Survey of Core Computing Facilities

Bruce Roe BROE at AARDVARK.UCS.UOKNOR.EDU
Tue Apr 2 09:39:00 EST 1991


Fellow Netters:

         I presently am trying to deal with the "powers that be" regarding
 funding for our centralized computing facility for genetic research.
 The University of Oklahoma provides the VAX 6250, *free* computer time,
 and user training for VAX usage.  The Oklahoma University Genetic Computer
 Group has both on-line and hard copy documentation for the programs listed
 below, maintains and updates the programs, databases and help, and provides
 phone and e-mail user help.
 
         If you are responsible for a similar computer facility I would
 greatly appreciate your responses to the following questions:
 
         1. What is your budget and who supplies the monies?
         2. What is available at your facility?
 	3. Who uses your facility?
 
 My answers to these questions follows.
 Thanks for any and all responses.
 
   **************************************************************************
  *  Bruce A. Roe                    Professor of Chemistry and Biochemistry *
  *  Dept. of Chem. and Biochem.     INTERNET: BROE at aardvark.ucs.uoknor.edu  *
  *  University of Oklahoma          BITNET:   BROE at uokucsvx                 *
  *  620 Parrington Oval, Rm 208     AT&TNET:  405-325-4912 or 405-325-7610  *
  *  Norman, Oklahoma 73019          FAXnet:   405-325-6111                  *
   **************************************************************************
 
 
 I. BUDGET FOR THE OKLAHOMA UNIVERSITY GENETIC COMPUTER GROUP FACILITY
 
 	A yearly budget of $150K was originally proposed for the University
 of Oklahoma Genetic Computer Group as part of a State grant to the Medical
 School to establish a  "Center of Excellence in Molecular Medicine".  This
 center consists of several core facilities, among them a Computing Core 
 Facility.  The original budget was cut to $33K/yr. and has been at that level
 since 1989.  All our hardware and computer time is supplied by the university.
 Thus there is no money for upgrading the existing hardware which is needed
 because of the increased usage.  This reduced budget means that there only
 are funds to support a part-time technician for maintaining the programs, 
 a part-time sect. for maintaining the documentation, and cover the costs of 
 the GCG and Staden programs and database updates.   I receive no salary or
 other funds for directing this center, helping users, etc.
 
 II. DESCRIPTION OF THE OKLAHOMA UNIVERSITY GENETIC COMPUTER GROUP FACILITY
 
         Funding for the "Center of Excellence in Molecular Medicine"
 begun on September 1, 1989.  One of the components of this center was
 to establish a common, centralized computer network which would allow
 individuals at Universities and Research Centers throughout Oklahoma
 to have free access to the University of Oklahoma Vax computer which
 contains an extensive set of DNA and protein analysis programs, the
 GenBank, EMBL, SwissProt, and NBRF databases, phylogenetic analysis
 programs and the usual electronic mail, text editors and other Vax
 capabilities.
 
         At present the Oklahoma University Genetic Computer Group
 facility contains:
 
 a. Computer programs from several sources which are extremely useful
         for genetic research, DNA analysis and protein studies.
         These programs include:
         GCG (Genetic Computer Group) programs by Dr. John Devereux,
           formally at the University of Wisconson.
         DNA and protein analysis programs, by Dr. Rodger Staden at the MRC,
           Cambridge, England.
         PHYLIP (Phylogeny Inference Package) by Joseph Felsenstein
           at Washington State Univ.
         FastA programs by Dr. Bill Pearson at Univ. Virginia.
         Various multiple sequence alignment programs.
         Various programs for rapid database searches, including
           direct e-mail searches of GenBank by GenBankMail, EMBL
           by EMBLMail, and Blast (from the NLM),
 b. The various data bases, i.e. GenBank, EMBL, SwissProt, and NBRF,
           and the programs used to search these data bases either
           in real time or in batch mode, or via e-mail to GenBank
           or EMBL computers.
 c. A VAX computer mail facility to improve rapid communications among
         the geographically distinct research groups.
 d. Computer support personnel to train the researchers in the new
         areas of the genetic engineering computer and to answer
         questions concerning the individual programs and facilities.
 e. A series of menus and on-line help files which provide a unique, user
         friendly interface to the available programs.  This interface reduces
         the difficulties usually encountered with main-frame computer usage.
 
 III. USERS OF THE OKLAHOMA UNIVERSITY GENETIC COMPUTER GROUP
 
         At present, there are 65 registered OUGCG user accounts.  Fifteen of
 these connect to OUGCG on average 2-4 hours/day while the remaining accounts
 are accessed on average once per week.  These registered users are at the
 University of Oklahoma Norman campus, University of Oklahoma Health Sciences
 Center OKC campus, Oklahoma Medical Research Foundation, Tulsa Univ.,
 Oklahoma State University, Noble Foundation, and Childrens Hospital of Tulsa.
 Of-campus users connect to the Norman campus VAX via the InterNet (MidNet)
 or via dialup.

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