Atlas User Interfaces to Accelerate Data Access

How can we design user interfaces that make data access effective and efficient? Introduces http://vitessce.io!

Transcript

1. Atlas User Interfaces to
   Accelerate Data Access
   @ngehlenborg ∙ http://gehlenborglab.org
   Human Cell Atlas General Meeting 2022
   Nils Gehlenborg, PhD
   Harvard Medical School
   

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2. Background
   Insights from Data Coordination Center projects
   NIH 4D Nucleome Consortium (Phase 1 & 2): 4DN DCIC

   PI: Park; since 2015
   NIH Human BioMolecular Atlas Program (Phase 1 & 2): HuBMAP HIVE

   PIs: Blood, Silverstein, Börner, Bar-Joseph, Gehlenborg; since 2018
   NIH Cellular Senescence Network: SenNet CODCC

   MPIs: Blood, Silverstein, Bar-Joseph; since 2021
   NIH Kidney Precision Medicine Project (Phase 2): KPMP KMAP

   MPIs: Krenzler, Himmelfarb; starting 2022
   

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3. How can we design
   user interfaces that make
   data access effective and efficient?
   

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4. How can we design
   user interfaces that make
   data access effective and efficient?
   

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5. How can we design
   user interfaces that make
   data access effective and efficient?
   deliver insight and minimize effort?
   

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6. How can we design
   user interfaces that make
   data access effective and efficient?
   do science and do it quickly?
   

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7. What are we doing in HuBMAP to
   accelerate data access?
   

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8. Data Knowledge
   HuBMAP Data Portal Human Reference Atlas
   - Data Ingestion and Curation
   - Uniform Processing Pipelines
   - Molecular Data Visualization
   - …
   - Common Coordinate Framework
   - Spatial Information about Samples
   - ASCT+B Tables
   - …
   HuBMAP View of the Cell Atlas World
   

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9. What cell types are where in the body?
   How are they spatially organized?
   What information was used to establish this?
   How reliable is this information?
   Where is the data behind this?
   …
   

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10. Data Knowledge
    HuBMAP Data Portal Human Reference Atlas
    - Data Ingestion and Curation
    
    - Uniform Processing Pipelines
    
    - Molecular Data Visualization
    
    - …
    - Common Coordinate Framework
    
    - Spatial Information about Samples
    
    - ASCT+B Tables
    
    - …
    HuBMAP View of the Cell Atlas World
    

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11. Deliver Insight and Minimize Effort
    Do science and do it quickly
    Deliver Insight
    - Provide data visualization tools
    
    - Enable queries across datasets (work in progress)
    
    - Integrate data analysis tools (work in progress)
    Minimize Effort
    - Maximize browser-based portal capabilities, minimize clicks to action
    

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12. Data Visualization Tools
    Deliver Insight
    

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14. Data Visualization Tools
    Deliver Insight
    

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15. Data Visualization Tools
    Deliver Insight
    

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16. Data Visualization Tools
    Deliver Insight
    

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17. Data Visualization Tools
    Deliver Insight
    

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18. Data Visualization Tools
    Deliver Insight
    

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19. Data Visualization Tools
    Deliver Insight
    MS Keller et al., 2021

    doi:10.31219/osf.io/y8thv
    Vitessce

    http://vitessce.io
    

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20. Data Visualization Tools
    Single Dataset Visualization
    Deliver Insight
    

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21. Data Visualization Tools
    Single Dataset Visualization

    Clustering, segmentation, cell type assignments, etc. for single assay for single
    sample but multiple analysis outputs
    Deliver Insight
    

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22. Data Visualization Tools
    Single Dataset Visualization

    Clustering, segmentation, cell type assignments, etc. for single assay for single
    sample but multiple analysis outputs
    Multi Dataset Visualization

    Multiple samples of single assay, multiple assays for single sample, etc.
    Altas Visualization

    UIs to test hypotheses, build models, and make predictions
    Deliver Insight
    

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23. Queries Across Datasets
    Deliver Insight
    TS Liaw & N Gehlenborg, 2022

    Proceedings of the Design
    Society, 2, 221-230.
    doi:10.1017/pds.2022.24
    

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24. Queries Across Datasets
    Deliver Insight
    

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25. Queries Across Datasets
    Deliver Insight
    

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26. Queries Across Datasets
    Deliver Insight
    

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27. Queries Across Datasets
    Deliver Insight
    

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28. Queries Across Datasets
    Deliver Insight
    

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29. Queries Across Datasets
    Deliver Insight
    

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30. Queries Across Datasets
    Deliver Insight
    

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31. Queries Across Datasets
    Deliver Insight
    

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32. Queries Across Datasets
    Deliver Insight
    

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33. Queries Across Datasets
    Deliver Insight
    

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34. Queries Across Datasets
    Deliver Insight
    

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35. Queries Across Datasets
    Deliver Insight
    

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36. Data Analysis Tools
    Deliver Insight
    Jupyter Notebooks and workspaces in HuBMAP Data Portal
    Focus on computational analysts
    - Support cutting edge work
    - Extensible solution that enables community contributions
    - Combine HuBMAP data with user data
    - Use HuBMAP infrastructure for computation and storage
    - Enable pick up where portal UI functionality leaves off
    

