Not to beat a dead horse, but, more VADMS ...
Steve Thompson: VADMS genetics
THOMPSON at WSUVMS1.CSC.WSU.EDU
Wed May 12 12:27:34 EST 1993
Attention BioNetland -
In the weeks following my posting of the compilation of the VADMS support
discussion, several additional comments and letters came in. To keep those
interested in this ongoing situation up to date, I have prepared another
summary. The enclosed comments are only those that were sent personally to me;
at least twenty more were sent directly to the "bigshots" without sending me a
copy. I will not repeat anything from the previous compilation and urge any
interested parties who missed the previous discussion to either use Gopher or
USENET for more information (or write me personally for the previous summary).
As always, the enclosed comments are purely the opinions of the identified
authours and do not constitute the official policy of any employing agency.
thompson at wsuvms1.csc.wsu.edu
P.S. Still no word from Central Administration or Systems and Computing
regarding final decisions! They'll probably string us out as long as
possible; the new fiscal year begins July 1 around here.
I'll keep you posted.
Kirk Schnorr at tournesol.versailles.inra.fr sent Dr. Tom Mueller, Director of
Systems and Computing, the following letter:
This letter is intended to express my strong support for the VADMS
program. In 1990, I was the teaching assistant for the Computer
techniques in [Molecular] biology course (BC/BP 578). As one of the
benefactors of a central biocomputing facility during my graduate
studies, I would like to express my views about VADMS before any
decisions involving reorganization or adjustment of funding of the
VADMS program are made. You probably have received letters of support
for the program from various sources and this may be just one more but
one thing worth considering is the three years of experience I have had
with European biocomputing. What I have learned is that a central
biocomputing facility, with proper staff, is not only desirable but
essential for most molecular biology disciplines. In this age,
research institutions are rapidly becoming either RhavesS or Rhave
notsS in this area. Those without central biocomputing facilities are
increasingly unable to compete with better supported institutes. The
Europeans have learned this lesson, in large part, from the success of
biocomputing facilities in the United States such as VADMS.
The value of VADMS is not only the investment of a central and
therefore more cost efficient hardware facility but also the staff. In
biocomputing it is very difficult to find individuals with expertise in
computer science and computational biology. Susan Johns is simply the
best biocomputing system manager I know of. Steve Thompson supplements
Susan's skills with very strong genetic computer analysis skills. In
addition Steve provides individual and on site instruction of all of
the latest and important analysis programs. I consider him extremely
valuable to VADMS. I am unable to count the numerous individuals I
come across on INTERNET usergroups who waste precious time or are
unable to fulfill their research goals because they lack someone like
Steve to give them expert knowledge. I know that WSU has to face severe
budget retraints for this year but I hope that you will keep in mind
the points I have mentioned in your decision making process. Mainly, I
believe that VADMS is functioning well with its present organization,
staff and equipment. Severe cuts to VADMS or lowering WSU's commitment
to it by transferring it to a smaller department face the real risk of
crippling VADMS so that it is of little use to anyone. From there, WSU
risks the chance of being one of the Rhave notS research institutions
that are unable to compete in this vital interdisciplinary area.
Sincerely, Dr. Kirk M. Schnorr
Mark Reboul at CUCCFA.CCC.COLUMBIA.EDU continued his insightful discussion:
I offer a couple more thoughts on the notion of charging for computing
resources (in case you find yourself in that extremity). Specifically,
I identify some "moral" dilemmas that come with that turf, which ought
to be thought about carefully before proceeding.
If right now the users get to use your computers for free, then you
can freely encourage them to experiment, to try things out, to vary
program parameters to help clarify their effects on output. In short,
you can encourage the users to learn about what they're doing by trial
But once usage charges are applied, the users will be constrained
against "playing around" on the system -- which all experienced users
know is the only way to truly learn what's going on. You will no
longer be able to say with a straight face something like, "Why don't
you run that FastA job with some different settings of the wordsize
parameter and see how they affect the results?"
This is definitely a problem I have in my job. I'm supposed to either
teach the users what to do or teach them how to teach themselves --
without actually doing the work for them -- but with these huge user
charges applied by the management, I can only say something very
wishy-washy like, "What you really need to do is run this program with
different parameter settings and see what happens; however, I
understand your boss will get mad if you run up a bill which is
somehow too large. So I don't know what to tell you, except for Good
Needless to say, our facility has no policy statement on this issue,
neither formal nor informal, and it makes my job harder, or at least
less satisfying. When I know that the best way to learn is by doing
yet I cannot honestly recommend that doing.... There's no solution to
My suggestion to you is, you need to think about this in advance.
