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Spring 2006

Using computers...liberally

by Elizabeth R. Altick ’75

Exposure to computers as undergraduate researchers morphed into love of three alumni

One wouldn’t ordinarily associate the words “passion” and “infatuation” with F&M’s Martin Library of the Sciences. Or becoming “enamored” while working on a research project. But several graduates fondly recall how their early encounters with computers in biology and medicine changed their lives.

Their initial excitement led them to enter one of the most promising cutting-edge fields in science: biomedical informatics, the study of information management in healthcare and life sciences. Initially applied to clinical medicine, biomedical informatics dealt with the ever-increasing volume of medical knowledge and assisted clinicians in taking care of patients through information technology.

The advent of high-throughput methodologies in genetics and molecular biology demanded significant advances in computational power and techniques, and informatics rose to the challenge. “Bio” was added to the name as new approaches to analyzing the vast amounts of data produced by endeavors such as the human genome project and the discovery of new drugs.

Matvey Palchuk, M.D., M.S., ’94

From Belarus to high technology

Matvey Palchuk, M.D., M.S., ’94 arrived in Lancaster from Pinsk, Belarus, in 1990, speaking very little English. His family came to Lancaster as refugees from the former Soviet Union.

“I never dreamed there was a glimmer of hope to enroll in a private school to pursue my pre-med education,” he explained. “Happily, some absolutely wonderful friends had the courage and foresight to introduce me to F&M.”

To learn to think and write in English, Palchuk took a writing course with then-professor Joseph Voelker ’68, who would not accept handwritten work and strongly suggested using computers. “Coming from a small town in the USSR, I’d never seen a personal computer,” Palchuk said. “They were something from the realm of science fiction.”

He went to the library, where a student computer consultant sat him down at a Mac, brought up a white screen of a word processor, told him to type, and walked away. “That’s when I fell in love,” he said. “I tried every command and opened every window, and by the next semester I was a computer consultant, eventually with my own office. I was kind of a computer doctor, holding the hands of my ‘patients’ who were afraid of losing their files or being unable to print.”

In his senior year, Professor Richard Fluck, suggested that he and Palchuk do research on digital light microscopy. “Back in 1994, I didn’t know what RAM, framegrabbers, or even the World Wide Web were,” explained Fluck, who is now associate dean of the faculty and the Dr. E. Paul & Frances H. Reiff Professor of Biology. “I said I’d teach him what I knew about light microscopy, if he’d teach me about computers.”

With Palchuk’s assistance, Fluck soon had enough computing power on his desk to collect digital images. With that as a starting point, Palchuk later helped Fluck and Kathleen Triman, professor of biology, write a grant proposal to the National Science Foundation for funds to buy microscopes, computers, video cameras, and framegrabbers for an imaging lab, which has been a boon to both their teaching and research.

Palchuk’s infatuation with computers persevered through his medical training at the University of Pittsburgh School of Medicine and a residency in internal medicine, eventually leading him to a medical informatics fellowship program at Harvard and MIT. Currently working as a product manager and a senior medical informatics specialist at Partners HealthCare in Boston, he specializes in designing electronic health record (EHR) systems.

“EHRs will eventually eliminate the slew of paperwork involved in practicing medicine and make information about patients as well as general medical knowledge readily available to clinicians at the point of care,” Palchuk explained. “It will improve patient safety, enhance the quality of care, increase efficiency, and reduce costs.”

While Palchuk does not see patients, he believes that combining his medical knowledge and expertise in information management helps many patients at the same time, rather than one at a time.

“The students were awestruck”

Intending to become an orthopedic surgeon, Albert Park ’99, enrolled in F&M on the recommendation of physician colleagues of his mother. In the last year of his pre-med training, he worked with Professor Triman on a project involving bioinformatics, which led him to change the course of his career.

“Albert single-handedly designed and implemented a searchable format for the Ribosomal RNA Mutation Database I had created in 1994,” said Triman. This unique database contains information about mutations (changes in the sequence) at precise locations in ribosomal RNA in E. coli and other organisms. Phenotypic (physically detectable changes) information and bibliographical citations are also included for each mutation.

“Albert was recognized for his work and presented it himself at the American Society for Biochemistry and Molecular Biology annual meeting in San Francisco in 1999,” Triman said.

A few years ago, Triman asked Park to teach a one-day advanced molecular biology seminar. He introduced the students to bioinformatics and demonstrated the use of new search engines employed by the pharmaceutical companies.

“The students were awestruck,” Triman recalled. “Albert’s presentation and the students’ enthusiastic response to it inspired me to devote one quarter of the course to bioinformatics the following year and every year since.”

