From owner-embldatabank@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.embldatabank Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 6 Jun 1996 02:00:53 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 154 Sender: daemon@net.bio.net Distribution: world Message-ID: <199606060900.CAA19238@net.bio.net> NNTP-Posting-Host: net.bio.net BIOSCI is about halfway to its funding goal!! I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We are only about halfway to our funding goal and need to raise further funds to avoid having to curtail services at net.bio.net. Fundraising is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we will be getting newer and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Please contact us for further details. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5500 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 800 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. Ads can also be displayed on various combinations of other BIOSCI/bionet newsgroups. Please contact us at biosci-help@net.bio.net for details. ---------------------------------------------------------------------- From owner-embldatabank@net.bio.net Thu Jun 06 23:00:00 1996 Newsgroups: embnet.general,bionet.molbio.embldatabank Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!news From: Matteo diTommaso Subject: Naming EMBL Daily Updates & NIs Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Fri, 7 Jun 1996 22:58:52 GMT Lines: 39 Content-Type: TEXT/PLAIN; charset=US-ASCII Mime-Version: 1.0 Organization: European Bioinformatics Institute X-Newsreader: NEWTNews & Chameleon -- TCP/IP for MS Windows from NetManage Daily Updates ------------- The following naming convention will be used at the EBI for the naming of daily update files to the EMBL Nucleotide database. Each release is given a number. The June release of the EMBL database will be Release 47. The next update to appear will be the first one to apply to release 47. All updates to this release will be sequentially numbered. r47u001.dat.Z r47u002.dat.Z r47u003.dat.Z This change from the date based numbering scheme allows us to issue more than one update per day. This will allow us, if necessary, to keep the size of updates below a given maximum and makes it easy for users to determine whether or not any updates have been missed. NIDs ------ The first entries containing NI numnbers will begin to appear this evening. The NI line shows the Nucleotide Sequence ID number this number is associated with the exact sequence in the entry and only changes when the sequence changes. This sequence number is essential for the building of secondary sequences (e.g a chromosome sequence which is constructed by concatenating parts several existing sequences). Using the NI numbers it is possible to point to the version of the sequence being used in the construction. The process of adding NI numbers to the EMBL database included a full comparison of all sequences in GenBank and EMBL databases to ensure that the sequences in both databases are the same. Matteo diTommaso -------------------------------------------------------- E-mail: ditommaso@ebi.ac.uk WWW: http://jupiter.ebi.ac.uk/~tommaso/ EMBL Outstation - European Bioinformatics Institute Hinxton Hall, Hinxton, Cambs, CB10 1RQ United Kingdom -------------------------------------------------------- From owner-embldatabank@net.bio.net Thu Jun 06 23:00:00 1996 Newsgroups: bionet.molbio.embldatabank,embnet.general Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!stoehr From: stoehr@ebi.ac.uk (Peter Stoehr) Subject: EMBL 47 begins Sender: news@ebi.ac.uk (Mr news) Message-ID: <1996Jun7.164823@ebi.ac.uk> Date: Fri, 7 Jun 1996 16:48:23 GMT Lines: 33 Organization: European BioInformatics Institute Today we have begun to build release 47 of the EMBL Nucleotide Sequence Database. Below are some details of relevance to those concerned with managing local databases of sequence updates. The actual 'freeze' time for EMBL 47 was 6-JUN-1996 08:16 BST The last daily update file which will be included in release 47 is ftp://ftp.ebi.ac.uk/pub/databases/embl/new/960606.dat.Z The naming scheme for update files on the EBI anonymous FTP server will change today. This scheme is re-posted in a separate message. As announced previously in database release notes, the following changes are introduced at release 47 and users