plone4bio STABLE is out !

We have released a new stable release of plone4bio, with BioSQL support.

Plone4bio 1.0 announcement

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 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@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@biodec.com
  •  WWW: http://www.biodec.com
  •  Phone: (+39)-051-0548263
  •  Fax: (+39)-051-7459582