Mind the Gap
Pittsburgh Supercomputing Center's MARC Program Helps Minority-Serving Institutions Prepare Students for 21st Century Biology Careers
August 12, 2013
In 1996, Ricardo González Mendez decided to revamp his skills and expertise in bioinformatics—using advanced computing techniques on biological problems. In the process, he learned something alarming: American biology education was in danger of becoming a two-class system.
A gap is developing, the University of Puerto Rico (UPR) School of Medicine professor realized. The top-tier institutions understand that bioinformatics will soon be a job requirement in much of biology. And they have expended their considerable resources to create bioinformatics classes, degree programs and research centers. Among the other institutions, many realized as well that a bioinformatics crisis was coming. Their students were in danger of being left behind, whether they wanted to pursue academic research, industrial positions or even teach. But the schools had neither the expertise nor the resources to respond.
“There is a total disconnect between the top-tier research schools and the minority or not-so-rich schools,” Gonzalez warns.
Today’s biologists are generating incredible amounts of data. The European Bioinformatics Institute alone, for example, now stores 20 petabytes of life sciences data — enough to fill nearly a quarter of a million top-line iPads. Understanding that much data can only be accomplished with computers.
“People are starting to come to the realization that either they modernize their skills, or they’re not going to get more funding,” Gonzalez says.
Gonzalez enlisted the then-director of PSC’s biomedical initiative, David Deerfield, who with PSC’s Hugh Nicholas and Alex Ropelewski wrote a 2001 National Institutes of Health Minority Access to Research Careers (MARC) grant to help students at minority-serving institutions study bioinformatics. Gonzalez was the PSC MARC program’s first faculty liaison. After Deerfield’s tragic death in 2006, he took on an expanded role as co-principal investigator with Nicholas.
Initially, the program focused on helping institutions establish a single bioinformatics course on campus. “The focus of the current grant is on working with five minority-serving [partner] institutions to get concentrations in bioinformatics on their campuses,” says Ropelewski. “It’s basically a multi-course work series that’s established officially, so that someone can minor in bioinformatics, for example.” The program fills gaps in students’ knowledge base — teaching biologists about computers, and computer scientists about biology.
PSC’s MARC program has enjoyed a number of successes. The students are “publishing in really good journals, getting funded from various agencies, and … going on to graduate programs, post-doctoral fellowships and positions in industry and government that are very good,” Gonzalez says. “We are not as big as some [of the top] programs, but we produce the same kind of quality.”
One of PSC MARC’s most exciting facets is a 10-week summer program, in which students from participating institutions come to PSC to carry out bioinformatics research projects. Here we present a sampling of this year’s students and their efforts.
Grabbing the Brass Ring
People had plenty of advice for Tevin Reed, an incoming senior at North Carolina Agricultural and Technical State University, about what not to major in. His band director warned about the grim employment prospects for a brass musician. Reed’s sister, an information technology major, always seemed to need another expensive tool for her projects. But in computer science, she told him, “As long as you have your laptop you can always do your homework.”
Reed found he loved computer science. “I’m not going to say I was the best at it, but I could actually understand what the teachers were saying on the first day,” he says.
Reed’s MARC project was to use the wxWidgets library to make the open source GeneDoc Windows program work on any operating system. PSC’s Hugh Nicholas, the late David Deerfield and Alex Ropelewski developed program specifications and Nicholas’ son Karl coded GeneDoc, which visualizes, highlights and rigorously compares DNA, RNA and protein sequence alignments. Reed hopes to help biologists get more consistent computational results no matter what kind of computer they use.
“It was very helpful” having the program’s authors available in working out the inevitable glitches, Reed says. “Once I finish it, I’ll talk with Alex and Hugh and see how they want to distribute it.”
Getting a Better Vantage Point
From atop Ingrid Montes-Rodriguez’s grandparents’ house in Ciales, in the mountains of Puerto Rico, you can see both the Atlantic Ocean to the north and the Caribbean Sea to the south.
“It’s really beautiful,” says Montes-Rodriguez, a PhD student in Juan López Garriga’s chemistry lab at the University of Puerto Rico, Mayagüez, who is currently doing her research work at the UPR Medical Sciences Campus. When the pressure of grad school gets to her, she heads for Ciales, and her family.
Her dad is a master of “tough love” advice: “He just says, ‘Well, you have to do it! What are you going to do, cry?’”
Thanks in part to that advice—and a PSC MARC summer project with Graham Hatfull’s lab at the University of Pittsburgh—Montes-Rodriguez has begun decoding the genetic material of the clam L. pectinata, a major focus of López Garriga’s team.
L. pectinata, which grows in mudflats throughout the Caribbean, survives levels of hydrogen sulfide that would kill most animals. It does this in part by producing a unique kind of hemoglobin, which attaches to that “rotten egg” chemical instead of oxygen.
Montes-Rodriguez hopes that comparing the genome of the clam with the DNA of other species will help explain how the unique hemoglobin evolved, and what other protective mechanisms the species has developed.
Putting the “Tech” in Biotech
Michael Thompson loves the gadgets.
“To be honest, I really love technology,” says the incoming Jackson State University senior. “I’m just fascinated by it.”
As a freshman Thompson wasn’t sure what he wanted to study. But he’d scored high in biology in the Mississippi state high school tests, and when Raphael Isokpehi, director of Jackson State’s Center for Bioinformatics and Computational Biology, invited him to visit Isokpehi’s lab he decided to check it out.
“There were a lot of computers but I didn’t notice any microscopes or anything like that,” Thompson says. “I thought, ‘That’s weird.’” That’s where, for the first time, Thompson found out that he could do biology and engage in his love of technology.
At the MARC summer workshop, Thompson continued his project from Isokpehi’s lab, studying the universal stress proteins (USPs) in the Clostridia bacteria. USPs are an important part of an organism’s defense against stresses such as antibiotics. Because of that, they’re an important target for treating food poisoning, colitis, tetanus and other diseases caused by Clostridia.
“Being able to have Alex, Hugh and Pallavi [Ishwad, PSC’s Education Program director] guide me in the right direction has been amazing,” Thompson says. “I feel like I can take a lot back home and teach others.”
Not all the success stories in this summer’s MARC program involve MARC students.
Jonathan Strickland, a recent high school graduate of the Pittsburgh Science and Technology Academy, knew that he wanted to work with computers. It’s probably fair to say, though, that after a senior project at PSC he’s aiming considerably higher in the industry—and it started with this year’s summer employment.
“I kind of pictured having a summer job at Arby’s,” he says. But the now-University of Arizona Honors College freshman and full scholarship recipient found himself on a different track. Working with PSC’s Alex Ropelewski, he did a project analyzing what factors affect the RNA sequence assembly program Trinity’s performance on supercomputers (See p. X). “I guess I did a good job, because Mr. Ropelewski asked me if I wanted to work at PSC this summer” helping with the MARC program.
So Strickland helped keep the MARC workshop running smoothly. He did some purely gopher tasks. But he also set up user accounts for the MARC students. He even helped out with the Python programming language class, which he himself learned during his senior project experience.
“Working at PSC is great,” he says. “I’m actually doing stuff that’s meaningful.”