From andreas.biegert at googlemail.com  Fri Dec  8 13:00:00 2006
From: andreas.biegert at googlemail.com (Andreas Biegert)
Date: Fri, 8 Dec 2006 19:00:00 +0100
Subject: [BioRuby] Contributing to BioRuby
Message-ID: <fd0847170612081000h1a5ebba7s902b5c95b653b3cf@mail.gmail.com>

Hi,

I am a graduate student in bioinformatics at the University  of Tuebingen,
Germany. In the last three years, two bioinformatics students and me have
been working at the  Max-Planck-Institute for Developmental Biology in
Tuebingen on the development of a  Bioinformatics Toolkit for  Protein
Sequence Analysis (http://toolkit.tuebingen.mpg.de, Publication:
http://nar.oxfordjournals.org/cgi/reprint/34/suppl_2/W335).  The  Toolkit
classes and modules are written entirely in Ruby and the web part is based
on the RubyOnRails web-framework. Currently, we are in the process of
streamlining the codebase and workflow. Since BioRuby offers such a
convenient access to common bioinformatics utilities and functionality we
would like to use it in our Toolkit, for example for sequence parsing and
reformatting.  Unfortunately some of the functionality we need, such as the
sequence formats that are used throughout the tools in the Toolkit seem to
be yet unsupported by BioRuby (e.g. CLUSTAL, A2M, A3M). Would it be possible
for me to contribute to BioRuby and extend such functionality? Thanks for
providing the bioinformatics community with this great library!

Best Regards,
Andreas

From ktym at hgc.jp  Sun Dec 24 14:07:38 2006
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Mon, 25 Dec 2006 04:07:38 +0900
Subject: [BioRuby] BioRuby 1.1 pre1 release
Message-ID: <013EDFC4-C6C5-439C-9CBB-5024BBA51403@hgc.jp>

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/