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Tuesday, October 8, 2013

Does every new biology PhD student need to learn how to program?

The answer is Yes!
see the paper from Nature Biotech


Box 1: Does every new biology PhD student need to learn how to program?

Durbin: That's a little like asking is it good for a molecular biologist to know chemistry. I would say that computation is now as important to biology as chemistry is. Both are useful background knowledge. Data manipulation and use of information are part of the technology of biology research now. Knowing how to program also gives people some idea about what's going on inside data analysis. It helps them appreciate what they can and can't expect from data analysis software.
Trapnell: It's probably not just that experimental biologists need to program, but it's also enormously helpful when computational folks learn how to do experiments. For me, for example, coming from a computer science background, the opposite way of thinking was hard to learn. How do I learn to argue with wet-lab data? How do I learn what to trust, what to distrust, how to cross-validate things? That's a radically different way of thinking when you're used to proofs and writing code and validating it on a computer.
Krzywinski: To some, the answer might be “no” because that's left to the experts, to the people downstairs who sit in front of a computer. But a similar question would be: does every graduate student in biology need to learn grammar? Clearly, yes. Do they all need to learn to speak? Clearly, yes. We just don't leave it to the literature experts. That's because we need to communicate. Do students need to tie their shoes? Yes. It has now come to the point where using a computer is as essential as brushing your teeth. If you want some kind of a competitive edge, you're going to want to make as much use of that computer as you can. The complexity of the task at hand will mean that canned solutions don't exist. It means that if you're using a canned solution, you're not at the edge of research.
Robinson: Yes. Even if they don't program in their research, they will have to use software and likely will communicate with software developers. It helps tremendously to have some basic knowledge. Additionally, in the research environment, the ability to do basic tasks in the Linux/Unix environment is essential.
Rasband: All scientists should learn how to program."

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