Now, a related issue is that, once user charges start to be applied,
it suddenly becomes cheaper for the users to do certain types of
sequence analysis OFF your system, on any of the many currently free
resources for sequence analysis accessible over the network. This may
be fine for your experienced users, but once again we face a dilemma
in teaching the non-experienced or infrequent users.
They may not be able to manage with all these different interaction
styles and formats which have proliferated with all the services and
interfaces. You certainly will not have the time to hold their hands
in these matters. Almost every week, some new free service is
announced. Even for an expert, it's impossible to keep up.
The obvious alternative is for you to teach them the one, consistent,
local way of doing things (e.g., GCG), and then when an individual
user becomes advanced enough to ask about the outside resources, you
give him some limited information and he goes off to learn it on his
own. The seemingly "immoral" part is that, out of trying to keep your
job manageable, you have implicitly forced the majority of users to
use the costly method, which benefits your own operation no less!,
when a much cheaper method (almost free) exists.
So this sort of thing also weighs heavily on my conscience, and there
seems to be no easy solution for it (in this money-centered world).
Again, I suggest you give it some thought in advance.
Finally, there is something to keep in mind, which may ultimately
mitigate that last concern. I believe it is inevitable that, sooner or
later, these network-accessible resources will no longer be useable
for free. There are two factors here.
First, whoever it is that provides network data communications around
the world is sooner or later going to start charging more for it, and
that cost will become reflected back on your users, either in a gross
sense or perhaps to be itemized with their individual network
accesses. Columbia pays big bucks to be hooked into the worldwide
network, which cost is now spread diffusely through general overhead
costs, but there is already talk about itemizing network access costs
on a per-facility basis. It cannot be avoided, and it seems as
reasonable as anything else.
The other factor is that these remote suppliers of computing
resources, be they government or otherwise, may eventually become
sufficiently burdened with computing requests that they will decide to
start charging for the use of their programs and CPU time. Again, it
seems as reasonable as anything else. NCBI has already stated publicly
that they might have to start charging for Blast Client connections to
cruncher.nlm.nih.gov's Blast Server, if the demand for service
continues to grow (as we know it will).
So that is my final (?) thought for today, that as you plan for the
future, you allow for the distinct possibility that your users may
eventually have to pay for network access and certain remote
computing. Note that these charges can develop independently of
whether your own plight forces you to charge your users for local
When our non-novice users come to us asking about remote computing
resources, basically what we tell them is, Use the services freely,
but keep in mind, they probably won't be free forever.
to which I directly replied to him:
Thanks again for the comments. In all likelihood we will end up charging for
services rendered. Your "moral" dilemmas are noted and are particularly
relevant since our users are not presently charged for anything except
some printing jobs.
One of the VERY important points that I try and get across in the course that
we teach as well as in daily consultations is just how vital it is too
experiment with the very parameters that you mention. There is NOT one right
way to do things. There are many. That is where the experimental method and
subjective biological understanding comes in in our game --- you know that very
well. How can we be honest with our users and only describe one way?!
Hopefully a way around it is to avoid cpu charges in lieu of some type of a
subscription and for collaborative efforts a by-job contractual fee. That way
the user would still be encouraged to be online, learning, as long as his lab's
P.I. felt any bio-computing service is worthwhile. The real dilemna that we
are having is just how steep a service fee we can get away with. Yes, you have
had luck with high user fees, but not all installations have been as fortunate.
You are right, this whole area requires much forthought!
Likewise, net services as well as local personal computer packages do become
more attractive, but as you point out, only experienced users are good enough
to cope with the bewildering array of formats, networks and servers
successfully enough to utilize all of what is available. And the commercial
local pc/Mac packages are either quite limited or very expensive. Of course
teaching everybody a common ground is the logical alternative; here it is GCG,
although we do have internet/GCG interfaces such as BLASTMail installed. But
you are right, if people begin paying for cpu, GCG, used properly, becomes
expensive. What's a person to do? And, yes, even the network connections may
one day become expensive. Along with everything else in the world, people will
A previous student of ours, Sudhi, from our neighboring institution, the
University of Idaho, wrote me:
I read the message sent by you and Susan. I am really surprised to
learn that the VADMS facility is likely to be trimmed. I strongly hope
that VADMS would continue to exist the way it has existed so far.
