[Biojava-l] BioInformatics toolbox.

[Iain Darroch]

On Tue, 9 Apr 2002, Matthew Pocock wrote:

> Mario Gianota wrote:
> > 
> > The moment, the _very_ moment that bio-Java  gets an IDE and an accompanying
> > web page with some reassuring screenshots is pretty much when you'll see the
> > user base expand to extremely healthy numbers. Until that day, bio-Java is
> > for expert Java programmers only --which is a shame really, isn't it?
> > 
> > 
> > --Mario Gianota
> 
> I like that prophecy. The issue realy is over what visual paradigm to 
> chose, and which group of people have the time to glue it all together. 
> Things like javascript, python and beanshell can all be used as 
> scripting languages embedded within java apps. Some of the biojava 
> classes fit nicely into the traditional beans framework (did I just say 
> traditional about a java programming model?). Some of it does not, and 
> it would be inapropreate to shoehorn it in there - e.g. the symbol 
> tokenizers would suck for performance if they were beans.

 
> It's actualy quite easy to come up with a control-flow language that 
> would allow users to draw directional pipes connecting files to 
> processors to agregators to visualisation tools to output files etc. 
> etc. ad nausium and do sensible optimizations over this framework, but 
> who has the time to write the gui & glue code?
>

I think people at Cardiff wrote something called PSE which was a way of
visually handling the flow of data to solve a particular problem. 
http://www.cs.cf.ac.uk/PSEweb/overview.htm

You have a repository of components (biojava) and you select the ones you
need and direct the flow from one to the other.

I agree that a flow based structure represented graphically should be
intuiative and easy to use.

I look forward to more input to this area.  I think it is very important.

Iain