[BioPython] Biopython Citation

[Harry Mangalam]

On Thursday 08 February 2007 18:20, Sebastian Bassi wrote:
> On 2/8/07, Julius Lucks <lucks at fas.harvard.edu> wrote:
> > There is a nice article covering the strengths and weaknesses of
> > BioPython, BioPerl and BioJava aimed at guiding a novice user:

Thanks :)

> Yes, but BioPython grew a lot from 2002.

So have the other bio-projects. For example, I noted BioRuby in 
passing but didn't include it in the survey - it's now gone to 
release 1.0, some kind of a step.  It certainly is time for a 
re-review.   What would be quite nice is a longish paper, perhaps in 
an e-format, with a short form published on paper.  If key personnel 
from each of the Bio-efforts contributed what they think are the 
strengths and weaknesses of their own approach, it would be extremely 
useful to a new crop of students.

Some of the problem in choosing a bio, as I mentioned in the paper, is 
dependent on the language itself, some is the approach to the 
problem.  Certainly, contributors to each group read each others 
lists and can best lay out their arguments.

Some of the attraction to users is also dependent on how the different 
distributions tend to package the contributions and the frequency 
that they're updated.  I haven't checked the biopython releases 
recently, but the Ubuntu distro, for example, does a very good job of 
packaging popular perl modules, with the result that I haven't had to 
resort to CPAN for a very long time.  Just my (possibly mistaken) 
impression, but Python utilities and modules seems to be a little 
less well packaged, at least by Ubuntu.

-- 
Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, 
UC Irvine 92697  949 824 0084(o), 949 285 4487(c) 
harry.mangalam at uci.edu
-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847(o) 949 285 4487(c) (email for fax)
                   hjm at tacgi.com  [plain text preferred]