[Biojava-l] BioInformatics toolbox.

[Mario Gianota]

> "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