Katy Börner, distinguished professor of engineering and information science at the Luddy School of Informatics, Computing, and Engineering, has received a $1.5 million award from the National Institutes of Health to continue her research with the Human BioMolecular Atlas Program Consortium, an NIH effort to map the human body at a single-cell resolution.
Börner, who also is the director of IU’s Cyberinfrastructure for Network Science Center, has been part of the consortium since its inception. The award will fund research in machine learning and data visualization and significantly scale up existing user interfaces for human tissue data registration and exploration. In addition, the award will expand research by Luddy Associate Professor Paul Macklin on PhysiCell, a large-scale, 3D simulation designed to model how cells grow, divide, interact, and die.
“The construction of a computable Human Reference Atlas requires close collaboration of experts from engineering and science departments, different institutions and countries,” Börner said. “HuBMAP is proud to partner with 16 international consortia, and we look forward to expanding the number and diversity of tissue data used to understand healthy aging in women and men.”
HuBMAP’s tools and maps are openly available for research to accelerate understanding of the relationships between cell and tissue organization and function, as well as human health. Visitors can find the data and the evolving human reference atlas at portal.hubmapconsortium.org.
HuBMAP is a consortium of 18 diverse collaborative research teams across the United States and Europe, including researchers from the Luddy School of Informatics, Computing, and Engineering. HuBMAP values secure, open sharing and collaboration with other consortia and the wider research community. The consortium is managed by a trans-National Institutes of Health (NIH) working group of staff from the NIH Common Fund; National Heart, Lung, and Blood Institute; National Institute of Biomedical Imaging and Bioengineering; and the National Institute of Diabetes and Digestive and Kidney Diseases.
The HuBMAP Consortium recently announced its latest data portal update, complete with new data, interactive visualization tools, and additional organs as researchers expand their effort to build a cellular atlas of the human body. HuBMAP’s tools and maps are openly available to the public and seek to accelerate understanding of human cells and tissues. Since the inaugural data release last September, Consortium collaborators have been expanding the information available to the research community via the Data Portal, and there are now a total of 11 organ types from 58 donors, totaling 494 samples and 512 datasets available. In addition to new data, new tools and functionality make the portal easily searchable, with innovative mapping and visualization features.
“Technologies developed by HuBMAP researchers provide data that uniquely span a wide range of spatial scales, from single cells to whole organs, and molecular classes including metabolites, lipids, proteins, and nucleic acids,” said HuBMAP Steering Committee co-chair and PI of the Tissue Mapping Center at Vanderbilt University Jeff Spraggins. “These data are enabling new possibilities for integration and analysis that will provide a deeper understanding of the molecular drivers of health and disease.”
As part of the Common Coordinate Framework (CCF), users can now browse organ locations through the Exploration User Interface (CCF-EUI) or spatially register a tissue sample with the Registration User Interface (CCF-RUI). The ASCT+B (anatomical structures, cell types, and biomarker) Reporter, another feature in development by the Consortium and its partners, is a state-of-the-art visualization tool presenting relationships between various anatomical structures and cell types.
Two more tools complete the latest round of updates, though some researchers have been taking advantage of these innovations for some time now. The Azimuth web application inputs a counts matrix of gene expression in single cells, and performs normalization, visualization, cell annotation, and differential expression (biomarker discovery). The Vitessce visual integration tool for exploration of spatial single cell experiments supports diverse spatial and non-spatial omics and imaging data types and integrates with a wide range of analysis workflows. Among many other new features, Vitessce now offers support for visualizing 3D volumes via raycasting and direct visualization of annData objects. Outside the data portal, Vitessce can easily be deployed in other environments, for example, Jupyter Notebooks or standalone websites. There are some datasets on the portal that highlight the capabilities of Vitessce, such as this CODEX dataset and this Lightsheet microscopy dataset. In collaboration with the NYGC Mapping Component, Vitessce visualizations for all Azimuth reference datasets have been made available as well.
The Consortium and its members will continue to enhance the data portal to ensure its accessibility and provide innovative tools for researchers within and beyond the HuBMAP community, as the available data continues to evolve. Future releases will include expanded tools, new organs, and additional datasets.
The availability of new HuBMAP tools and data was made possible by the collaborative efforts across HuBMAP Consortium including:
- Common Coordinate Framework, Exploration User Interface, and Registration User Interface development by HuBMAP HIVE Indiana University Mapping Component, led by Katy Börner.
- Azimuth creation and development by HuBMAP HIVE New York Genome Center Mapping Component led by Raul Satija
- Vitesse creation and development by HuBMAP HIVE Harvard Medical School Tools Component led by Nils Gehlenborg
- Data processing and pipeline development by HuBMAP HIVE Carnegie Mellon University Tools Component, led by Ziv Bar-Joseph
- Data ingest, data management, infrastructure, and project coordination and communication provided by HuBMAP HIVE Pittsburgh Supercomputing Center/University of Pittsburgh Infrastructure Component, led by Phil Blood and Jonathan Silverstein
- HuBMAP data is provided by Tissue Mapping Centers, Transformative Technology Development, and Rapid Technology Implementation teams. Learn more about these teams and the research specialties.