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plone4bio (1.1)
- plone4bio download link: http://plone.org/products/plone4bio/releases
- Homepage of plone4bio: http://plone.org/products/plone4bio
- plone4bio repository: http://www.plone4bio.org/svn/plone4bio.buildout
- Description source: http://www.plone4bio.org/
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.
