Is David Steffen and elitist bigot?

Foteos Macrides MACRIDES at WFEB2.BITNET
Fri Dec 20 11:58:00 EST 1991


>In article <9112191757.AA02256 at genbank.bio.net> MACRIDES at WFEB2.BITNET
>                                                    (Foteos Macrides) writes:
>[...]

>Hmm, I had to go back several messages to even figure out what this
>was all about.  What I found was:
>
>I said:
>[...]

>Then Fote said:
>[...]

>My comments:
>
>(1) I stand by my position.
>[...]

>David Steffen

        The message in question pre-dated any of the above and had expired in
David's NEWS reader.  He successfully tracked it down by doing a search for
'outsiders' with WAIS in the bionet.general archive.  It took him only a few
seconds.  I feel very proud of him!!!

        Again, I assert that he is not a bigot.  He is a very assertive, real
live human being.  At the Worcester Foundation, we love assertive people.

        Below is a review of WAIS which David posted some time ago in
bionet.software/BIO-SOFT.  Within the present context, I believe it qualifies
as an ANNOUNCEMENT or DISCUSSION of broad interest to biologists, suitable for
inclusion in any of the forums associated with any of the bionet.general
reorganization plans.  At the time, I must admit, I myself (mis?)interpreted
it as a CHAT dressed in a SCHOLAR's clothing, and to actually be saying:

        "Hi guys and gals.  I just managed to download the WAIS sources.  The
documentation is written in a style that only Fote used to deal with, but I
managed to get it installed and running all by myself.  I don't immediately
see what's so useful about it, but if Rob says its great I'll keep playing
with it and see if it is.  Aren't you all proud of me 8-)."

        Everybody needs to do this kind of thing -- celebrate one's
accomplishments with others --  and will find some pretext or context in which
to do it.

        I celebrated with David by taking up precious disk space (back then;
the WFEB just bought many gigabytes more disk space) to save it in its
entirety locally on our system.

        Hmm, maybe I should have gone with by heart instead of my head and
voted for Plan C.

        Maybe I should be posting this stuff to bionet.neuroscience/NEUR-SCI
(I guess, in my own field, its so hard for me to put out anything but highly
polished manuscripts; I still have a long way to go yet 8-).

                                Fote

=========================================================================
 Foteos Macrides           Worcester Foundation for Experimental Biology
 MACRIDES at WFEB2.BITNET     222 Maple Avenue, Shrewsbury, MA 01545

                            Know thyself.
=========================================================================

David Seffen's CHAT?, ANNOUNCEMENT?, DISCUSSION?:
=================================================

From:   edu%"steffen at mbir.bcm.tmc.edu"  2-OCT-1991 17:45:16.50
To:     software at genbank.bio.net
Subj:   A cynic's review of WAIS

              A Cynic's Review of WAIS

************************************************************
*                 EXECUTIVE SUMMARY                        *
*                                                          *
*   As Rob Harper has said, WAIS is a nifty way of         *
* searching remote databases, and may well represent the   *
* wave of the future.  However, my experiences with        *
* WAIStation 0.6.2 for the Mac suggest that this           *
* program/system/whatever may not yet be ready for the     *
* working biologist.                                       *
*   If you have a remote database that you positively must *
* search, which is accessible in no other way, or if you   *
* just like to play with new toys, go ahead and jump in    *
* now; but be prepared for some work and frustration.      *
* Otherwise, leave it to the computer pioneers to get      *
* things going before jumping aboard.                      *
************************************************************

Disclaimer:  All this is only my opinion; Baylor has nothing
to do with any of it.  I am not an expert on WAIS; consider
this a Pournellesque review.  If you insist on the liberal
use of IMHO, hit "N" now.  If this review makes you mad
enough to flame, flame yourself.  If you  flame me and as a
result I do something rash, my wife and kids will sue you.

