This blog has migrated to a new more awesome home at Biorelated.  All future posts will be written at this new biorelated location. 


Announcing scribl-rails

PfEMP1 domains drawn with scribl

Sometimes back I had mentioned about scribl javascript framework for drawing bioinformatics glyphs on HTML5 canvas. If you are a Rails developer you will be happy to know that I have written  scribl-rails, an asset helper for including scribl in your application asset pipeline.


Add the following to your gemfile:

gem 'scribl-rails' 

ran bundle install from the application directory

Add the following directive to your Javascript manifest file (application.js):

//= require scribl 

Enjoy using scribl-rails and creating cute bio-graphics! Many thanks to Chase Miller for the awesome library!

For more information and development check out the scribl-rails at github

Goodbye Steve Jobs


                                     Steve Jobs 1955 – 2011

You inspired and awed with equal measure. I admired your insight,courage and knack for walking along the unbeaten path.

Use Scribl to draw genomic glyphs on HTML5 canvas

The Scribl library by Chase Miller is an awesome and a promising Javascript library for visualizing biological sequence information and rendering it on the web. Scribl  generates biological charts of genomic regions, alignments, and assembly data. The library is under continuous development and I have been able to use it for some internal projects!

A very nice list of examples and introduction is available at the home page and the wiki provides an elaborate user guide!

Happy biology!

Keep track of Bioruby plugins

Biogems.info is a new site for keeping track of new and existing Bioruby plugins. Plugins are separate code libraries that split functionality out of the Bioruby main tree. The idea is to have a core Bioruby release and to allow Ruby developers to contribute to Bioruby through plugins. According to Bonnal, the maintainer of biogem (the bio-plugin crafting tool),  plugins are separately maintained and may represent experimental or work in progress.

To read more about Bioruby plugin system please refer to the wiki page on plugins.

Happy biology!

Bioruby 1.4.2 released!

The Bioruby development team has continued to work tirelessly to bring us the latest release of the Ruby bioinformatics library commonly referred to as bioruby. A list of all the new changes is available  here . One of the most pleasant news for beginners is that the Bioruby tutorial has been updated thanks to Michael O’Keefe and Pjotr Prins. The Release is largely a bug fix release with updates on web services from SOAP to REST interfaces. Upgrading to the latest release is easy…
gem update bio
gem install bio

Happy biology!

Processing netMHCII-pan prediction output

Like most informatics throughput methods, epitope prediction generates a lot of output and in a not so friendly format suitable for subsequent analysis. I considered writing a parser for the output using Ruby, but would that not take long? A simple vim function that I added to my .vimrc file to format the output and use a single keystroke worked the magic and saved time.

" formating output from netMHCII-pan program
function! FormatNetmhcOutput()
   g/^\#/norm dd 
   g/^--/norm dd
   g/^Protein/norm dd
   g/^pos/norm dd
nmap   ;h  :call FormatNetmhcOutput()

This function can be called by pressing the ; and h key when in normal mode. It removes comments and provides a csv output that can be read with a simple R directive.

data <– read.csv("file.csv") 

sample output