Atlas User Interfaces to Accelerate Data Access @ngehlenborg ∙ http://gehlenborglab.org Human Cell Atlas General Meeting 2022 Nils Gehlenborg, PhD Harvard Medical School
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
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? …
Data Visualization Tools Single Dataset Visualization Clustering, segmentation, cell type assignments, etc. for single assay for single sample but multiple analysis outputs Deliver Insight
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
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
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
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
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!
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!
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.
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
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 [email protected] if interested!