Hacker News Reader

pjotrpon FOSDEM 2023 is live now

I love FOSDEM. The vibe, the speakers, the audience, the place. I always learn things and it helps set the agenda for the next year(s). We organised one of the devrooms and it was amazing. And note it is all done by volunteers: from the organisers all the way to the people cleaning toilets. Thank you all!

pjotrpon From Ruby to Node: Overhauling Shopify’s CLI for a better developer experience

Looks like it is mostly deployment issues they are fighting. I suggest to use a true deployment tool like GNU Guix.

pjotrpon Challenge to crack homomorphic encryption of genotypes and phenotypes

And $1,000 for the winner.

pjotrpon Why Docker Is Not Yet Succeeding Widely in Production

Docker for reproducible Science is an intermediate solution. While a Docker image can be moved and rerun (with some luck) the content of a Docker image is actually not transparent.

Reproducibility implies being able to regenerate the full container including software version control and visibility of the full dependency chain all the way down to BLAS and glibc! You can't do that by using apt, rpm, Perl CPAN, rubygems, Python pip and the like. None of these package managers have been designed for true isolation of packages and full reproducibility. That is why today people go with Docker. The shortcomings of these package managers drive people to Docker.

The technology for regenerating exact Docker containers exists in the form of GNU Guix and/or Nix packages. The fun fact is that when using GNU Guix, Docker itself is no longer required.

Watch GNU Guix.

pjotrpon A farewell to bioinformatics (2012)

The bio in bioinformatics is the important bit. Informatics plays second fiddle, even in the name. Very few will appreciate your beautiful code, but many will appreciate you finding a cure for cancer. That is the reality of bioinformatics, most of the code has a short shelf life. If you luck out, your software may live longer, as is the case with samtools. That samtools code is crappy is true, still the much cleaner code alternatives, sambamba and bamtools, are not much used! Go figure.

Maybe bioinformatics is not the place to aim for great informatics. We do bioinformatics because of love of science first and foremost. This is frontier land, the wild west, and it pays to play quick and dirty. I would suggest to hang on to some best practices, e.g. modularity, TDD and BDD, but forget about appreciation. Dirty Harry, as a bioinformatician you are on your own.

To be honest, in industry it is not much different. These days, coders are carpenters. If you really want to be a diva, learn to sing instead.