Suggestions and Feedback? Email us at krembil.centre@camh.ca
The Krembil Centre for Neuroinformatics at CAMH || Looking for more? Email us at krembil.centre@camh.ca
The full schedule:
- kcni-school-lessons
- The full schedule:
- 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 4: Brain Microcircuit Simulations of Depression (July 8, 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)
Day 1: Welcome! Understanding clinical research questions and reproducible science (July 5, 2021)
Instructors: Erin Dickie, Sean Hill, Dr Victor Tang, Dr Brett Jones
TA's: Sejal Patel, Kevin Kadak, Taha Morshedzadeh, Kevin Witczak
Computing Environment:
- we will use our custom rstudio docker, available from dockerhub
edickie/kcnischool-rstudio:latestclick here for install instructions. - Also grab Erin's reproducibility slides from here
| Time (EST) | Session | |
|---|---|---|
| 9:00-10:30 | Lecture 1: Welcome and Orientation | Watch on Crowdcast |
| 10:30-10:45 | Morning Break | Join us in gather.town |
| 10:45-12:15 | Lecture 2: Problems and opportunities in the diagnosis and treatment of major depression | Watch on Crowdcast |
| 12:15pm-1:00pm | Lunch Break | Join us in gather.town |
| 1:00-2:30pm | Workshop 1: Guiding principles for FAIR and open science | Watch on Crowdcast |
| 2:30-2:45pm | Afternoon Break | Join us in gather.town |
| 2:45-4:15pm | Workshop 2: Tools for Reproducible Science | Watch on Crowdcast |
| 4:30-5:00pm | Daily Social Chat? / Q & A | Join us in gather.town |
Day 2: Applied ethics in machine learning and mental health (July 6, 2021)
Instructors: Daniel Buchman, Marta Maslej & Laura Sikstrom
Computing Environment:
- we will use our custom rstudio docker, available from dockerhub
edickie/kcnischool-rstudio:latestclick here for install instructions.
| Time (EST) | Session | |
|---|---|---|
| 9:00-10:30 | Lecture 1: Introduction to AI Ethics | Watch on Crowdcast |
| 10:30-10:45 | Morning Break | Join us in gather.town |
| 10:45-12:15 | Lecture 2: Fairness and Health Equity | Watch on Crowdcast |
| 12:15pm-1:00pm | Lunch Break | Join us in gather.town |
| 1:00-2:30pm | Workshop 1: Research Design, Data Collection, Model Construction and Validation | Watch on Crowdcast |
| 2:30-2:45pm | Afternoon Break | Join us in gather.town |
| 2:45-4:15pm | Workshop 2: Analysis, Interpretation and Knowledge Exchange and/or Translation | Watch on Crowdcast |
| 4:30-5:00pm | Daily Social Chat? / Q & A | Join us in gather.town |
Day 3: Fundamental methods for genomic and single-cell transcriptome analysis (July 7, 2021)
Instructors: Dr. Shreejoy Tripathy & Dan Felsky
TA's: Sonny Chen, Micaela Consens, Amin Kharaghani, Keon Arbabi
Computing Environment: we will continue to use our custom rstudio docker, available from dockerhub edickie/kcnischool-rstudio:latest [click here for install instructions]
| Time (EST) | Session | |
|---|---|---|
| 9:00-10:30 | Lecture 1: Basics of Genotype, Central dogma, GWAS, and Polygenic Risk Scores | Watch on Crowdcast |
| 10:30-10:45 | Morning Break | Join us in gather.town |
| 10:45-12:15 | Lecture 2: Transcriptomics at the single-cell and bulk level level | Watch on Crowdcast |
| 12:15pm-1:00pm | Lunch Break | Join us in gather.town |
| 1:00-2:30pm | Workshop 1: Intro to transcriptomic data types, including single-cell and bulk RNAseq | Watch on Crowdcast |
| 2:30-2:45pm | Afternoon Break | Join us in gather.town |
| 2:45-4:15pm | Workshop 2: Explore cellular changes in major depression using bulk and single-cell RNAseq data | Watch on Crowdcast |
| 4:30-5:00pm | Daily Social Chat? / Q & A | Join us in gather.town |
Day 4: Brain Microcircuit Simulations of Depression (July 8, 2021)
Instructors: Etay Hay & Frank Mazza
TA's TBA
Computing Environment: we will use our custom python/neurophysiology docker, available at dockerhub edickie/kcnischool-jupyter. go here for more info on setting up the environment
| Time (EST) | Session | |
|---|---|---|
| 9:00-10:30 | Lecture 1: Modeling brain microcircuits activity in health and depression | Watch on Crowdcast |
| 10:30-10:45 | Morning Break | Join us in gather.town |
| 10:45-12:15 | Lecture 2: Simulating EEG from brain microcircuits in health and depression | Watch on Crowdcast |
| 12:15pm-1:00pm | Lunch Break | Join us in gather.town |
| 1:00-2:30pm | Workshop 1: simulating neurons, microcircuits and EEG signals | |
