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Promoting Open Science in the University (OSBD 2016)

Jake VanderPlas
December 05, 2016

Promoting Open Science in the University (OSBD 2016)

This talk gives a broad overview of the various initiatives to promote open science at the University of Washington, through the interdisciplinary eScience institute.

Jake VanderPlas

December 05, 2016
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  1. @jakevdp
    Jake VanderPlas
    Promoting Open Science
    in the University
    Jake VanderPlas; @jakevdp
    OSBD, Dec 5, 2016

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  2. @jakevdp
    Jake VanderPlas
    Barriers to Open Science in the University
    Incentives:
    Little incentive for academics to devote time to openness.
    Career paths:
    Relevant skills are more highly valued outside academia.
    Education:
    Undergraduate and graduate curricula lag in data science.
    Interdisciplinarity:
    Siloization of disciplines leads to missed opportunities.

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  3. @jakevdp
    Jake VanderPlas

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  4. @jakevdp
    Jake VanderPlas
    Original Core Faculty Team
    Data Science
    Methodology
    Biological
    Sciences
    Environmental
    Sciences
    Social
    Sciences
    Physical
    Sciences
    Cecilia Aragon
    Human Centered
    Design & Engr.
    Magda
    Balazinska
    CSE
    Emily Fox
    Statistics
    Carlos Guestrin
    CSE
    Bill Howe
    CSE
    Jeff Heer
    CSE
    Ed Lazowska
    CSE
    David Beck
    Chem. Engr.
    Tom Daniel
    Biology
    Bill Noble
    Genome Sciences
    Josh
    Blumenstock
    iSchool
    Mark Ellis
    Geography
    Tyler McCormick
    Sociology, CSSS
    Ginger Armbrust
    Oceanography
    Randy LeVeque
    Applied Math
    Thom
    Richardson
    Statistics, CSSS
    Werner Stuetzle
    Statistics
    Andy Connolly
    Astronomy
    John Vidale
    Earth & Space
    Sciences

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  5. @jakevdp
    Jake VanderPlas
    2014 Kickoff Event:
    137 posters from
    30 UW departments!

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  6. @jakevdp
    Jake VanderPlas

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    Jake VanderPlas

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    Jake VanderPlas

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    Jake VanderPlas

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  10. @jakevdp
    Jake VanderPlas
    eScience Major Support:
    Gordon and Betty Moore Foundation & Alfred P. Sloan Foundation
    - $38 million over 5 years, split between
    UW, NYU, and UC Berkeley
    Washington Research Foundation
    - $9.3 million over 5 years for faculty & postdocs
    - $7.1 million to the closely-aligned
    Institute for Neuroengineering
    University of Washington
    - $550,000/year for staff support
    - $600,000/year for faculty support
    National Science Foundation
    - $2.8 million over 5 years for graduate program
    development and Ph.D. student funding (IGERT)

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  11. @jakevdp
    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    Addressing the Problems
    This level of support has given eScience opportunity to
    explore many aspects of these challenges . . .
    Six interrelated “Working Groups”
    - Career Paths and Alternative Metrics
    - Education and Training
    - Software Tools, Environments, and Support
    - Reproducibility and Open Science
    - Data Science Ethnography
    - Working Spaces and Culture.

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  12. @jakevdp
    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    Incentivizing Open Research Practices
    Rewarding open/reproducible research
    with “Open Science Badges”
    One of the ideas being explored by
    our Reproducibility working group
    https://osf.io/tvyxz/wiki/home/

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  13. @jakevdp
    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    Incentivizing Open Research Practices
    http://joss.theoj.org/
    Code as a first-class
    research product
    (on par with traditional publications)
    - Short papers, review focused on code
    - Submitted & reviewed in the open on GitHub
    - Makes code citeable and indexable by
    traditional tracking services

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  14. @jakevdp
    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    New Academic Career Paths
    Jake VanderPlas
    Director of Research,
    Physical Sciences
    PhD Astronomy
    Ariel Rokem
    Data Scientist
    PhD, Neuroscience
    Valentina Staneva
    Data Scientist
    PhD, Applied Math
    Bernease Herman
    Data Scientist
    BS Stats, Formerly
    Amazon &
    Morgan-Stanley
    Data Scientists (full support)
    Research Scientists (partial support)
    Bryna Hazelton
    Research Scientist
    PhD Astrophysics
    Andrew Gartland
    Research Scientist
    PhD Biostatistics
    Vaughn Iverson
    Research Scientist
    PhD Oceanography
    Anthony Arendt
    Research Scientist
    PhD Geophysics
    Joe Hellerstein
    Sr. Data Science Fellow
    PhD Computer Science
    Formerly Microsoft
    Research, Google, IBM
    Watson
    Dave Beck
    Director of Research,
    Life Sciences
    PhD Medicinal
    Chemistry
    Rob Fatland
    Director Cloud & Data
    Solutions
    PhD Geophysics,
    formerly NASA &
    Microsoft Research
    Britta Fiore-Gartland
    Director of Ethnography
    PhD Communication
    Research Faculty
    Research IT
    Ethnography of
    Data Science

