kcni-school-lessons
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
How to use git to clone this repo to your own computer
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.gitThe 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: 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?
Day 1: Welcome! Understanding clinical research questions and reproducible science (July 5, 2021)
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 slides | 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 slides | 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 slides | 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 |
Day 2: Applied ethics in machine learning and mental health (July 6, 2021)
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 |
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 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 slides | 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 |
Day 4: Simulating Brain Microcircuit Activity and Signals in Mental Health (July 8, 2021)
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 slides | 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 |
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
- Or open the code in google colab
| Time (EST) | Session | |
|---|---|---|
| 9:00-10:30 | Lecture 1: Introduction to neuroimaging connectomics slides | 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 |
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 [email protected] 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 slides | 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 |
Day 7: Digital Health and Population-Based Data Resources (July 13, 2021)
Instructors: Daniel Felsky, Abhi Pratap & Joanna Yu
TA's: Marta Maslej, Grace Jacobs, Mohamed Abdelhack, Amin Kharaghani, Milos Milic, Earvin Tio
Computing Environment:
Workshop 1 today 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.
- Step 1: Create an account on synapse - https://www.synapse.org/#!RegisterAccount:0
- Step 2: Become Certified (allows to upload data to synapse) by passing the synpase quiz to show you understand data use principles - https://www.synapse.org/#!Quiz:Certification
Workshop 2 will demonstrate how to use the synapse platform for analysis for a combined analysis of several restricted access datasets. Getting access to all these datasets is more time consuming than would be feasible for any student in this course, but we hope that students will find the demostration useful.
| 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 (Note: a "certified" synpase account is required for all code to run) | Watch on Crowdcast |
| 2:45-4:15pm | Workshop 2: Introduction to interactive methods (demonstates a workflow using several resticted access datasets) | 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: Marta Maslej, Mohamed Abdelhack, Amin Kharaghani, Milos Milic, Earvin Tio
Computing Environment:
| 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 |
Ways to connect with TA's instructors and classmates!
- 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
Are you looking for the 2020 content?
The 2020 Summer School content is archive in the 2020 release https://github.com/krembilneuroinformatics/kcni-school-lessons/releases/tag/2020.