BioWidget meeting

[Steve A. Chervitz]

In general I agree with the comments Georg and SteveB made about 
the relationship between Perl and Java. I just want to clear up a few 
things:

Georg Fuellen wrote:

> a generic object interface could help; last I heard some study saying
> that simple concepts like Javabeans may outcompete COBRA really soon.

The real battle is between Java's Remote Method Invocation and CORBA. 
JavaBeans is a component architecture for building applications.

>   <li> Java applet security problems are ``inherent'' in the design of the
>        language (but Perl is "catching up".. ;-)  (((Hint at Penguin)))

Are you implying that Perl is becomming MORE secure? Also, what is 
Penguin?

>   <li> Java is not "Free Software"

The BioWidget Consortium intends to create a repository of free software 
in the same spirit as the Free Software Foundation. Bytecode as well as 
source code is to be freely available for all submitted "bioWidgets". 
Note that a bioWidget is not an application but a small reusable 
graphical component which could be assembled into an application. If 
someone creates a novel application using bioWidgets he could sell it 
and charge a fee to support it. At least this was the thinking as of the 
last meeting this past January.

>   <li> "Inferno"/"Limbo" is coming up anyway :-)

What is Inferno/Limbo?

>   <li> Java is nice for designing user interfaces, while Perl
>        acts behind the scenes...

SteveB wrote:

> I like to think of it this way:  Perl is good for slurping 
> and munging data; Java is good for presenting it.
> ...
> The main thing I would add is that most of biological data management is
> "munging the data into a reasonable format" -- most of my time coding is
> probably spent not on the acutal algorithms, but on trying to collate 
> the data.  This is where Perl really excels.

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?


SteveC