From owner-embldatabank@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!not-for-mail From: Eugene Kolker Newsgroups: bionet.molbio.embldatabank Subject: Recomb98: Registration Date: 6 Jan 1998 00:09:40 -0000 Lines: 8 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <68rso4$1i1@mserv1.dl.ac.uk> Original-To: embl-db@dl.ac.uk CALL FOR RECOMB 98 Registration Registration is now starting for RECOMB 98. Please visit our website for registration instructions: http://www.mssm.edu/biomath/recomb98.html If you do NOT want to be in our mailing list, please reply with Subject line "Recomb98: remove". From owner-embldatabank@net.bio.net Mon Jan 05 22:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.embldatabank Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 6 Jan 1998 02:00:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199801061000.CAA23147@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. 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. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-embldatabank@net.bio.net Wed Jan 07 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.direct.ca!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!stoehr From: stoehr@ebi.ac.uk (Peter Stoehr) Newsgroups: bionet.molbio.embldatabank,embnet.general Subject: EMBL release 53 available Date: 8 Jan 98 15:41:04 +0000 Organization: European BioInformatics Institute Lines: 208 Distribution: embnet Message-ID: <1998Jan8.154104@ebi.ac.uk> NNTP-Posting-Host: earth.ebi.ac.uk Release 53 of the EMBL Nucleotide Sequence Database is now available from the EMBL-EBI ftp site: ftp://ftp.ebi.ac.uk/pub/databases/embl/release This release is already installed on other EBI query/search servers, SRS/Blast/Fasta. A few extracts from the release notes follow, but they can be read in full at: ftp://ftp.ebi.ac.uk/pub/databases/embl/release/relnotes.doc or http://www.ebi.ac.uk/ebi_docs/embl_db/relnotes53/relnotes.html For those who maintain local copies using our cumulative update file in ftp://ftp.ebi.ac.uk/pub/databases/embl/new/cumulative.dat.Z, please note that this file will be changed to include only post- release 53 data on Friday Jan 9th at 15:00 GMT (ie it gets smaller then). Regards, Peter Stoehr EMBL-EBI -------- 1 RELEASE 53 The EMBL Nucleotide Sequence Database was frozen to make Release 53 on the 16th December 1997. The release contains 1,917,868 sequence entries comprising 1,281,391,651 nucleotides. This represents an increase of about 8% over Release 52. A breakdown of Release 53 by division is shown below: Division Entries Nucleotides ----------------- ------- ----------- Bacteriophage 1388 2188305 ESTs 1343796 496603984 Fungi 18137 44602064 GSSs 100154 49099107 HTG 1868 102763872 Human 74384 139022655 Invertebrates 28126 107524431 Organelles 24715 22870076 Other Mammals 14429 13785092 Other Vertebrates 13145 14653255 Plants 22136 37736590 Patent 91221 29511807 Prokaryotes 42666 102750354 Rodents 37043 46489741 STSs 51172 17685717 Synthetic 2424 5377292 Unclassified 2380 2387088 Viruses 48684 46340221 ----------------- -------- ------------ Total 1917868 1281391651 ----------------- -------- ------------ 1.1 EST Database Files In order to keep the size of the data files within reasonable limits for handling purposes, we have split the EST division into several files. At this release we have created one extra files of EST data named EST14.DAT. Additional files will be added in subsequent releases as appropriate. 1.2 Feature Table Qualifiers 1.2.1 New SOURCE Qualifier /specimen_voucher This new source feature qualifier valid at this release indicates the source of a sample , eg a museum identification tag, of the sequenced material. Qualifier /specimen__voucher="text" Definition an identifier of the individual or collection of the source organism and the place where it is currently stored, usually an institution. Value format "text" Example /specimen__voucher="Smith s. n. 4-IV-1995 (U. S. Natl. Herbarium)" 1.2.2 New /focus This new source feature qualifier valid at this release defines the main source feature for records with more than one source feature (e.g. proviral/cellular sequences) Qualifier /focus Definition defines the preferred source feature for records that have more than one source feature Value format none Example /focus Comment this qualifier is to be used only if there is more than one source feature. The preferred source feature is used to determine which organism is displayed in the SOURCE and ORGANISM lines and to determine the EMBL division in which it is placed. For sequences derived from more than one organism, and therefore containing more than one 'source' feature key, the /focus qualifier will be attached to the source key which represents the major organism, that which was the focus of the sequencing effort. If no translation table is specified, the organism with /focus will define the translation table. 2 FORTHCOMING CHANGES 2.1 Nucleotide And Protein Identifiers 2.1.1 Nucleotide Indentifiers The NI linetype of the EMBL flat-file format currently contains a unique identifier for the nucleotide sequence. While the sequence remains the same, so does the value of this identifier. When a sequence change occurs, however minor, a new NI value will be assigned whilst the accession number on the AC line may remain unchanged. These identifiers are collaboratively maintained with GenBank and DDBJ, for example: NI g21954 It has become clear from users and other database groups that confusion has been created about the relationship between these identifiers and the GenBank 'gi' numbers. It has been decided therefore to introduce a new system of nucleotide identifiers of the form 'accession.version', eg: X12345.3, where the accession number part will be stable, but the version part will be incremented if the sequence changes. Subject to synchronisation of this change with GenBank and DDBJ, we plan to implement this new form of nucleotide identifier during 1998. 