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

[Chris Fields]

On Feb 6, 2008, at 9:28 AM, Colosimo, Marc E. wrote:

> <rant>
> What is biology in python or more to the point why is there yet  
> another
> mailing list (Web site?) for biology in python?

The BioPython group primarily focuses on the BioPython suite of  
tools.  Other groups might address more general computational issues  
which may or may not pertain to BioPython.

There are similar efforts with perl.

>> From looking at their archive messages:
>
> 1. Need to establish python/biology community.....
>
> Isn't that what BioPython is? If not, why not?
>
> I'll also point out that there is "CoreBio" a python toolkit for
> writing computational biology applications
> <http://code.google.com/p/corebio/>
>
> I don't want to subscribe to another mailing list, install another
> suite of code, keep track of another Web site.
> </rant>

...

You don't have to if you don't want to.  This was probably cross- 
posted by Andrew to bring in discussion on this paper with like-minds  
from BioPython.

BTW, Andrew et al, speaking as a perl/BioPerl programmer, I also think  
it's a terribly researched and written piece; surprised it got past  
the reviewers.  Programming language 'shootouts' are always  
controversial (anything with a 'my language is better that yours'  
conclusion is bound to cause arguments).  One would think a shootout  
means setting strict rules and having the best/brightest put forward  
their qualifying code, but clearly in this case that didn't happen.

chris