BioWidget meeting

[Georg Fuellen]

SteveC:

SteveC wrote,
> Georg Fuellen wrote:
> > 
> > SteveC wrote,
> > > I very much agree. I have a number of examples of how I am using Perl 
> > > and Java in precisely this manner. One of the big issues with the BioWidget 
> > > folks is to avoid getting caught up in sematics. "Drive sematics out," they 
> > > say (after David Searls). They want to create a semantically neutral system 
> > > for displaying and manipulating graphically any kind of genomic data. But 
> > > at some point you must deal with the semantics of biological objects 
> > > (primarily, this is a data model issue, I believe). I think Perl is well 
> > > suited to deal with semantic issues. This could be a good angle to present 
> > > at the conference. For example, we could cast Perl as an intermediary 
> > > between a semantically complex biological object and a semantically neutral 
> > > Java bioWidget.  What do you think?
> > 
> > This looks exciting, but I'm not clear in which way the 
> > ``semantically complex biological object'' is represented, so that Perl can
> > act as an intermediary between this object and a Java bioWidget.
> 
> I'm not quite sure myself, but the basic idea would be to use a parallel 
> object schema in both the Perl and Java to facilitate mapping between 
> Perl and Java objects. 

Did you see:
>>>>>>>>>
From: schuller+news@lunatech.com (Bart Schuller)
Subject: Re: Perl CORBA IIOP module?
Date: 10 May 1997 13:12:31 GMT
Organization: Lunatech Research

[comp.lang.perl is long dead, Newsgroups trimmed]

In article <5kqng8$rqo$1@inet16.us.oracle.com>,
Oracle News 2 <rpang@us.oracle.com> wrote:
>
>A related question.  Is there any CORBA-Perl mapping definition underway
>right now?  I understand that Perl does not have the notion of datatypes
>which makes such a mapping difficult.  Has anyone thought about how to
>overcome this difficulty?

I've set up a mailinglist to discuss these issues, as well as my own
implementation of CORBA in Perl. The list is at cope-request@lunatech.com
Details on htpp://www.lunatech.com/cope/

For your question: A CORBA mapping is not hard. Perl does have plenty of
datatypes, it's just that they are not strongly typed.

For example, a short and a string will both map to the same perl datatype
(a scalar). But a stub method knows that for example the CORBA object
expects a short and so interprets the parameter as a short. You could
hand this method a string and it will probably be interpreted as 0. That's
a case of "Don't do that, then". After all, the IDL for the method told you
it expects a number.

The same goes for other datatypes. I represent structs as associative-
arrays. What happens if you put more keys in them? That's undefined.

The bottom line is: as long as you remember that you're talking to a
strongly typed system and play by the rules of that system, all will
be fine.

-- 
Bart Schuller                  schuller+sig@lunatech.com At Lunalabs, where the
Lunatech Research              http://www.lunatech.com/  future is made today..
Partner of The Perl Institute  http://www.perl.org/    Linux http://www.li.org/
<<<<<<<<<

This seems to touch some of the issues re: strongly-typed Java <-> Perl...
 
> > Also, am I right that ``semantically neutral'' means that a bioWidget
> > can display any piece of data that conforms to a certain syntax, or ?
> 
> Yes. A bioWidget is expected to conform to an common API that allows
> for various display tasks such as selection, highlighting, and coordinated 
> scrolling/zooming. This permits a consistent interface across widgets. 
> At some level, though, there has to be some semantic tie-in so that a 
> specific bioWidget knows how handle the peculiarities of biological 
> information from a specific domain. One could imagine there being 
> subtypes of bioWidgets that specify more about the domain data which 
> would act as a base class for all widgets of that type (e.g., 
> SequenceWidget, MapWidget).
> 
> Check the bioWidget homepage for more about this:
> http://goodman.jax.org/projects/biowidgets/consortium/

I hope to take an intensive look at all this in a month or so.

> Regards,
> SteveC

best wishes,
georg