Mind to Market

Monday, December 17, 2007

Modeling Biology

As someone who promotes the ideas and technologies of computational biology, I am regularly confronted by skeptics who either doubt the value or the capabilities of computational models of biology. There is a perception of a computer either churning for days to determine what a trained scientist can figure out in a few minutes or the inability of the program to provide a correct result to a seemingly simple problem.

Perhaps this is an issue of setting expectations. The cases above expect either too much or too little from computational modeling. As a first pass a computer model should be expected to perform those tasks that are already being done manually by scientists. Every scientist, even those who have never written a line of code, has some mental model of the biological systems she is working with. The mental models may be complex and subtle, i.e. difficult to express explicitly, but they can be expressed nevertheless.

Terry Quatrani writes in a recent Dr. Dobb's Journal article entitled Agile Modeling: No, It's Not an Oxymoron, that computer models are useful both by enabling communication with other team members and by focusing the thought process. She points out that 93 percent of agile team members sketch on the whiteboard, definite proof of modeling. If you're a scientist sketching on a white board or notepad, you're a modeler.

So why bother with the arduous process of converting those sketches into millions of lines of code? Although the sketches may contain genius, they are difficult to transfer, reproduce, extend, integrate or eventually, simulate. Although they contain the essence of thought, they lack the conveniences and efficiencies that modern information technologies provide us with.

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