From owner-srs@net.bio.net Wed Jul 07 12:26:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!paloalto-snf1.gtei.net!su-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.corridex.com!hub1.ispnews.com!hermes.visi.com!news-out.visi.com!news.maxwell.syr.edu!oleane!jussieu.fr!news!not-for-mail From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: need help for SRS5 about links Date: Wed, 07 Jul 1999 15:18:52 +0200 Organization: INFOBIOGEN Lines: 32 Message-ID: <378353BB.AE12990@infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: caroll.infobiogen.fr 931353532 18844 193.52.226.4 (7 Jul 1999 13:18:52 GMT) X-Complaints-To: newsmaster@infobiogen.fr NNTP-Posting-Date: 7 Jul 1999 13:18:52 GMT X-Mailer: Mozilla 4.61 [en] (X11; I; SunOS 5.6 sun4u) X-Accept-Language: en Hello, I find a problem of link between to banks A and B. I need to build the link to bank B with one or two fields. exemple: link between UNIGENE and SWISSPROT $link:[@UNIGENE_DB type:index to:@?SWISSPROT_DB fromField:@DF_BAcc toField:@DF_PID weight:11] $link:[@UNIGENE_DB type:index to:@?SWISSPROT_DB fromField:@DF_BAcc toField:@DF_Accession weight:11] In this case , the link is done only with the last way (DF_accession) Thanks for your help in advance, Jean-Marc -- --------------------------------------------------- Jean-Marc PLAZA INFOBIOGEN - CNRS 7, rue Guy Moquet BP8 94801 VILLEJUIF Cedex, France tel: +33 45 59 52 39 fax: +33 45 59 52 50 e-mail: plaza@infobiogen.fr --------------------------------------------------- From owner-srs@net.bio.net Fri Jul 09 10:13:00 1999 Path: biosci!CNET.CO.KR!leu44 From: leu44@CNET.CO.KR (pyrt8te) Newsgroups: bionet.software.srs Subject: Grandma's and businessman's new Internet tool. Date: 9 Jul 1999 04:13:15 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <199907091162WAA18240@ymutoas.scala.se> NNTP-Posting-Host: net.bio.net Headline: With the iPhone even your Grandmother can surf and send email instantly-but wait until you see how it speeds up your business. Copy: Now your grandmother can get wired, your wife can divorce the desktop, your 6-yr. old can email your mom and you can increase your efficiency. The iPhone (as seen in PCWORLD, Red Herring, Baltimore Sun News) comes plug and play with a 56k modem, zero boot-up time, retractable laptop-size keyboard, 7.4 inch tiltable touchscreen, built-in digital answering machine and 2 lines. (Use the phone while sending email or surfing.) Did we say plug and play? Just $399. The king (pc) is dead. Long live the king (iPhone). For info on how to buy or sell call 603-537-0751, fax 603-537-0753, mail: iphone4u@bigfoot.com ADVD58E27-Exgh58S49 Mailz-Complyant V3.2 From owner-srs@net.bio.net Sun Jul 11 15:24:00 1999 Path: biosci!rutgers!nntp.upenn.edu!newsserver.jvnc.net!209.130.129.214!nntp.frontiernet.net!nntp.primenet.com!nntp.gctr.net!howland.erols.net!news.megsinet.net.MISMATCH!news.corecomm.net!not-for-mail From: another_better_way@hotmail.com Newsgroups: bionet.software.srs Subject: ACAD for Linux ... Message-ID: <307111999115709sforge@mcs.net> Lines: 14 Date: Sat,10 Jul 1999 19:21:33+2000 NNTP-Posting-Host: 216.214.39.146 X-Trace: news.corecomm.net 931709707 216.214.39.146 (Sun, 11 Jul 1999 11:15:07 CDT) NNTP-Posting-Date: Sun, 11 Jul 1999 11:15:07 CDT Look at this web page to learn more about ACAD for Linux !!! http://209.218.86.64/linux.html If you know someone who can be interested in that please tell him or her about this web page. Thank you for your time. From owner-srs@net.bio.net Mon Jul 12 17:34:00 1999 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!news.megsinet.net.MISMATCH!news.corecomm.net!Wfsdfsdf.com From: outo@Wfsdfsdf.com Newsgroups: bionet.software.acedb,bionet.software.gcg,bionet.software.srs Subject: ADULTS ONLY! 88358 Message-ID: <12079911.2701@Wfsdfsdf.com> Organization: hfjfyhfg