There is still time to register for the 2021 school (July 5-14, 2021) - register directly at the Chrowdcast event link https://www.crowdcast.io/e/kcni-summer-school-2021
Note that some of the tutorial content and data is located within "submodules" - or pointers to other repo's. To get EVERYTHING use:
git clone --recurse-submodules https://github.com/krembilneuroinformatics/kcni-school-lessons.git- 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: Simulating Brain Microcircuit Activity and Signals in Mental Health (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)
- Ways to connect with TA's instructors and classmates!
- Are you looking for the 2020 content?
Instructors: Sean Hill, Dr Victor Tang, Dr Brett Jones, Erin Dickie, & Sejal Patel
TA's: Kevin Kadak, Taha Morshedzadeh, Kevin Witczak
Computing Environment:
- we will be introducing our rstudio and jupyter docker environments, available from dockerhub
edickie/kcnischool-rstudio:latest&edickie/kcnischool-jupyter:latestour docker setup instructions. - Also grab Erin's reproducibiltiy slides from here
- launch rstudio binder example
- launch jupyter binder example
| Time (EST) | Session | |
|---|---|---|
| 9:00-10:30 | Lecture 1: Welcome and Orientation + Neuroinformatics across scales - Sean Hill | Watch on Crowdcast |
| 10:45-12:15 | Lecture 2: Problems and opportunities in the diagnosis and treatment of major depression - Drs Victor Tang & Dr Brett Jones download slides as pdf | 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 - Erin Dickie & Sejal Patel | Watch on Crowdcast |
| 2:45-4:15pm | Workshop 2: Tools for Reproducible Science - Erin Dickie & Sejal Patel rstudio example  jupyter example |
Watch on Crowdcast |
| 4:30-5:00pm | Daily Social Chat? / Q & A | Join us in gather.town |
Instructors: Daniel Buchman, Marta Maslej & Laura Sikstrom
Computing Environment:
- setup instructions and code in the day2 folder
- we will use our custom rstudio docker, available from dockerhub
edickie/kcnischool-rstudio:latestdocker instructions - open rstudio in binder
| Time (EST) | Session | |
|---|---|---|
| 9:00-10:30 | Lecture 1: Introduction to AI Ethics | Watch on Crowdcast |
| 10:45-12:15 | Lecture 2: Fairness and Health Equity slides | 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 |
| 2:45-4:15pm | 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 |
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 docker instructions
Run rstudio in binder
| 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 | 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 |
| 2:45-4:15pm | 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 |
Instructors: Etay Hay & Frank Mazza
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 You can also run the tutorial code intercatively in binder
| Time (EST) | Session | |
|---|---|---|
| 9:00-10:30 | Lecture 1: Simulating brain microcircuit activity in mental health | Watch on Crowdcast |
| 10:45-12:15 | Lecture 2: Simulating EEG from brain microcircuits in mental health | Watch on Crowdcast |
| 12:15pm-1:00pm | Lunch Break | Join us in gather.town |
| 1:00-2:15pm | Workshop 1: Simulating and analyzing spiking from neurons and microcircuits | Watch on Crowdcast |
| 2:30-4:00pm | Workshop 2: Simulating and analyzing EEG signals from brain microcircuits | Watch on Crowdcast |
| 4:00-5:00pm | Daily Social Chat? / Q & A | Join us in gather.town |
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
- Or open the code in google colab
| Time (EST) | Session | |
|---|---|---|
| 9:00-10:30 | Lecture 1: Introduction to neuroimaging connectomics | Watch on Crowdcast [ ] |
| 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] |
| 2:45-4:15pm | 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 |
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 day6 folder
| Time (EST) | Session | |
|---|---|---|
| 9:00-10:30 | Lecture 1: Modelling Cognition using Bayesian Inference | Watch on Crowdcast |
| 10:45-12:15 | Tutorial 1: Modelling Abnormal Beliefs (Delusions) | Watch on Crowdcast |
| 12:15pm-1:00pm | Lunch Break | Join us in gather.town |
| 1:00-2:30pm | Lecture 2: Integration of Neuroimaging and Electrophysiological Data | Watch on Crowdcast |
| 2:45-4:15pm | Tutorial 2: Modelling Neuroimaging Data | Watch on Crowdcast |
| 4:30-5:00pm | Daily Social Chat? / Q & A | Join us in gather.town |
Instructors: Daniel Felsky, Abhi Pratap & Joanna Yu
TA's: Marta Maslej, Grace Jacobs, Mohamed Abdelhack, Amin Kharaghani, Milos Milic, Earvin Tio
Computing Environment: we will continue to use our custom rstudio docker, available from dockerhub edickie/kcnischool-rstudio:latest our docker setup instructions
| Time (EST) | Session | |
|---|---|---|
| 9:00-10:30 | Lecture 1: Digital Health for Mental health | Watch on Crowdcast |
| 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 |
| 2:45-4:15pm | Workshop 2: Introduction to interactive methods | Watch on Crowdcast |
| 4:30-5:00pm | Daily Social Chat? / Q & A | Join us in gather.town |
Instructors: Daniel Felsky & Abhi Pratap + All Instructor Panel
TA's: Marta Maslej, Mohamed Abdelhack, Amin Kharaghani, Milos Milic, Earvin Tio
Computing Environment: we will continue to use our custom rstudio docker, available from dockerhub edickie/kcnischool-rstudio:latest our docker setup 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 Discussion - Moderated by | Watch on Crowdcast |
| 2:45-4:15pm | Final Social Hour? | Watch on Crowdcast |
| 4:30-5:00pm | Social Chat? / Q & A | Join us in gather.town |
- join the conversation with school instructors on slack slack invite link
- come speak to us during the breaks in gather.town gather.town link
- start a conversation about this content in our github discussions board
- Remember you can always re-watch content after the session ends on Chrowdcast Chrowdcast Link
The 2020 Summer School content is archive in the 2020 release https://github.com/krembilneuroinformatics/kcni-school-lessons/releases/tag/2020.