DS 6559: Biomedical Cloud Computing Seminar (SIS code: 19817; 1 credit hour)
Meets: Tuesdays, 3:30 to 4:45pm
Room: New Cabell Hall 338
Instructor: Tim Clark
Please seek instructor permission through SIS only.


Biomedical computing is currently being driven by combined laboratory and data science paradigms such as genotype/phenotype analysis for Precision Medicine. Rapid declines at > 5X the Moore’s Law rate in the cost of molecular sequencing have led to new insights based on enormous volumes of data.  Many large-scale analytics are being migrated from bespoke architectures to cloud platforms, with several unique demands on these environments.

NIH has recognized this need and initial work has begun on a cloud-of-clouds / cloud-agnostic data analytics platform for the major NIH funded genotype/phenotype and model organism datasets and associated analysis platforms. Cloud computing is rapidly increasing its footprint in the life sciences R&D industry in conjunction with advanced data analytics.

This seminar will discuss theory and applications of biomedical cloud computing.  We will be reading and discussing important literature in the field, with guest presentations by leading experts. Planned topics include NIH's cloud strategy; major computational platforms; reproducibility; workflow abstraction & interoperability; FAIR data and PHI; Identifiers, ontologies and metadata; authentication & authorization; and differential privacy.

The seminar will coordinate with Data Science Institute seminars given by leading experts, and will provide class participants the opportunity to interact with them in small-group discussions. 

Among the planned visiting experts for this class will be:

  • Stan Ahalt, Ph.D. - Director of the Renaissance Computing Institute (RENCI); Professor of Computer Science at UNC Chapel Hill; Director, Biomedical Informatics Service of the North Carolina Translational and Clinical Sciences Institute; and Dr. Steering Committee Head for the National Consortium for Data Science.
  • Vivien Bonazzi, Ph.D. - Senior Advisor for Data Science at National Institutes of Health (NIH). Program Leader for the NIH Data Commons; formerly Program Director in Computational Biology and Bioinformatics at the National Human Genome Research Institute (NHGRI).
  • Carl Kesselman, Ph.D. - Dean's Professor of Industrial and Systems Engineering and Professor of Industrial and Systems Engineering, Computer Science, and Preventive Medicine; Information Sciences Institute Fellow; and Director, Informatics Division, Information Sciences Institute, University of Southern California.
  • Maryann Martone, Ph.D. - Professor of Neuroscience, University of California San Diego, Principal Investigator of the Neuroscience Information Framework project, a US national project to establish a uniform resource description framework for neuroscience, and the NIH/NIDDK Information Network.

The course will be taught by Timothy Clark, Ph.D., Associate Professor of Public Health Sciences and Associate Research Director for Neuroinformatics at the UVA Data Science Institute. Dr. Clark has 28 years of experience in biomedical data science applications, at the NIH, in the biotech industry, and in academia.