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

[Andrew Dalke]

On Feb 8, 2008, at 3:23 PM, Bruce Southey wrote:
> I strong concur with Andrew that we need to focus solely
> on the merit of the paper not the journal or review process.
   ...
> Really the problem exists at the author level because
> you can not expect the reviewers to know all languages.

Hmm.  The reviewers don't need to know all the languages.  I don't.   
But I know enough about some of the languages to tell there's  
methodological errors.

If the reviewers can't review the content of the paper, then what's  
the point of having reviewers?

So I think the reviewers do share some of the blame with the authors.

I've also elsewhen on this list complained that improving software  
development skills in computational biology and chemistry isn't seen  
as being important, except in the abstract. The philosophy is that  
code's okay as long as it works, with little concern about the time  
it takes to implement the code, overall performance, maintainability,  
security and other factors.

That's not something that can be addressed in a response to this  
paper.  :)


> 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.

The peer-review system is based on several ideas:
   - if it's not published, it didn't happen
   - peer-review for publication provides the first level of validation
   - others should review and reproduce the paper ...
   - ... and publish any problems found

Peer review doesn't stop when the paper is published.

				Andrew
				dalke at dalkescientific.com