Understanding the brain with open data and open source software

Ariel Rokem, University of Washington eScience Institute

Slides available at: https://arokem.github.io/2019-05-07-NWDSS/

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Data-driven research

Data science training

Building a community of practice: open, reproducible, rigorous and ethical


Normal behavior is supported by brain connectivity

Analysis
Interpretation

Observatory-driven science

Sloan Digital Sky Survey
Image from Sloan Digital Sky Survey By Donald Pelletier [CC BY-SA 4.0 ], from Wikimedia Commons

The era of "brain observatories"

    Allen Institute for Brain Science

    Human Connectome Project (HCP),
    (2012-2015), N = ~1,200

    Healthy Brain Network (HBN),
    (2016--),   N = ~10,000

    Adolescent Brain Cognitive Development,
    (2016--),   N = ~10,000

    UK Biobank,
    (2018--),   N = ~500,000

Opportunities

New data sets will enable important new discoveries

Data-driven discovery

Challenges

Data arriving at unprecedented volume, variety and velocity

=> Need new tools and approaches to process, analyze and interpret

=> New sociotechnical structures sustain data science approaches

Open source software is a necessary complement to brain observatories

Open-source software for science

Python: an ecosystem for scientific computing

Free and open source

High-level interpreted language

Very wide adoption

Python in Astronomy (ADS)

NIPY: Neuroimaging in Python

A community of practice

Many different projects and individuals

Focus on commons

Shared resources that are maintained collectively and available to anyone

Diffusion MRI

Rokem et al. (2017), Journal of Vision
Rokem et al. (2015), PLoS One

Diffusion MRI

Isotropic diffusion
Rokem et al. (2017), Journal of Vision
Rokem et al. (2015), PLoS One

Diffusion MRI

Anisotropic diffusion
Rokem et al. (2017), Journal of Vision
Rokem et al. (2015), PLoS One

Diffusion statistics

Mean diffusivity
Fractional anisotropy
Principal diffusion direction
Rokem et al. (2017), Journal of Vision
Rokem et al. (2015), PLoS One

Amyotrophic Lateral Sclerosis (ALS)

Open source diffusion MRI


Comprehensive
Thoroughly tested
Well-documented


Eleftherios Garyfallidis (Indiana University)

Open to users

Open to contributors

Distributed collaboration

Challenges for scientific software

Sustainability

Quality assurance


Rigorously evaluate open source software

Provide a canonical citation for software that meets these standards

Sharing and exploring large datasets on the web


Jason Yeatman

Adam
Richie-Halford

Josh Smith

Anisha
Keshavan

AFQ-Browser

Automatic data sharing

Further exploration

How do I get involved?

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Neuroinformatics Special Interest Group

Discussions

Tutorials

Code reviews

...

Neurohackademy


A Summer Institute in Neuroscience and Data Science (=> 2021)

Contact information

http://arokem.org
arokem@gmail.com
@arokem
github.com/arokem