will see these from now on in daily updates. - a new flat-file division HUM (for human data) replaces PRI (primate). Non-human primate data will be represented in the MAM (other mammal) division. - a new line-type NI is introduced to contain a stable identifier for a nucleotide sequence. This will almost certainly be the last database release before we have to move to the new accession number format. For further detail, see previous release notes in: ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.doc or http://www.ebi.ac.uk/ebi_docs/embl_db/relnotes46/relnotes.html Peter Stoehr EMBL - EBI From owner-embldatabank@net.bio.net Sun Jun 09 23:00:00 1996 Path: biosci!agate!spool.mu.edu!usenet.eel.ufl.edu!newsfeed.internetmci.com!chi-news.cic.net!cougar.olivet.edu!reed-006.olivet.edu!dginn From: dginn@olivet.edu Newsgroups: bionet.molbio.embldatabank Subject: Rat Type I collagen cDNA probe needed Date: Mon, 10 Jun 1996 14:38:44 +1000 Organization: Olivet Nazarene University Lines: 10 Message-ID: NNTP-Posting-Host: reed-006.olivet.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev B] Greetings, I am looking for a plasmid probe with a cDNA sequence for Rat Type I collagen gene [alpha1(I) and/or alpha2(I)]. Does anyone know where I could get ahold of this probe - either a company or a laboratory? Thanks a lot! Dwight Ginn Olivet Nazarene University From owner-embldatabank@net.bio.net Wed Jun 26 23:00:00 1996 Newsgroups: embnet.general,bionet.molbio.embldatabank,ebi.announce Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!stoehr From: stoehr@ebi.ac.uk (Peter Stoehr) Subject: Notice of Accession Number format change Sender: news@ebi.ac.uk (Mr news) Message-ID: <1996Jun27.143711@ebi.ac.uk> Date: Thu, 27 Jun 1996 14:37:11 GMT Lines: 57 Organization: European BioInformatics Institute This message is to announce that we plan to release in the next few days into the EMBL Nucleotide Sequence Database a DNA sequence record with the new Accession Number format consisting of 2 letters plus 6 digits (eg AB123456). This entry will be distributed via the daily/weekly/cumulative update mechanism on our anonymous FTP server, as well as being available from EBI network servers. This change was announced by the International Nucleotide Sequence Databases (DDBJ/EMBL/GenBank) in June of last year and in all subsequent issues of the database release notes. See the text below or link to the URL http://www.ebi.ac.uk/ebi_docs/embl_db/relnotes47/forthcoming_changes.html#acc This single record will give you the opportunity to ensure that your various programs, scripts or retrieval software you may be using are working the expected way when such records come your way. Regards, Peter Stoehr EMBL -EBI ------------- Notice of Accession Number Format Change Nucleotide Sequence Database Collaborative Agreement 31 May 1995 Currently, accession numbers used by the nucleotide sequence databases consist of one prefix letter followed by 5 digits. EST projects and projects to add patent data have accelerated the need to extend the accession number space. It is projected that the databases will run out of accession numbers within 8 to 10 months. It is clear that: * As much notice as possible should be given to users and software developers. * The change should make a large enough space that another change will not be necessary in the foreseeable future. * The accession number should continue to be readily identifiable as a DDBJ/EMBL/GenBank accession number. The collaborators concluded that: * A new form of accession number will be created, defined as an 8-character alphanumeric string, beginning with two upper case letters and followed only by digits (e.g., SR004562). Leading and trailing zeros are significant. The letter 'O' will not be used. * Existing 6-character accession numbers will remain as they are, and will never be transformed to an 8-character form. * New accession numbers will not be used before February 1, 1996. The groups agree to avoid using new accession numbers as long as possible after that. The International Nucleotide Sequence Databases DDBJ/EMBL/GenBank From owner-embldatabank@net.bio.net Wed Jun 26 23:00:00 1996 Newsgroups: embnet.general,bionet.molbio.embldatabank,ebi.announce Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!stoehr From: stoehr@ebi.ac.uk (Peter Stoehr) Subject: EMBL 47 available Sender: news@ebi.ac.uk (Mr news) Message-ID: <1996Jun27.144204@ebi.ac.uk> Date: Thu, 27 Jun 1996 14:42:04 GMT Lines: 32 Organization: European BioInformatics Institute Release 47 of the EMBL Nucleotide Sequence Database is built and available via the following EBI network servers: - anonymous FTP server ftp://ftp.ebi.ac.uk/pub/databases/embl/release - SRS WWW server http://www.ebi.ac.uk/srs/srsc - FASTA server, FASTA@ebi.ac.uk or URL: http://www.ebi.ac.uk/searches/fasta.html - email server, NetServ@ebi.ac.uk Release notes are available in: ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.doc (plain text) http://www.ebi.ac.uk/ebi_docs/embl_db/relnotes47/relnotes.html (html) For those who install local copies of the database, note particularly the following: 1. Database files. There is an additional EST file EST6.DAT; we have removed the primate division (PRI); we have added a new division HUM for human sequence data, consisting initially of files HUM1.DAT and HUM2.DAT. 2. A new line-type NI is introduced in all entries. 3. Release 47 is about 16% bigger than release 46 (by nucleotide count) 4. Entries containing the new '2+6' accession number format will appear very soon now in updates distributed between releases 47 and 48. 5. We will update the contents of the update directory on the EBI anonymous FTP server ftp.ebi.ac.uk/pub/databases/embl/new this evening Thursday June 27th to: - remove all pre-release 47 update files. - replace the cumulative.dat.Z file by one containing only post-release 47 data (it will become smaller !). Regards, Peter Stoehr EMBL - EBI From owner-embldatabank@net.bio.net Thu Jun 27 23:00:00 1996 Path: biosci!ynu.edu.cn!hongluo From: hongluo@ynu.edu.cn (hongluo) Newsgroups: bionet.molbio.embldatabank Subject: helpac Date: 28 Jun 1996 04:48:48 -0700 Organization: Yunnan University Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <31D46C59.6247@ynu.edu.cn> NNTP-Posting-Host: net.bio.net Help. From owner-embldatabank@net.bio.net Thu Jun 27 23:00:00 1996 Newsgroups: bionet.molbio.embldatabank Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!uranus.ebi.ac.uk!redaschi From: Nicole Redaschi Subject: Update: SynCron - tools for maintaining synchronised copies of the EMBL Nucleotide Sequence Database Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Fri, 28 Jun 1996 11:17:53 GMT Content-Type: TEXT/PLAIN; charset=US-ASCII Mime-Version: 1.0 Organization: European Bioinformatics Institute Lines: 48 Update: SynCron - tools for maintaining synchronised copies of the EMBL Nucleotide Sequence Database ----------------------------------------------------------------------------- We observe that many people still download the full cumulative update file (cumulative.dat) from the EBI ftp site rather than incremental updates. To promote usage of the incremental EMBL update files, the EBI and the Swiss EMBNet node have jointly developed the SynCron tools in order to allow you to regenerate the cumulative update file at your site reliably from incremental updates. The tools make use of 'transaction listings' that describe the update, insert and delete operations to the EMBL Nucleotide Sequence Database as represented in the flat-file updates. There is one listing for each update file (available from ftp://ftp.ebi.ac.uk/pub/databases/embl/new/list/), and the naming scheme is the same as for incremental and cumulative updates with the extension ".lis". Using these tools it should be possible to keep a copy of the EMBL Nucleotide Sequence Database that exactly matches the contents of the database in operation at the EBI for external services, with manual intervention required only in the event of some failure in network transfer of the file, etc. The programs have recently been updated to facilitate the initial configuration. SynCron is available by anonymous ftp from: UNIX Version: ftp://ftp.ebi.ac.uk/pub/software/unix/listtools/SynCron_004.tar.gz VMS Version: (backup/gzip) ftp://ftp.ebi.ac.uk/pub/software/vms/listtools/SynCron_004.bck-gz OR (tar/compress) ftp://ftp.ebi.ac.uk/pub/software/vms/listtools/SynCron_004.tar_Z (The _004 version number will change as the programs are updated.) Matteo diTommaso and Nicole Redaschi Database Programming Group EMBL Outstation The European Bioinformatics Institute E-mail: ditommaso@ebi.ac.uk, redaschi@ebi.ac.uk Reinhard Doelz Biozentrum - University of Basel EMBnet Node Switzerland