[Pipet Devel] Re: The Loci Project

J.W. Bizzaro bizzaro at bc.edu
Tue Jul 20 08:19:35 EDT 1999

Hello Thomas.

I'm sorry that I took so long to get back to you.

Thomas Junier wrote:
> All I can say is that I'm very pleased, but I sincerely wonder if I can be of
> any help, because I know close to nothing about Python (I'm more of the C/Perl/
> Java world), as to CORBA, DOM and XML I have some idea about what they do, but
> not much. Of course, I could start learning all this. :-)

Python is being used as a glue language for Loci.  Knowledge of it would be
helpful but should not be required.  We are aiming for a language-neutral
system, a la CORBA.  So, we're not forcing anyone to pick up a book on Python
and start reading ;-)

> > I
> > think what you have done is an important building block for Loci.
> Well, I'm all the more pleased, but since it's based on Perl and Java, won't it
> be hard to integrate it into Loci ?

Regarding language, as long as a "translator" can connect to CORBA, the language
shouldn't matter.  If we use SEView (or a derivative), we will have to work
these object models into it.

I think we could also use your help with defining a generic "translator" for
I/O.  The definition should be such that someone can write one in the language
of their choosing.  We can take a look at SEView and make sort of a generic
algorithm that can be used as a blueprint.  (That might even be publishable.)

> So my answer is that I'm interested, but I'm not sure how I can be useful. If I
> first have to learn Python, CORBA, XML and friends, it'll be some time before I
> can be productive, I'm afraid. On the other hand, if my Perl/C/Java skills can
> be put to use, that would allow me to start working sooner.

Well, most of us will need a lesson in CORBA.  C works well with Python, and
we're sure to have a bit of it in Loci.  Actually, most Loci developers are C
coders and only a few joined knowing Python, CORBA, etc.  We have a few Perl
hackers here too, but Python has some obvious strengths for what we need to do.

> One thing I could not find on the Loci page: what kind of collaboration do you
> have with EMBOSS ?

Peter Rice, the coordinator of EMBOSS, reads our list and I read theirs.  (He's
sure to read this :-)  And we've corresponded a few times, but that's about it. 
If I can take the liberty to speak for them, they are developing a command-line
based system much in the spirit of the GCG Wisconsin Package.  They have chosen
not to choose a GUI because there are several existing that can interface with
the EMBOSS command-line (Loci could be on that list but doesn't really
"exist").  We would like to make translators (here's where you guys come in) to
interface EMBOSS with Loci, but EMBOSS has taken no official position on Loci.

BTW, have you spoken to Philipp about Loci?  I did not get a message back from
him.  Does he still work with you?

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                   |                                    |
                   |           J.W. Bizzaro             |
                   |      jeff at bioinformatics.org       |
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                   |       THE OPEN COLLABORATORY       |
                   |    FOR MOLECULAR BIOINFORMATICS    |
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