How much programming should a biologist know?

August 16, 2007

Tiago’s blog is fast becoming a favorite. He responds to an interview with Alexei Drummond and I figured I’d respond to him.

First things first, I am not a biologist, just a physical chemist who has been in the biological sciences for a long time. So programming/scripting, etc are part of what I did in my scientific career from the beginning. I do believe that there are some level of computational skills all biologists must possess, but unlike Tiago, I think the number of scientists who know how to script is actually going to go down. It is becoming less common to find many scientists, even those who do part time molecular modeling, who have ever using a *NIX machine. Many OSX users don’t even know the best part of the OS, the ability to open a shell.

The alternative is to use interfaces that are between the scientist and the script, simple drag and drop interfaces that can be used to do many of the same things (workflow engines for example). Many of those are still to complex, but if a scientist has a basic understanding of data flow and the methods behind the madness, tools that give them access to workflows are the way to go, or so I think.

On the flip side, I do believe that hacks like yours truly would have benefited greatly from some formal software development training. Being able to write good code is important. Just look at the number of great academic packages that are a nightmare to maintain and completely bloated.

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Posted by Deepak Singh | Filed Under Education, Informatics, Science 

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