October 2009
1 post
April 2009
1 post
Run the current R script from vim with F2
:map <F2> <Esc>:w<CR>:!R —slave —file=%<CR>
January 2009
1 post
October 2008
1 post
“You will not go far wrong if you remember two simple guidelines at all times:
...”
– The layout of formal tables from the booktabs package for LaTeX
September 2008
1 post
Batch run mysql queries at command line
mysql -u user -ppassword database -t -e "source sql-file"
August 2008
1 post
Starfish, Rake, and Sun Grid Engine
It’s dirty, but it’s a first attempt at starting parallel jobs using a rake task.
July 2008
2 posts
Install a Ruby Gem without sudo access
gem install gem_name --install-dir=~/.gems/
Makers of GitHub, release a paste bin with git... →
June 2008
6 posts
Great LaTeX thesis template →
Strategy for using git in a workflow →
Times Higher Education - Curse.com or... →
The evolution of a Ruby programmer →
A very Ruby in-joke
1 tag
Example bioinformatics data validations
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'
1 tag
Example bioinformatics log file
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...
May 2008
5 posts
Go West, Young Man: Does Open Access Really Matter... →
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.
1 tag
Simple Ruby markdown script using BlueCloth and...
#!/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
Y[A-Z]{2}\d{3}[CW](-[AB])? Revisions welcome
Git pull messages show you your hard work
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 ++++++++++...