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Enabling Infectious Disease Transmission Research

KRISP News - 2017-07-27

KRISP Researcher and Fulbright scholar Dr. Eduan Wilkinson news from the US: HiPerGator supercomputer 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.'

Taylor Paisie is studying Cholera in Haiti and Fulbright scholar at University of Florida Eduan Wilkinson is analyzing factors generating HIV transmission in South Africa

Taylor Paisie and Eduan Wilkinson sequencing Cholera whole genomes in Prof. Marco Salemi's laboratory, University of Florida.

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.'

Eduan Wilkinson, FulBright Scholar using HiPerGator supercomputer to HIV data from South Africa

Dr. Eduan Wilkinson using HiPerGator supercomputer in Florida to analyze large HIV datasets from South Africa.

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 HiPerGator 2017-2018 brochure.


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