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Enabling Infectious Disease Transmission Research

PHOTO: Ph.D. candidate Taylor Paisie at her desk in UF's Emerging Pathogens Institute.

HiPerGator is enabling infectious disease transmission research in UF’s Emerging Pathogens Institute. Among the research underway at the EPI are two studies by graduate students: Taylor Paisie is studying Cholera in Haiti and Fulbright scholar Eduan Wilkinson is analyzing factors generating HIV transmission in South Africa. Paisie, originally from Ohio, says HiPerGator is integral to her work:

“I look at disease patterns of the past in order to understand the global clinical and epidemiological patterns of the disease,” said Paisie. “I can’t analyze samples without HiPerGator. Its power allows us to sequence whole genome samples and continue working while the data is being analyzed on our computers.”

In addition to researching Cholera, the Salemi Lab also includes Eduan Wilkinson, a postdoc studying HIV transmission in his native South Africa. Wilkinson is able to run 16,000 very large sequences on HiPerGator in one week, thanks to UFIT’s ability to optimize job scripts and provide exceptional software.

“The methods that we use to look at viral strains are extremely powerful,” said Wilkinson. “By analyzing sequences we can construct relationships between pathogens so we can see what’s driving the transmission. We can also use these methods to evaluate how public health interventions are impacting the epidemic.”

Faculty and affiliated staff and students interested in utilizing HiPerGator may attend a Research Computing walk-in session, held each Wednesday at the Informatics Institute. A list of consulting and training services provided by Research Computing is available in the 2017-2018 brochure.