After graduating from F&M, Park earned an advanced degree in bioinformatics at Boston University. He is now a staff scientist at Dyax Corp, in Cambridge, Mass., a biotech company focusing on medical advances in the areas of inflammation and oncology. There, Park is involved in high-throughput drug screening, i.e., writing computer programs that analyze data generated by automated robotics that rapidly “perform the thousands of experiments” necessary to formulate new drugs.

What’s in the cards for computer science?

Richard A. Fluck, associate dean of the faculty and the Dr. E. Paul & Frances H. Reiff Professor of Biology, talks about the future of computer science at Franklin & Marshall.

(right) Vivek Abraham and Professor Fluck working in the lab, 1992. Photo by Dan Marschka.

Q Does the College have plans to offer a major in computer science?
A We do envision a major in computer science. This vision is based on an internal study and external review by computer scientists from three liberal arts colleges. For this major to be viable, we will need three full-time computer scientists. We currently have two faculty in the mathematics department who teach courses and do research in computer science. However, one of the professors also teaches mathematics courses so his formal commitment to computer science is equivalent to 60 percent of a full-time position.

Q Would the major involve study in fields other than biology and math?
A We expect that faculty in other departments would teach courses that would support a major. The chemistry department could address cheminformatics, and a psychology course could focus on cognitive science. Computer science majors might also study artificial intelligence and robotics; and computer science is also relevant to geology, economics, and business.

Q In addition to two additional tenure-track faculty members, what will it take to create this major?
A Computer science is a laboratory science and needs equipment (for both teaching and research) and the support staff to maintain it. The College’s broader needs in the area of information technology were described in a 2005 report that underscored the importance of maintaining our centralized systems and improving network robustness and security. We also need to plan for replacing equipment and to expand on what we call “technology-enhanced classrooms.” The projected cost of these and related projects is about $7.3 million over six years.

Q When do you think the computer science major will be available?
A We envision that the new major will be in place within the next three to five years.

A lucky day

Vivek Abraham, Ph.D., ’94, was also in F&M’s pre-med program. He is now with Abbott, north of Chicago, where he, like Park, is immersed in high-throughput drug screening.

“I’ve always had an unexplainable fascination with cells and microscopic imaging,” Abraham said. “From a purely scientific standpoint, an image is worth a thousand words. I worked with Professor Fluck for almost all my time at F&M. We studied the early development of the fish embryo using time-lapse video microscopy.”

Vivek Abraham, Ph.D., ’94

Fluck vividly recalled the first day he met Abraham. “When Vivek showed up at my door—literally—it was a lucky day for both of us. He told me he was working in the dining hall and wanted to know if he could do research instead. Luckily for him (and me) I had about $300 in research money that enabled him to start tracking the movements of subcellular particles via time-lapse video microscopy.”

Like much research, the work was tedious and demanding, but within a few weeks Abraham had identified three classes of movements. His careful work and results became the foundation for projects that involved Fluck and numerous students for the following eight years.

“I cannot say enough about Professor Fluck’s mentorship during and after my college years,” Abraham explained. “He gave me every opportunity to develop and pursue the things I was excited about, including finding an excellent graduate program. I’m also grateful for having him introduce me to one of the premier biological research institutions in my junior year.”

Abraham went on to graduate school to earn a Ph.D. in the laboratory of D.L. Taylor at Carnegie Mellon University. He then joined Cellomics, a biotechnology company focused on developing tools for fully automating microscopic imaging and image analysis of cells. “These tools enable large scale cell biological experimentation that simply could not be attempted using traditional manual microscopy, such as rapidly screening through several thousand chemical compounds for the ones that have a specific effect on cells that indicates drug-like potential,” he explained.

Abraham recently joined the Department of Biological Screening at Abbott in the Global Pharmaceutical Research and Development Division. His primary responsibility is to apply automated cellular imaging tools to drug discovery to best determine which chemical compounds show the highest therapeutic potential during the early stages of drug discovery.

Maintain the momentum

Using computers for research during their undergraduate days changed the career choices of these graduates. That’s why they feel so strongly that today’s students also need that type of computer experience, so they can find careers that interest them.

“I think F&M as a liberal arts college would benefit by continuing to ensure that all the disciplines are fully supported with state-of-the-art computational tools,” Abraham said. “I speak from the perspective of becoming excited after seeing what these tools could deliver in my area of interest.”

Not only will this type of support propel the next generation of Franklin & Marshall students into important cutting-edge fields, it might even help them fall in love—with computers, that is.