From: Jacob Fugal <lukfugl@...>
Date: 2006-08-22T05:25:04+09:00
Subject: Re: Been there, done that - language shootout

On 8/21/06, Isaac Gouy <igouy@yahoo.com> wrote:
> Jacob Fugal wrote:
> > On 8/18/06, Isaac Gouy <igouy@yahoo.com> wrote:
> > > Jacob Fugal wrote:
> > > > That's the *current* page for the FASTA benchmark, so maybe
> > > > that page just needs to be updated to remove that constraint?
> > >
> > > Jacob, why would we want to remove that constraint?
> >
> > Either remove or update to point to a current (not "/old/") benchmark.
> > I don't care either way...
>
> Jacob, why would we want to remove that constraint, and what problem
> would be solved by "update to point to a current (not "/old/")
> benchmark" ?

Note this portion of the prior conversation:

Jacob Fugal wrote:
> On 8/10/06, Caleb Clausen <vikkous@gmail.com> wrote:
> > On 8/10/06, Eric Hodel <drbrain@segment7.net> wrote:
> > > My assertion is correct.  The fasta benchmark says:
> > >
> > > > Each program should:
> > > > [...]
> > > > * generate DNA sequences, by weighted random selection from the
> > > > alphabets (using the pseudo-random number generator from the random
> > > > benchmark)
> >
> > I did not see this test named 'random' when I looked through the
> > alioth site earlier today... and I still don't see any links to it
> > from that site. (I did find it by following your link, however.)
> >
> > I notice that your second link contains the word 'old'. Perhaps this
> > benchmark has been withdrawn? If so, I submit that your criticism was
> > true in the past, but no longer is.
>
> I agree that the presence of "/old/" (vs. "/gc4/") in the URL probably
> indicates that the "random" benchmark has been removed from most
> locations.

The problem I see is that the current incarnation of the FASTA
benchmark page makes reference to another benchmark that *appears* to
have been deprecated. This possible deprecation is manifest in the
presence of the word "old" in the URL combined with the assertion
(which I'll admit I haven't verified) that there is no other link to
the benchmark on the site. The reliance of the FASTA benchmark on the
Random benchmark, to me, is not an issue. The reliance of the FASTA
benchmark on a possibly *deprecated* Random benchmark is the issue.
This issue can be resolved by:

1) Removing the reliance
2) Updating the FASTA benchmark to reference a non-deprecated Random benchmark
3) Clarifying that the Random benchmark is not, in fact, deprecated
4) Something else I haven't considered (I'm not omniscient, and don't
pretend to dictate what the Shootout must do :)

[I had assumed previously that the deprecation of the Random benchmark
was certain in my previous posts, which is why I didn't previously
mention option 3. I didn't mention option 4, because I assumed it was
implied, but I state it here for completeness.]

Now, between those four options, I don't care which you do. You know
what the Random benchmark is and whether it's necessary and/or
deprecated a lot better than I do. I was just mentioning possible
options to resolve the issue that I noticed in the conversation above.
I'm fine with letting you choose which option to pursue.

Jacob Fugal