[Biojava-l] BioInformatics toolbox.

[Schreiber, Mark]

Hi -

I made a bit of an off hand comment before to Michael about making some
of the core Biojava interfaces into valid java beans. I have thought of
it before but shyed away as many of the Biojava interfaces didn't seem
very beanable. However that may have been because I was a bit naïve
about the Biojava interfaces and some of the bean technologies. It would
certainly make biojava a very powerful addition to the Bioinformaticists
IDE. The ability to drag and drop Biojava objects into your program
could be very useful for people wanting rapid prototyping /results.

Perhaps some of the Biojava designers might want to comment on the
beanability of some of the core interfaces.

Mark

"friends don't let friends use vi"

> -----Original Message-----
> From: Mario Gianota [mailto:mario.gianota@bookkeeperseye.com] 
> Sent: Tuesday, 9 April 2002 12:59 p.m.
> To: Michael L. Heuer
> Cc: biojava-l@biojava.org
> Subject: Re: [Biojava-l] BioInformatics toolbox.
> 
> 
> 
> > "friends don't let friends use IDEs"
> >
> > The netbeans project has been advocating this angle for 
> some time now, 
> > with little to no success.  The Eclipse IDE doesn't have the 
> > development community that netbeans does, and it's much less unix 
> > friendly.
> >
> > see
> >
> > > http://netbeans.org/about/third-party.html
> >
> > Look -- there's even one for bioinformatics
> >
> > > http://bioinf.gla.ac.uk/biobeans/
> >
> 
> Correction, there is a web page with lofty ideas that hasn't 
> been updated since August of last year. In other words, there 
> is nothing for biologists in this area and I'm honestly not 
> surprised: have you ever tried to strip NetBeans down to its 
> bare minimum ?
> 
> Whilst IDEs may be considered harmful by programmers that 
> were raised on make, a command line editor and a compiler 
> there exist a substantial number of programmers that cannot 
> work without an IDE. There is every indication that the 
> majority of biologists, though capable of writing Java 
> programs, cannot produce working Java code outside of an IDE 
> because the setup and deployment is too complex. Result ? 
> They'll re-use other people's bio-PERL scripts because that's 
> much simpler to do.
> 
> In the component software industry the trend is towards 
> supplying mini-IDEs with the components. For example, F1Java 
> the spreadsheet component from www.actuate.com includes a 
> designer bundled with the component. I would suggest that an 
> API as complex as bio-Java could only benefit from a 
> dedicated IDE, or at the very least, a collection of wizards 
> to automate some common tasks.
> 
> 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
> 
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> http://biojava.org/mailman/listinfo/biojava-l
> 
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