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 information.
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 Enjoy. 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 [email protected] 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, [email protected], that you can join here: http://ackbar.biodec.com/cgi-bin/mailman/listinfo/p4b -- .*. finelli /V\ (/ \) -------------------------------------------------------------- ( ) Linux: Friends dont let friends use Piccolosoffice ^^-^^ -------------------------------------------------------------- Era uno che per sembrare un genio avrebbe dovuto essere completamente diverso. Beppe Viola _______________________________________________ Product-Developers mailing list [email protected] http://lists.plone.org/mailman/listinfo/product-developers
