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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.

						Steve Thompson
						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
    & error.

    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
    this conflict.

    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
eventually pay.


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
    this crisis.

    I thank you and Susan for helping me to say 'Thanks to VADMS' in a
    different way.

    Sincerely, Sudhi 
    M.R. Sudarshana 
    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.


      					 David Morgan
                                         Brandeis University
      					 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

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