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Comment by acomjean | Hacker News Reader

I've started working in Bioinformatics. The languages in use and libraries seem to by Perl/Python and some java. Except for the stuff that needs to be fast, then its C. Although I notice some movement to use Rust instead of C (having installed some C based tools having package management would be glorious).

It would seem the concurency model of go would be a great fit for a lot of those existing python/perl tools. My searchingg for projects show it hasn't really taken off in this domain. I might start rolling my own packages.

How is the package management in Go? Data structures and String manipulation? And is does that concurency scale across nodes (al la MPI)?

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I'm a computational biologist that recently ported our webserver (genestation.org) from Tripal (PHP/Drupal) to Go. The performance gains were huge, but the simplicity of development and deployment was even better. I'd strongly recommend Go for a biology web server. However, Biogo is not remotely as far along as Biopython or Bioperl. Also, Perl beats Go for ease of string handling. Unfortunately, there is no equivalent to Numpy/Scipy in Go. Despite these areas of weakness in the ecosystem, I have switched to Go entirely except for one-liners and one-off parsing in Perl.

> Unfortunately, there is no equivalent to Numpy/Scipy in Go.

We're trying! https://groups.google.com/forum/#!forum/gonum-dev github.com/gonum . Bug reports and contributions encouraged.

Thanks. They new site is snappy.

Tripal I had never heard of. It uses "Chado" db schema which I have heard of (though flybase) which while flexible isn't always performant.

Performance gains and simplified development are so appealing (I have 12 tools to maintain in Java/perl/php)..

Biogo is what I was looking for. https://github.com/biogo/biogo

You said above you 'may start rolling your own packages'. If you're interested in helping develop the numeric ecosystem, please come join us at gonum https://groups.google.com/forum/#!forum/gonum-dev github.com/gonum.

Dan (the lead developer of biogo) is very competent and I'm sure would love bug reports and PRs in biogo as well.

Chado does have substantial performance problems for use as a webserver backend. We use elasticsearch for full-text search and as JSON document store, which improves performance substantially.

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