The syllabus for the 12-week online course is available as a Google Doc.
Details on the ABCD-ReproNim AI/ML Course can be found here.
Please review our instructions and recommendations for ABCD Data Access.
Each week includes three recorded videos: an ABCD lecture, a ReproNim lecture, and a pre-recorded Q&A session.
ABCD lectures will emphasize understanding different data sources and types available in the ABCD dataset.
ReproNim lectures will emphasize data tools, resources, and strategies for reproducible analytics.
A supplemental reading list of recommended related publications has been distributed by each instructor.
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Week 1 - January 10, 2022
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event
ABCD: Introduction to the ABCD Study®
ABCD Study® Design and Objective
ABCD CC, DAIC, and Study Sites
Protection of Human Subjects
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event
ReproNim: Introduction to ReproNim
"The Reproducibility Problem"
Re-Executability at the Publication Level
Introduction to the ReproStack
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Week 2 - January 17, 2022
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event
ABCD: Data Access, NDA, and DEAP
DAIRC, Data Access, and NDA
DEAP Access and Use
Site and Vendor Effects
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event
ReproNim: Git & Basics
Command Line/Shell
Version Control Systems and Git
Package Managers and Distributions
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Week 3 - January 24, 2022
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event
ABCD: Sampling, Recruitment, and Retention
Inclusion/Exclusion Criteria
Sampling and School Selection
Description of Sample
Recruitment and Retention
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event
ReproNim: Containers & ReproEnv
What are Containers?
Docker and Singularity
The ReproNim Reproducibility Stack
Container Management
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Week 4 - January 31, 2022
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event
ABCD: Imaging Measures
Experimental Set-Up and MRI Vendors
Imaging Protocol and Pulse Sequences
Quality Assurance
fMRI Task Description
Data Harmonization
Minimally Processed Pipelines
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event
ReproNim: Pre-Registration and P-Hacking
What Forms a Good Question in Neuroimaging?
Pre-Registrations: Why, Why Not, When?
Reminder on the Classical Null Hypothesis Testing Framework
Common Pitfalls and Mis-Interpretations of P-Values
What Makes the Risk of Error Inflate?
Can We P-Hack in a Machine Learning Framework?
This session includes a bonus presentation and Q&A on ABCD Data Access given by the NIMH Data Archive (NDA).
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Week 5 - February 7, 2022
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event
ABCD: Neurocognitive Assessments
Description and Rationale for Neurocognitive Battery
Intelligence, Cognitive Control, and Reward
Methodological Considerations
Variations in Assessments Across Time Points (e.g., Baseline, 6-Month, 1-Year, etc.)
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event
ReproNim: FAIR Data/Semantic Markup 1
What is FAIR?
Implementing the FAIR Principles
Web of Data and Linked Data
Data Publishing
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Week 6 - February 14, 2022
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event
ABCD: Substance Use Assessments
Description and Rationale For Substance Use Battery
Substance Use Module Methods
Measurement Tools
Variations in Assessments Across Time Points (e.g., Baseline, 6-Month, 1-Year, etc.)
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event
ReproNim: Semantic Markup 2
Data Semantics – Why?
Data Semantics – How?
The NeuroImaging Data Model (NIDM)
pyNIDM – Python Utilities to Manipulate and Query NIDM
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Week 7 - February 21, 2022
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event
ABCD: Demographic, Physical, and Mental Health Assessments
Description of Demographic Information
Description and Rationale for Physical Battery
Description and Rationale for Mental Health Battery
Parent Assessments and Teacher Reports
Minimization of Participant and Family Burden
Variations in Assessments Across Time Points (e.g., Baseline, 6-Month, 1-Year, etc.)
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event
ReproNim: Scientific Questions and Statistical Issues
Effect Size and Variation of Effect Sizes in Brain Imaging
Statistical Power
Model Selection
The Positive Predictive Value
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Week 8 - February 28, 2022
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event
ABCD: Culture and Environment Assessments
Description of Culture and Environment Measures
Culture and Environment Group Membership
Proximal Social Environment
Social Interactions
Variations in Assessments Across Time Points (e.g., Baseline, 6-Month, 1-Year, etc.)
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event
ReproNim: Data Versioning and Tranformation with DataLad
Why Should Data Be Versioned?
Simple DataLad Tranform: Retrieve, Compute, Store Results
Create a Dataset
Using DataLad with Containers on the Dataset
Rerunning and Checking Analysis Differences
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Week 9 - March 7, 2022
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event
ABCD: Biospecimens
Biospecimen Description and Rationale: Hair Samples, Baby Teeth, Saliva, Blood
Data Collection Protocol and Methodological Considerations
Storage and Analysis
Variations in Biospecimens Across Time Points (e.g., Baseline, 6-Month, 1-Year, etc.)
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event
ReproNim: Reproducible Workflows & Analyses
The Need For and the Problems With Computational Flexibility
Introduction to Scalable Analysis with Dataflow Tools
Introduction to Regression Testing and Software Changes
Automated Provenance Tracking
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Week 10 - March 14, 2022
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event
ABCD: Novel Technologies – Mobile, Wearable, and Social Media
Background and Rationale for Novel Technologies
Mobile and Wearable Technologies
Social Media Data
Data Capture, Preprocessing, and Analysis Approaches
Variations in Biospecimens Across Time Points (e.g., Baseline, 6-Month, 1-Year, etc.)
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event
ReproNim: ReproMan – Execution and Environment Manager
Creation and Management of Computing Environments in Neuroimaging
Distributed Computing: HPC and Cloud
Re-Execution
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Week 11 - March 21, 2022
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event
ABCD: Visualizing ABCD Data
Basics of Plotting Data in Python
Manipulating Basic Plots and Figure Objects
Displaying Statistical Results in Plots
Data and Dataframe Manipulation
Plotting Brain Data in Python
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event
ReproNim: ReproPub: The Re-Executable Publication
Spectrum of Reproducibility and Definitions
Re-Executability as a Key Element of Reproducibility
Provenance and Core Research Objects: Data, Workflow, Computational Environment, Results, Statistical Assessments
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Week 12 - March 28, 2022
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event
Analytic Approaches: Longitudinal Modeling and Quantifying Change
What is Longitudinal Modeling?
Common Statistical Models of Longitudinal Change
Developmental Questions and Applications
Available (and Missing) Software Packages and Tools
Troubleshooting and Gaps in the Literature
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event
Analytic Approaches: Reproducible Practices in Machine Learning
Individual Differences Analyses
Machine Learning Basics
Training/Testing Approaches
Generalization
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Project Month: April 4 - April 29, 2022
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event
April 4: Overview and Discussion
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April 8: Project Pitches
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event
April 11-14: Work on Projects
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April 15: Progress Report
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April 18-21: Work on Projects
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April 22: Progress Report
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April 25-27: Wrap Up Projects
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April 28 & 29: Final Presentations