Study of PSC Internship Shows a Need To Go Beyond Traditional Outreach

July 19, 2016

Bringing more minority students into the bioinformatics training pipeline may require a major rethink of STEM outreach to minority-serving institutions (MSIs) and more funding, a team from the University of Puerto Rico and PSC reported today at the XSEDE16 supercomputing conference in Miami.

“A large number of schools, students and faculty do not have the computational or bioinformatics skills necessary to carry out competitive biomedical genomics research,” says the University of Puerto Rico, Medical Sciences’ Ricardo Gonzalez Mendez, first author of the peer-reviewed paper accompanying the presentation. “We’re giving a series of recommendations including re-thinking the biology curricula in terms of competencies needed for bioinformatics and STEM careers, to increase the amount of instruction that builds analytical and computational, and Next-Generation Sequencing analysis skills to train novices in these areas.”

The group surveyed students from MSIs before and after an intensive two-month summer internship in bioinformatics at PSC. PSC’s internship, funded by the National Institutes of Health’s Minority Access to Research Careers (MARC) program, raised participating students’ bioinformatics skills across the board. But more telling was the students’ lack of previous exposure to basic bioinformatics skills. Despite being among the top students at their institutions, before the internship began 27 percent ranked at the “novice” level in performing sequence database searches or multiple sequence alignments; 59 percent were ranked no higher than a “basic” level of skill in either. For a set of nine specialized Next-Generation Sequencing skills surveyed, between 68 percent and 91 percent ranked only as novices.

These skills are important, the researchers note, because having some exposure to them is necessary to maximize the benefits obtained from the typical one- to two-day outreach program, let alone embark on successful bioinformatics study.

“Our whole mindset needs to change with the goal in mind,” says coauthor Pallavi Ishwad, education program director at PSC. “Most of these students still think, ‘I’m studying biology,’ or ‘I’m studying computer science.’ But you need to think about combining these skillsets for a successful career in the 21st century.”

Top-ranked colleges and universities have largely made this transition, according to coauthor Alexander Ropelewski, director of PSC’s Biomedical Applications Group. But the transition to offer multidisciplinary coursework early in the academic curricula is absent at MSIs, which educate some 58 percent of minority students.

“What is needed is much more intense training that gets the MSI faculty to the point that they can effectively transition the coursework to emphasize the building of quantitative skills needed by the biomedical workforce,” he says.

XSEDE16 is the NSF XSEDE project’s fifth annual conference. The conference showcases the discoveries, innovations, challenges and achievements of those who use and support XSEDE resources and services, as well as other digital resources and services throughout the world. The theme of XSEDE16 is “Diversity, Big Data & Science at Scale: Enabling the Next-Generation of Science and Technology.” The UPR/PSC team’s presentation is part of the first track ever of presentations on Diversity and Development in the workforce at XSEDE meetings.

Assisting Bioinformatics Programs at Minority Institutions: Needs Assessment and Lessons Learned—A Look at an Internship Program