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

[Bruce Southey]

Hi,
I strong concur with Andrew that we need to focus solely on the merit
of the paper not the journal or review process.  There were some
issues that should have been caught but, given the results provided,
these may not have resulted in the main component of the paper Really
the problem exists at the author level because you can not expect the
reviewers to know all languages.

I think that it may be best to directly ask the editors to consider 'a
letter or short communication' by providing solid supporting material.
Also to point out 'The Computer Language Benchmarks Game'
(http://shootout.alioth.debian.org/ ) so that this paper is very
limited and not novel at all. Personally, I would just ignore this
paper because I don't think it should have the attention it getting -
let it remain uncited rather than draw more attention to it.

Regards
Bruce


On Feb 7, 2008 10:45 PM, Andrew Dalke <dalke at dalkescientific.com> wrote:
> On Feb 6, 2008, at 2:35 AM, Titus Brown wrote:
> > 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.
>
> I've got something written up.  It's mostly complete.  100 lines,
> plus a summary I haven't figured out yes.  What should I do with it?
>
> Options:
>
>   - publish (BMC Bioinformatics has a $1,870 fee - that ain't gonna
> happen)
>
>   - I don't see a letters to the editor column, or anything similar.
> The closest is
>         Queries about content, submissions, or the review process
> should be
>         directed to editorial at biomedcentral.com
>
> I really want to complain about their lack of rigorous peer review.
>
>
>    - I see there's a spot for comments at
>    http://www.biomedcentral.com/1471-2105/9/82/comments
>
> Does anyone use that?  Or is there some place else which is better?
>
>    - blog it
>
> Anything else?
>
> Also, does anyone want to look over my draft version?  This is a
> public list and I would rather the comments not be widely
> disseminated yet.
>
> I'm also not sure about the politics of dissing BMC Bio's editors and
> peer reviewers skills on reviewing this paper.  Not that I publish,
> but how do I make it the most effective?
>
>
>                                 Andrew
>                                 dalke at dalkescientific.com
>
>
>
>
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