NIH to Fund Mapping System for Human Tissues
PSC and Pitt to Build Computing Infrastructure for Molecular Atlas; Will Allow Biologists to Explore the Human Body in Cellular Detail
Sept. 26, 2018
A collaboration of Pittsburgh institutions will play a key role in enabling biologists to explore the human body in exquisite detail. By flipping among digital maps of different features revealed by modern molecular biology and imaging techniques, scientists will be able to chart a path through human health and disease using massive datasets that would otherwise be too complex to navigate. The Pittsburgh Supercomputing Center (PSC), a program of Carnegie Mellon University and the University of Pittsburgh, and the Department of Biomedical Informatics (DBMI) at Pitt’s School of Medicine are undertaking the work as part of $54 million in funding by the National Institutes of Health (NIH) for the Human BioMolecular Atlas Program (HuBMAP).
NIH will support PSC and Pitt DBMI with an initial $598,000 to integrate, host, and provide secure access to high-resolution, 3D biomolecular tissue data along with tools and services for searching, analyzing and visualizing these as maps. HuBMAP will help scientists gain insight into health, disease and aging. Initial funding covers a nine-month setup phase of what is expected to be a four-year program scaling up to full production, followed by an additional four-year production phase. Future developments of the project will involve additional funding for PSC and DBMI.
In developing the infrastructure to support HuBMAP, PSC and Pitt DBMI will work together with a number of other teams as part of the HuBMAP Integration, Visualization, and Engagement (HIVE) Collaboratory. These other teams will focus on engaging with stakeholders, creating the tools and services that will be hosted and made available on the HIVE open data platform, and developing a common framework for orienting the various tissue maps in the spatial context of the human body. The ultimate aim of the NIH-funded HuBMAP will be to offer scientists an interactive atlas of multilayered maps that provide complementary views of the human body at the cellular level, similar to how Geographic Information Systems used by businesses and public safety and government planning officials layer multiple data sets and views over the same physical space.
“The Human Biomolecular Atlas, through the hybrid computational infrastructure we’re creating to support it, will open the door to understanding our bodies at the most fundamental level, enabling insights into health, disease, and aging,” says Nick Nystrom, principal investigator for the Infrastructure Component of HIVE and PSC’s Interim Director. “This is an incredible opportunity that will unlock access to data, allowing talented researchers nationwide to generate new discoveries.”
The organization, specialization and cooperation of different cells within the tissues of a healthy human body have a profound impact on tissue growth, function and aging. These factors can also indicate the emergence of disease. Yet understanding important high-resolution features of cells in tissues remains a challenge. Recently developed technologies, including many supported through NIH programs, allow researchers to study and map the organization of all cells within tissues or organs across the human body. HuBMAP will provide a framework that ultimately is expected to support complete mapping of the entire body and making the data available to the research community.
“We’re pleased to further deepen our close relationship with PSC via this national cyber-infrastructure project,” says Jonathan C. Silverstein, Principal Investigator, Pitt DBMI. “We are especially excited to work with HuBMAP and HIVE collaborators, including NIH, to build HuBMAP’s secure and highly flexible research data portal and computational environment.”
The HIVE Infrastructure Component will need to archive various types of massive high-resolution imaging, genome sequencing and other data and make these data available to a diverse array of stakeholders worldwide. These data will also need to be made available alongside other major scientific data resources available at various institutions and in public clouds. In response to these needs, PSC and Pitt DBMI are planning to develop a flexible and scalable hybrid cloud infrastructure that will combine the strengths of high performance computing (HPC) and public clouds, providing stakeholders with uniquely-effective storage and co-located compute resources for depositing, accessing, querying, searching, analyzing and visualizing HuBMAP data independently or in conjunction with other data sets.
“We’re looking forward to engaging with our collaborators in HuBMAP and the HIVE, along with the scientific community, to develop a flexible, high-value resource,” says Phil Blood, PSC’s Senior Director of Computational Biology. “We intend to enable the fulfillment of HuBMAP’s vision to transform our understanding of tissue organization and function.”
The HuBMAP is funded by the NIH Common Fund. It is managed by a trans-NIH working group and led by staff from the 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.
Read a press release from Carnegie Mellon School of Computer Science about their HuBMAP grant.