'A Farewell to Bioinformatics'
Readers may take a look at this reddit thread containing many good discussions on bioinformatics. The leading article is very negative about bioinformatics, but it had the good impact of bringing in valuable comments. Especially, the comments from chilloutdamnit and chrismiller are quite informative.
Do our readers agree about this on code optimization?
I’m in the field of bioinformatics to improve human health and understand deep biological questions. I care about reproducibility and accuracy in my code, but 90% of the time, I could give a rat’s ass about performance. I’m trying to find the answer to a question, and if I can get that answer in a reasonable amount of time, then the code is good enough. This is especially true when you consider that 3/4 of the things I do are one-off analyses with code that will never be used again. (largely because 3/4 of experiments fail - science is messy and hard like that). If given a choice between dicking around for two weeks to make my code perfect, or cranking out something that works in 2 hours, I’ll pretty much always choose the latter. (“Premature optimization is the root of all evil (or at least most of it) in programming.” –Donald Knuth)
That said, when we do come up with some useful and widely applicable code, we do our best to optimize it, put it into pipelines with robust testing, and open-source it, so that the community can use it. If his lab never did that, they’re rapidly falling behind the rest of the field.
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Ycombinator thread on the same topic got even bigger. Their community is more in agreement with Fred, the frustrated ex-bioinformatician. Here are two sample comments from the thread -
My experience working as a scientific programmer is this: my colleagues aren’t forthcoming. I could list case after case of failure to document or communicate crucial details that cost me days, weeks and even months of effort. But I won’t, until I have another job lined up. If I were in the author’s position (I’m in another field), I would insist that my colleagues– all of them, in whatever field I ended up working, were forthcoming about their work. This is non-negotiable. Being over-busy is no excuse. (It may be an excuse for not being forthcoming, but right or wrong, I couldn’t care less –I would not work with such people if I could avoid it, for whatever reason.)
Academia rewards journal publication and does not adequately reward programming and data collection and analysis, although these are indispensable activities that can be as difficult and profound as crafting a research paper. At least the National Science Foundation has done researchers a small favor by changing the NSF biosketch format in mid-January to better accommodate the contributions of programmers and “data scientists”: the old category Publications has been replaced with Products.
Naming is important to administrators and bureaucrats. It can be easy to underestimate the extent to which names matter to them. Now there is a category under which the contribution of a programmer can be recognized for the purpose of academic advancement. Previously one had to force-fit programming under Synergistic Activities or otherwise stretch or violate the NSF biosketch format. This is a small step, but it does show some understanding that the increasingly necessary contributions of scientific programmers ought to be recognized. The alternative is attrition. Like the author of the article, programmers will go where their accomplishments are recognized.
Still, reforming old attitudes is like retraining Pavlov’s dogs. Scientific programmers are lumped in with “IT guys.” IT as in ITIL: the platitudinous, highly non-mathematical service as a service as a service Information Technocracy Indoctrination Library. There is little comprehension that computer science has specialized. For many academics, scientific programmers are interchangeable IT guys who do help desk work, system and network administration, build websites, run GIS analyses, write scientific software and get Gmail and Google Calendar synchronization running on Blackberries. It is as if scientists themselves could be satisfied if their colleagues were hired as “scientists” or “natural philosophers” with no further qualification, as opposed to “vulcanologist” or “meteorologist” (to a first order of approximation).
I have some experience working at a genomics research company and I’ll broadly +1 Fred’s experience about the industry, although in less negative terms. I got out before I got jaded, so my perspective is a bit more “oh, that’s a shame” than his. I really like genetics, bioinformatics, hardware, deep-science, and all that but the timing and fit wasn’t right.
The tools are written by (in my experience) very smart bioinformaticians who aren’t taught much computer science in school (you get a smattering, but mostly it’s biology, math, chemistry, etc.). Ex:
http://catalog.njit.edu/undergraduate/programs/bioinformatic…
http://www.bme.ucsc.edu/bioinformatics/curriculum#LowerDivis…
http://advanced.jhu.edu/academic/biotechnology/ms-in-bioinfo…
The tools themselves are written by smart non-programmers (a very dangerous combination) and so you get all sorts of unusual conventions that make sense only to the author or organization that wrote it, anti-patterns that would make a career programmer cringe, and a design that looks good to no one and is barely useable.
Then, as he said, they get grants to spend millions of dollars on giant clusters of computers to manage the data that is stored and queried in a really inefficient way.
There’s really no incentive to make better software because that’s not how the industry gets paid. You get a grant to sequence genome “X”. After it’s done? You publish your results and move on. Sure, you carve out a bit for overhead but most of it goes to new hardware (disk arrays, grid computing, oh my).
I often remarked that if I had enough money, there would be a killing to be made writing genome software with a proper visual and user experience design, combined with a deep computer science background. My perfect team would be a CS person, a geneticist, a UX designer, and a visual designer. Could crank out a really brilliant full-stack product that would blow away anything else out there (from sequencing to assembly to annotation and then cataloging/subsequent search and comparison).
Except, I realized that most folks using this software are in non-profits, research labs, and universities, so - no, there in fact is not a killing to be made. No one would buy it.
