Bioperl: article for Dr. Dobb's Journal

[Ewan Birney]

On Fri, 9 Oct 1998, Lincoln Stein wrote:

> Hi All,
> 
> I'm writing an article for Dr. Dobb's Journal on Perl and Molecular
> Biology.  I thought I'd post the draft here for comments.  It just
> came back from the editor with the comment "loved it, but it's way too 
> long."  Any ideas what parts should be chopped out?
> 
> Lincoln
> 

It's a very nice article. How much do you need cut out? Here are some
suggestions:

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 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.

This should save alot of space.


Two content points:

a) I think the bio.perl.org site is the better site to reference about
bioperl.

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).


Does this help? It is just my $0.02





Ewan Birney
<birney@sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/

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