Reply-To: changer95@aol.com Lines: 15 Date: Monday, 12 Jul 1999 11:27:01 -0600 NNTP-Posting-Host: 216.214.77.203 X-Trace: news.corecomm.net 931803872 216.214.77.203 (Mon, 12 Jul 1999 13:24:32 CDT) NNTP-Posting-Date: Mon, 12 Jul 1999 13:24:32 CDT Xref: biosci bionet.software.acedb:2462 bionet.software.gcg:3622 bionet.software.srs:1531 This is for Adults Only: http://207.240.225.250 * 18+ Only Please! . * Newsgroups: bionet.software.srs Subject: Protein IDs Date: 15 Jul 1999 12:17:59 +0100 Organization: The Sanger Centre Lines: 33 Message-ID: NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 932037647 14025 193.60.84.160 (15 Jul 1999 11:20:47 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 15 Jul 1999 11:20:47 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 I spent a while this morning trying to track down entry '[TREMBLNEW-ID:AAD17483]' which disappeared when I updated SPTREMBL and TREMBLNEW. It is now in SPTREMBL, and I found it eventually as '[SPTREMBL-ACC:Q9Z6I5]' What I would really like to do is find it by using the TREMBLNEW id which should appear as a Protein-ID (prd) in the protein databases and EMBL. Sadly, there is by default no Protein-ID index for swissprot, swissnew, sptrembl or tremblnew. Is anyone out there indexing Protein-IDs for the protein databases? It is there hiding in the DR lines. If there is no 'standard' way I can invent something. SRS5 (as EMBL is indexed on the EBI's FTP server) does index /protein_id in the feature table, but SRS6 only does /db_xref which is the obsolete pid not used in TREMBLNEW - so I can find it by '[embl-prd:AAD17483*]' (that "*" is a nuisance and very confusing to users - just because of the ".n" after - I would prefer to index just the prefix because you only ever get the 'latest' version of the protien in the database). Curiously, DATABANKS at EBI does not seem to include the EMBL feature fields in its index. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Fri Jul 16 13:23:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newsfeed.cwix.com!193.190.198.38!news.belnet.be!newsfeed.wirehub.nl!psiuk-p2!uknet!psiuk-n!goya.lionbio.co.uk!not-for-mail From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: Protein IDs Date: Fri, 16 Jul 1999 14:31:58 +0100 Organization: Lion Bioscience Lines: 89 Message-ID: <378F344E.59834C38@lionbio.co.uk> References: NNTP-Posting-Host: dix.lionbio.co.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en Peter Rice wrote: > > I spent a while this morning trying to track down entry > '[TREMBLNEW-ID:AAD17483]' which disappeared when I updated > SPTREMBL and TREMBLNEW. > > It is now in SPTREMBL, and I found it eventually as > '[SPTREMBL-ACC:Q9Z6I5]' > > What I would really like to do is find it by using the TREMBLNEW id > which should appear as a Protein-ID (prd) in the protein databases and EMBL. > > Sadly, there is by default no Protein-ID index for swissprot, > swissnew, sptrembl or tremblnew. Is anyone out there indexing > Protein-IDs for the protein databases? It is there hiding in the DR > lines. If there is no 'standard' way I can invent something. > > SRS5 (as EMBL is indexed on the EBI's FTP server) does index > /protein_id in the feature table, but SRS6 only does /db_xref which is > the obsolete pid not used in TREMBLNEW - so I can find it by > '[embl-prd:AAD17483*]' (that "*" is a nuisance and very confusing to > users - just because of the ".n" after - I would prefer to index just > the prefix because you only ever get the 'latest' version of the > protien in the database). > > Curiously, DATABANKS at EBI does not seem to include the EMBL feature > fields in its index. > OK - it seems to make sense to index protein ids. This is how you can do it in SRS6: To index protein_id in embl: Define a ProtID field in srsgen.i: $DF_ProtID=$SrsField:[ProteinID short:prd] In embl.is, add the production: ftprd: ~ {$In:[ftvals c:qual] $Out} /\/protein_id="([0-9a-zA-Z]+)/ {$Wrt:[s:$1]} ~ (if you want to include the version number in the value to be indexed, use "/\/protein_id="([0-9a-zA-Z\.]