[BioPython] Biopython Citation

[Harry Mangalam]

That's a really excellent overview.  My only (non)critique is that 
since there's so much to cover that you couldn't possibly have 
covered each in the kind of detail it deserves.  

Maybe the proper way to do this is to wikitize the paper, allowing 
supporters and users to fill in the gaps.

Again, great job - sorry I missed this when it came out.

Harry

On Thursday 15 February 2007 08:55, Hilmar Lapp wrote:
> 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]
> > _______________________________________________
> > BioPython mailing list  -  BioPython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython

-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847(o) 949 285 4487(c) (email for fax)
                   hjm at tacgi.com  [plain text preferred]