== The problem ==

Bioinformaticians have some very powerful toolsets, like
[http://www.bioperl.org BioPerl], [http://www.biopython.org Biopython],
[http://www.biojava.org Biojava] or the the NCBI web services, but lack a
flexible software solution for the integrated management of biosequence data.
We think that [http://www.plone.org Plone] can be the right platform to build it and
that it has great potential to become a software of choice for the management
of biological data. 

== Sequences as first-class citizens ==

Plone4bio is a bunch of Plone products developed to bridge this gap: they let
people add '''sequence records''' as first-class citizens to the [http://www.plone.org Plone] CMS, stored either in the ZODB or in any BioSQL compliant
database. Sequences can be quite complex objects, with lots of metadata that
need to be displayed pictorially, but all the complexity is hidden to the
end-user.

The management of biological data is a complex task, that faces many
integration issues. As of today, researchers have had no choice but either
using public services such as [http://www.ensembl.org Ensembl] (which have lots
of features, but which lack powerful content management capabilities), or store
their data on local databases, accessing it with programs (probably written
using [http://www.bioperl.org BioPerl], [http://www.biopython.org BioPython] or
[http://www.biojava.org Biojava]). Or worse, storing data and partial results
in textual files, spreadsheets, and so on. Moreover, for several institutions,
privacy and secrecy of research require that no public services can be used.

== Use BioSQL to organize your data ... ==

A standard has been developed, called [http://www.biosql.org BioSQL], to define
a database-independent schema to store biological sequence data, and all the
major Bio* libraries have modules to access data stored in a BioSQL database.
What researchers are still lacking are a way of accessing these sequences which
does not require writing SQL queries, and do not require programming expertise
to just have a plot of the sequence features.

== ... and Plone to explore them ! ==

Plone4bio let people browse [http://www.biosql.org BioSQL] databases from
within Plone and allows integrating data which are stored in a database system,
showing their metadata, indexing them and drawing pictures of features,
together with the native data of a state-of-the art CMS . For the first time
researchers have a place where all the relevant information about their
research can be stored, organized, searched and managed, regardless them being
PDF or Office files, images, sequence records or predictions.

== In the future ==

In BioDec we are expanding the Plone4bio capabilities with further specialized
content types, like those required to manage antibodies and PCRs: of course the
really cool feature is the integration with sequence data in BioSQL format. If
we succeed we could have the first open-source Bioinformation Management System
used by academia and companies, and it will be based on Plone, too !