Snacker News

You can Bash that

August 20, 2015

It’s well known that the Unix shell allows for some amazing feats of brevity. But did you know it was possible to perform diffs on biological molecules designed protein structures, transcribe DNA to RNA, and perform other computational biology feats from your command line? What follows is some fun with Unix in computational biology.

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Scaling biology with techniques from computer science

August 1, 2017

Computation has become a central part of biology. These days, if you have biological questions, you are more than likely going to use computers, sequencing, and laboratory automation to answer them.

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The Unix shell as a biologist sees it

September 10, 2017

This post began as a simple question: “How do I make this script I just wrote accessible on the command line?” The answer took us on a journey. Along the way, we learned a lot about what exactly the “command line” is, and how it’s useful for humans doing research and engineering in biology.

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Switching to fish from bash

May 21, 2017

As someone who starting computing as a teenager in 2000 with the “public beta” of Mac OS X, my first shell was GNU Bash. Seventeen years later, I still use Bash every day.

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Python generators for biologists

August 24, 2017

The use of generators is an intermediate programming topic that comes up again and again in biological codebases. In short, a generator lets you store some code to run later. In biological codebases, generators are excellent for times when you would like to go through all the elements in some collection and operate on all of them, and then collect the result of all the operations into another list.

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How to become a computational biologist

August 1, 2017

Computation has become a central part of biology. These days, if you have biological questions, you are more than likely going to use computers and laboratory automation to answer them.

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Advice for biologists learning about coding: don’t learn outdated technology

July 20, 2017

As a biologist who learned how to code to solve my problems and answer biological questions, here’s some advice to those like me: don’t learn outdated technology.

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How to run Rosetta with SLURM on a high-performance compute cluster

Feb 21, 2016

Rosetta’s sampling methodology allows searching protein sequence functional space (which is extremely rugged). To effectively use Rosetta, high performance computing (cluster computing) is necessary to carry out many sampling trajectories in parallel.

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