Bioperl: article for Dr. Dobb's Journal

Ewan Birney
Fri, 9 Oct 1998 23:21:15 +0100 (BST)

On Fri, 9 Oct 1998, Andrew Dalke wrote:

> Ewan Birney <> said
> > To be honest I think the OOP stuff is more important than the
> > algorithm and the fact that perl is the *ideal* language to glue
> > and provide a development 'framework' is v. important.
> *Ahem*.  You might want to stay away from religious issues like
> that  :)  (I know, this is the bioperl list, but I'm here
> because I want to keep up on computational chemistry and biology
> development environments, even though I currently do most of my
> programming in Python.)

<embarrassed> I think the word *ideal* was a little too strong
there. It should be more *pragmatic* or a decent option. Python
is also a very good option (should we start a bio-python project? 
--> only joking). But I think that there are a number of people
who don't see how robust you can make perl - it is for more than
scripts. Though I wouldn't write a server in perl... </embarrassed>

> > I'd go OOP-Perl to say that it is more than a web/systems
> > glue language.
>   But doesn't implementing alignment code in Perl shows that
> just as well as showing it's use for OO development?  Still,
> I would tend to agree that my interest is in how you set
> up a large system using data encapsulation and all those other
> CS buzzwords, which corresponds to the part:

I don't think implementing DP in perl shows much expect that perl
doesn't do clever optimisations for this sort of algorithm (re:
lincoln's comment that it was slow and big). Perhaps PDL would be
efficient... I'm not sure. DP was made for C - laying your memory
out correctly, allowing the optimiser to do crazy things with your
inner loop. Perhaps I'm just a little too addicted to my C code.

> > Programmers who prefer the object paradigm can use Perl to
> > create object-oriented classes and methods.
> Which to me is a more important thing than the details of an
> standard algorithm which are found in an earlier DDJ and in
> Knuth.

I agree with Andrew.

Ewan Birney

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