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37. Data Analysis Tools
    Deliver Insight
    Today
    Create and download Jupyter
    Notebooks to execute locally
    or in Google Colab
    

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38. Data Analysis Tools
    Deliver Insight
    Today
    Create and download Jupyter
    Notebooks to execute locally
    or in Google Colab
    

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39. Data Analysis Tools
    Deliver Insight
    Today
    Create and download Jupyter
    Notebooks to execute locally
    or in Google Colab
    

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40. Data Analysis Tools
    Deliver Insight
    Today
    Create and download Jupyter
    Notebooks to execute locally
    or in Google Colab
    

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44. Data Analysis Tools
    Deliver Insight
    Today
    Create and download Jupyter
    Notebooks to execute locally
    or in Google Colab
    

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45. Data Analysis Tools
    Deliver Insight
    Today
    Create and download Jupyter
    Notebooks to execute locally
    or in Google Colab
    

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46. Data Analysis Tools
    Deliver Insight
    Today
    Create and download Jupyter
    Notebooks to execute locally
    or in Google Colab
    Near Future
    Create and execute Jupyter
    Notebooks in Jupyter Lab in
    HuBMAP infrastructure
    

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47. Data Analysis Tools
    Deliver Insight
    Today
    Create and download Jupyter
    Notebooks to execute locally
    or in Google Colab
    Near Future
    Create and execute Jupyter
    Notebooks in Jupyter Lab in
    HuBMAP infrastructure
    

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48. Deliver Insight and Minimize Effort
    Do science and do it quickly
    Deliver Insight
    - Provide data visualization tools
    
    - Enable queries across datasets (work in progress)
    
    - Integrate data analysis tools (work in progress)
    
    Minimize Effort
    - Maximize browser-based portal capabilities, minimize clicks to action
    

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49. Deliver Insight and Minimize Effort
    Do science and do it quickly
    Deliver Insight
    - Provide data visualization tools
    
    - Enable queries across datasets (work in progress)
    
    - Integrate data analysis tools (work in progress)
    
    Minimize Effort
    - Maximize browser-based portal capabilities, minimize clicks to action
    Deliver Insight
    - Provide data visualization tools
    
    - Enable queries across datasets (work in progress)
    
    - Integrate data analysis tools (work in progress)
    
    Minimize Effort
    - Maximize browser-based portal capabilities, minimize clicks to action
    
    - Optimize task-based creation of data downloads (work in progress)
    

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50. Task-Based Creation of Data Downloads
    Minimize Effort
    Interactive Mockup
    

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52. Task-Based Creation of Data Downloads
    Minimize Effort
    Interactive Mockup
    

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53. What are some takeaways of
    this work?
    

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54. Deliver Insight and Minimize Effort
    Contributor Interdependencies
    UI designers and developers are high value customers of any atlas data
    management and analysis infrastructure developed.
    UI designers and developers must deliver use cases that drive infrastructure
    development.
    UI
    Infra-
    structure
    User interfaces must not be an afterthought and coordination is critical!
    

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55. Deliver Insight and Minimize Effort
    Contributor Interdependencies
    UI
    Infra-
    structure
    Data
    Analysis
    Tools
    Data
    Vis
    Tools
    UI designers and developers are high value customers of any atlas data
    management and analysis infrastructure developed.
    UI designers and developers must deliver use cases that drive infrastructure
    development.
    User interfaces must not be an afterthought and coordination is critical!
    

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56. Deliver Insight and Minimize Effort
    Contributor Interdependencies
    UI
    Infra-
    structure
    Data
    Analysis
    Tools
    Data
    Vis
    Tools
    

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57. Deliver Insight and Minimize Effort
    Charting a Roadmap for Atlas User Interfaces
    Tier 1: View Data

    UIs to understand what questions can be asked
    Tier 2: Explore Data

    UIs to generate hypotheses
    Tier 3: Analyze Data

    UIs to test hypotheses, build models, and make predictions
    Cell atlas UIs are typically somewhere between Tier 1 and Tier 2 today.
    

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58. Challenges
    The Wild West of Cell Atlases
    Sociological
    - Diverse user audiences with different goals: user research is hard
    
    - Diverse teams contribute expertise to atlas building: coordination is hard
    Technological
    - Diverse data schemas, formats, and tools in use: integration is hard
    Scientific
    - Diverse analysis questions: science is not always easy
    

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59. Opportunities
    Calling up the Community
    Collaborate on shared challenges in atlas user interface development
    - Share use cases, personas, and other user research artifacts
    - Agree on common data schemas and formats
    Consider APIs user interfaces
    - Many analysts will interact with data primarily through APIs and serving
    their needs for efficient data access will accelerate science
    What else can we do?
    Postdoctoral Fellow
    (Senior) UI/UX Developer

    (Senior) Software Developer
    Apply for a
    position in
    my lab as a
    Email nils@hms.harvard.edu if interested!
    

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