Michael Barton

Starfish, Rake, and Sun Grid Engine

Tue, 12 Aug 2008 12:00:57 -0400

It’s dirty, but it’s a first attempt at starting parallel jobs using a rake task.

Install a Ruby Gem without sudo access

Thu, 24 Jul 2008 11:29:48 -0400

gem install gem_name --install-dir=~/.gems/

Makers of GitHub, release a paste bin with git support - Gist

Tue, 22 Jul 2008 06:37:11 -0400

Makers of GitHub, release a paste bin with git support - Gist

Great LaTeX thesis template

Thu, 19 Jun 2008 13:00:01 -0400

Great LaTeX thesis template

Strategy for using git in a workflow

Wed, 18 Jun 2008 14:57:52 -0400

Strategy for using git in a workflow

Times Higher Education - Curse.com or blessing.net? Or be silent and take up stamp collecting

Mon, 16 Jun 2008 08:43:12 -0400

Times Higher Education - Curse.com or blessing.net? Or be silent and take up stamp collecting

The evolution of a Ruby programmer

Mon, 16 Jun 2008 08:05:55 -0400

The evolution of a Ruby programmer: A very Ruby in-joke

Example bioinformatics data validations

Tue, 03 Jun 2008 06:26:10 -0400

validates_true_for :alignment, :logic => lambda {

re = Regexp.new(/\d+\s\d+/) ! re.match(alignment) },

:message => 'Alignment field should not contain alignment count and length'

validates_format_of :alignment,

:with => /F(Y[A-Z]{2}\d{3}[CW](-[AB])?)/,

:message => 'Alignment should contain an S. cerevisiae gene'

Example bioinformatics log file

Tue, 03 Jun 2008 06:26:00 -0400

W, [2008-06-03T11:29:39.719022 #29112] WARN — : Load gene: Q0075 is not a valid coding ORF

W, [2008-06-03T11:29:40.642888 #29112] WARN — : Load alignment: No yeast ORF found in MYBR098W alignment

W, [2008-06-03T11:29:42.254248 #29112] WARN — : Load alignment: YDR474C is not a verified ORF

W, [2008-06-03T11:29:42.585707 #29112] WARN — : Load alignment: YER087C-A is not a verified ORF

Go West, Young Man: Does Open Access Really Matter in the Long Run?

Thu, 29 May 2008 07:08:51 -0400

Go West, Young Man: Does Open Access Really Matter in the Long Run?

Using lighthouse to manage a research project

Thu, 29 May 2008 06:35:00 -0400

Using lighthouse to manage a research project: Lighthouse has a simple interface that is intuitive. The ticketing system dovetails well with Github. It’s nice to be able to create a ticket for some thing that needs doing, then fix it and point to the Git patch that does the fix.

Simple Ruby markdown script using BlueCloth and RubyPants

Mon, 19 May 2008 11:26:15 -0400

#!/usr/local/bin/ruby

require 'rubygems'
require 'bluecloth'
require 'rubypants'

puts RubyPants.new(BlueCloth.new(File.open(ARGV.shift).read).to_html).to_html

Yeast gene reqular expression

Thu, 08 May 2008 08:03:10 -0400

Y[A-Z]{2}\d{3}[CW](-[AB])?

Revisions welcome

Git pull messages show you your hard work

Sun, 04 May 2008 07:08:04 -0400

Updating 60661c5..f7326c6
Fast forward
 .gitignore            |    2 ++
 Rakefile              |   22 ++++++++++++++++++++++
 analysis/project.rake |   28 ++++++++++++++++++++++++++++
 config/environment.rb |   16 ++++++++++++++++
 controller/main.rb    |    8 +++++++-
 model/project.rb      |   12 ++++++++++++
 start.rb              |   16 +++-------------
 view/index.haml       |   10 ++++++++++
 8 files changed, 100 insertions(+), 14 deletions(-)