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

[Peter]

Paulo Nuin wrote:
> I will comment on my blog and if permitted I would like to include
> everyone's view about it.

I've tried to leave a comment on BioMedCentral, but this only
scratched the surface.  Am I right in thinking the authors have not
made any of their sample input files available?  In the case of the
multi GB Blast file, this is perhaps justified.  Also I didn't see any
timing script.

Cory Tobin wrote:
> The methodology of this paper was a complete disgrace and lacked any
> scientific objectivity.  If they actually wanted to be somewhat
> objective they should have found people who are adept in each of those
> languages and told them to write the fastest code they could.

As their paper's slant was about comparing performance, then yes, they
should have used equally skilled programmers for each language.  There
is a debatable justification for keeping the code "simple" and
avoiding extreme optimization at the cost of readability - but setting
this fairly across different languages is a thorny issue in itself.

Peter
P.S. Hello from Biopython