The Biomedical Applications Group at the PSC pursues leading edge research in high performance computing in the biomedical sciences and fosters exchange between PSC expertise in computational science and biomedical researchers nationwide. The Biomedical Applications Group also engages in outreach activities at both the local and national level.
Scientists in the Biomedical Applications Group develop computational methods and tools and conduct research on biomedical systems at the cell and tissue level with a focus on neural systems such as the brain and the central nervous system. Our flagship outreach effort is a MARC funded program aimed at developing bioinformatics programs and academic courses at MARC institutions leveraging our expertise in bioinformatics.
Projects and Collaborations
- The National Center for Multiscale Modeling of Biomedical Systems (MMBioS)
The Biomedical Applications Group is a member of MMBioS, which develops tools to advance and facilitate cutting-edge research at the interface between high performance computing technology and the life sciences. The overarching goal of MMBioS is the predictive multi-scale modeling of the spatiotemporal organization and evolution of neurosignaling systems and events. As collaborators in MMBioS we contribute to the development of a variety of computational software and methods for the biomedical community:
- New methods and tools for large scale image registration and analysis such as AlignTK
- MCell and CellBlender, software tools for developing and simulating spatially resolved cell models using particle based Monte Carlo algorithms
Minority Access to Research Careers (MARC)
The MARC program developed bioinformatics programs and academic courses at MARC institutions, leveraging our group’s expertise in bioinformatics. In collaboration with minority serving partner institutions, we created a special technology transfer and outreach program to help increase minority participation in biomedical research.
The primary aim of the project was to increase minority participation in biomedical research through a broadly-based program synergistically formulated to assist minority serving institutions establishing bioinformatics programs ranging in size from a single course to a degree program. Our program was unique in being both situated external to a Minority Serving Institution (MSI) and in its focus on building and sustaining curricula and research programs at partner MSIs.
The collaborative effort assisted scientists at MSI’s through four main activities:
- Bioinformatics Summer Institute: An annual intensive two-week Summer Institute in Bioinformatics at the Pittsburgh Supercomputing Center open to faculty and graduate students at minority serving institutions. The session focuses on preparing faculty to incorporate bioinformatics into their teaching and research.
- Bioinformatics Summer Internship: An annual mentored research program at the Pittsburgh Supercomputing Center for students that have completed bioinformatics training on their local campus to receive guidance on a self-selected research problem involving bioinformatics and next generation sequencing.
- Bioinformatics Online Learning Environment: The development of interdisciplinary training modules and related course materials for the fields of Biology, Computational Science and Mathematics.
- Curriculum Improvement: A partnership to improve the curriculum at Minority Serving Institutions by providing aide and assistance to MSI’s establishing bioinformatics programs and adding bioinformatics components into coursework.
MCell and CellBlender development is supported by the NIGMS-funded (P41GM103712) Multiscale Modeling of Biological Systems (MMBioS) Center established by the Department of Computational and Systems Biology at the University of Pittsburgh, the Pittsburgh Supercomputing Center, the Computational Neurobiology Laboratory at the Salk Institute and Carnegie Mellon University.
Left: MCell simulation of synaptic vesicle release at the frog neuromuscular junction. It was generated via CellBlender.
Bridges-2, PSC's newest supercomputer, funded by a $10-million grant from the National Science Foundation, is up and running!