Clark University - Clarknews winter 2004
From information to knowledge: A new concentration in bioinformatics helps students learn how to solve complex scientific problems
By Judith Jaeger
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Just a few of the faculty involved in Clark's new bioinformatics concentration: Computer Scientist Arthur Chou (left), mathematical statistician Laura Bernhofen, biologist David Hibbett, computer scientist Li Han, Mathematics and Computer Science Department Chair Lawrence Morris and chemist David Thurlow
Photo by Frederick Peck |
With the completion of the human genome project and ongoing research initiatives in the life sciences, scientists have access to more biological information than ever before. While this flood of data is creating more opportunities for scientific discovery and innovation, it also brings with it new challenges—namely, how to turn information into knowledge.
Clark undergraduates will soon ply their skills on such challenges as part of the new bioinformatics concentration, which begins this spring. According to Lawrence Morris, chair of the Math and Computer Science Department, bioinformatics is a burgeoning field that has grown considerably with the progress of the human genome and other genome projects. The data produced by these projects are central to advancement in many areas of molecular biology and biochemistry, as well as to the development of new drugs, vaccines, gene therapies and other discoveries in the biomedical and biotechnology industries. But the volume and complexity of this data is so great that researchers are turning to mathematicians and computer scientists to develop tools to store, manage and analyze it.
"New problems are coming out of biology that require sophisticated math and computer science," Morris says. "And it’s important for math and computer science students to realize that their learning can be applied to other disciplines."
Morris describes bioinformatics as "the nexus of math, computer science and life sciences." More specifically, he points to the National Institutes of Health definition of the field—"the research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze or visualize such data." Clark’s program is built on this definition, Morris says, and is designed to introduce students to paradigms and algorithms from mathematics and computer science for solving such problems in the life sciences. An algorithm is a precise set of instructions that enables a computer to solve a problem. For example, a sorting algorithm tells a computer how to sort information.
The concentration rests in the Math and Computer Science Department and brings together faculty from the Chemistry and Biology departments. By taking a variety of courses in these disciplines, Morris says, math and computer science students will learn how to work with scientists to solve complex, data-driven problems in biology and chemistry, and science students will learn about computational tools that are available to them.
The interdisciplinary advantage
While several colleges and universities offer bioinformatics programs, Morris notes that many of them are at the graduate level, with only a few schools offering courses to undergraduates. In addition, Morris and the other faculty involved with the concentration believe that Clark’s interdisciplinary atmosphere is particularly well-suited to providing a high-quality bioinformatics concentration.
"We actually sat down with the scientists and talked to them about what we could do," Morris says. Clark recently earned a grant from the National Science Foundation for a new computing cluster, for example, that involved co-principal investigators from the Biology, Chemistry, Physics and Math and Computer Science departments, with support from Clark’s Information Technology Services office. This computing cluster will be used, in part, to support the bioinformatics concentration.
"Clark has a history of providing good quality programs that involve multiple departments," adds chemist David Thurlow, who is part of the working group that developed the bioinformatics concentration. Thurlow says that Clark’s biochemistry/molecular biology major, which involves at least 10 faculty members from the Biology and Chemistry departments, served as the model for the bioinformatics program.
While bioinformatics is often associated with biology, Thurlow says it also has important applications for chemistry, particularly for biochemistry and molecular biology.
"DNA sequencing is absolutely essential for modern-day biochemistry and molecular biology students. That’s where it all starts," he says.
In his research into protein structures, Thurlow uses software developed through bioinformatics to design cloning experiments, analyze available data, identify interesting biological systems with which to work and for molecular modeling. Thurlow says the concentration has a large emphasis on computer programming, making it the perfect concentration for students interested in programming and biochemistry/molecular biology and an important draw for prospective students already interested in these areas.
Active learning at work
The bioinformatics concentration also illustrates the benefits of the synergies between teaching and scholarship that are so prevalent at Clark. The program essentially grew out of faculty members’ experience working with bioinformatics in their research.
Computer scientist Arthur Chou, for instance, became involved with bioinformatics while helping researchers at the University of Massachusetts Medical Center who were developing an HIV vaccine. The researchers were examining an envelope protein—the protein that surrounds the HIV virus—and wanted to analyze its gene sequence. The researchers had the sequence, Chou explains, but needed a computer scientist to develop an algorithm to analyze it. Similar analyses and techniques are used in drug development, he says, and can also be used to analyze how patients react to a drug. Chou adds that many cancer-fighting drugs are designed using bioinformatics.
"This is what caught my attention—how exciting the whole field is in taking abstract math and computer science and using it to solve important medical problems," Chou says. "I saw my knowledge put to use."
After this experience, Chou wanted to learn more about the kinds of life-science research problems that would benefit from bioinformatics. He also wanted to learn more about the terms and vocabulary biologists use, in order to fully understand the issues in their research and be able to talk about those issues using biological terms. Chou went back to the classroom, sitting in on a biology course taught by biologist David Hibbett last spring. Ensuring that math, computer science and science students know how to talk to each other about their specific fields is an important focus of the concentration, Chou says, and all students in the concentration are required to take at least one biology course. The introductory bioinformatics course offered this spring will be taught by Chou and Hibbett, with units on protein structures and molecular visualization taught by Thurlow, chemist Don Nelson and computer scientist Li Han.
"The challenge will be to find the common ground where we can talk about the problems and solutions," Chou says.
How information is changing biology
In addition to the analysis and synthesis of sequence data, Chou explains, bioinformatics is also used in the development of phylogeny, or evolutionary trees. Hibbett, for example, is developing a phylogeny of fungi and uses bioinformatics to compare DNA sequences of different organisms, mine data from a databank and manipulate that data, and to trace the evolution of different genes and gene sequences. This past summer, Moran Schonfeld ’03, one of Chou’s students, developed a computer program for Hibbett that automates the process of mining a data bank and retrieving, screening and analyzing the data.
