[BioPython] biopython in ZOPE

[Jeffrey Chang]

Yes, there's definitely interest here in wrapping biopython code in
Zope objects.  My feeling is that the best way to do this is to build
a Zope product that accesses biopython.  That way, you can just
distribute the product and let people embed biopython functionality
into Zope-based websites.  However, I'm really just a Zope newbie, so
you could probably come up with better solutions than I.

I believe Johann Visagie came up with the idea maybe two years ago.
However, there's been a dearth of people who have both the skills and
the time to put it together!

Jeff



On Thu, Mar 28, 2002 at 12:15:52PM +0100, Danny Navarro wrote:
> 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
> modules.
> 
> 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
> Zclasses?
> 
> ...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:
> 
> http://www.biopython.org/pipermail/biopython-dev/2002-January/000802.html
> 
>     ==================================================
>     > Biopython zope objects complete with interface (Blast, .....) and
>     output
>     > (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
>     for
>     > 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!  :-)
>     ===================================================
>     
> http://www.biopython.org/pipermail/biopython/2000-August/000350.html
>     
>     ===================================================
>     And here's the kicker:
>     
>     - Existing Python modules can be imported into Zope's namespace and
>     be
>       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
>     Biopython
>       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
>     site
>       could actually contribute towards the Biopython project in a more
>     concrete
>       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.
> 
> Danny
> 
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