Post tagged: computational biology

Common tasks in Galaxy

It's all there in the documentation, but sometimes it's hard to find. This document gives you another place to look.

So how do I ...

... create admin users?

Curiously, the identity of admin users is hardcoded into the Galaxy configuration file. (Which makes it secure, I guess, but separate from the …

Galaxy toolsheds

Galaxy toolsheds

Relatively painless tool-sharing

This is a more recent innovation in Galaxy, which can make it a somewhat confused one: the concept of the toolshed has changed over its lifetime, the documentation is incomplete, and there's a slightly strange emphasis in the documentation that exists. So …

Mile-high description

Toolsheds …

Language Wars

"What language would you recommend to introduce programming to an audience of life science students at a bachelor level?"

(Originally published on BiocodersHub)

Following several lengthy and passionate discussions in different venues on what language to use for teaching bioinformatics, I've started cutting and pasting my reply. And here it is.

You'll get a lot of different opinions on this because:

  • It's a religious issue. That is, it comes …

Hitchhikers guide to BioPython: SeqRecords

For the novice, more-than-raw sequences.

(Previously published on BiocodersHub.)

Previously I'd spoken about how Biopython represents sequence data with the Seq class. But there is also the SeqRecord class:

  • A Seq is just raw sequence data and information about what type of sequence it is.
  • A SeqRecord is a Seq and all the other information …

Galaxy miscellanea

Odds and ends and the surprising.


If you are serving the installation with a proxy redirect (e.g. the galaxy server is running on port 7070 but is being redirect by Apache to appear at port 80 on /galaxy), while you can access Galaxy at both addresses, login will …

Installing Galaxy

Setting up a production version of GMOD Galaxy for general use.

This presents one way to create an optimized production Galaxy instance. Variations are certainly possible and some of the choices presented are/were dictated by local culture. Certain settings may be more suitable for production or development environments. Nonetheless, this presents a start-to-stop process for installation and setup.

Note: this …