Welcome to Plone4Bio Project

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.

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 and as a predictor for coil-coil ready to be used.

Install and development information

There is a mailing list available for developers: http://ackbar.biodec.com/cgi-bin/mailman/listinfo/p4b

Requirements:

  • python2.4
  • python setuptools
  • biopython
  • PIL

To install plone4bio, run the following commands: 

svn co http://www.plone4bio.org/svn/biocomp.pscoils/trunk/ biocomp.pscoils
cd biocomp.pscoils
sudo python2.4 setup.py install
cd ..
svn co http://www.plone4bio.org/svn/plone4bio.buildout/trunk/ plone4bio.buildout
cd plone4bio.buildout
python2.4 bootstrap.py
bin/buildout -v
bin/instance fg

Documentation

For installation and documentation issues refer to these documents:

There is a mailing list available for discussion and help: http://ackbar.biodec.com/cgi-bin/mailman/listinfo/p4b

Miscellanea

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.

Plone4bio is a BioDec project.