cthomas@f.adelaide.edu.au (05/27/91)
Thanks to all those who replied to my query re status of DDBJ Flat Email server. As a result of your replies I was able to contact Mary Shimoyama (International Collaboration Supervisor) from DDBJ. Here is her reply re status of DDBJ Flat Email server Dr Connor J Thomas Dept Microbiology and Immunology University of Adelaide South Australia ----------------------------------------------------------------------------- Date: Mon, 27 May 91 09:57:22 JST From: mshimoya@ddbj.nig.ac.jp (Mary Shimoyama) Message-Id: <9105270057.AA18235@niguts.ddbj.nig.ac.jp> To: cthomas@f.adelaide.edu.au, mshimoya@ddbj.nig.ac.jp Subject: emailserver Dear Dr. Thomas, Thank you for your e-mail of May 26th. Unfortunately, at the present time DDBJ Flat Email server services are unavailable. We are in the process of developing a new Email server program and will inform you as soon as it is available. We also offer on-line service which is the most efficient way to access the database in DDBJ. If you are interested in on-line service, I would be glad to send you an application. Thank you for your interest in DDBJ and if I can be of any assistance or if you have any questions, do not hesitate to contact me. Sincerely, Mary Shimoyama
pgil@HISTONE.LANL.GOV (Paul Gilna) (05/28/91)
Connor and Michael, One postscript re DDBJ: All data processed by DDBJ (with the exception of confidential data) are passed to GenBank on a regular basis and incorporated immediately into the on-line flatfile servers and RDBMS satellites; These data are in turn propagated to EMBL and their distribution nodes. Hence data from DDBJ are available to users of the GenBank and EMBL sequence retrieval and searching facilities. Confidential data are passed to us either upon expiration of hold dates or when either of the three databases (or increasingly, the community) "spot" the published data. Regards, --paul Paul Gilna GenBank, Los Alamos
kramer@beasley.CS.ORST.EDU (Jack Kramer - Biophysics) (05/29/91)
In article <9105281658.AA02439@histone.lanl.gov> pgil@HISTONE.LANL.GOV (Paul Gilna) writes: > >One postscript re DDBJ: > >All data processed by DDBJ (with the exception of confidential data) >are passed to GenBank on a regular basis and incorporated >immediately into the on-line flatfile servers and RDBMS satellites; >These data are in turn propagated to EMBL and their distribution nodes. >Hence data from DDBJ are available to users of the GenBank and >EMBL sequence retrieval and searching facilities. Confidential >data are passed to us either upon expiration of hold dates or when >either of the three databases (or increasingly, the community) >"spot" the published data. > >Paul Gilna >GenBank, Los Alamos The real value of the DDBJ flat file server was not necessarily limited to the availability of just the DDBJ. It was the only site which provided anonymous ftp access to the distribution format data from "ALL" repositories. Most especially this included the NBRF/PIR data which the NBRF still refuses to connect to Internet since they would still rather ship the tapes and collect their "shipping and handling" charges. It was also very convenient to be able to access all the databases at one high bandwidth site. I am sorry to see that they too have now acceeded to the for profit crowd. Jack Kramer
POSTMAST@gunbrf.bitnet (05/30/91)
The National Biomedical Research Foundation is a non-profit foundation which
began the collection of protein sequence information with the "Atlas of Protein
Sequence and Structure" in 1968 and maintains the Protein Identification
Resource entirely through grants from the NIH, NLM, and NSF. We are required
to distribute the PIR sequence databases on a cost recovery basis.
On several occasions we have had correspondence with Jack Kramer, formerly at
the University of Miami and now apparently at Oregon State, concerning
network access to the PIR database. Dr. Winona Barker, Dr. David George and I
have all always responded in a courteous and friendly manner to his private
messages and BioNews postings. Here is some of the reply that Dr. George
sent to Jack Kramer after his bulletin board outburst at the announcement
of the PIR Network Server last autumn.
------------------------------------------------------------------------
Jack Kramer November 29, 1990
Molecular Biology Computing
University of Miami
jkramer@molbio.med.miami.edu
Dear Jack,
I am very sorry that the PIR is not up to the standards of GenBank and the rest
of the world. However, while GenBank's budget was dramatically increased so
that they might modernize, our budget over the past eight years has barely kept
pace with the cost of living; I'm sure you are aware that the amount of
sequence data has accumulated at a somewhat faster pace.
