[Bioperl-l] question about the nature of bioperl

[Ewan Birney]

>
> also i think there is a niche for a nice procedural (yes, the horror)
> module (or a class Util type module with procedural style calls) for a lot
> of core bioinformatics stuff. You know, often I just want to say
> $aa = translate("ATG");
> rather than have to go through a bunch of bureaucratic object middlemen.
>

I agree. We have Bio::Perl but it is not rich enough (and not pointed out
enough in the docs) and we should play this up - quick-and-dirty Bioperl!


[snip]


>
> Ewan will no doubt say I've been in berkeley too long and am out of my
> tree and live in a world where code writes itself and i don't have to come
> in to work... but i am a little perturbed by the direction the OO
> technology bandwagon has led the whole software industry up this cul de
> sac of ever more complex and unnecessary middleware and convoluted
> techniques, design patterns are just formulae to turn programmers into
> macro processors. at the end of the day it's just passing data around -
> maybe bioinformatics should just ignore the mainstream software industry
> and get back to computer science fundamentals.
>

I agree/disagree and in any case this is just philosophical ramblings - I
am actually very excited about trying out more "just the data m'am"
approaches but


   - the magic of semantic interpretation has to happen somewhere, and it
has to involve effectively "ifs" (branches) and "fors"
(loops/agregration/decomposition)  and at some point either a little bit
of maths and/or string manipulation. In my view this magic is best
represented as a series of abstract imperative programming languages, but
"hidden" as much as possible to look almost functional. You can do this
via declaritive things which then code generate or drive runtime systems
but I think thats programming by proxy...


   - people always ends up having abstractions - those abstactions nearly
always look like objects (ish). Or rather -objects is a sensible
imperative language abstraction and other sensible abstractions are nearly
always interconvertible (though... all have pluses and minuses)


   - You're free to start BioProlog or BioLisp or something and if it
works --- great! Bioperl is unsurprisingly going to be somewhat Perl
object like and I see no other sane way of constructing it.



Anyway - roll on ontologies and declarative data approaches. I'm all for
getting my feet wet...







> But realistically speaking this won't happen. I do actually have to build
> working large scale bioinformatics software for a living (although you
> wouldn't think so from this ill though out rant..) and from that
> perspective bioperl has been a lifesaver.
>
> > Best regards,
> >
> > Nathanael Kuipers
> >
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