======================== INTRODUCTION =======================

  I have to confess: computers are a serious addiction of
mine.  Further, I have felt for a long time that something
other than Usenet newsgroups was necessary for taking full
advantage in the promise implicit in the vast resources
potentially available on Internet; something that saw data
not as transient messages, but rather as relatively stable
bodies of knowledge.  So when one of my net.heros, Rob
Harper, began raving about the greatest thing in searching
remote databases, something called WAIS, and further, when
Bionet made the archives of the bionet newsgroups WAIS-
accessible, how could I avoid jumping on the bandwagon?  My
addiction notwithstanding, however, I am a working biologist,
and thus I had to get some positive results with a reasonable
effort if I was going to be able to use this new thing.
Downloading the Mac version of the program from Thinking
Machines Corporation (which they provide *ABSOLUTELY FREE*,
Thanks, Thinking Machines!), guided by the clear instructions
given by Rob Harper, went relatively straightforwardly.
However, initial attempts to USE the program to search for
useful database were aggravating, time consuming and largely
unsuccessful.  Further effort has indicated to me that at the
present time, use of the program is too complex and too
unreliable, and resources accessible with WAIS are too sparse
to allow me to recommend this program as a working tool.
However, I hope WAIS really is the wave of the future, for if
WAIS-compatible resources become more generally available,
and if some of the bugs get worked out of the system, this
will become a must-use technology.

======================= WHAT IS WAIS? =======================

  I am not going to try to reiterate the thorough
descriptions of WAIS posted to the net by Rob Harper, or the
beautiful manual provided for WAIStation *WITHOUT COST* from
Thinking Machines, or the rather hyperbolic but informative
article in the May 1991 issue of Byte.  However, I will note
that after reading the information provided by all three of
these sources, I was still confused.  This is a problem I
frequently have when reading computer documentation; that it
is is completely clear if I already understand what is being
described, but totally opaque if I don't.  Nothing for it,
then, but to download WAIStation for the Mac from Thinking
Machine's computer, and see if I could figure the sucker out
by playing with it.  After several hours of work I have been
partially successful, and the following description of WAIS
is based on that experience.

1) What does WAIS do?

  WAIStation for the MAC, *ONCE YOU SET IT UP*, logs onto
remote databases, and allows you to search them.

2) What do you mean, "remote databases"?

  Potentially, there are lots of answers to this question,
but I will start by talking about just one remote database as
an example.  If you are even reading this message, you are
probably familiar with the Bionet newsgroups.  One database,
located on the genbank computers in California, consists of
all of the messages ever posted to these newsgroups.

  For me, one of the most useful of the bionet newsgroups is
bionet.molbio.methds-reagnts.  In this newsgroup, people
discuss things like difficulties ligating PCR fragments and
the solutions thereto, experience with different brands of
PCR machines, different stains for detecting DNA on gels, and
so forth.  Problem is, you may not be interested in a
particular topic when it comes up, but 6 months later be
desperately interested.  For example, you decide to buy a PCR
machine and  wonder if anyone has discussed their experiences
with different brands of machines on the newsgroup.  Perhaps
you think you remember reading something like this, but
didn't save the messages, or perhaps you have just
subscribed.  All the past messages are saved on the Bionet
computers.  This is one database.  WAIS is one way in which
you can search through this database.  //Need an example
search//.

3) What other databases are there?

  Several, but not so many at present useful to biologists.
Perhaps the first I should mention is the "database of
databases" maintained at Thinking Machines.  Thinking
Machines maintain several other example databases on their
machines.  However, the ones potentially useful to biologists
are incomplete; they are included as examples only.  If you
use Rob Harper's BioBits, all of the back issues of this are
available on his computer in Finland.  In addition to the
bulletin board database, discussed above, there is also a
"biojournals" database on the Bionet computer, which I
haven't played with yet; I would assume that access to
Medline (which most of us have) might make the biojournals
database less essential.  For me, the only truly useful
databases available RIGHT NOW are the Bionet bulletin board
database and the BioBits databases.  (Many of the other
databases are fun, however.)

4) How is WAIS different from what exists now?

  WAIS is different from what exists now in several ways.

First: It is my understanding that it is much easier to make
a WAIS-searchable database than it is to make other kinds of
remote searchable databases (e.g. Medline).  In addition, I
understand that the WAIS protocols have been placed into the
public domain , or at least are available to those who want
to use them.  Thus, many people will have a sufficient level
of expertise (Rob Harper, the folks at Bionet, NOT David
Steffen) to produce a WAIS-compatible database with
relatively modest effort.  What this will (hopefully) mean in
the future is that more databases will be available.

