[Biopython-dev] biopython in ZOPE volunteer

Danny Navarro d.navarro at bmb.sdu.dk
Thu Mar 28 06:27:12 EST 2002

Hi all,

I am a "curious" biochemistry/bioinformatics undergraduate student who
always have liked very much computers and specially Open Source. 

Right now, I am able to write some code in Python and Perl, I have some
skills administrating Debian servers,... and I know more "just for fun"
computer things. 

But I don't know what can I do to be useful for the open bioinformatics
community. I would like to help to make it stronger.

One thing I am very enthusiastic about is the idea of wrapping biopython
modules in ZOPE, so that you can construct web sites with ZOPE and at
the same time provide bioinformatics web services using biopython

What it'll be really cool woud be the intercommunication between
biopython and ZOPE APIs. To do this:

would be better to extend ZOPE adding a "biopython product" using

...or would be better the implementation in the biopython API the
accession to the ZOPE one? (like bioperl with MySQL)

... or both might be required?

I have seen some recent messages in the mailing list archive regarding
to this matter:


    > Biopython zope objects complete with interface (Blast, .....) and
    > (BioXML,....)
    > Bioperl zope objects complete with interface (T-coffee) and output
    > (BioXML, GAME, ...)
    > Web maintainers could just install the products and Voila.
    > Biopython ZClasses (and maybe BioPerl objects?) could be
    subclassed for
    > special uses through properties interface.
    > The output of one zope product could be fed into another allowing
    > complex scripts.
    > A weird example.
    > From Swissprot chose trypsin->fasta->phylogeny->align each
    > group->consesus for each group->common restriction enzymes, .....
    I think these are the sort of ideas that need to be shared with the
    Biopython (and possibly Bioperl) developers!  :-)
    And here's the kicker:
    - Existing Python modules can be imported into Zope's namespace and
      exposed to the Web.  With a little bit of wrapping, it may
    eventually be
      possible to build a set of reusable "web widgets" to wrap
      objects.  This is still a very vaguely formed idea, but it is
    where I think
      I would like to work towards, eventually.  It would mean that the
      could actually contribute towards the Biopython project in a more
      manner than just providing PR.
    Now firstly...  do we have the go-ahead to start spending some time
    on this?
    Jeff?  :-)
Ok, so these kinds things I would really like to do.

So if you want a quick learner volunteer to colaborate in this possible
project just say me what I can do, please.


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