BioWidget meeting

[Georg Fuellen]

SteveC wrote,
> 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 

Personally, I don't think there will be a safe way for remote code execution
for years to come; that holds for Java as well as for Perl. (There's been
a lot of discussion in comp.risks, http://catless.ncl.ac.uk/Risks, about this.)

> Penguin?

See http://www.oasis.leo.org/perl/exts/security/Penguin.dsc.html

> >   <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.

Thanks for pointing this out! All the better if we want to have an interface
to bioWidgets at some point.

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

See http://inferno.lucent.com:80/inferno/index.html

> >   <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?

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.
Also, am I right that ``semantically neutral'' means that a bioWidget
can display any piece of data that conforms to a certain syntax, or ?

> SteveC

best wishes,
georg