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Atlas User Interfaces to Accelerate Data Access

Atlas User Interfaces to Accelerate Data Access

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

Nils Gehlenborg

June 28, 2022
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  1. Atlas User Interfaces to Accelerate Data Access @ngehlenborg ∙ http://gehlenborglab.org

    Human Cell Atlas General Meeting 2022 Nils Gehlenborg, PhD Harvard Medical School
  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
  3. How can we design user interfaces that make data access

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

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

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

    effective and efficient? do science and do it quickly?
  7. What are we doing in HuBMAP to accelerate data access?

  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
  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? …
  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
  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
  12. Data Visualization Tools Deliver Insight

  13. None
  14. Data Visualization Tools Deliver Insight

  15. Data Visualization Tools Deliver Insight

  16. Data Visualization Tools Deliver Insight

  17. Data Visualization Tools Deliver Insight

  18. Data Visualization Tools Deliver Insight

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


    doi:10.31219/osf.io/y8thv Vitessce
 http://vitessce.io
  20. Data Visualization Tools Single Dataset Visualization Deliver Insight

  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
  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
  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
  24. Queries Across Datasets Deliver Insight

  25. Queries Across Datasets Deliver Insight

  26. Queries Across Datasets Deliver Insight

  27. Queries Across Datasets Deliver Insight

  28. Queries Across Datasets Deliver Insight

  29. Queries Across Datasets Deliver Insight

  30. Queries Across Datasets Deliver Insight

  31. Queries Across Datasets Deliver Insight

  32. Queries Across Datasets Deliver Insight

  33. Queries Across Datasets Deliver Insight

  34. Queries Across Datasets Deliver Insight

  35. Queries Across Datasets Deliver Insight

  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
  37. Data Analysis Tools Deliver Insight Today Create and download Jupyter

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

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

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

    Notebooks to execute locally or in Google Colab
  41. None
  42. None
  43. None
  44. Data Analysis Tools Deliver Insight Today Create and download Jupyter

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

    Notebooks to execute locally or in Google Colab
  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
  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
  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
  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)
  50. Task-Based Creation of Data Downloads Minimize Effort Interactive Mockup

  51. None
  52. Task-Based Creation of Data Downloads Minimize Effort Interactive Mockup

  53. What are some takeaways of this work?

  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!
  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!
  56. Deliver Insight and Minimize Effort Contributor Interdependencies UI Infra- structure

    Data Analysis Tools Data Vis Tools
  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.
  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
  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!