[Biopython-dev] biopython web interface

[Andrea Pierleoni]

>
> 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