[bip] Bioinformatics Programming Language Shootout, Python performance poopoo'd

[Bruce Southey]

Hi,
The concern that I have is that showing incorrect code or results is
not usually a constructive approach. A far bigger concern for me is
what is actually being compared. Looking at the code for C (and
pretending to understand Perl), I don't think that the same algorithm
is being implemented in each language! For example, the readFasta.py
involves a list of classes that I don't think is done in the other
languages - anyhow it is also so inefficient that it is trivial to
reduce its time by nearly half. Also, the code don't seem to have any
error checking ability or test ability to assess if the code is even
correct.

I found it more disturbing the lack of literature review including
different papers (http://www.cis.udel.edu/~silber/470STUFF/article.pdf
or http://page.mi.fu-berlin.de/prechelt/Biblio/jccpprtTR.pdf ) or
sites that do valid comparisons of the languages (
http://scutigena.sourceforge.net/ or
http://shootout.alioth.debian.org/). Most of these are dated but none
show the differences that occurs in this manuscript.

Regards
Bruce


On Feb 5, 2008 7:35 PM, Titus Brown <titus at caltech.edu> wrote:
> On Tue, Feb 05, 2008 at 06:38:19PM -0500, Paulo Nuin wrote:
> -> I will comment on my blog and if permitted I would like to include
> -> everyone's view about it.
>
> Well, the mailing list archives are open and searchable, so I'm sure
> you're welcome to do so ;)
>
> -> I have found some othe "strange" stuff too, but I can't say I am that
> -> expert on Python to weigh that much.
>
> I suspect that the code could use some systematic code review; "we"
> (i.e. someone else :) could even write up something semi-formal if it
> turns out that the results are bogus.
>
> --titus
>
>
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