2.1.2 Protein Identifiers Protein identifiers are currently assigned to all CDS features in the nucleotide sequence database and are found in the feature table qualifier /db_xref, eg: /db_xref="PID:e123456789" As for nucleotide identifier values (above), confusion resulted amongst users concerning the relationship of these to GenBank 'gi' numbers also assigned to CDS features. To clarify this, and to adopt a comparable scheme of identifiers for both nucleotides and proteins, the collaborating databases have decided to create a new feature table qualifier /protein_id, eg: /protein_id="AAA12345.1" This form of identifier also allows easier tracking of changing protein identifiers by external databases than the previous PIDs. This qualifier consists of a stable ID portion (3+5 format with 3 positions letters and 5 numbers) plus a version number after a decimal point. The version number will change only when the protein sequence coded by the CDS changes, while the stable part will remain unchanged. This qualifier will be valid only on CDS features which translate into a valid protein. Subject to synchronisation of this change with GenBank and DDBJ, we plan to implement this new form of protein identifier during 1998. 2.2 Feature Table Qualifiers 2.2.1 New /protein_id As mentioned above a new feature table qualifier /protein_id will be created: Qualifier /protein_id="" Definition Protein Identifier, issued by International collaborators. This qualifier consists of a stable ID portion (3+5 format with 3 positions letters and 5 numbers) plus a version number as the decimal point. Example /protein_id="AAA12345.1" Comment Only when the protein sequence coded by the CDS changes, the version number will change, while the stable part will remain unchanged. This qualifier is valid only on CDS features which translate into a valid protein. The list of 3-letter prefixes will be maintained by EBI Subject to synchronisation of this change with GenBank and DDBJ, we plan to implement this new form of protein identifiers during 1998. 2.2.2 /translation And Related Feature Qualifiers The collaborating databases DDBJ/EMBL/GenBank have decided that translation related qualifiers should only be used with the primary CDS feature key. These translation related qualifiers are: /codon /codon_start /exception /translation /transl_table /transl_except Starting at release 54, translation related qualifiers will only be valid with the CDS feature key and will be removed from the following list of non-CDS features: C_region D_segment exon J_segment mat_peptide N_region sig_peptide S_region transit_peptide V_region V_segment From owner-embldatabank@net.bio.net Wed Jan 14 22:00:00 1998 Path: biosci!agate!ihnp4.ucsd.edu!sdd.hp.com!vixen.cso.uiuc.edu!howland.erols.net!news-peer.gip.net!news.gsl.net!gip.net!peerfeed.ncal.verio.net!Supernews60!supernews.com!uunet!in4.uu.net!news.anet-chi.com!not-for-mail From: toddc-NoSpAm@NoSpAm-anet-dfw.com (Todd C.) Newsgroups: bionet.molbio.embldatabank Subject: PEDANT ? Date: Thu, 15 Jan 1998 22:22:19 GMT Organization: ANET Internet Services Lines: 6 Message-ID: <34be8c0f.106732849@news.anet-dfw.com> Reply-To: toddc-NoSpAm@NoSpAm-anet-dfw.com NNTP-Posting-Host: 206.103.93.55 X-Newsreader: Forte Free Agent 1.1/32.230 Does anyome know what happened to PEDANT. Is it no longer publicly accessable? http://pedant.mips.biochem.mpg.de/frishman/pedant.html From owner-embldatabank@net.bio.net Mon Jan 19 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!news.maxwell.syr.edu!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!not-for-mail From: "Open Windows (John Dawson)" Newsgroups: bionet.molbio.embldatabank,bionet.molbio.genbank Subject: Mitochondrial DNA Concordance - new URL Date: Tue, 20 Jan 1998 12:05:18 +0000 Organization: Open Windows (mail-order book service) Lines: 10 Message-ID: <34C492F7.7C4C@cam.ac.uk> Reply-To: Open@ajcox.demon.co.uk NNTP-Posting-Host: jld.sidg.pwf.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) CC: kmiller@sscf.ucsb.edu Xref: biosci bionet.molbio.embldatabank:1061 bionet.molbio.genbank:2865 Please note that the Mitochondrial DNA Concordance formerly found at http://alishaw.sscf.ucsb.edu/~kmiller is now at http://sscf.ucsb.edu/~kmiller because of a change of machine names. We apologise for any inconvenience. The Concordance is now being updated; the next version should be ready by the end of March 1998. John Dawson JLD1@cam.ac.uk Kevin Miller kmiller@sscf.ucsb.edu From owner-embldatabank@net.bio.net Mon Jan 26 22:00:00 1998 Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!tome From: tome@ebi.ac.uk (Patricia Rodriguez-Tome) Newsgroups: bionet.software,bionet.general,bionet.molbio.embldatabank Subject: BioCatalog release 5.6 Date: 27 Jan 1998 16:52:13 GMT Organization: European Bioinformatics Institute (EMBL) - UK Lines: 21 Distribution: world Message-ID: <6al3bt$9km$1@niobium.hgmp.mrc.ac.uk> Reply-To: tome@ebi.ac.uk NNTP-Posting-Host: sol6.ebi.ac.uk Xref: biosci bionet.software:20376 bionet.general:29230 bionet.molbio.embldatabank:1064 Release 5.6 of the Biocatalog is out., it contains now 555 entries. As always the Web server is : http://www.ebi.ac.uk/biocat Ascii files are available at : ftp://ftp.ebi.ac.uk/pub/databases/biocat Submissions are welcome, use the form at : http://www.ebi.ac.uk/biocat/biocat_form/html For contact please email biocat@ebi.ac.uk -- ======================================================================= Dr. Patricia Rodriguez-Tome | URL: http://www.ebi.ac.uk The EMBL Outstation, Hinxton - The European Bioinformatics Institute Wellcome Trust genome Campus, Hinxton | Tel: +44 (0)1223 494 409 Cambridge CB10 1SD, UK | Fax: +44 (0)1223 494 468 ========================================================================