[ 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
SOCKSIFIED UNIX NETWORK ENTREZ CLIENTS
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:
sockd 188.8.131.52 255.255.255.0
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,
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.
DATA ENCRYPTION AVAILABLE FOR U.S. AND CANADIAN USERS
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.
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