Jun
16th
Mon
16th
The evolution of a Ruby programmer
A very Ruby in-joke
Jun
3rd
Tue
3rd
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'
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 alignment: YER087C-A is not a verified ORF
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.
May
19th
Mon
19th
Simple Ruby markdown script using BlueCloth and RubyPants
#!/usr/local/bin/ruby
require 'rubygems'
require 'bluecloth'
require 'rubypants'
puts RubyPants.new(BlueCloth.new(File.open(ARGV.shift).read).to_html).to_html
May
4th
Sun
4th
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 ++++++++++
8 files changed, 100 insertions(+), 14 deletions(-)
