker)

Watch on Youtube
slides
11:00-12:30pm
Workshop 2: Tools for Reproducible Science - 
Erin Dickie, Sejal Patel

R with Rmarkdown (walk through)

Python in ipython notebooks (walk through)

     -also google colab

The fancy bits:

  - building your own binder environments

  - building your own containers (docker & singularity)

Watch on YouTube

github code

rstudio example Binder jupyter example Binder


Register for the Virtual Q&A

3:30pm EST

Applied Ethics in Machine Learning and Mental Health 

Register for Virtual Q&A  - June 14, 2022 3:30pm EST

2022 Watch Party Time

EST

Topic
VideoMaterials
9:00-10:30am
Lecture 1: Introduction to AI Ethics - 
Daniel Buchman
Watch on  YouTube (1:22:07)
slides
10:30-12:00pm
Lecture 2:  Fairness and Health Equity - 
Laura Sikstrom
Watch on Youtube (1:06:36)
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

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

Register for Virtual Q&A  - June 20, 2022 1:00pm EST

Computing environment: Python (jupyter)

Watch Party  
Time (EST)
Session
InstructorVideoMaterials
9:30-11:00am
Lecture 1: Digital Health for Mental health
Abhi Pratap
Youtube (1:20:28)
11:00-12:30pm
Workshop 1: accessing reproducible datasets from Synapse as part of integrated workflow
Abhi Pratap
YouTube (1:15:12)
All videos previously recorded July 13th, 2021 as part of the KCNI Summer School


The workshop demostates how to work with the Synapse platform.

Workshop 1 will use push and pull data to the synapse platform for sharing biomedical datasets using the synapseClient python package. In order to be able to run all the commands in tutorial 1, a "verified" synapse account is required. For folks who are not able to create an account or get certified before the session tomorrow the instructor will cover the concepts for tractable data analysis that can still be generally applicable beyond synapse platform. Getting a Verified Account is a two step process.


Fundamental Methods for Genomic Analysis

Register for Virtual Q&A  - June 22, 2022 10:30am EST

New Live webinar on add mixture modeling  - June 22, 2022 11:30am EST - Register here!

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. 
Watch Party Time (EST)
Session
InstructorVideoMaterials
June 21, 1pm
Lecture 1: Basics of genotype, central dogma, GWAS, and polygenic risk scores
Dan Felsky
YouTube (1:28:17)
June 22, 9amDan Felsky
YouTube (1:27:18)
code (GitHub)
own timeWorkshop 2: Calculation of polygenic risk scores in PRSiceDan FelskyYouTube (1:53:34)code (GitHub)

June 22, 11:30am

(Live! - register here)

Considering population stratification and admixture in modern GWAS; concepts and toolsDan FelskyRegister 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

Register for Virtual Q&A  - June 22, 2022 3:30pm EST

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.
Watch Party Time (EST)
Session
InstructorVideoMaterials
June 21, 2:30pm
Lecture 1:  Transcriptomics at the single-cell and bulk level level
Shreejoy Tripathy
YouTube (1:29:08)
slides
June 22, 12:30pm
Workshop 1: Intro to transcriptomic data types, including single-cell and bulk RNAseq
Sonny Chen
YouTube (1:19:17)
June 22, 2:00-3:30pm
Workshop 2: Explore cellular changes in major depression using bulk and single-cell RNAseq data
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

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


Watch Party Time (EST)

June 23, 2022

Session
InstructorsVideoMaterials
9:00-10:30am
Lecture 1: Simulating brain microcircuit activity in mental health
Etay Hay & Frank Mazza
YouTube (1:20:43)
slides
10:30-12:00pm
Lecture 2: Simulating EEG from brain microcircuits in mental health
Etay Hay & Frank Mazza
YouTube (1:11:04)
slides
12:30-2:00pm
Workshop 1: Simulating and analyzing spiking from neurons and microcircuits
Etay Hay & Frank Mazza
YouTube (1:39:51)
2:00-3:30pm
Workshop 2: Simulating and analyzing EEG signals from brain microcircuits
Etay Hay & Frank Mazza
YouTube (1:30:41)

All videos previously recorded July 8th, 2021 as part of the KCNI Summer School


Neuroimaging Connectomics

Register for Virtual Q&A  - June 29, 2022 11:30am EST

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

Watch Party Time (EST)

June 29, 2022

Session
InstructorsVideoMaterials
8:30-10:00am
Lecture 1: Introduction to neuroimaging connectomics
Erin Dickie & John Griffiths
YouTube (1:47:22)
slides
10:00-11:30am
Workshop 1: Calculating Neuroimaging Connectomes
Erin Dickie & John Griffiths
YouTube (1:39:04)
All videos previously recorded July 9th, 2021 as part of the KCNI Summer School



Whole-Brain Modelling

Register for Virtual Q&A  - June 30, 2022 3:30pm EST

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

Watch Party Time (EST)

June 30, 2022

Session
InstructorsVideoMaterials
12:30-2:00pm
Lecture 2: Intro to whole-brain modelling (Lecture)
John Griffiths
YouTube (1:24:44)

2:00-3:30pm
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


Bayesian Models of Learning and Integration of Neuroimaging Data

Register for Virtual Q&A  - June 28, 2022 3:30pm EST

Presented by Andreea Diaconescu and the Cognitive Network Modelling (CogNeMo) Group

Coding Language: MATLAB more setup info


Watch Party Time (EST)

June 28, 2022

Session
InstructorVideoMaterials
9:00-10:30am
Lecture 1: Modelling Cognition using Bayesian Inference
Andreea Diaconescu
YouTube (1:28:14)
slides
10:30-12:00pm
Workshop 1:  Modelling Abnormal Beliefs
Daniel Hauke
YouTube (1:15:04)
code (github)
12:30-2:00pm
Lecture 2: Integration of Neuroimaging: Dynamic Causal Modelling for fMRI and EEG Data
Andreea Diaconescu, Colleen Charlton
YouTube (1:32:42)
slides
2:00-3:30pm
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
InstructorVideoMaterials

Lecture 1: Population-based resources and the BrainHealth Databank
Joanna Yu
YouTubeslides

Workshop 1: Introduction to interactive methods
Daniel Felsky
YouTube (1:24:30)

Lecture 2: Types of integrative research and Whole Person Modelling
Daniel Felsky
YouTube (1:28:14)

Workshop 2: SNF / Subtyping
Daniel Felsky
YouTube (1:21:38)

2020 Summer School Overview




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