[Biojava-l] BioInformatics toolbox.

[Matthew Pocock]

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?

The changeability framework gives us a huge tool for visualising data 
rippling through a network of data sources and processors, and I'm sure 
that these could be projected into a javabean world with a little 
tweaking (not sure we even need too many adapter classes). But it would 
be even better if the visual tools could work with our properties and 
events natively.

In your view, which APIs or functionality should be visualy active so 
that joe-blogs can start clicking biojava apps together? What are your 
simple use cases? Any idea how it should look visualy?

Matthew