| Watch on Crowdcast | ||
| 2:30-2:45pm | Afternoon Break | Join us in gather.town |
| 2:45-4:15pm | Workshop 2: exercises | Watch on Crowdcast |
| 4:30-5:00pm | Daily Social Chat? / Q & A | Join us in gather.town |
Day 5: Whole-Brain Modelling and Neuroimaging Connectomics (July 9, 2021)
Instructors: Erin Dickie & John Griffiths
TA's Shreyas Harita, Jerrold Jeyachandra, Kevin Kadak
Computing Environment: we will use our custom python/neurophysiology docker, available at dockerhub edickie/kcnischool-jupyter. go here for more info on setting up the environment
| Time (EST) | Session | |
|---|---|---|
| 9:00-10:30 | Lecture 1: Introduction to neuroimaging connectomics | Watch on Crowdcast |
| 10:30-10:45 | Morning Break | Join us in gather.town |
| 10:45-12:15 | Workshop 1: Calculating Neuroimaging Connectomes | Watch on Crowdcast |
| 12:15pm-1:00pm | Lunch Break | Join us in gather.town |
| 1:00-2:30pm | Lecture 2: Intro to whole-brain modelling (Lecture) | Watch on Crowdcast |
| 2:30-2:45pm | Afternoon Break | Join us in gather.town |
| 2:45-4:15pm | Workshop 2: simulating whole-brain activity, EEG, evoked responses, brain stimulation | Watch on Crowdcast |
| 4:30-5:00pm | Daily Social Chat? / Q & A | Join us in gather.town |
Day 6: Bayesian Models of Learning and Integration of Neuroimaging Data (July 12, 2021)
Instructors: Dr. Andreea Diaconescu
TA's: Colleen Charlton, Daniel Hauke, Peter Bedford, Povilas Karvelis
Compute Environment: MATLAB.
- All students in the interactive stream should have been emailed a link to a temporary MATLAB license that can be used for this course. Contact KCNI.School@camh.ca with any questions.
- Additional setup instructions are available in the day5 folder
| Time (EST) | Session | |
|---|---|---|
| 9:00-10:30 | Lecture 1: Bayesian Models of Learning | Watch on Crowdcast |
| 10:30-10:45 | Morning Break | Join us in gather.town |
| 10:45-12:15 | Turorial 1: Hierarchical Gaussian Filter and Simulating Learners | Watch on Crowdcast |
| 12:15pm-1:00pm | Lunch Break | Join us in gather.town |
| 1:00-2:30pm | Lecture 2: Computational Modelling of EEG Data | Watch on Crowdcast |
| 2:30-2:45pm | Afternoon Break | Join us in gather.town |
| 2:45-4:15pm | Tutorial 2: Single-trial EEG Modelling | Watch on Crowdcast |
| 4:30-5:00pm | Daily Social Chat? / Q & A | Join us in gather.town |
Day 7: Digital Health and Population-Based Data Resources (July 13, 2021)
Instructors: Daniel Felsky, Abhi Pratap & Joanna Yu
TA's: Marta Maslej, Akshay Mohan, Grace Jacobs
Computing Environment: we will continue to use our custom rstudio docker, available from dockerhub edickie/kcnischool-rstudio:latest [click here for install instructions]
| Time (EST) | Session | |
|---|---|---|
| 9:00-10:30 | Lecture 1: Digital Health for Mental health | Watch on Crowdcast |
| 10:30-10:45 | Morning Break | Join us in gather.town |
| 10:45-12:15 | Lecture 2: Population-based resources and the BrainHealth Databank | Watch on Crowdcast |
| 12:15pm-1:00pm | Lunch Break | Join us in gather.town |
| 1:00-2:30pm | Workshop 1: accessing reproducible datasets from Synapse as part of integrated workflow | Watch on Crowdcast |
| 2:30-2:45pm | Afternoon Break | Join us in gather.town |
| 2:45-4:15pm | Workshop 2: Introduction to interactive methods | Watch on Crowdcast |
| 4:30-5:00pm | Daily Social Chat? / Q & A | Join us in gather.town |
Day 8: Integrative research methods and Final Panel Discussion (July 14, 2021)
Instructors: Daniel Felsky & Abhi Pratap + All Instructor Panel
TA's: Mohamed Abdelhack, Marta Maslej
Computing Environment: we will continue to use our custom rstudio docker, available from dockerhub edickie/kcnischool-rstudio:latest [click here for install instructions]
| Time (EST) | Session | |
|---|---|---|
| 9:00-10:30 | Lecture 1: Types of integrative research and Whole Person Modelling | Watch on Crowdcast |
| 10:30-10:45 | Morning Break | Join us in gather.town |
| 10:45-12:15 | Workshop: SNF / Subtyping | Watch on Crowdcast |
| 12:15pm-1:00pm | Lunch Break | Join us in gather.town |
| 1:00-2:30pm | Group Panel Discussion | Watch on Crowdcast |
| 2:30-2:45pm | Afternoon Break | Join us in gather.town |
| 2:45-4:15pm | Final Social Hour? | Watch on Crowdcast |
| 4:30-5:00pm | Social Chat? / Q & A | Join us in gather.town |
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