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  15. @jakevdp
    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    New Academic Career Paths
    2-year/3-year
    postdoctoral fellowships
    across a range of
    departments.
    Joint mentorship:
    domain + methodology.
    Focus on high-impact
    researchers who will push
    boundaries in both areas.
    Post-doctoral Fellowships

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    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    New Academic Career Paths
    Example: Mario Juric, Astronomy
    - Data Management Lead for LSST
    - Professor of Astronomy, UW
    - Sr. Fellow at UW eScience
    Working on scalable software infrastructure
    for the LSST project, especially regarding
    the formation, structure, and evolution of the
    Milky Way.
    Faculty position half-funded through
    eScience, half through Astronomy.
    (one of six such appointments across
    campus)
    Interdisciplinary Faculty

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    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    New Academic Programs
    Undergraduate Level:
    “Transcriptable option” for students across
    departments.
    Masters Level:
    Stand-alone evening masters program aimed
    at working professionals.
    PhD Level:
    “Data Science specialty” for graduate students
    across disciplines.

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    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    New Interdisciplinary Courses
    http://uwseds.github.io/

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  19. @jakevdp
    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    IGERT/eScience Graduate Fellows
    Cecilia Noecker
    Genome Sc. & ML
    Matt Murbach
    ChemE & ML Ryan Maas
    CS & Astro
    Alex Tank
    Stats & Allen Inst.
    for Brain Science
    Grace Telford
    Astro & Stats
    Will Gagne-Maynard
    Oceanography & MSR
    eScience Graduate
    Fellows – first cohort

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    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    Extracurricular Training
    - Short trainings, workshops, and bootcamps
    - Annual “Hack Weeks” (e.g. AstroHackWeek,
    GeoHackWeek, NeuroHackWeek)
    - Informal seminar series (e.g. Python in
    Geosciences)
    - International coding sprints (e.g. Python in
    Astronomy)

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    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    Data Science Studio

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    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    Restoring the “Water Cooler”
    full 6th floor

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    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    Office Hours

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  24. @jakevdp
    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    Research Incubator
    Quarter-long, in-Studio projects,
    engagement two days per week
    - Each team: 1 project lead + 1 eScience
    Data Scientist
    - 4-6 concurrent teams: Network effects
    among cohort beyond 1:1 interactions

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  25. @jakevdp
    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    Research Incubator
    Developing a Workflow for Managing Large Hydrologic Spatial Datasets to
    Assist Water Resources Management and Research
    Project Lead: Nicoleta Cristea, Civil and Environmental Engineering
    eScience Liaisons: Anthony Arendt, Rob Fatland
    Methods for Characterizing Human Centromeres
    Project Lead: Siva Kasinathan, UW School of Medicine
    eScience Liaison: Andrew Fiore-Gartland, Bryna Hazelton
    Target Detection for Advanced Environmental Monitoring of Marine Renewable
    Energy
    Project Lead: Emma Cotter, Mechanical Engineering
    eScience Liaison: Bernease Herman
    Improved Stimulation Protocols for Sight Restoration Technologies
    Project Leads: Ione Fine, Geoffrey M. Boynton, UW Psychology
    eScience Liaison: Ariel Rokem
    AralDIF: A Cloud-based Dynamic Information Framework for
    the Aral Sea Basin
    Project Lead: Amanda Tan, Department of Oceanography
    eScience Liaisons: Rob Fatland, Anthony Arendt

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  26. @jakevdp
    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    Data Science for Social Good
    Four teams
    supported each
    summer
    Teams include:
    - Project Leads (1-2 from each org.)
    - DSSG Student Fellows (4 per team)
    - Data Science Leads (1-2 per team)
    - Stakeholders

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  27. @jakevdp
    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    Data Science for Social Good
    - Open Sidewalk Graph for Accessible Trip Planning
    - Assessing Community Well-being through Open Data and Social
    Media
    - Predictors of Permanent Housing for Homeless Families
    - Rerouting Solutions and Expensive Ride Analysis for King County
    Paratransit
    - Mining Online Data for Early Identification of Unsafe Food
    Products
    - Use of ORCA data for improved transit system planning and
    operation
    - Global Open Sidewalks: Creating a shared open data layer and an
    OpenStreetMap data standard for sidewalks
    - CrowdSensing Census: A heterogenous-based tool for estimating
    poverty
    2015
    2016

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  28. @jakevdp
    Jake VanderPlas
    Incentives
    Career Paths
    Education
    Interdisciplinarity
    Data Science for Social Good

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  29. @jakevdp
    Jake VanderPlas

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  30. @jakevdp
    Jake VanderPlas
    Email: [email protected]
    Twitter: @jakevdp
    Github: jakevdp
    Web: http://vanderplas.com/
    Blog: http://jakevdp.github.io
    Thank You!

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