From: kristoff@net.bio.net (David Kristofferson)
Newsgroups: bionet.molbio.genbank
Subject: Re: BLAZE survey
Date: 8 Jan 93 18:56:00 GMT
Organization: BIOSCI International Newsgroups for Biology

MCKMICP@YaleVM.YCC.Yale.Edu (Michael McKenna) writes:

>As the original poster (I do exist) I have to admit that I was seeking
>the kind of qualitative information that was posted in the BLAZE survey.
>Since the survey clearly originated from MasPar, I didn't interpret the
>post as a manipulative advertisement.

Thanks for speaking up here!!  I'm getting tired of dodging arrows
singlehandedly.

Some people have commented to me privately after seeing this exchange
that I should stand back and let these groups be "self-administering."
When the deck is stacked about 500:1 on the academic versus the
commercial side in these forums, my standing back means in essence
that the academic and government side wins by default and never has
its views challenged.  To this invitation to remove myself, I reply
politely, "No thank you!"  Of course, I will not be surprised if some
day grant reviewers take this action unilaterally (as I have already
had many pleasant experiences along these lines 8-).

>Having read some of the literature that compares various algorithms,
>the articles tend to sort into two classes:
> 
>     1) Theoretically based papers discussing the various mathematical
>        merits of one algorithm versus another. The authors are likely to
>        have an investment in their favorite tool, and it's not always clear
>        (to me) how the math translates to the real world
>     2) Very general papers which look at two or three sequences and
>        draw conclusions about algorithm strengths from a limited database.
> 
>It seems to me that all the algorithms have their unique strengths and
>weaknesses- and this is going to be strongly sequence dependent. That
>is why I made the original post, in an attempt to discern the relative
>strengths of the programs for different applications.

Although I have been an administrator for the last six years and not
an active researcher in this field, my original background included
physics and physical chemistry plus a lot of math up through partial
differential equations and integral transforms.  I also did a postdoc
in the UCSF Macromolecular Structure Group with Bob Stroud and a
second with Marc Kirschner modelling the dynamics of microtubules, so
I am not intimidated by the field of molecular biology computing.

I have looked at several search programs in my capacity as manager of
first BIONET and then GOS.  To be quite frank, my somewhat summary and
inexpert impression of this field as a whole is that there is a often
a lack of good controls along with inflated claims about the worth of
programs (and we have probably been guilty of this ourselves at times
to be honest).  Those who need to use these programs are generally not
in a good position to be able to judge the theoretical merits, and thus
word-of-mouth information from a large cross-section of users is
probably *more* believable to them.  You are also right in stating that
sequence-specific dependencies can play a significant role in this
*art*.

>Phil Stamm's post from MasPar was interesting in that it derived from
>many sources and had different reponses. It is tainted somewhat by the
>commercial connection, but more, I thought, by the unwieldiness of the survey
>results.
> 
>Dave Kristofferson e-mailed me and mentioned a summary that Doug Brutlag had
>written; does anyone have a copy of this file or any other comparative
>reference for that matter.

My mention refered to the research paper that Doug and others at IG
and Maspar are putting together.  As I said previously, they were not
ready to release these results yet unfortunately.

>I never thought I'd see a flame-war in bionet.molbio.genbank!

You must be an infrequent reader of this group 8-).  This is still
where the real action is 8-)!

>Michael McKenna  MCKMICP@YaleVM.YCC.Yale.edu
>I do exist-- really...

I never lost my faith in this fact 8-).  Amen.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net
Newsgroups: bionet.molbio.genbank