[BioRuby] BioRuby 1.1 pre1 release

[Toshiaki Katayama]

Dear BioRuby users and developers,

Merry Christmas! (I don't trust any religion other than science, although.)


I have just put the latest BioRuby package as a BioRuby pre-v1.1 release.

  http://bioruby.org/archive/bioruby-1.1.0-pre1.tar.gz

Please play with it and report us if you find any problem.


* Phyloinformatics support

This release includes some phyloinformatics libraries (Bio::Tree,
Bio::Newick, Bio::Nexus etc.), which are developed during the
Phyloinformatics hackathon held in this December at NESCent, Durham, NC.
See http://hackathon.nescent.org/ more details and some photos.


* BioRuby shell on Rails

BioRuby v1.1 also comes with completely re-written BioRuby shell on Rails.
Now, you can use BioRuby within the web browser with AJAX (you just need
to install Ruby on Rails). Try

  % bioruby --rails testproj

and type-in some ruby programs in the text box.

  a = 123
  seq = getseq("atgc" * 10).randomize
  pep = seq.translate

Console (irb enhancemnet) version of the BioRuby shell is still available.
Try

  % bioruby --irb testproj
  bioruby> demo

and see how it works. You can continue with objects created during the irb
session in rails mode just by restarting (and vice versa).

  % bioruby --rails testproj

More complex operations can also be done in the shell. For example,
if you have installed RSRuby (http://rubyforge.org/projects/rsruby),

  require 'rsruby'
  r = RSRuby.instance
  r.install_packages("ape")
  r.library("ape")
  r.example("plot.phylo")

will work even in the rails mode. In this case, you will find generated
figure as a 'Rplots.ps' file in your 'testproj' directory.
I'll try to display these images or other appropriate representation of
objects in the web interface.


TODOs before the final v1.1 release includes:

* Change license from LGPL to Ruby's 
  (I'll ask for each developer on this in the separate mail, but
  if you have any *objection* to this, please let me know ASAP).
* Finishing English/Japanese tutorial to follow changes on shell on Rails
* Update sample/ directory


You have any comments or suggestions, please let us know.


P.S.
* I'll make refactoring on wiki site, and will give a write account
  to any of you interested.
* I'll reply to emails which I coludn't find enough time to write back
  (especially to Jan, sorry).
* I heard that the BioRuby's BLAST XML parser can fail with 2.2.15.
  If you have same problem, please let us know with your error log and data.

Regards,
Toshiaki Katayama
--
Human Genome Center, Institute of Medical Science, University of Tokyo
4-6-1 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan
tel://+81-3-5449-5614, fax://+81-3-5449-5434
BioRuby project     http://bioruby.org/
GenomeNet/KEGG      http://www.genome.jp/
Human Genome Center http://www.hgc.jp/