+)/" as regular expression in the production) In embl.i, add the field to be indexed to $EmblFeature_Format: $Field:[$DF_ProtID token:ft index:str indexToken:ftpid tableToken:ftpid] To index the protein_id field in swissprot/sptrembl, add this production to swissprot.is: protid: ~ {$In:[fields c:link] $Out} (tag (/EMBL;[^;]+; +([A-Z0-9]+)/ {$Wrt:[s:$1]} | ln )*)* ~ and add to the $SWISSPROT_FORMAT in swissprot.i the field: $Field:[$DF_ProtID index:str code:link indextoken:protid] And finally - to introduce hyperlinks: add a new hyperlink definition to href.i: prdR:$Href:[$EMBL_DB field:$DF_ProtID] edit swissprot.is - look for the occurenceof pidR, and replace it by prdR We will incorporate these changes in the next release of SRS6 Martin Hilbers -- ----------------------------------------------------- Martin Hilbers Customer Support Specialist LION Bioscience Main: +44 (0) 1223 224 700 Sheraton House Phone: +44 (0) 1223 224 711 Castle Park Fax: +44 (0) 1223 224 701 Cambridge CB3 0AX UNITED KINGDOM Email:hilbers@lionbio.co.uk ----------------------------------------------------- From owner-srs@net.bio.net Fri Jul 16 14:42:00 1999 Path: biosci!ROSA.ESB.UCP.PT!piy96 From: piy96@ROSA.ESB.UCP.PT (ytukay2) Newsgroups: bionet.software.srs Subject: ADV: Is the Government covering up the "Y2K" crisis? Date: 16 Jul 1999 08:42:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 78 Sender: daemon@net.bio.net Distribution: world Message-ID: <19990716593EAA19305@kloeswez.cs.technion.ac.il> NNTP-Posting-Host: net.bio.net To be removed, just email tvmoto@bigfoot.com -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* Every Citizen deserves to know the truth and the facts about the Y2K computer problem. Many governmental officials have spoken to the public on the topic of Y2K for the purpose of not creating any panic to the communities. Unfortunately, this governmental approach on the problem is provoking a passive attitude and creating a false sense of security within Citizens with respect to this extremely vital issue! Do not be deceived! How much do you really know about the year 2000 computer crisis? Take a look at the following statements made by the U.S. Senator Robert F. Bennett (R-Utah), Chairman of the Senate Special Committee on the Year 2000 Technology Problem: "The financial services industry is particularly susceptible to the Year 2000 problem. Without reliable systems... interest could be miscalculated, stock trades could vanish, and customers could have difficulty accessing their account balances or their credit cards." The Year 2000 problem -- or the inability of computers to recognize dates beyond 1999 -- could potentially cause national and worldwide computer systems to shut down or make major mistakes at the beginning of the next century". "While I do hope the FAA is doing as well as it says, experience has taught me to be suspicious of easy answers and quick fixes," he added. "One example is the recent overstatement by the Department of Defense, exposed when its Inspector General reported that 70 percent of the mission critical systems the department deemed to be Y2K compliant were, in fact, not." Take a look at the following statement relating to the business community: "Businesses that fail to properly correct their systems could be committing corporate suicide," Bennett said. "The biggest Y2K headache of all could be the legal fees and lawsuits that cripple America's employers and working people long after the Y2K bug has been chased from computer hardware and software." As a consumer or a business owner you have the right to obtain