After reading the message, I brought the situation to the attention of
my major advisor Dr. Phil Berger. Incidentally, he was already aware of
this, and he told me that he has tried to draw the attention of
Bact/Biochem faculty by circulating copies of your message.
While, I will do exactly what you have suggested me to do, in addition
I am going to draw the attention of the GPSA at the UOI, and our Dept.
Head, Dr. L. O'Keefe, and also of the Dean of Graduate School at UOI.
I hope that the situation would improve if UOI can get 'entangled' in
I thank you and Susan for helping me to say 'Thanks to VADMS' in a
Dept. of PSES, Univ. of Idaho, Moscow, ID 83844
And David Morgan at auriga.rose.brandeis.edu sent me the following comment
(along with his enclosed letter to a couple of the "bigshots"):
The following letter has been e-mailed to Tom Mueller and to Tom
George. I hope it has some sort of good effect, and that the powers
that be don't really fuck up a good thing without realizing it. Let me
know what happens.
Dear Dr. Mueller, (Dear Dr. George,)
I am writing in response to a notice I received via electronic mail
concerning the future of the VADMS facility at WSU. My name is David
Morgan and I was a non-tenure track faculty member in the
Biochemistry/Biophysics Program from summer 1988 to fall 1990. I
obviously do not know the exact conditions which have lead the
administration to consider a reorganization of VADMS, but I do know
the strengths of the current program and its unique status relative to
WSU. I have stayed in close contact with both Keith Dunker and Steve
Thompson since I left WSU and I know that the course which VADMS offers
has grown enormously since I taught a lecture or two in the spring of
1990. I am also aware from contacts with several other people at WSU
that the services offered by VADMS to the research community in general
have been invaluable over the past few years. From my experiences at
other universities and in talking with other people in the field, I
have become aware of how truely unique the VADMS facility is: although
many universities have various software systems and data bases
available, no other university to my knowledge has any sort of
organization whose purpose is to help the rest of the university
utilize these 'available' resources. For example, Dr. R. Macnab at
Yale University asked me to do him a favor: he wanted a sequence
comparison done for several new open reading frames his group had
sequenced, and the most recent sequence data base available at Yale is
at least a year out of date. While I am certain that someone at Yale
has access to the most recent sequence information, it is rather
telling that the chairman of their biochemistry department had to ask a
friend at another university to help him with the search. Here at
Brandeis, we are fortunate to have up-to-date access to various
molecular biology data bases, but there is essentially no support
staff for using any of them: I was able to help Dr. Macnab due to my
experiences at WSU and to my interactions with the VADMS staff there.
I am also certain that had I needed any of the expertise of the VADMS
staff, I could have called upon them to offer whatever help they could.
My own field is structural biology, which includes diffraction
techniques, molecular modelling and various molecular graphics
techniques. The resources here are quite good, but the support staff
is non-existant: everytime I need to learn a new system, I am forced
to find a graduate student or post-doc who has the time, talent and
inclination to teach me how to use the 'available' resources. This is
the role Susan Johns performs at VADMS (along with general system
upkeep), and is one for which Steve Thompson is ill equiped (even if he
had the time to deal with such problems, which I am assured he does not
by both Keith Dunker and Steve himself). In addition, as I am
painfully aware from experiences with our own computer network here at
Brandeis, it is both desirable and necessary to have a staff member
whose job is to baby-sit the computers: to maintain the software and
the hardware, to keep the users happy by adding and removing users and
managing disk storage problems, to make sure 'simple' changes in one
place don't completely foul-up the remainder of the system, and to
allow the system to grow and expand in necessary and useful directions.
If one combines this role with that of teaching a course, and acting as
support staff for the university for both molecular biology and
structural biology, it seems clear that this is too much work for a
single individual to accomplish.
As mentioned, I do not know all the factors leading to the proposed
reorganization of VADMS, and I realize that the bugets for universities
in general are very tight. However, I strongly urge you to examine
very carefully the effects of your actions on the role VADMS plays at
WSU and to consider that your actions might lead to the demise of an
important and unique resource on your campus. Please do not do
anything which the WSU community will regret at some future date.
Waltham MA 02254
dgm at auriga.rose.brandeis.edu
In response to the onslaught of support letters Central Administration sent the
following political no-speak announcement out to all whom sent letters in:
From: WSUCSC PROFS Administrator
SUBJECT: VADMS Reconfiguration All PROFS News Announcement
Concerns about proposed budget cuts and reconfiguration of the
Visualization, Analysis and Design in Molecular Sciences (VADMS) Center
have been expressed by some members of the University community.
