[BioPython] biopython in ZOPE

[Danny Navarro]

The only thing I know about Medusa is that it is an asynchronous server
framework which comes with web and FTP servers written in Python. I know
also that Zserver comes from medusa.

I know that Apache is faster and it has a module for python CGIs. I
didn't check exactly what is the advantage of Medusa over Apache.


On Thu, 2002-03-28 at 12:36, Eugene Leitl wrote:
> 
> Have you had a look at Medusa?
> 
> On 28 Mar 2002, 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
> >
> > _______________________________________________
> > BioPython mailing list  -  BioPython@biopython.org
> > http://biopython.org/mailman/listinfo/biopython
> >
> 
> -- Eugen* Leitl <a href="http://leitl.org">leitl</a>
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