Kjiersten Fagnan on the JGI’s Genome Citation Service That Tracks Genomes Across Research
March 28, 2023
Kjiersten Fagnan is an applied mathematician enamored of biology’s messy datasets. Now, as chief informatics officer at the Department of Energy Joint Genome Institute (JGI), located at Lawrence Berkeley National Laboratory, she finds bioinformatics' computational and data challenges very different from applied math or partial differential equations. Fagnan is the newest guest on the Trends from the Trenches podcast, speaking with host Stan Gloss of BioTeam about JGI’s Genome Citation Service, a new offering that connects the broader community with the organization’s massive data resources and infrastructure.
Fagnan talks about the centralized data management system JGI deployed 10 years ago in response to exponential data growth and the questions it forced the organization to ask about the quality and utility of the data it produces and manages. “One of our goals is to see… the impact of the data generated amplified through reuse of the data,” she says. Fagnan also discusses JGI’s strategic collaboration with NamesforLife to create a unique global identifier to help researchers link work on the same microbe even as naming conventions change over time. Additionally, she talks about why perfection is the enemy of reality and JGI’s immediate and long-term plans for the Genome Citation Service.
Kjiersten Fagnan, PhD, MBA, Chief Informatics Officer, U.S. Department of Energy Joint Genome Institute
Kjiersten Fagnan began working with JGI in 2012 as a NERSC bioinformatics computing consultant after completing a petascale postdoctoral fellowship at NERSC and LBL’s Computational Research Division. As a postdoc, her research focused on stable and accurate computational methods for reacting subsurface flows and evolved into scalable methods for scientific data analysis. In 2014, Dr. Fagnan became the JGI-NERSC Engagement Lead, focusing on adapting JGI workloads to run on supercomputing hardware and working closely with staff to understand the data-intensive nature of JGI workloads.
Dr. Fagnan was appointed CIO of JGI in 2016 and, in 2018, was hired as JGI’s Data Science and Informatics department head. In 2018, Dr. Fagnan was part of the Gordon Bell prize-winning team at the Supercomputing conference, SC’18, led by researchers at Oak Ridge National Laboratory. In addition, Dr. Fagnan has been the Distinguished Speaker at IBM Research in Almaden, where she presented work related to distributed data and workflow management. Dr. Fagnan is also a co-PI for the National Microbiome Data Collaborative, where she leads infrastructure and user-centered design efforts.
Host Bio
Stan Gloss
As co-founder and Evangelist of BioTeam, Stan Gloss has been working to tell the stories of the intersection of science, data and technology since 2002. Gloss joined with fellow founding partners Bill Van Etten and Chris Dagdigian to form BioTeam in 2002 following his tenure in business development with AVAKI Corporation, a pioneer in global grid software solutions, and Blackstone Computing, a computing and IT consulting company for scientists, Gloss led the sales initiative that launched the company in the life sciences market. Gloss earned his MS at the University of Buffalo and was a department chairman and faculty member at Quinnipiac University.
A life science IT consulting firm at the intersection of science, data, and technology, BioTeam builds innovative scientific data ecosystems that close the gap between what scientists want to do with data—and what they can do. Learn more at www.bioteam.net.