[Pipet Devel] DOM/gdome update

J.W. Bizzaro bizzaro at bc.edu
Sat Jul 10 01:17:13 EDT 1999

Justin Bradford wrote:
> I've contacted the author of gdome, and am actively tracking its
> development. Unfortunately, little is being done with it currently. Most
> of its development is being driven by gill (an SVG application).

Hi Justin.  Who's the author of gdome?

> Anyway, I've talked to the primary author of gdome. His plans for the
> sliding DOM have been set aside, and they are currently concentrated on
> implementing a straight DOM interface over CORBA. He was very interested
> in my ideas on a simple wire protocol (something that would not require
> CORBA, necessarily), and I'll be getting back to him with a proposal for
> an intelligent client-side gdome interface (which resolves many of the
> problems with DOM over CORBA).

Hmmm.  I don't recall if you mentioned a "wire protocol" before on this list. 
Feel free to share the proposal with us when it's ready.

> However, the first priority for this side of development is probably
> python bindings to CORBA. I'll be checking into that this weekend. With
> the new design, supposedly new language bindings are not too difficult.

Great.  Did you post on the ORBit list that you'll be working on the bindings? 
The Python newsgroup might be a good place to announce that too.

> Hopefully, I can get something working soon which will allow use of
> GNOME's CORBA stuff. We can use the convential gdome system for the
> interim, and eventually, the new, more efficient (but not quite
> traditional DOM) interface will be available for implementing our various
> tools.

Neeto.  But I think most of us will need a primer on using CORBA and DOM.  Is
there some documentation that you think would be helpful?

> Is everyone ok with the idea of a centralized gdome system holding the
> Loci data? Plugins (viewers, editors, etc) all deal with the data via the
> gdome interface. It offers some very cool benefits with little (Loci
> unique) code, so as event notification, locking, etc.

The last messages I posted from Ferdinando pointed out that there are quite a
few guys around with somewhat similar plans for Gnome.  If we all work together,
we will have something that much better and sooner.  And I think if we decide to
use Gnome, we should get more than just our feet wet and try to work on some
Gnome development (blur the line between Gnome and Loci).  This way we will
understand the system better and get to know (and maybe get some help from) the
Gnome developers.  Some of those guys (and some of you guys :-) are way ahead of
me, and I'd love to work with them.

> I've been busy at Genentech lately, but I just wrapped up a project, so I
> can hopefully do something for Loci now, besides write emails about what
> I'm going to do ;)


> And for anyone who cares, Genentech (the original biotech company, based
> in San Francisco) is a very cool place. And it looks like they're going to
> give me a job next January, and probably pay for grad school.  The
> bioinformatics/biocomputing departments are expanding rapidly for anyone
> looking for jobs :)



P.S. We got 301 hits on the Loci page Friday, due mostly to the Freshmeat post. 
And there are 2 new subscribers to the list.
                   |                                    |
                   |           J.W. Bizzaro             |
                   |      jeff at bioinformatics.org       |
                   |                                    |
                   |       THE OPEN COLLABORATORY       |
                   |    FOR MOLECULAR BIOINFORMATICS    |
                   |                                    |
                   |     http://bioinformatics.org/     |
                   |                                    |

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