[BioPython] biopython in ZOPE

[Danny Navarro]

I think the best approach is going to be the creation of a Zclasses
reusing biopython modules instead of trying to implement the accesion to
Zope API from biopython modules.

I have to go deeper in the Zclass documentation know exactly how to do
it.

Danny

On Fri, 2002-03-29 at 05:55, Jeffrey Chang wrote:
> 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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