Network Entrez 3.010

Jonathan Epstein epstein at gold.nlm.nih.gov
Mon Jan 30 14:40:26 EST 1995

[ this message was also e-mailed to the Network Entrez administrators ]

The long-awaited new Network Entrez clients have now been released, and
may be found in the normal location, in the /entrez/network directory
of the ncbi.nlm.nih.gov anonymous FTP site.  VAX executables (excluding
OSF/1) may be found in the /entrez directory on the ncbi.unh.edu anonymous
FTP site, courtesy of Will Gilbert of the University of New Hampshire.

Significant changes include:

(1) A new netentcf configuration program.  This program is compatible with
    CD-ROM releases Entrez 13.0 and higher, and is (hopefully) easier to
    use than the older netentcf program.  Note that the README file has
    also changed to reflect the new program.

(2) Minor performance improvements for low-speed network connections when
    performing Boolean operations.

(3) A fix to the serious "missing docsum" problem, where some document
    summaries would fail to appear within the document window.

(4) Support for the SOCKS proxy mechanism with UNIX Network Entrez clients
    [ see below ]

(5) By popular demand, the addition of a "Date" field.  This makes it easier
    to narrow-down searches, especially when working with the EntrezBigMed

(6) The ability to track any delays which occur while connecting to the
    Dispatcher.  Since, for example, some European users report that they
    experience long delays when running Network Entrez during the afternoon,
    these new delay statistics will help me to determine whether the problem
    is network-related or NCBI-related.

(7) On-the-fly MEDLINE neighboring.  This feature is currently disabled for
    most users pending Beta-testing; please contact me if you would like
    to Beta-test this feature.

In addition, U.S. and Canadian users can now build encryption-capable Network
Entrez clients for their own use; see below.

The new Network Entrez clients resided for a few weeks in the 
"/entrez/network/new" directory.  If you have already installed this
version (version 3.010) there is no need to re-install it.  Otherwise,
please install this new software, and disseminate it as widely as
possible among your user base, as soon as you are satisfied with its

UNIX users: note that I have not built as many different UNIX clients
as in the past.  If you experience difficulties using the clients provided,
then please provide me with the following information:
  (1) The operating system which is in use (SunOS, Solaris, SGI IRIX, and
      OSF/1 on Dec alphas are supported)
  (2) The output of the command "ldd Nentrez"
  (3) Whether you are using X11R4 or X11R5.
I will attempt to post suitable binaries upon request.

The Entrez 14.0 dataset was also posted a few days ago for both Network
Entrez and WWW Entrez users; I regret the delay in making this data

  I am pleased to announce that all of the new posted UNIX Network Entrez
  clients are SOCKSified.  This means that they can run successfully behind
  a firewall, where a SOCKS daemon exists at the edge of the firewall.  The
  Network Entrez software determines at runtime whether or not to use a
  SOCKSified method of communicating with NCBI's Dispatcher, based upon the
  presence or absence of the file /etc/socks.conf.  On systems without this
  file, the Network Entrez software should run as it has in the past.  On
  systems where /etc/socks.conf is present, it should be configured to
  permit access to the appropriate NCBI computers.  At present, this means
  that the following line should be added to /etc/socks.conf:
  Also note that the SOCKS_SERVER environment variable must be set to point
  to the hostname of your SOCKS daemon.
  If these constraints are incompatible with your SOCKS environment, you
  can build Network Entrez from its source code in the NCBI toolbox,
  in ncbi.nlm.nih.gov:/toolbox/ncbi_tools.
  We hope to make SOCKSified clients for other platforms available in
  the not-too-distant future, subject to time availability and technical
  Many thanks to Rick Blevins of Merck for his help in testing this out
  in a real firewall environment, and to Don Holt of Glaxo for confirming
  this correct operation.
  If you have trouble running SOCKSified Network Entrez, please verify the
  proper operation of your SOCKS environment using other SOCKSified
  applications prior to contacting NCBI.


  For U.S. and Canadian users who might be concerned about the security of
  their Network Entrez data which traverses the Internet, it is now
  possible to build Network Entrez in a manner which causes all communications
  to be encrypted.  The encryption uses DES cypher-block-chaining, where
  the DES key is pseudorandomly selected by the Network Entrez client
  software, and is securely transmitted to the Network Entrez server using
  public key encryption.  The private key for the public key encryption only
  exists on NCBI's Dispatcher computers.  The public key appears in the
  Network Entrez software releases in the "data" directory, as well as in
  the NCBI toolbox and on the Entrez CD-ROMs, release 11.0 and higher.  The
  public key file is named "pubkey.enc".
  Due to U.S. export regulations, NCBI cannot post encryption-capable
  software for anonymous FTP.  U.S. and Canadian users who wish to use
  encryption-capable Network Entrez will need to build Network Entrez from
  source code in the NCBI toolbox, and follow the instructions in the
  toolbox's network/encrypt/README file to obtain the RIPEM/RSAREF source
  Since Network Entrez consists of keyword searches of public data, it is
  unlikely that users will need to use data encryption.  There may, however,
  be concerns about transmitting private sequence data over the network for
  BLAST searches.  Since the same encryption scheme will be used in the
  forthcoming Dispatcher-based network BLAST client/server software,
  interested users and developers may wish to preview the encryption methods
  We would like to thank James Bidzos, President of RSA Data Security, Inc.,
  for granting permission to use the software from the RSAREF encryption
  libraries for this application and to Mark Riordan for maintaining
  the RIPEM/RSAREF distribution site.

I will be happy to answer technical queries; please direct general queries
and IP registration updates to net-info at ncbi.nlm.nih.gov.  U.S. users:
please provide your phone number when contacting me, as I prefer to use
the telephone when possible.

As always, thanks for your interest in Network Entrez.

Sincerely yours,

- Jonathan

Jonathan Epstein                                epstein at ncbi.nlm.nih.gov
National Center for Biotechnology Information   Phone: (301)496-2475
National Library of Medicine                    Building 38A, Room 8N805
National Institutes of Health                   8600 Rockville Pike
                                                Bethesda, MD 20894

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