Second: WAIStation makes it easy to search databases in very
useful ways.  For example, *ONCE YOU SET IT UP*, it is easy
to search multiple databases with the same question in one
step.  If you get a list of articles, only one of which is
what you were looking for, WAIStation allows you to ask for
"more articles just like this one" (but see below!).

============= SOUNDS GREAT!  WHAT'S THE CATCH? ==============

1) Learning how to set up WAIS can be a task!

  I get the impression that the authors of WAIStation expect
that their software will be set up by an "expert" before the
end user messes with it; in particular, they don't expect the
end user to be adding sources.  (Do you have someone who will
set WAIS up for you if you ask them to?  I don't.)  Quoting
from the manual (the "WAIStation User Guide 0.57"):

  "Sources are generally available to everyone at a given
   site.  Questions, on the other hand, generally belong to
   individuals."

  "Your System Administrator will have arranged to have some
   or all of your site's sources updated at regular
   intervals."

In support of my suspicion, there is no information about
adding new sources in the manual.  Thus, the first couple of
hours I spent playing with WAIS was spent trying to figure
out how to add bionet as a source.  After studying Rob's
posts I thought I got it right.  No luck.  I kept getting
error messages like:

"Connection Failed - Unable to Access Remote Database"
           -or-
"Configuration Error - Unable to Access Remote Database"

Turns out, my difficulties were aggravated by:

2) Flakey network connections!

  Decided to spend a Saturday afternoon messing with WAIS
before trashing it.  After messing with things, SUCCESS!
Went home.  Came in Monday and:

"Connection Failed - Unable to Access Remote Database"
"Configuration Error - Unable to Access Remote Database"

Tuesday, it works again.  It is very difficult to figure out
the right and wrong way of doing things if the systems
imposes errors on top of the ones you are making.

3) Nifty features give weird results!

  One of the major claims to fame of WAIS is that searching
with keywords is just the start; once you find a reference
you like, WAIS will find more like it.
Use "article like/text like" with bboards gives unpredictable
results.  Every time I do this, the list of references I gets
gets worse, not better.  In particular, one post in
particular, (a post to bionet.general from
wchutt at monsanto.com on 24 Dec 90 12:16:33 GMT) always shows
up as the best match.  Turns out this is a garbled message
which is a concatenation of a bunch of different messages to
different bulletin boards (many not related to bionet).  This
concatenation seems to make it a trap for these kinds of
searches.

  In several hours playing with WAIStation and the bionet
bulletin boards, I have found that only the simple keyword
searches give good results.

  Finally, it appears that not all of the advertised features
of WAIStation work yet and that some important features were
not included.  I can't be sure of this, as I am still
learning to use the program.  This isn't a complaint, as this
is still a pre-release version, but I just wanted to let
y'all know: this is still a pre-release version.

================ I'M GOING FOR IT; ANY TIPS? ===============

Everything I say here assumes you are using a Mac connected
to Internet via MacTCP.  If this is not you, sorry, I can't
help.

1) When you ftp to think.com to retrieve WAIStation, you will
find two candidates:
WAIStation-0-61.sit.hqx
WAIStation-0-62.sit.hqx
Presumably, the -62 is the more recent version of the
program.  However, there is stuff in the -61 package which is
not in the -62 package; you might want to download both.

Also, you might want to get wais-overview-docs.sit.hqx, which
contains additional documentation.

If wading through all this seems like a chore and
professional suicide, remember; I WARNED YOU!

2) The two sources you will want right away are the bionet
bulletin boards, and BioBits.  The information you need to
install these are as follows:

bionet bulletin boards:
----------------------

CONTACT:   Mac TCP ...
           Address: 134.172.3.160
              Port: 210

DATABASE:  biosci

biobits:
-------

CONTACT:   Mac TCP ...
           Address: nic.funet.fi
              Port: 210

DATABASE:  biobit

======================== IN CONCLUSION ======================

  Although I cannot give an unqualified recommendation to
WAIS at present, I'm going to leave it on my hard disk.
Heck, everyone has to have some fun once in a while, right?
Besides, I guess I believe that someday it WILL be an
essential tool for biologists, and the time I spend mastering
it now will put me ahead of the competition.  That's my
excuse, anyway.

--
David Steffen
Department of Cell Biology, Baylor College of Medicine, Houston TX 77030
Telephone = (713) 798-6655, FAX = (713) 790-0545
Internet = steffen at mbir.bcm.tmc.edu



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