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Q&A: Carnegie Mellon's Robert Murphy Discusses Goals, Benefits of New Computational Biology Degree

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Carnegie Mellon's Robert Murphy

NEW YORK (GenomeWeb) –  Carnegie Mellon University's School of Computer Science has launched a new bachelor's degree program in computational biology that is expected to begin accepting new students starting next fall.

The new program, which is under the auspices of the school's computational biology department, adds to existing doctoral and master's degree programs. According to CMU, the curriculum will provide students with a solid foundation in both computer science and experimental biology and help them make connections between the two fields. They'll also have the opportunity to participate in computational biology research projects with faculty.

Students who complete the major will be competitive candidates for doctoral programs in a range of biomedical areas including computational biology, systems biology, and quantitative biology, for industry positions with pharmaceutical and biotechnology companies, and for careers as physicians who are well equipped to understand and apply genomic medicine in their practices.

The program is directed by Phillip Compeau, an assistant teaching professor and co-developer of a six-course specialization in bioinformatics on the educational technology website Coursera. That course, developed in collaboration with Pavel Pevzner, a professor of computer science and engineering at the University of California, San Diego, is designed to teach core bioinformatics principles and concepts to biologists and computer sciences. These researchers are also responsible for developing Rosalind, a bioinformatics education platform that challenges users to solve problems that address concepts in biology and programming.

This week, GenomeWeb spoke with Robert Murphy, head of the computational biology department, about the new program. What follows is an edited version of the conversation. 

Let's start with the most obvious question. Why are you launching this program?

We have had a program in computational biology since the late eighties. That program was developed at a time when we didn't really have much coursework in computational biology. I taught the only course we had in computational biology and the curriculum for that program was basically biology, computer science, and that was it. We have a department of computational biology now, we have a lot more coursework that's available and we have an updated view of what computational biology students need.

What we have also done is realize that one of the important pools of students that would be good computational biology majors are students that are competitive for entry into our School of Computer Science. As a school, we've been looking for ways to diversify the interests of the undergraduates specifically in the school. And offering other majors is one of the ways in which we can do that. So on the one hand, we have a very exciting curriculum that we've developed for the new program and we have also made arrangements [to] admit students into the School of Computer Science who are interested in computational biology. We think that we have a good vision for what that education should look like and we think that a lot of students will find that attractive.

I should also note that there is tremendous demand from industry, medicine, and academia for people who have exactly the interdisciplinary skills that our program provides.

You already have doctoral and master's programs in computational biology, so why do you need a defined bachelor's degree as well?

We have observed that students who come through a computational biology program as undergraduates or who had significant exposure to both computer science and biology as either undergraduates or master's students are in a much better position when they go into a PhD program. By contrast, students who come in with just computer science find it daunting to learn the essence of biology as well. [A] computational biology education should be about not just teaching computer science and then describing some current open problems in computational biology and letting students work on those problems, but [also] to train students to be able to frame problems on their own, and that requires a deep understanding of computer science and biology. That's the reason that we feel that it's important to enable students to be prepared in both of these disciplines and be familiar with the essence of computational biology as it is now.

What does your curriculum offer that would make it worthwhile for a student to enroll in the program instead of just taking basic computer science and biology courses?

Any major potentially involves making compromises between different courses. When it comes to, for example, a biology degree or computer science degree, there are a number of courses that are required that would make it hard for someone to take a lot of computational biology courses. With this curriculum, we've made judgements about what are the most important parts of computer science that computational biologists need and the most important parts of biology and put those in. That has left room for putting in courses that cover the current state of computational biology. We are hoping with this curriculum that we will prepare students not only for graduate programs in computational biology and related disciplines but also that the undergraduates would be very well prepared for going directly into jobs in industry and startups in this space. And they would be as well prepared as master's students from many other programs. Further, we think there is also a place for undergraduates who are interested in premedical programs to take this major because the future of medicine is also computational.

One of the professors involved with your program also helps run a MOOC on the Coursera site. Will there be opportunities to bring resources from that effort into the classroom?

One of the things that the online course can do a very good job on is getting people interested in this field. They may have enough training from the online course to get a certain type of job, but if they are really interested and want to take it to the next level, then this is the kind of degree that would enable that. It depends on whether we are talking about a high school student taking one or more online courses and then deciding that they want to major in computational biology or if it's somebody that's already graduated and then realizes that this is something that's interesting. There is also a place for using modules from online courses as supplements in regular university courses.

Is there a specific benefit that you see this program bringing to the Computational Biology Department at Carnegie Mellon?

Two ways. One, we have a very long tradition of undergraduate research at Carnegie Mellon. Many of these undergraduates will be interested in doing research and that will provide additional students who are interested in working in research projects with our faculty. We also see our mission as a department being to promulgate and disseminate a much more computationally driven vision of experimental biology and medicine that these students will be exposed to and will be advocates for.

Can you provide some examples of specific research projects that students could take part in?

Each of our faculty have specific projects that they have identified that would be appropriate for undergraduates to work with them on. I have students working with me. What my lab works on is building models of cells directly from microscope images. Those models are not reconstructions of an individual image but generative models of that particular cell type so that you can incorporate information from many different cells into that model. That's an open-source project, and I have undergraduates working with me on constructing components of machine-learning modules that learn parts of the cell from images. Another possibility is working with one of our newest faculty members, Dr. Andreas Pfenning. His group works on neurogenomics, learning the relationship between genome variation and neurological diseases such as Alzheimer's. They focus especially on identifying genome variation in regulatory regions.

Are you hiring new staff to help with teaching courses?

The short answer is no. We have been hiring computational biology faculty for a number of years and hired Philip Compeau, who will be the advisor for this program, last year. One reason we are putting this program in place now is that we are already teaching enough courses to really provide a strong education in the discipline of computational biology and we already have enough faculty for that.  But we are continuing to hire tenure-track faculty in various research areas. 

When will you start taking in students?

We'll be accepting students in this cycle for enrollment this coming fall, so students can apply now. 

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