[Biojava-l] BioInformatics toolbox.

[Mario Gianota]

>
> On Tue, 9 Apr 2002, Mario Gianota wrote:
>
> > 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 ?
>
> Yes, actually I have on more than one occassion.
>
> I was able to successfully pull out from netbeans some but not all of the
[snip]
Thanks for the references.

> > 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.
>
>
> The biojava library, javadocs, and example code integrate well into any of
> a number of java IDEs -- netbeans, forte, codewarrior, jde, jbuilder &c.
> as is.

Yes, but these tools are still too complicated for biologists to use. As
programmers we take a good deal of what we know for granted and cannot
afford to assume that the concepts we have in our heads have a corresponding
approximation in the head of the average biologist because the biologists
frequently haven't got the first idea of what we're talking about.

I suppose the correct phrase would be biology-centric for an IDE that is
wholly devoted to Biologists. No specialized programming knowledge required.
Such an IDE would have an emphasis on point & click, dragging, mouse
gestures and so on and would deliberately go out of its way to hide the
programming side of things and provide most of its functionality with visual
metaphors.

>
> If you're advocating beanification of all the biojava classes with drag
> and drop of SimpleSVMClassifierModels and the like, I really don't see
> that as the desired interface for working with bioinformatics data.  IDEs
> work well for painting guis, not so well for algorithm development.
>

I've always shied away from the Beans framework. My primary concern is with
finding ways to visualize large amounts of data. I want the tools to be
point & click with very little programming required because I know that the
majority of biologists don't have the time to get their heads around
complicated programming frameworks, or paradigms. For an indication of where
I am coming from on the bioinformatics side see www.bookkeeperseye.com/ged3d
for an example of a three D visualizer in development. It's still very
early, I'm afraid.

My idea is this: provide an IDE that is geared towards developing visual
models of data sources. Parsers are associated with data sources and all
parsers can have data transformation filters attached to them which
implement a basic renderable interface so permiting the data to be
visualized. The IDE is plugin based in that additional parsers, renderers
and filters can be downloaded and plugged in. The filters offer a means to
transform the data through algorithmic means after it has been parsed and
before it hits any of the visualization components --so the entire process
from data aquisition to data transformation and visualization works on a
pipeline principle. This is a simple model which I believe that biologists
could get their heads around. The idea of 'pluggable' data transformation
algorithms shouldn't be too esoteric for them and it is a small step from
there towards getting the biologists to write their own plugins. This is why
I was looking at Eclipse.


>
> > 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?
>
>
> It's good for job security.  :)

Thank heavens for complex technology eh ? ;)

>
>
> Seriously though -- if you see areas in the API that need improvement,
> clarification, or simplification, please point them out to the list.  The
> biojava community is very receptive to useful suggestions.
>
> And most receptive to source code patches or submissions.

Okay. In the meantime, I have 25,000 lines of code that urgently needs
refactoring so if you're feeling generous... ;)

Warm regards,

--Mario