[BioSQL-l] Announcing Plone4bio 1.0

[Ivan Rossi]

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Plone4bio 1.0 announcement
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BioDec is pleased to announce the new stable release of plone4bio.

Plone4bio is a project to provide an integrated environment where it
is possible to manage and analyze biological sequences within the
Plone (http://plone.org) content management system.

What's new
----------

In this release we have added a major feature, namely a product that let
Plone act as a web interface to a BioSQL database.

BioSQL (http://www.biosql.org/) is a generic relational model covering
sequences, features, sequence and feature annotation, a reference
taxonomy, and ontologies (or controlled vocabularies): a BioSQL database
(as you know) can be used seamlessly from BioPerl, BioPython, BioJava,
and BioRuby.

A BioSQL databases is connected with a standard connection string to a
plone4bio adapter, and then the content of the BioSQL database can be
searched, using the Plone internal search engine and the plone
collections, it can be browsed, including the usual graphical mapping of
the features on the sequence, and in general handled by the standard
Plone CMS machinery.

Download and Project page
-------------------------

The software is available at http://www.plone4bio.org 
The documentation is available at http://www.plone4bio.org/trac/wiki/Install
The SVN repository is available at http://www.plone4bio.org/svn/

plone4bio mailing list: http://ackbar.biodec.com/cgi-bin/mailman/listinfo/p4b

plone4bio demo site (read-only): http://p4bdemo.biodec.com

Installation notes
------------------

The package to install to have a full plone4bio site running is
plone4bio.buildout

The plone4bio.base is just the package that defines a skeleton
predictor: deriving from that it is possible to integrate any other
application and visualize all the results together.

biocomp.pscoils is an example predictor, encapsulating the pscoils
algorithm by Fariselli et al. available at http://www.biocomp.unibo.it/
It is intended both as an example on how to integrate one's own
predictor in the plone4bio framework and as a ready-to-use predictor for
coiled-coils.

Requirements:

  - python2.4
  - python setup tools (Debian users: the python-setuptools package)
  - BioPython
  - PIL
  - BioPerl for some graphics

Further information
--------------------

Either the web site or the mailing list p4b at biodec.com

For installation and documentation issues refer to README.txt and INSTALL.txt
files from the archive or the script published on the plone4bio wiki site.

plone4bio is published under the GPL.

To contact BioDec S.r.l.:

  - Email: info at biodec.com
  - WWW: http://www.biodec.com
  - Phone: (+39)-051-0548263
  - Fax: (+39)-051-7459582



--
Ivan Rossi, PhD - ivan AT biodec dot com OR ivan dot rossi3 AT unibo dot it
BioDec Srl, Via Calzavecchio 20/2, I-40033 Casalecchio di Reno (BO), Italy
Phone: (+39)-051-0548263 - Fax: (+39)-051-7459582 - http://www.biodec.com