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NIAID/ACE - OSG collaboration leads to a successful virtual training session

Hannah Cheren
May 2, 2022

The U.S. National Institute of Allergy and Infectious Diseases (NIAID) and the African Centers for Excellence in Bioinformatics and Data-Intensive Science (ACE) partnered with the OSG Consortium to host a virtual high throughput computing training session for graduate students from Makerere University and the University Of Sciences, Techniques, and Technologies of Bamako (USTTB).

Map of Africa with Mali and Uganda Highlighted
Map of Africa; Mali and Uganda are highlighted where their respective flags point. Image credit: © 2010 Roland Urbanek. Flags are edited in and overlayed on the image. on Flickr.

Five thousand miles and seven time zones were no obstacle for forty-one dedicated researchers from Uganda and Mali participating in their first high throughput computing training session using the OSG high throughput computing services. On February 15, bioinformatics graduate students and faculty members from Makerere University in Uganda and the University Of Sciences, Techniques, and Technologies of Bamako in Mali engaged in a customized training session over Zoom led by Christina Koch, an OSG Research Computing Facilitator.

Dr. Mariam Quiñones, Dr. Darrell E. Hurt, Mr. Chris Whalen, and the ACE Global Operations Team within NIAID’s Office of Cyber Infrastructure and Computational Biology (OCICB) spearheaded this cross-continent collaboration between the OSG Consortium, the NIAID, and ACE, which supports bioinformatics training for graduate students and other researchers at Makerere University and USTTB. The ACE Global Operations Team works closely with the ACE Center Directors and instructors to identify gaps and provide supplemental hands-on training to the students. The NIAID ACE Global Operations Team recognized a need for additional computing resources to train graduate students and knew precisely where to turn.

Envisioning the power of a partnership between the OSG Consortium and the ACE community, Quiñones approached OSG Research Facilitation Lead Lauren Michael with the idea of a high throughput computing training session for the students and faculty within the ACE program.

NIAID’s previous success with running computational work on the Open Science Pool (OSPool) led Quiñones to think the impact might even reach beyond students trained by the ACE program. Predicting the spread of this adoption of OSG services, Quiñones remarks, “[w]e hope some of the faculty and associated staff actively generating data from data-intense research projects will begin to use the OSG services.”

In preparation for the training, OSG’s Research Facilitation Team planned to go beyond the usual introduction to the OSPool. This time around, the team designed a new tutorial that incorporated the BWA software, a tool commonly used in bioinformatics and familiar to the students. Koch, who led the training session, notes that the “goal of using the tutorial was to give the students hands-on experience using software that would be relevant to the kind of work they are already doing for their research.”

Building off Koch’s thoughts, Michael explains: “Given the shared bioinformatics needs of the students, we wanted to make sure the content went beyond our general New User Training format by encouraging conversation among training participants and using examples they’d connect with.” Reflecting, she adds: “It seemed to pay off, given the level of engagement.”

Through numerous public-private partnerships with the NIAID, African institutions, governments, and private-sector companies, ACE aims to enhance access to computational capabilities and infrastructure and provide training in data science and bioinformatics. This access will empower researchers and students to accelerate biomedical research and drive discoveries that could impact the treatment, prevention, and diagnosis of diseases in Africa and across the globe.

And while high throughput computing and the OSPool can play an essential role in advancing the bioinformatics behind some of these efforts, Michael emphasizes that the benefits are undoubtedly mutual for the OSG consortium:

“By working with ACE, engaging with participants, and adding documented bioinformatics examples to our resources –– we are better poised to support other researchers doing similar work and flexibly customize our training materials for other domains. We’re deeply grateful for this partnership.”

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