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> the biologists first come up with the first concept of the tool, which is purely focused on ensuring good results. After this first iteration is completed, en

> the biologists first come up with the first concept of the tool, which is purely focused on ensuring good results. After this first iteration is completed, engineers then come in and rewrite the tool using modern engineering practices with things like speed and reliability in mind. I think that is already accepted as good practice, and the way most people in the field work, which is part of the reason why the field is in this shoddy state right now. Because in reality, most of the time those engineers don't exist and it will never advance to the second stage, but will still be used regardless. And even if you manage to find an engineer for your team, the same problem exists in many layers down your stack. As with most other kinds of software, the biologists should be treated as customers (or trained up to be skilled-enough engineers), as it is done in other disciplines. To create good accounting software you also wouldn't propose to have the accountant write the initial version of the software, would you? > Many of the projects that are critical to the foundation of genomics are reaching or have eclipsed the ten-year mark. How much longer can we expect these individuals to single-handedly maintain these code bases? What you propose sounds more like "hey, be the next idiot that commits to maintaining critical software for nothing", rather than any systemic change. The ugly secret of bioinformatics is the same one as in broader tech: Most of it runs on the backs of unpaid OSS maintainers (in this case a handful of motivated PIs that carve out some of their time for that). If you want to have good software in the sciences, you first have to solve the OSS funding problem. PS: the `user-select: none;` on your page is really annoying

jltsiren 4y ago
> As with most other kinds of software, the biologists should be treated as customers (or trained up to be skilled-enough engineers), as it is done in other disciplines. To create good accounting software you also wouldn't propose to have the accountant write the initial version of the software, would you? Accounting is a bit different, because it has already been invented. There are standards and best practices for it. In bioinformatics, writing software is often a research activity. You write software to determine what the software should do, and then you adjust your ideas and rewrite it. The person writing the first version(s) of the software is a researcher – at least in practice if not by job title.
- hobofan 4y ago
  Accounting is not a static thing, and is also constantly changing with new legislation and financial instruments popping up. Most bioinformatics tasks nowadays are not any more "creative" in their research. Specifically in the last few years a good chunk of the research is just okayish application of ML research to their field of research. For many specific problem sets in the natural science informatics disciplines, you can just stay up-to-date on ML trends and release a new paper that applies them every few years, in an almost automatable way.
  - jltsiren 4y ago
    There is a good chunk of research like that, but there is also a good chunk of research where the "biologist as a customer" model does not work. In research like that, it's the job of the person writing the software to figure out which biological problems they are trying to solve and how.

jltsiren 4y ago

> As with most other kinds of software, the biologists should be treated as customers (or trained up to be skilled-enough engineers), as it is done in other disciplines. To create good accounting software you also wouldn't propose to have the accountant write the initial version of the software, would you? Accounting is a bit different, because it has already been invented. There are standards and best practices for it. In bioinformatics, writing software is often a research activity. You write software to determine what the software should do, and then you adjust your ideas and rewrite it. The person writing the first version(s) of the software is a researcher – at least in practice if not by job title.

hobofan 4y ago
Accounting is not a static thing, and is also constantly changing with new legislation and financial instruments popping up. Most bioinformatics tasks nowadays are not any more "creative" in their research. Specifically in the last few years a good chunk of the research is just okayish application of ML research to their field of research. For many specific problem sets in the natural science informatics disciplines, you can just stay up-to-date on ML trends and release a new paper that applies them every few years, in an almost automatable way.
- jltsiren 4y ago
  There is a good chunk of research like that, but there is also a good chunk of research where the "biologist as a customer" model does not work. In research like that, it's the job of the person writing the software to figure out which biological problems they are trying to solve and how.