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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 simp

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.

acomjean 11y ago
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 https://github.com/biogo/biogo
- howeman 11y ago
  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 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.
- biomcgary 11y ago
  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.
howeman 11y ago
> Unfortunately, there is no equivalent to Numpy/Scipy in Go. We're trying! https://groups.google.com/forum/#!forum/gonum-dev https://groups.google.com/forum/#!forum/gonum-dev github.com/gonum . Bug reports and contributions encouraged.

acomjean 11y ago

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 https://github.com/biogo/biogo

howeman 11y ago
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 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.
biomcgary 11y ago
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.

howeman 11y ago

> Unfortunately, there is no equivalent to Numpy/Scipy in Go. We're trying! https://groups.google.com/forum/#!forum/gonum-dev https://groups.google.com/forum/#!forum/gonum-dev github.com/gonum . Bug reports and contributions encouraged.