[BioPython] biopython to jython for literature miner

[Jeffrey Chang]

The classes to access NCBI should work.  People have reported using
parts of Biopython with Jython successfully with no modifications at
all.

I'm not sure which modules of Biopython are most widely used.  In
general, Jython should work fine, except where extensions classes are
used (such as the Martel parsing framework), and where Python 2.2 is
required (Jython only supports 2.1, I believe).  In general, though,
Biopython doesn't make very advanced use of Python 2.2, and parts that
are 2.2 specific should be relatively easily rewritten to work with
2.1.

Jeff




On Sun, Aug 11, 2002 at 02:39:47PM -0700, Kasian Franks wrote:
> I was thinking of starting with bio.www.ncbi. However
> my experience tells me that if I developed a 100%
> jython version it would not be completely compatible
> with biopython. Before I charge through a long term
> jython dev session I'd like to know approx how much of
> biopython I can expect to be compatible with jython or
> vice versa. I'm assuming in the future this question
> will be irrelevant, but for now I'd like to know that
> if I invested in a full jython integration effort that
> I will also be able to use the most useful biopython
> modules. Specifically, are the most widely used
> modules of biopython compatible with jython?
> 
> --- Jeffrey Chang <jchang@smi.stanford.edu> wrote:
> > Which part of Biopython are you using?  Is there
> > something specific
> > you need ported to Jython?
> > 
> > Jeff
> > 
> > 
> > On Sun, Aug 11, 2002 at 11:56:11AM -0700, Kasian
> > Franks wrote:
> > > I've been working on some tools related to
> > biomedical
> > > literature mining and information retrieval e.g.
> > > PubMed, OMIM, Swissprot, Genbank etc.
> > > In the process I've accumulated quite a few python
> > and
> > > tcl based libs, API and db interfaces for
> > gene/protein
> > > annotation, genomic database/knowledge management
> > and
> > > gene to disease mapping. I'm going to make a 100%
> > > Jython version. Has anyone done much work on
> > porting
> > > biopython components to Jython?
> > > 
> > > check it out, http://64.163.147.146/~kasian/fp and
> > let
> > > me know what you think...
> > > 
> > > Thanks
> > > -Kasian Franks  
> > > 
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> 
> 
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