Psst! I've posted some details about my notebook setup here.

Shell pipelines in Python

The UNIX shell is an indispensible tool for project organization and data management in bioinformatics. I spend a lot of time in the shell, and having picked up on a lot of time-saving techniques over the years it might just be my favorite computing environment.

The shell has its limitations, however. Piping, the very feature that gives the shell its ...

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Filter stderr while piping in UNIX

Permalink: 2015-12-14 by Daniel S. Standage in blog tags: shell

Nifty trick for filtering stderr in the middle of a shell pipeline.

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Reading roundup

Roundup of links to interesting reads from the last couple of weeks.

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Random gene distribution: follow up

I recently sketched out some notes on random placement of genomic intervals. Here I show a more concrete implementation

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Some notes on random gene distribution

I've been looking at statistics of gene spacing, but as of yet have not compared these to benchmarks of "randomly" distributed genes. Here I sketch out a few rough notes on the topic.

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Consortium authors in EndNote

Today I was reformatting a manuscript and changing from a numbered citation style to an author/date citation style. In doing so, I found some issues with my EndNote references library that had gone unnoticed before since they were tucked away in the reference list. One of the issues involved citation of a paper with a single consortium author, designated ...

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A model invited speaker

Today I had the privilege of attending an excellent departmental seminar from an invited speaker. I've seen plenty of great seminars in grad school but I've also experienced my fair share of seminars that were...less than phenomenal. The content of the talk was interesting, and the speaker's presentation was engaging, but there were a couple of ...

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Group meeting feedback

I gave a group meeting today on my iLocus work, and got some good feedback from the group.

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Cleanup: supplementary tables for our genome paper

We submitted a genome paper to Genome Biology over the weekend. I'm going through our repository and tidying things up, and I realized I have not had a chance to record my notes on several of the supplemental tables providing a comparison of genome features across seven species. I'll go ahead and do so here.

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New lab notebook setup: my motivation

Permalink: 2015-11-17 by Daniel S. Standage in blog tags: meta

My first research blog was a self-hosted Wordpress blog run from an Ubuntu server in our lab. I was initially enamored by the supposed control and flexibility this gave me, but when I changed institutions a year or so later I was not quite as enamored with the work that went into migrating the content, nor the time I spent ...

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