[Bioclusters] Nomenclature (was Re: Call for information.)

Ivo Grosse bioclusters@bioinformatics.org
Thu, 18 Apr 2002 11:15:45 -0400

Hi Joe,

Joe Landman <joe.landman@mscsoftware.com> wrote on Wed, 17 Apr 2002:

> On Wed, 2002-04-17 at 10:58, Ivo Grosse wrote:
> > Yes, thanks to make that clear.  Hence, my question about recent Blast 
> > benchmarks on P3s and P4s and Athlon-MPs meant: does anyone have those 
> > 3 numbers (or sets of numbers) for SINGLE nodes?
> This is of course, not a simple question to answer properly.
> I am trying to create a set of benchmarks which would be helpful in this
> As soon as I have time, I will try to package up my tests for people to
> try on their own.  This will eventually be part of a informatics
> performance metric project to be hosted on the bioinformatics.org site.


Could -- in the meantime -- some other people from the list just 
publish their "small and not complete and not systematic" benchmark 
results?  All of those results together could give (all of) us a better 
picture than each individual test alone.  Just specify in detail

- the hardware platform,

- the compiler & compiler options, and

- the Blast parameters (which set of query sequences?, which database?, 
repeat-masked or not?, which E-value?, etc.).

That would be super.  Thanks!



Likewise, did anyone do benchmark tests with Gibbs sampling or other 
bioinformatics algorithms other than Blast?