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Krembil Centre for Neuroinformatics Summer School
Solving Problems in Mental Health using Multi-Scale Computational Neuroscience
JULY 5-9th, 12-14th, 2021.
Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health
The full schedule:
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The full schedule:
- clinical research questions and reproducible science
- ethics machine learning and mental health
- methods genomic single-cell transcriptome analysis
- Simulations of Depression
- research methods
Day 1: Welcome! Understanding
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Clinical Research Questions and Reproducible Science (July 5, 2021)
Instructors: Erin Dickie, Sean Hill,
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Sejal Patel, Victor Tang,
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Brett Jones
TA's:
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Kevin Kadak, Taha Morshedzadeh, Kevin Witczak
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- we will use our custom rstudio docker, available from dockerhub
edickie/kcnischool-rstudio:latest
click here for install instructions. - Also grab Erin's reproducibility slides from here
Time (EST) | Session |
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9:00-10:30 | Lecture 1: Welcome and Orientation | | 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 | | 12:15pm-1:00pm | Lunch Break | Join us in gather.town |
1:00-2:30pm | Workshop 1: Guiding principles for FAIR and open science | |
2:30-2:45pm | Afternoon Break | Join us in gather.town | 2:45-4:15pm | | | 4:30-5:00pm | Daily Social Chat? / Q & A | Join us in gather.town
Day 2: Applied
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Ethics in
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Machine Learning and Mental Health (July 6, 2021)
Instructors: Daniel Buchman, Marta Maslej & Laura Sikstrom
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- we will use our custom rstudio docker, available from dockerhub
edickie/kcnischool-rstudio:latest
click here for install instructions.
Time (EST) | Session |
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9:00-10:30 | Lecture 1: Introduction to AI Ethics | |
10:30-10:45 | Morning Break | Join us in gather.town | 10:45-12:15 | Lecture 2: Fairness and Health Equity | |
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 | | 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 | | 4:30-5:00pm | Daily Social Chat? / Q & A | Join us in gather.town
Day 3: Fundamental
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Methods for
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Genomic and
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Single-Cell Transcriptome Analysis (July 7, 2021)
Instructors:
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Shreejoy Tripathy & Dan Felsky
TA's:
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Keon Arbabi, Sonny Chen, Micaela Consens, Amin Kharaghani
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Time (EST) | Session |
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9:00-10:30 | Lecture 1: Basics of Genotypegenotype, Central central dogma, GWAS, and Polygenic Risk Scorespolygenic risk scores | |
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 | |
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 | | 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 | | 4:30-5:00pm | Daily Social Chat? / Q & A | Join us in gather.town
Day 4: Simulating Brain Microcircuit
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Activity and Signals in Mental Health (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 |
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9:00-10:30 | Lecture 1: Modeling Simulating brain microcircuits microcircuit activity in mental health and depression | | 10:30-10:45 | Morning Break | Join us in gather.town |
10:45-12:15 | Lecture 2: Simulating EEG from brain microcircuits in mental health and depression | |
12:15pm-1:00pm | Lunch Break | Join us in gather.town | 1:00-2:30pm | Workshop 1: simulating neurons, microcircuits and EEG signalsSimulating and analyzing spiking from neurons and microcircuits | |
2:30-2:45pm | Afternoon Break | Join us in gather.town | 2:45-4:15pm | Workshop 2: exercisesSimulating and analyzing EEG signals from brain microcircuits | | 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 |
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9:00-10:30 | Lecture 1: Introduction to neuroimaging connectomics | |
10:30-10:45 | Morning Break | Join us in gather.town | 10:45-12:15 | Workshop 1: Calculating Neuroimaging Connectomes | |
12:15pm-1:00pm | Lunch Break | Join us in gather.town | 1:00-2:30pm | Lecture 2: Intro to whole-brain modelling (Lecture) | |
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 | | 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:
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Andreea Diaconescu
TA's: Colleen Charlton, Daniel Hauke, Peter Bedford, Povilas Karvelis
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Compute Environment: MATLAB.
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Time (EST) | Session |
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9:00-10:30 | Lecture 1: Bayesian Models of Learning | | 10:30-10:45 | Morning Break | Join us in gather.town |
10:45-12:15 | Turorial 1: Hierarchical Gaussian Filter and Simulating Learners | |
12:15pm-1:00pm | Lunch Break | Join us in gather.town | 1:00-2:30pm | Lecture 2: Computational Modelling of EEG Data | |
2:30-2:45pm | Afternoon Break | Join us in gather.town | 2:45-4:15pm | Tutorial 2: Single-trial EEG Modelling | | 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: Mohamed Abdelhack, Grace Jacobs, Amin Kharaghani, Marta Maslej,
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Milos Milic, Earvin Tio
Time (EST) | Session |
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9:00-10:30 | | |
10:30-10:45 | Morning Break | Join us in gather.town | 10:45-12:15 | Lecture 2: Population-based resources and the BrainHealth Databank | | 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 | | 2:30-2:45pm | Afternoon Break | Join us in gather.town |
2:45-4:15pm | Workshop 2: Introduction to interactive methods | | 4:30-5:00pm | Daily Social Chat? / Q & A | Join us in gather.town
Day 8: Integrative
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Research Methods and Final Panel Discussion (July 14, 2021)
Instructors: Daniel Felsky & Abhi Pratap + All Instructor Panel
TA's: Mohamed Abdelhack,
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Amin Kharaghani, Marta Maslej, Milos Milic, Earvin Tio
Time (EST) | Session |
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9:00-10:30 | Lecture 1: Types of integrative research and Whole Person Modelling | | 10:30-10:45 | Morning Break | Join us in gather.town |
10:45-12:15 | Workshop: SNF / Subtyping | |
12:15pm-1:00pm | Lunch Break | Join us in gather.town | 1:00-2:30pm | Group Panel Discussion | |
2:30-2:45pm | Afternoon Break | Join us in gather.town | 2:45-4:15pm | Final Social Hour? | | 4:30-5:00pm | Social Chat? / Q & A | Join us in gather.town |