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Well, it looks like one of the biggest problems in computational biology has finally blown up in our face. I work in a very similar field to the one discussed
by veddox 6y ago
Well, it looks like one of the biggest problems in computational biology has finally blown up in our face.
I work in a very similar field to the one discussed here - ecosystem modelling. And much of the code I see is probably of a similar quality to Neil Ferguson's model. (Although I haven't had a detailed look at his work.) For all you angry devs out there, I have three comments:
1. Yes, we have a problem with code quality, and no, this should not be acceptable where policy-relevant decisions of such magnitude are concerned. (Although one should bear in mind that all science is flawed and its achieved reliability will always be limited by constraints of time/budget/etc.)
2. However, changing the status quo is really hard. Specifically, the two greatest changes that are needed are to teach proper software development practices to students in the natural sciences (just like we teach lab technique), and/or make it easier to get funding for software developer positions in a research team. This sounds easy, and ought to be easy, but both run counter to some pretty entrenched ideas held by the "old folks at the top" in universities and funding bodies. (Believe me, I'm speaking from experience :-/ )
3. But yes, we are working on it. The debate is growing, and there's a new generation of computational biologists with much closer ties to computer science who are trying to shake things up a bit. In some sense, we are several decades behind the wider CS world in the techniques we use, but we're catching up. And at the same time, we're starting to develop some of our own methods of quality control (such as pattern-oriented modelling).
- veddox 6y agoIf you're interested, here is some further reading: * DeAngelis, D. L., & Grimm, V. (2014). Individual-based models in ecology after four decades. F1000prime Reports, 6(June), 39. https://doi.org/10.12703/P6-39 https://doi.org/10.12703/P6-39 * Grimm, V., Berger, U., DeAngelis, D. L., Polhill, J. G., Giske, J., & Railsback, S. F. (2010). The ODD protocol: A review and first update. Ecological Modelling, 221, 2760–2768. https://doi.org/10.1016/j.ecolmodel.2010.08.019 https://doi.org/10.1016/j.ecolmodel.2010.08.019 * Grimm, V., & Railsback, S. F. (2011). Pattern-oriented modelling: A ‘multi-scope’ for predictive systems ecology. Philosophical Transactions of the Royal Society B, 367(1586), 298–310. https://doi.org/10.1098/rstb.2011.0180 https://doi.org/10.1098/rstb.2011.0180 * Nowogrodzki, A. (2019). How to support open-source software and stay sane. Nature, 571(7763), 133–134. https://doi.org/10.1038/d41586-019-02046-0 https://doi.org/10.1038/d41586-019-02046-0 * Wilson, G., Bryan, J., Cranston, K., Kitzes, J., Nederbragt, L., & Teal, T. K. (2016). Good Enough Practices in Scientific Computing. 1–30. http://arxiv.org/abs/1609.00037 http://arxiv.org/abs/1609.00037