Atlas User Interfaces to Accelerate Data Access

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

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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
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
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
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!