• Edit 2017-01-09: provide upgrade path to Pulse …

Here are my notes for setting up an Ubuntu VM to work on some web applications. This is intended to be a sandbox for development, so I'll err on the side of convenience (at …

Illumina provides a program for demultiplexing sequencing output called bcl2fastq. They get a gold star for releasing the source - the downside is that they release binaries only for RHEL/CentOS, and no build instructions for Ubuntu. So …

I learned a bit about list creation in elisp today. Here's how you join a list of strings in elisp:

(mapconcat #'identity '("" "path" "to" "someplace") "/")

But I learned (thanks to legoscia on stackoverflow) that simply replacing an element in the list with a variable results in an error:

(let ((path …

• Edit 2015-07-26: added a section on date formatting
• Edit 2016-07-11: add reference to Tidy Data

This post contains the content of a lecture prepared for Laboratory Medicine residents as part of a series on medical informatics.

Probably not as efficient as using the sqlite3.Row class, but works when actual dict objects are required. Adapted from https://docs.python.org/2/library/sqlite3.html.

import sqlite3

def dict_factory(cursor, row):
    return {col[0]: row[idx] for idx, col in enumerate(cursor.description)}

con = sqlite3.connect(":memory …

Never one to pass up the opportunity for yak-shaving, I thought I'd finally try to settle on a publishing platform for various notes and other content that I have scattered about …

These are my notes that I took while setting up a …

Notes to myself about installing R packages.

install.packages(c("ape","sqldf","ROCR"), repos="http://cran.fhcrc.org/", dependencies=TRUE, clean=TRUE)

source("http://bioconductor.org/biocLite.R")
biocLite(c("Biostrings","BSgenome …