BioWidget meeting

Georg Fuellen fuellen@dali.Mathematik.Uni-Bielefeld.DE
Mon, 12 May 1997 18:45:20 +0000 (GMT)


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: (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$rqo$>,
Oracle News 2 <> 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
Details on htpp://

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         At Lunalabs, where the
Lunatech Research      future is made today..
Partner of The Perl Institute    Linux

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:

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

> Regards,
> SteveC

best wishes,