In the second year of PIR operation, we noted that it would be impossible to
keep pace with the incoming data without additional funding to modernize our
methods and to moderately expand our staff. Although we have pleaded every year
since, no such additional funding was forthcoming.
We attempted to rectify the situation when the PIR grant came up for renewal;
however, NIH council finally approved twenty to thirty percent less than we
requested, which amounted to only a modest increase. Unfortunately, even this
amount was not actually awarded. In each year since the renewal (which began
February 1989), some administrative misunderstanding resulted in the actual
award being some 20% less than the council recommendations. In 1989, after
considerable lobbying, we were able to recover almost the full award by
applying for supplements from the NLM, but this required some additional work
that would not necessarily have been required if the grant had been fully
funded. We were not able to repeat this for the past year and it seems unlikely
that we will get any relief in the coming year.
If you are worried about where your US tax dollars are going, you are looking
in the wrong place; we have simply not been given sufficient support to provide
adequate services. I would be grateful if you would write to congress, because
we have apparently exhausted all possible appeals to the National Library of
Medicine, who now administers the grant.
We regret that we must charge for distribution; however, under the PIR grant,
we must operate distribution services on a cost recovery basis. I can assure
you that you are not the only one that is frustrated; however, until we can
obtain sufficient and stable funding, there is little else that we can do.
As for your concern over FTP access to the data: because of the size of our
operation and other security considerations, it is necessary for us to
independently maintain our own computer system. While recognizing this
necessity, the NIH council inadvertently eliminated the computer support
personnel (system manager, operator, etc.) from our budget and little funds
were made available for the personnel time required for the installation of new
equipment. Therefore, an Internet connection could only be installed by
stealing time from other database activities. Moreover, efficient FTP access
cannot be provided without the development of specialized hooks into the
database. Given limited resources, we had to set priorities and made the
decision that it was more important to solve the data backlog problem than to
concentrate on providing rapid access to a data set that was updated only
infrequently. With the introduction of Section 3 of the database, we have
essentially solved the backlog problem; if we could recover of the 20% cut, we
would be able to completely eliminate the backlog within the coming year and
make the data available within a few weeks of publication. We have now begun to
seriously address the accessibility problem. As John Garavelli has written to
you, we have set up an E-mail server and hope to establish a system for FTP
transfer within the coming months.
Again, I am sorry for any inconveniences that this situation may caused you;
however, under the circumstances we are having some difficulty providing any
database at all.
Sincerely,
David George
Director of Computer Operations
Protein Identification Resource
National Biomedical Research Foundation
GEORGE@GUNBRF.bitnet
------------------------------------------------------------------------
On that and one other occasion after informing Jack Kramer of the particular
circumstances of our network situation, he posted statements that were
misleading or that he then knew to be false on the BioNews bulletin boards.
Jack Kramer may at one time have been a user of the PIR On-Line service, while
we were able to offer that service for free. But when we had to begin
recovering costs for our services, he was not a paying user. Interestingly,
after the PIR Network Server was announced as a free service last autumn, Jack
Kramer has not been among the hundreds of users getting prompt network
responses to their thousands of PIR, GenBank and EMBL database queries and
sequence searches. Nor has he apparently used the FTP site maintained by Dan
Davison at the University of Houston which has our current database. Whatever
the origins of Jack Kramer's antipathy to the staff of the NBRF, his
irresponsible behavior in making these repeated verbal attacks only call his
motivations into question.
We intend to continue providing the scientific community with high quality,
annotated and current protein sequence databases, and now that Internet access
is available to the NBRF, we will try, as we can afford to expend the limited
time and resources of our small staff, to provide more direct and responsive
database access through sites distributed around the country. And yes, Jack,
you can get the free, instantaneous gratification you have been seeking.
------------------------------------------------------------------------
Dr. John S. Garavelli
Database Coordinator
Protein Identification Resource
National Biomedical Research Foundation
Washington, DC 20007
POSTMASTER@GUNBRF.BITNET