Hibbett says the huge amount of data now available to scientists is one of the key ways biology has changed.
"A challenge for biology is to turn that information into knowledge," Hibbett says. "Every biologist needs to be capable of manipulating information, and there are areas of biology that are otherwise difficult to address."
According to Hibbett, bioinformatics was already being worked into the undergraduate biology program. In the same way that every biologist needs some knowledge of molecular biology, he says, biologists also need some knowledge of bioinformatics. A large part of that knowledge, Hibbett explains, is an awareness of the data and bioinformatics tools that are available.
"This goes for students who are going to graduate school, and if they’re going to work at a biotechnology company," he says.
Opening doors to new career options
The biomedical and biotechnology industries are becoming viable career options for math and computer science majors, says mathematical statistician Laura Bernhofen.
"A typical question from math students is ‘what can I do with my math?’" says Bernhofen, who helped develop the bioinformatics concentration. While math majors have traditionally gravitated toward business, finance or physics, bioinformatics gives a math major a new perspective on where mathematical tools can be applied, she says. The recent decline in the information-technology industry is also causing computer science students to seek alternative career options. She notes Clark’s close proximity to biomedical and biotechnology industry centers in Worcester, Cambridge and Boston.
Bernhofen, for instance, has worked with researchers at the Informatics Center at the Massachusetts Biomedical Initiative, formerly the Center for Computational Molecular Biology, in Worcester, investigating statistical models of gene expression data.
"Traditionally trained biologists don’t have the math, computer-science or statistical skills to deal with all the data coming out of the genome projects," she says. "Biologists are realizing that they need more math to analyze the types of problems that are currently arising."
Bernhofen says the concentration is designed to give math and computer science students the knowledge they need to communicate more effectively with scientists, and to give students in the life sciences additional analytical tools.
Complex problems with satisfying solutions
Li Han works with the third major area of bioinformatics—molecular modeling. Specifically, Han develops computer algorithms to show how proteins move from one state to another.
Han, who specializes in computer simulation and robotics, is not new to bioinformatics. Han’s Ph.D. research combined her computer science knowledge with biomedical engineering in her work on a robotic hand that used computer algorithms to find paths of motion. This translates easily to protein modeling, she says. A human hand and a protein are both linkage systems, she explains, which means the math and computer models that show motion in a hand are very similar to the models that show motion in a protein. Like Chou, Han enjoys seeing her computer-science knowledge impact other disciplines.
"This is a very exciting field, and it has more of a general impact on human life," says Han, who adds that this also makes the field attractive to students. "The problems are very complex, and they are interesting to students."
Applying knowledge to real-world problems
Although the concentration didn’t officially start until this spring, Han has already been working with students in a bioinformatics seminar and advising those students on research projects. Mario Fonseca ’04, for example, began working with Han last semester on an independent study in bioinformatics. Fonseca is developing graph-related algorithms to help reveal insights into how proteins fold back to their original shapes. In developing these algorithms, he is also focusing on gathering and processing this information more efficiently.
When Fonseca entered Clark, he considered majoring in a science but chose to major in computer science instead. Bioinformatics, he says, allows him to study science and apply his computer-science knowledge at the same time.
"It’s great that students can cross majors and apply their learning in another area," says Fonseca, who also took a biology course last semester to enhance his study of bioinformatics. "I’m also fortunate to be working with Professor Han, who has the experience to give me the right kind of advice."
Fonseca hasn’t quite narrowed his plans for what he will pursue after graduation, but he is confident that his study of bioinformatics will serve him well.
"Even if I don’t go into bioinformatics, I can take what I’ve learned and apply it to any career," he says.
Bioinformatics and the liberal arts
Marc Snyder ’04 is also participating in Han’s bioinformatics seminar. Snyder, a Traina Scholar and computer-science major, began working with bioinformatics in the spring 2003 semester. He worked with researchers at the University of Massachusetts Medical School who were studying the folding behavior of the alpha subunit of tryptophan synthase, a protein involved with E. coli. Snyder assisted the researchers by creating computer algorithms to extract data about this protein for use in other computer applications that give the researchers a better understanding of the protein’s behavior.
This past summer, Snyder used the stipend from his Traina Scholarship to support his research into different computer programs used in molecular modeling and extracting data from gene sequences. He surveyed approximately 11 different software programs to see how they could be used in scientific research and wrote guides to each of the programs that will serve as references for the bioinformatics course this spring. Currently, Snyder is working on his honors thesis, which focuses on homology modeling, the process of comparing a structurally unknown amino acid sequence to a sequence with a known structure to generate a hypothetical structure of the unknown protein.
But you won’t find Snyder in a lab after graduation in May. In a typically unconventional Clark twist, Snyder plans to earn a law degree—using his background in bioinformatics to pursue a career in biotechnology law.
"When I came to Clark, I was pulled between technology and law," says Snyder, who will graduate with a concentration in law and society. While his research activities have confirmed his desire to pursue law rather than the lab, Snyder says he is grateful for having the opportunity to pursue both.
"That’s why I chose Clark," he says. "I wanted the liberal-arts education. It’s been perfect for me."
Chou says Snyder is a great example of the particular advantage to studying bioinformatics in a liberal-arts environment.
"Students can learn all of this as a cultural background for what they want to study in graduate school or pursue professionally," Chou says. "We also want to train our students to be scientists, not just technicians. We want them to become leaders in their fields."
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