[Biopython-dev] KEGG support

[Giovanni Marco Dall'Olio]

On Wed, Feb 10, 2010 at 9:12 PM, Kyle <kellrott at gmail.com> wrote:

> I think external library dependancies should be avoided unless necessary.
>  Would a tool like wsdl2py produce code that isn't dependent on an
> installed
> library? Alternatively, suds is LGPL based, could we just cannibalize the
> source code for the important classes?
>

Honestly I think that the best solution would be to make an external module
to extend the basic biopython and to link it on the biopython's web page.
The core biopython should provide objects and infrastructures for biological
data, but then the additional functionalities should go on separate modules
linked on the biopython's web page, taking inspiration from BioConductor and
installed with easy_install or a derivate.
If we keep on maintaining a constrain that all biopython modules should have
the same dependencies, then it is impossible to make anything more complex
than the basic stuff, and then biopython won't never be useful as it may be.
You can't make a good library for using WSDL services with SOAPpy, or plot
nice graphics without matplotlib, or store data in HDF5 format, and there
are many other examples. Bioinformatics is a very general word, people
working on it have a big variety of needs, and it is difficult to accomplish
it all with few dependencies.

-- 
Giovanni Dall'Olio, phd student
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)

My blog on bioinformatics: http://bioinfoblog.it