plone4bio

Warning

This product has not had a release in over 1 year and may no longer be maintained.

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

Project Description

BioDec is 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 a web-based integrated environment where it is possible to manage and analyze biological sequence data. The plone4bio package provides the possibility by adding new content types to the Plone CMS.

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, 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 ready-to-use predictor for coiled-coils.

Requirements

1. python2.6 (the older version worked with plone3, so it required python2.4: we strongly suggest to use the new plone4-based version)
2. python setup tools (the python-setuptools Debian package)
3. biopython
4. PIL
5. bioperl for some graphics

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/

Further informations

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.

BioDec S.r.l. is an Italian company

• Address: BioDec S.r.l.; via Calzavecchio 20/2; I-40033 Casalecchio di Reno (BO), Italy.
• Email: info@biodec.com
• WWW: http://www.biodec.com
• Phone: (+39)-051-0548263
• Fax: (+39)-051-745958

Disclaimer

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.