The syllabus for the 13-week online course is available as a Google Doc.

Please review our instructions and recommendations for ABCD Data Access.

Pre-recorded lectures each week will include an ABCD and a ReproNim lecture.

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 will be distributed by each instructor.

We will meet one hour per week on Fridays at 1pm EST (10am PST).

  • Week 1 - October 16, 2020

  • event

    ABCD: Introduction to the ABCD Study®

    ABCD Study® Design and Objective

    ABCD CC, DAIC, and Study Sites

    Protection of Human Subjects

  • event

    ReproNim: Introduction to ReproNim

    "The Reproducibility Problem"

    Re-Executability at the Publication Level

    Introduction to the ReproStack

  • Angie Laird (she/her)

  • David Kennedy (he/him)

  • Week 2 - October 23, 2020

  • event

    ABCD: Data Access, NDA, and DEAP

    DAIRC, Data Access, and NDA

    DEAP Access and Use

    Site and Vendor Effects

  • event

    ReproNim: Git & Basics

    Command Line/Shell

    Version Control Systems and Git

    Package Managers and Distributions

  • Wes Thompson (he/him)

  • Dorota Jarecka (she/her)

  • Week 3 - October 30, 2020

  • event

    ABCD: Sampling, Recruitment, and Retention

    Inclusion/Exclusion Criteria

    Sampling and School Selection

    Description of Sample

    Recruitment and Retention

  • event

    ReproNim: Containers & ReproEnv

    What are Containers?

    Docker and Singularity

    The ReproNim Reproducibility Stack

    Container Management

  • Hugh Garavan (he/him)

  • Dorota Jarecka (she/her)

  • Week 4 - November 6, 2020

  • 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

  • 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?

  • Damien Fair (he/him)

  • JB Poline (he/him)

On Friday, November 6, we will host a bonus session presentation and Q&A on ABCD Data Access given by the NIMH Data Archive (NDA).

This will extend our regularly-scheduled synchronous meeting by 30 minutes.

  • Week 5 - November 13, 2020

  • 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.)

  • event

    ReproNim: FAIR Data/Semantic Markup 1

    What is FAIR?

    Implementing the FAIR Principles

    Web of Data and Linked Data

    Data Publishing

  • Susan Tapert (she/her)

  • Maryann Martone (she/her)

  • Week 6 - November 20, 2020

  • 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.)

  • event

    ReproNim: Semantic Markup 2

    Data Semantics – Why?

    Data Semantics – How?

    The NeuroImaging Data Model (NIDM)

    pyNIDM – Python Utilities to Manipulate and Query NIDM

  • Krista Lisdahl (she/her)

  • David Keator (he/him)

  • Week 7 - January 15, 2021

  • 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.)

  • 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

  • Deanna Barch (she/her)

  • JB Poline (he/him)

  • Week 8 - January 22, 2021

  • 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.)

  • 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

  • Raul Gonzalez (he/him)

  • Adina Wagner (she/her)

  • Week 9 - January 29, 2021

  • 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.)

  • event

    ReproNim: ReproNim – Execution and Environment Manager

    Creation and Management of Computing Environments in Neuroimaging

    Distributed Computing: HPC and Cloud

    Re-Execution

  • Kristina Uban (she/her)

  • Yaroslav Halchenko (he/him)

  • Week 10 - February 5, 2021

  • 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.)

  • 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

  • Kara Bagot (she/her)

  • Satra Ghosh (he/him)

  • Week 11 - February 12, 2021

  • 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

  • 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

  • Kirstie Whitaker (she/her)

  • Julianna Bates (she/her)

  • Week 12 - February 19, 2021

  • 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

  • event

    Analytic Approaches: Reproducible Practices in Machine Learning

    Individual Differences Analyses

    Machine Learning Basics

    Training/Testing Approaches

    Generalization

  • Tara Madhyastha (she/her)

  • Gaël Varoquaux (he/him)

  • Week 13 - February 26, 2021

  • event

    Collaborative Project Proposals

    Overview and Discussion

  • Angie Laird

  • David Kennedy

  • Satra Ghosh

  • JB Poline

  • Project Week - March 8-12, 2021

  • event

    Collaborative Projects