[BioPython] Biopython Citation

[Hilmar Lapp]

BTW Jason and I wrote a relatively high-level review last summer:

Briefings in Bioinformatics 2006 7(3):287-296
http://dx.doi.org/10.1093/bib/bbl026

It's not a Bio* comparison paper, though. In fact, it rather tries to  
highlight the strengths of various toolkits and standards in the life  
sciences.

	-hilmar

On Feb 14, 2007, at 9:08 PM, Harry Mangalam wrote:

> 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]
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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