[Pipet Devel] BioML vs BSML

J.W. Bizzaro bizzaro at bc.edu
Sun Jan 24 16:40:10 EST 1999

Harry Mangalam wrote:
> :) I'm sorry for having caused the early morning convulsions, Jeff.  I'm
> just trying to get a handle on the big picture.  I wasn't actually suggesting
> replacing Python with perl for the central technology, but rather as one of
> the toolsets that supports your central technology.  The problem I see with
> being too doctrinaire as to the languages used is that you run the risk of
> alienating some that support your model and see alternative ways of
> accomplishing a task (that may have already been solved with great effort)
> using another approach and as long as using it doesn;t conflict with your
> central goal, I don't see the problem.

I don't want to be misunderstood regarding my position on various languages. 
One of the main goals of Loci is to provide a framework to unify many bio tools
of different languages.  ***But can we keep just the core of Loci virgin
Python?  It will be hard enough allowing all sorts of languages to be attached
to the core.

> Hear, hear.  That's all I'm suggesting.  However, IMHO excluding biosequence
> artists on the basis of what language they choose is certain to make for bad
> blood in the community and that's not what we want.  As long as there's a
> standard way for the components to interact, anything that contributes to
> the effort should be considered.  Speaking of which, one of the things that
> attracted me to this approach was it's close coding and thematic relation to
> the GNOME project.  One way to rationalize the different language issue
> would be build the components using the GNOME's ORBit definition, which is a
> lightweight, lo-memory, GPLed, CORBA-compliant ORB (albeit written in C, but
> I'm not sure that would affect much). Info is at:

Yes, we have considered CORBA and ORBit.  Right now there is no decent free
implementation of CORBA for Python.  But there is an effort underway to make
Python bindings to ORBit, which we will consider.

It is not a bad idea.  CORBA may be the best way for tools of various languages
to connect to the Loci core without going thru the Gatekeeper.  So, we may very
well see various different GUI attached to Loci.  It's just that we won't do
anything like that for the _core_.

***Remember, the Loci core won't contain even one analysis tool!  We are
considering the core to be very small, consisting of Python/C GTK/GNOME modules.

J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/

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