[Product-Developers] plone4bio stable released

m at pavis.biodec.com m at pavis.biodec.com
Mon Sep 7 11:56:50 UTC 2009

Hi everybody

We released few days ago the stable release for the plone4bio
product. Here http://www.plone4bio.org/trac/ and there
http://plone.org/products/plone4bio you will find all the relevant

In a nutshell, plone4bio is a project to provide an integrated
environment where it is possible to manage and analyze sequences of
proteome or genome. In this release we have added a very important
feature, namely a product that let Plone act as an interface to a BioSQL
dataabase. 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 can be used seamlessly from BioPerl, BioPython, BioJava,
and BioRuby.

The main new content type defined by plone4bio is the Sequence. The
Sequence can be written by hand, imported from a FASTA file or accessed
through a BioSQL database. The Sequence can then be visualized, showing
its textual annotations data and its graphical features. It can be
searched, using plone built-in search engine. Then it is possible to
apply to the Sequence a program, called a predictor, that calculates the
probabilities of the sequence to have a given property (the property
that the predictor tries to determine) and to plot its results as new
features or annotations. For example a predictor can try to assess if a
protein sequence is trans-membrane, whether a signal peptide exists, and
so on.

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

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


p.s.: by `We' I mean BioDec (http://www.biodec.com) an Italian company,
specialized in bioinformatics. Feel free to contact me, or the company
at info at biodec.com for any problem or for any request about plone4bio:
we are looking for people interested in using our product in research or
academia and for ideas about extensions and improvements. There is a
mailing list, p4b at biodec.com, that you can join here:

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