Create New File in Finder with Alfred 2

April 4, 2013   

I have created a simple workflow for Alfred 2 which makes it easy to create a new text file in the frontmost finder window. Update – at the suggestion of a visitor – James Kachan – I have updated the workflow to automatically open the new file in a text editor. An alternative, more advanced workflow for Alfred 2 has also been created by Ian Isted.


Open Alfred 2, and type new followed by the name of the file. If you just type new, a file called ‘untitled.txt’ will be created.



Alfred  Downloads  Utilities  Mac OSX

Excel Template for Mapping Four 96-Well Plates to One 384-Well Plate

March 6, 2013   

Featured on Getting Genetics Done, this excel template helps you map 96 well templates to a single 384 well plate using Microsoft Excel.



Copy in Identifiers

A 384 well template is produced

And a summary table too.

Downloads  Genetics  wet lab  excel

Django models for Chado

January 9, 2013   

Here is my first stab at models for django of the Chado database schema

Available here on github gists.

Bioinformatics  Programming  Database gist

Install Tabix and Samtools on Mac

December 27, 2012   

I was having a tough time getting Tabix and Samtools installed on my mac – but found a very easy way to do it. You’ll have to install Homebrew and xcode.

xcode can be installed using the appstore.

Homebrew can be installed by copying and pasting the following into the terminal:

/usr/bin/ruby -e "$(curl -fsSL"

Next you type this:

brew tap homebrew/science
brew install tabix
brew install samtools

And you are done. Homebrew has easy commands for symlinking these too. These details are mentioned when you install items.

Bioinformatics  homebrew sequencing vcf


December 19, 2012   

The Variant Caller Format developed by the 1000 genomes project makes it easy to filter and manage large amounts of variant information for a set of subjects.

STATA offers an easy interface for sorting, filtering, and manipulating large datasets. I have developed a tool, vcf that makes it easy to import .vcf files into Stata (no easy task!).

The program does two challenging things to prepare the file for Stata:

  1. It Splits the INFO column (delimited by ; ) into seperate columns. This is necessary because STATA has a string limit of 244 characters and truncates this column otherwise.
  2. It recodes genotypic data, showing the genotypes of each individual.


ssc install vcf


I have only tested with STATA 12/SE. I believe it will also work with STATA 11 and perhaps earlier.


vcf using "path/to/file.vcf"


  1. While it is possible to read in very large files – this program cannot handle enormous VCF Files. I have successfully loaded in files that are a few gigabytes. Therefore ideally you’ll filter enormous VCF Files prior to using this.
  2. If your VCF Files has more than 9 alternative alleles, this program will incorrectly assign alleles beyond the 9th alternative allele.


This program is no longer supported.

Programming  STATA Programs  1000genomes STATA tool vcf