[Biopython-dev] biopython web interface

[Rodrigo Faccioli]

Hello,

The messages before described about BioPython and BioSQL projects.
Furthermore, they commented how you are able to develop your system with
those projects.

I would like to show the project which I have been working. Although you're
using web2py framework, I would like to show my project which don't use
framework, yet. We develop its front-end in jsp. However, its back-end is
written with BioPython. Please, see [1].

[1] http://glu.fcfrp.usp.br:8180/prometheus/

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-8739
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
Personal Blogg - http://rodrigofaccioli.blogspot.com/



On Sat, Apr 30, 2011 at 2:03 PM, Andrea Pierleoni
<andrea at biocomp.unibo.it>wrote:

>
> >
> > Message: 3
> > Date: Fri, 29 Apr 2011 08:34:34 -0500
> > From: Massimo Di Pierro <mdipierro at cs.depaul.edu>
> > Subject: [Biopython-dev] biopython web interface
> > To: <biopython-dev at biopython.org>
> > Message-ID: <57629245-F184-4143-8B18-80E69BC2C351 at cs.depaul.edu>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Hello everybody,
> >
> > I am new to biopython and I have some silly questions.
> >
> > Does biopython have a web interface?
> > If not, would you be interested in help developing one?
> > What kind of features would you be interested in?
> >
> > Reason for my question: I am a physicist and a professor of CS. I am
> > working with a few different groups to build a unified platform to bring
> > scientific data online. The main idea is that of having a tool that
> > requires no programming and scientists can use to introspect an existing
> > directory and turn it into dynamical web pages. Those pages can then be
> > edited and re-oreganized like a CMS. The system should be able to
> > recognize basic file types, group, tag and categorize them. It should
> them
> > be possible to register algorithms, run them on the server, create a
> > workflow. The system will also have an interface for mobile.
> >
> > Here is a first prototype for physics data that interface with the
> > National Energy Research Computing Center:
> > http://tests.web2py.com/nersc
> >
> > Since we are doing this it would be great to have as many community on
> > board as possible so that we can write specs that are broad enough.
> > We can do all the work or you can help us if you want.
> >
> > So, if you have a wish list please share it with me.
> >
> > Personally, I need to be educated on biopython since I do not fully
> > understand what are the basic file types it handles, what are the most
> > popular algorithms it provides, nor I am familiar with the typical usage
> > workflow.
> >
> > Massimo
> >
> >
> >
>
>
> Hi Massimo,
> BioPython itself is a python library, but a web interface would enable many
> functions to biological scientist with no programming expertise.
> There are some parts of the library that cope well with a
> web-interface/server,
> in particular the BioSQL modules.
> The BioSQL schema is a relational database model to store biological data.
> I do have working code for using the BioPython BioSQL functions (and more)
> with
> the web2py DAL, and I'm working on a complete web2py-based opensource
> webserver to store and manage biological sequences/entities.
> If you (or any other) are interested and want to contribute, let me know.
> There are  many things in common between what I'm doing and what you want
> to do,
> so maybe its a good idea to work together.
>
> Andrea Pierleoni
>
>
>
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