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plone4bio
Category: Educational, Layout and presentation, Miscellaneous, Services, Statistics & reporting
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Current release
No stable release available yet.
Experimental releases
Upcoming and alpha/beta/candidate releases
- Alpha releases should only be used for testing and development.
- Beta releases and Release Candidates are normally released for production testing, but should not be used on mission-critical sites.
- Always install on a separate test server first, and make sure you have proper backups before installing.
Project Description
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Code repositoryBioDec 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 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 and as a predictor for coil-coil ready to be used.
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.
Requirements
- python2.4
- python setup tools (the python-setuptools Debian package)
- biopython
- PIL
Download and Project page
The software is available at http://www.plone4bio.org
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)-051-7459582
