November Data Sharing and Reuse Seminar

Karthik Gangavarapu, Ph.D. will present "Advancing Outbreak Surveillance: From data integration to actionable insights" on November 8, 2024, from 12:00 p.m.–1:00p.m. ET.

About the Seminar

In response to the emergence of SARS-CoV-2 variants of concern, the global scientific community through unprecedented effort has sequenced and shared over 17 million genomes as of October 2024. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. More recently, wastewater sequencing has emerged as an alternative to sequencing clinical samples for cost-efficient genomic surveillance. We developed outbreak.info as a platform that uses publicly available clinical and wastewater-based genomic data to provide insights for researchers, public health officials, and the general public. We built scalable data pipelines to ingest heterogeneous sources of SARS-CoV-2 variant data and used the BioThings SDK to develop server infrastructure for widespread data dissemination via a high-performance API. Using this API, we provide interpretable visualizations through our web application and programmatic access to the processed data through our Python and R packages. Outbreak.info can be used for genomic surveillance and as a hypothesis-generation tool to understand the outbreaks at varying geographic and temporal scales.

About the Speaker

Karthik Gangavarapu is an Institute Investigator at Scripps Research, specializing in computational biology with an emphasis on infectious disease research. He has led large-scale collaborative projects that apply phylogenetic and phylodynamic methods to understand the transmission dynamics of rapidly evolving viruses, including Zika and SARS-CoV-2. He has developed widely used software for genomic epidemiology such as iVar and outbreak.info. He has also made important contributions to BEAGLE, a library that accelerates numerical calculations for statistical phylogenetics, used by sophisticated phylogenetics software such as BEAST.

About the Seminar Series

The seminar is open to the public and registration is required each month. Individuals who need interpreting services and/or other reasonable accommodations to participate in this event should contact Allison Hurst at 301-670-4990. Requests should be made at least five days in advance of the event.

The National Institutes of Health (NIH) Office of Data Science Strategy hosts this seminar series to highlight exemplars of data sharing and reuse on the second Friday of each month at noon ET. The monthly series highlights researchers who have taken existing data and found clever ways to reuse the data or generate new findings. A different NIH institute or center will also share its data science activities each month.