Hopefully, this will provide some background information on the
proposals being considered.
It is important to acknowledge that the Center has been in existence
since 1989 with an annual budget of $75,000/year from the Area 16
(Office of Vice Provost for Research and Dean of Graduate School)
during 1991-93 and $125,000/year during 1989-91. In addition to these
funds, Systems and Computing has contributed $60,000+ per year for the
past few years. Thus, the combined funding per year for this unit
(during 1989-93) has been in excess of most organized research units at
When VADMS was founded in 1989, we hoped that it would serve its
mission as a research and service organized research unit (ORU) as
envisioned in many planning documents that had preceded its development
(including its temporary status and funding through Area 16 as a
"laboratory") during the period 1985-89.
Since 1989, the VADMS Center has done a magnificent job of assisting
faculty and students in visualization, analysis,and design programs and
methods. The Center's user list has grown from a few to more than 100
investigators in units across campus. In addition, VADMS staff have
been instrumental in the development and instruction of graduate
students through Biochemistry/Biophysics 578, a course that has proven
useful to students in many academic areas at WSU. In summary, VADMS
service and teaching activities have been significant successes. In
contrast, VADMS has not been successful in attracting research funds or
in instituting a system for recovering partial costs through user fees,
despite encouragement from administration.
In 1992, a faculty committee was commissioned by Area 16 to conduct a
review of the VADMS Center. The Committee's report validated our
earlier assessments of the usefulness of the VADMS services to faculty
and graduate students and the value of the contributions of VADMS staff
to the BC/BP 578 course. Simultaneously, the Committee's report called
into question the expectation that the VADMS Center could succeed as a
research center. Thus, it became apparent that the original mission
developed for the VADMS Center, one of research and service, had now
shifted to service and teaching. And since ORU's do not have the
academic oversight appropriate for teaching functions, it was our
judgment that the Center's teaching function be shifted to an academic
unit such as the Department of Biochemistry and Biophysics.
Additionally, if the Center's mission now focuses exclusively on
service, then it should be considered for a budget modification
commensurate with this more narrow mission.
Accordingly, discussions were developed among Area 16 and College of
Sciences administration, and VADMS and Systems and Computing staffs.
From these discussions came a VADMS staff proposal for a "bare bones"
Area 16 budget of $51,944/year for the VADMS Center. From the earliest
discussions, Area 16 has offered to contribute $40,000/year to the
VADMS Center and to designate these funds for the College of Sciences
if its faculty were willing to support the service function of the
Center. To make up the difference between the $51,944 and $40,000, we
suggested a $100/year user fee for the >100 users on campus and
elsewhere. This fee might be assessed once yearly like a subscription
service fee and we have already talked to the Vice President for
Business Affairs who believes that the subscription fee concept can be
adopted by the Controller's Office.
The above scenario brings VADMS Center supporters up-to-date in our
conversations on the future of the Center. But, the book is not closed.
The Reconfiguration Committee will consider all of the above-noted
issues as it formulates recommendations to the President. Also, we
anxiously await a decision from Systems and Computing on its continuing
contributions to VADMS Center services. In the meantime, we value your
ideas and counsel on a future course of action--one that will assist
the University with its budget shortfall without extraordinarily
depriving WSU faculty and students of needed services.
me again, SMT:
So there you have it. The administration is giving excuses, based solely on the
almighty dollar, for its actions. Therefore, we, the non-PhD'ed staff of VADMS,
whom have performed in an exemplary manner in providing service to the
university scientific community in both research and education, as admitted even
by Central Admin', are being forced to suffer the consequences of not bringing
in grant dollars. Writing grants is not even a part of our job; the fact that
our faculty director, now a volunteer position, has been unsuccessful in his
endeavor to write funded grants, after the initial one which began VADMS, should
not deprive the entire university of our services. Oh well; nuff said. I'll
keep the boards informed on the ultimate resolve up here. Bye for now.
Sincerely, Steve Thompson
Steven M. Thompson
Consultant in Molecular Genetics and Sequence Analysis
VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory
Washington State University, Pullman, WA 99164-1224, USA
AT&Tnet: (509) 335-0533 or 335-3179 FAX: (509) 335-0540
BITnet: THOMPSON at WSUVMS1 or STEVET at WSUVM1
INTERnet: THOMPSON at wsuvms1.csc.wsu.edu
More information about the Mol-evol