I had some requests---Entrez/VMS summary (very long)

Steve Thompson: VADMS genetics THOMPSON at WSUVMS1.CSC.WSU.EDU
Wed May 19 15:47:19 EST 1993


Good Day Bio-Soft -

Okay, I know it's almost 1500 lines long, but I did have a few people request
my summary.  Go ahead and Delete it if you care not bother.  Sorry to
monopolize bandwidth and disturb routines.  Look for screen-wide strings of
##### to find major division breaks in the document.

						SMT


          =========================================================
          NCBI's _Entrez_: Sequences & References, on VAX/VMS; How?
          =========================================================




						edited by:
	  					Steve Thompson, May 1993
						thompson at wsuvms1.csc.wsu.edu 



This summary compilation attempts to describe various methods of installing and
operating NCBI's Entrez System on a VAX/VMS cluster.  The virtues and drawbacks
of several alternate approaches are discussed.  In all cases I  attempt to
emphasize methods of wide range, multi-user applicability.  Naturally, all
standard disclaimers hold and I apologize to any authors which I have neglected
to identify as well as to any who would have prefered that I not include their
thoughts on these matters.

The previous summer I had collected comments from a similar discussion on the
Bio-Soft BioNet board.  That summary, which follows in part below (see Appendix
for technical section from same discussion), seemed to imply that the only way
to get Entrez running on a VAX was in a windowing type environment,
specifically, with VMS/Motif.  I really blew it on identifying authors in this
old summary because I didn't realize that I would be including it in some later
document.  Sorry and thanks to all those valuable individuals who contributed!


################################################################################

    Subj:	Entrez for VMS/Motif ... where to look/what to grab to
                get a working version of Entrez on the VAX.
 
    Much From: jasper at vax.path.ox.ac.uk (Jasper Rees)

    Another option is the NCBI Entrez CD, for which there are clients
    for unix (all flavors, Sun and SGI clients are on the NCBI
    server), VMS (Motif 1.0A is required), Mac, and Windows (not just
    DOS). The software on the server compiled cleanly on VMS, Sun's
    probably require Motif to compile but the binaries are available,
    SGI binaries are there too, though this should be fine directly I
    guess: which makes it the first 'Open' software I can think of -
    for which I think NCBI deserve real praise!
 
    I guess I can get to a full report later today (I have a CD here,
    the software is installed, the ISO-9660 drivers are installed, I'm
    supposed to be writing a grant :( but it looks really neat, there
    are links betweeen the databases and the appropriate Medline
    entries and good things like this, so check it out! There is no
    sensible way (or reason to) move these databases from the CD's.
 
    Both the NCBI and DEC want to see Entrez running under VMS.
 
    I was able to build Entrez for VMS/Motif last week.  The source
    code was from the NCBI archive, no changes were made to this this
    code.  The "build" files provided are a series of DCL commands,
    MMS is not required. These files contained a couple of typo's,
    ommisions, and logicals needed to be added to find the X11 and
    Motif header files.
 
    For the impatient running VMS 5.5, there is an Anonymous FTP at
    "ncbi.wi.edu". Get the .EXE file and required ASN file.  We run
    TGV Multinet, VMS Image transfer mode will work from other
    Multinet sites and Wollongong site with a recent release.  There
    are also some better uncompress and tar tools in the [.UNIX-TOOLS]
    subdirectory.
 
    Of more critical concern is the ISO 9660 driver from DEC.  It is
    not fully functional under VMS 5.5.  Jasper Rees thinks there is a
    new release in the works, we'll wait to see what he finds out. 
    Currently, a single user can mount the CD, work with it then
    reboot to dismount it.  A little brutal, but OK for development on
    a single-user workstation. Also, the sales people don't know that
    much about it so here's the part number, YT-GS001-01, $275 (list).
  
    OK, the 5.5 compatible ISO-9660 driver is called F11CD, and
    several sources tell me to contact my DEC sales group for a part
    number and a price for media and documentation. License to use is
    included with VMS 5.5. I have yet to discover whether it media can
    be obtained as part of DECcampus style agreements, but its not in
    the listings I have. Nor is it on CONDIST.
 
    The early versions of VFS are reported to work properly using the
    RRD40 CD readers but mine are RRD42s, and I didn't get feedback on
    which version of VMS this was with. In that config they can be
    mounted /Cluster/System.
 
    Worth the reboot just to see the software! But don't spend money
    on the driver just to see this unless you have to.
 
    Thanks to Jasper (and Mr. Schneider at DEC) I found the ISO9660
    driver for VMS on September's CONDIST. Thanks to Will Gilbert for
    providing the VMS Entrez via anonymous FTP (look on ncbi.wi.edu).
 
    It works. Took all of five minutes to install the driver from DEC
    then a reboot. Works great on VMS 5.5 with the July, 1992
    Pre-release 6 Entrez CD-ROM.

################################################################################

Me again. SMT:  This left me dissatisfied for it would severly restrict our
user's access to the Entrez system.  The remainder of the discussion, which is
summarized below, occurred on the Bio-Soft BioNet board and was prompted by my
recent posting of the following query:

################################################################################

    Greetings BioNetLanders -

    From all I can gather (using Gopher and USENET) NCBI's _Entrez_
    system can only run on a VMS system if Motif and some type of
    windowing environment is utilized.  _Entrez_ is tremendously
    powerful with its "neighboring" and "hard link" concepts and could
    prove invaluable to many users on our campus if they had access to
    it.  No other system so painlessly merges the information
    available in Medline to sequence data.  The probability of getting
    many separate laboratories to purchase both the _Entrez_ CD's and
    CD readers for their own machines is nil.  Therefore, we desire to
    place the system on a distributed platform that all users could
    equally access.  In our case that limits our choice to VAX/VMS. 
    Our system already has the necessary CD readers and network
    connections. Yet few of our users have X-window server software on
    their machines, furthermore, many of our users ONLY have access to
    text or at most Tek graphics terminals.  Has anybody developed a
    text only interface to _Entrez_ ?!  The potential application of
    such an interface in enormous.  I would imagine that if one were
    developed, the demand would be substantial.

    Call to software developers!  Please heed this need to make NCBI's
    _Entrez_ system accessible to ALL biologists, not just those
    chosen few with seemingly bottomless computing resource budgets!

					Thank you for the time, Steve T

                              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


################################################################################

My VAX/VMS system manager replied to me:

    Thanks for the note Steve. You could have the CDs mounted on your
    Microvax and  have people have access to them with Motif from the
    cluster. If you had them use it from your platform, you would
    also have to buy motif for yours. But that doesn't seem
    necessary. -- Dean Guenther

So at least we wouldn't have to get Motif up on both the university's cluster
and our own MicroVAX (where our CD readers are).  Four main approaches were
suggested to solve our problem of getting Entrez out to as many people on campus
as possible.  In addition to my suggested comman



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