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plone4bio

plone4bio is a set of products to do bioinformatics within our preferred CMS, Plone.

We are pleased to announce a new plone project: plone4bio. As the name suggest it is intended as a set of products to do bioinformatics within our preferred CMS, Plone.

What is plone4bio

The rationale of the plone4bio project is to provide an integrated environment where it is possible to manage and analyze sequences of proteome or genome.
The plone4bio package provides the possibility to add a new content type, called sequence, than can be either written by hand or imported from a FASTA file, and to apply to that sequence a program, called predictor, that gives a back a plot of predicted probabilities for the sequence to have a given property (the property that the predictor tries to determine).
A predictor can try to assess if a protein sequence is trans-membrane, whether a signal peptide exists, and so on.

plone4bio.base

The plone4bio.base is a 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, incapsulating 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.

Requirements

  1. python2.4
  2. python setup tools (the python-setuptools Debian package)
  3. biopython
  4. PIL

Download and Project page

The software is available at http://www.plone4bio.org

Further informations

Either the web site or subscribe at 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.
This product is produced independently from the product Plone, and carries no guarantee from the Plone Foundation about quality, suitability or anything else. The supplier of this product assumes all responsibility for it.