Bioperl: article for Dr. Dobb's Journal
Fri, 9 Oct 1998 12:20:22 -0400
Ewan Birney writes:
> It's a very nice article. How much do you need cut out? Here are some
The article needs to be cut by about 50% (I'd actually asked to make
it a two-parter originally, but got turned down). If I cut out the
alignment stuff there will still need to be some substantial trimming
in the rest. Alternatively, I could focus on the alignment algorithm
entirely, and this is what the editor has suggested. I hate leaving
out all the OO stuff, however.
> In the biology bit, I don't think you need to explain replication except
> in perhaps a sentance about the fact that DNA is both a positive and
> negative image welded together, allowing for easy replication (should save
> you a bit of space).
I'll do that.
> I think your biggest saving would be to drop the alignment class stuff
> all together. It's sad because that's where this stops becoming simple
> datastructures and starts getting interesting (and of course, I find
> alignments v.interesting), but I think trying to explain OOP-perl,
> bioinformatics and dynamic programming all in one small article is taking
> on quite a job.
Do you think the alignment part is strong enough to stand on its own?
The code actually runs pretty slowly and uses a lot of memory (and
uses a horrible trick in which strings are turned into numbers
automagically). Maybe I should focus on the algorithm and then show
how it can be turned into an XS module.
> Two content points:
> a) I think the bio.perl.org site is the better site to reference about
Just sloppiness on my part. Thanks for catching that.
> b) I think the point about perl is that not only is it a rapid development
> cycle but that existing command line based solutions can be worked into
> it, as can C based APIs (a la AcePerl and the bioperl alignment
Very good point. I'll add that to the intro.
Lincoln D. Stein Cold Spring Harbor Laboratory
firstname.lastname@example.org Cold Spring Harbor, NY
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