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copied!<p>Let me preface this by saying that I'm a bioinformatician, so I see the things you're talking about all the time. There's some truth to the fact that many of these people are biologists-turned-coders who just don't have the exposure to best practices.</p> <p>That said, the core problem isn't that these people don't know about good practices, or don't care. The problem is that there is no incentive for them to spend more time learning software engineering, or to clean up their code and release it.</p> <p>In an academic research setting, your reputation (and thus your future job prospects) depends almost entirely on the number and quality of publications that you've contributed to. Publications on methods or new algorithms are not given as much respect as those that report new biological findings. So after I do a quick analysis of a dataset, there's very little incentive for me to spend lots of time cleaning up my code and releasing it, when I could be moving on to the next dataset and making more biological discoveries.</p> <p>I'll also note that the availability of funding for computational development is orders of magnitude less than that available for doing the biology. In a climate where only 10% of submitted grants are getting funded, scientists don't have the luxury of taking time to clean and release their code, when doing so doesn't help them keep their lab funded.</p> <p>So, there's the problem in a nutshell. As a bioinformatician, I think it's perverse and often frustrating. </p> <p>That said, there is hope for the future. With second-and-third generation sequencing, in particular, biology is moving into the realm of high-throughput discovery, where data mining and solid computational pipelines become integral to the success of the science. As that happens, you'll see more and more funding for computational projects, and more and more real software engineering happening.</p>

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