[Biopython-dev] biopython in ZOPE

Danny Navarro d.navarro at bmb.sdu.dk
Mon Apr 1 10:33:16 EST 2002

> It would be nice if we could use some bioperl stuff, they are quite mature and
> have lots of functionality. How to do that best in ZOPE, im not sure.
> ActiveState had some ZOPE-perl stuff, but it dosnt look very active now.

Hi Florian,

I totally agree with that. The new modules incorporated in the 1.0
realease are really impressive. But I like more Python... I started to 
learn programming with Perl but when I discovered Python I didn't have
any doubt about getting deep into it. I am not going to discuss here why
but what I mean is that I feel more comfortable working with Python than
with Perl. It'll be easier, at least to me, to wrap biopython modules in
Zope than the the bioperl ones.

But if anybody wants to do it, it should be possible. In theory you
could use pyperl to embed Perl code in Python and zoperl to access to
the Zope API. But as you said it doesn't seem to be maintained anymore
and I don't know if the Zope Perl scripts work properly.


I think the easiest way to incorporate the bioperl functionality is
first try to implement biopython modules in Zope classes. After that
then we could try to access bioperl and biojava through bioCORBA. But I
haven't tried bioCORBA yet and I can't assess the feasibility of this.


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