Bioperl: article for Dr. Dobb's Journal

Lincoln Stein
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
 > suggestions:

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 site is the better site to reference about
 > bioperl.

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
 > routines).

Very good point.  I'll add that to the intro.


Lincoln D. Stein                           Cold Spring Harbor Laboratory			                  Cold Spring Harbor, NY
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