quality information on how to confront the year 2000 computer crisis successfully. Do you have precise answers to the following questions? Is your personal computer or network going to survive the coming crash? Are your software and data files going to be DESTROYED by the "Millennium Bug"? Is your computer system fully YEAR 2000 COMPLIANT, even if it is new? Do you know how the "Electronic Data Interfacing" could severely harm consumers and businesses? Your business survival will depend on you obtaining quality information and FACTS. Learn how to protect your business against individuals and lawyers who may be currently preparing to file lawsuits against your business for not being fully Y2K compliant. Denying or ignoring the problem would be a foolish position to take. Learn why your computer compliance efforts should meet the internationally adopted standard BSI (British Standard Institution for Year 2000 Compliance) Learn more about the most recent technical Y2K problem found in personal computers and networks-- the "Crouch-Echlin Time Dilation Effect". Ignoring this problem can send your compliance efforts down the drain. How would you like to make $ thousands of dollars by taking advantage of the income opportunities originated by the year 2000 computer crisis. Obtain a FREE report on the facts and solutions to the upcoming Y2K computer crash. click here for your FREE report --Thank-You: for removal see above instructions From owner-srs@net.bio.net Fri Jul 16 14:42:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!dispose.news.demon.net!demon!colt.net!newspeer.clara.net!news.clara.net!newsfeed.nacamar.de!fu-berlin.de!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: Protein IDs Date: 16 Jul 1999 16:36:49 +0100 Organization: The Sanger Centre Message-ID: References: <378F344E.59834C38@lionbio.co.uk> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 932139370 4110 193.60.84.160 (16 Jul 1999 15:36:10 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 16 Jul 1999 15:36:10 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 Lines: 20 Martin Hilbers writes: > OK - it seems to make sense to index protein ids. > This is how you can do it in SRS6: > > In embl.i, add the field to be indexed to $EmblFeature_Format: > > $Field:[$DF_ProtID token:ft index:str indexToken:ftpid tableToken:ftpid] .... oops. Needs to be ftprd in both places, not ftpid -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Fri Jul 16 16:23:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!dispose.news.demon.net!demon!diablo.theplanet.net!psiuk-p2!uknet!psiuk-n!goya.lionbio.co.uk!not-for-mail From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: Protein IDs Date: Fri, 16 Jul 1999 17:02:19 +0100 Organization: Lion Bioscience Message-ID: <378F578B.63D23758@lionbio.co.uk> References: <378F344E.59834C38@lionbio.co.uk> NNTP-Posting-Host: dix.lionbio.co.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en Lines: 30 Peter Rice wrote: > > Martin Hilbers writes: > > > OK - it seems to make sense to index protein ids. > > This is how you can do it in SRS6: > > > > In embl.i, add the field to be indexed to $EmblFeature_Format: > > > > $Field:[$DF_ProtID token:ft index:str indexToken:ftpid tableToken:ftpid] > > .... oops. Needs to be ftprd in both places, not ftpid > Yes ofcourse........ Martin -- ----------------------------------------------------- Martin Hilbers Customer Support Specialist LION Bioscience Main: +44 (0) 1223 224 700 Sheraton House Phone: +44 (0) 1223 224 711 Castle Park Fax: +44 (0) 1223 224 701 Cambridge CB3 0AX UNITED KINGDOM Email:hilbers@lionbio.co.uk ----------------------------------------------------- From owner-srs@net.bio.net Mon Jul 19 08:00:00 1999 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 Jul 1999 02:00:15 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199907190900.CAA29696@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-srs@net.bio.net Mon Jul 19 13:48:00 1999 Path: biosci!ebi.ac.uk!stoehr From: stoehr@ebi.ac.uk (Peter Stoehr) Newsgroups: bionet.software.srs Subject: Splitting EMBL cumulative update file Date: 19 Jul 1999 07:48:24 -0700 Organization: EMBL-EBI Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: <3793394A.CF7D514A@ebi.ac.uk> NNTP-Posting-Host: net.bio.net Several sites have reported problems handling our EMBL cumulative update file when it grows beyond 2GB (uncompressed). The problems are either at the operating system level where the filesystem does not support >2GB files (sigh...), or SRS5 which does not seem to like indexing a file >2GB or so. Perhaps other application software has sproblems also. In *addition* to the cumulative.dat.gz files we make available on our FTP server, we now also split that dataset into smaller parts, namely: cum_1.dat.gz !all the cumulative file except the data in files below. cum_est1.dat.gz !ESTs cum_htg1.dat.gz !HTG cum_hum1.dat.gz !human (non-gss, non-HTG, non-EST) cum_gss1.dat.gz !GSS We chose this data division: - because it represents the current major division of data in the updates, or our best guess about what will happen in the coming months. - to try to keep the files below 2GB for as long as possible, eg before needing cum_hum2 etc - to avoid frequent changes. These filenames should last a while and contain some data even soon after a new full release. SRS icarus files (for example) should not need constant changing, and when they do we should be able to see it coming well beforehand. Those who 'mirror' our ftp.ebi.ac.uk/pub/databases/embl/new directory may wish to have either the full cumulative.dat.gz or the cum_* set ignored, in order to save some netwidth. The data contained is the same - we build the cum_* files from the cumulative.dat.gz file afresh each day. There is no correspondence between, say, cum_est1.dat and the est1.dat file of the full release. FYI the EBI SRS server now has the EMBLNEW dataset using these cum_* files. Regards, Peter Stoehr EMBL-EBI From owner-srs@net.bio.net Tue Jul 20 19:48:00 1999 Message-ID: <3794DF38.B8611882@lion-ag.de> Date: Tue, 20 Jul 1999 22:42:33 +0200 From: Morozov Organization: LION Bioscience AG X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.software.srs To: kurapkat@lion-ag.de Subject: SWISSPROT DE field is wrongly indexed? Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: base64 NNTP-Posting-Host: gate.lion-ag.de X-Trace: 20 Jul 1999 22:42:45 +0200, gate.lion-ag.de Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!dispose.news.demon.net!demon!newsfeed.nacamar.de!newsfeed.nacamar.de!f.de.uu.net!news.uni-stuttgart.de!news.belwue.de!news.farside.net!gate.lion-ag.de Lines: 28 SSBzdXBwb3NlIHRoYXQgc2Vjb25kIERFIGxpbmUgaXMgbm90IGFkZGVkIGludG8gdGhlIERF UyBmaWVsZA0KZHVyaW5nIGluZGV4aW5nDQoNCm1vcm96b3ZAY3J1bmNoMS5saW9uLWFnLmRl PiAgZ2V0eg0KJ1tzd2lzc3Byb3QtY2M6Y2hhbm5lbCpdIShbc3dpc3Nwcm90LWRlczpjaGFu bmVsKl0pJyAtZiAiaWQgZGVzInxtb3JlDQpJRCAgIDVIVDNfSFVNQU4gICAgIFNUQU5EQVJE OyAgICAgIFBSVDsgICA0NzggQUEuDQpERSAgIDUtSFlEUk9YWVRSWVBUQU1JTkUgMyBSRUNF UFRPUiBQUkVDVVJTT1IgKDUtSFQtMykgKFNFUk9UT05JTi1HQVRFRA0KSU9ODQpERSAgIENI QU5ORUwgUkVDRVBUT1IpLg0KSUQgICA1SFQzX01PVVNFICAgICBTVEFOREFSRDsgICAgICBQ UlQ7ICAgNDg3IEFBLg0KREUgICA1LUhZRFJPWFlUUllQVEFNSU5FIDMgUkVDRVBUT1IgUFJF Q1VSU09SICg1LUhULTMpIChTRVJPVE9OSU4tR0FURUQNCklPTg0KREUgICBDSEFOTkVMIFJF Q0VQVE9SKS4NCklEICAgNUhUM19SQVQgICAgICAgU1RBTkRBUkQ7ICAgICAgUFJUOyAgIDQ4 MyBBQS4NCkRFICAgNS1IWURST1hZVFJZUFRBTUlORSAzIFJFQ0VQVE9SIFBSRUNVUlNPUiAo NS1IVC0zKSAoU0VST1RPTklOLUdBVEVEDQpJT04NCi4uLi4uDQptb3Jvem92QGNydW5jaDEu bGlvbi1hZy5kZT4gZ2V0eiAiW3N3aXNzcHJvdC1pZDo1SFQzX0hVTUFOXSIgLWYgZGVzDQpE RSAgIDUtSFlEUk9YWVRSWVBUQU1JTkUgMyBSRUNFUFRPUiBQUkVDVVJTT1IgKDUtSFQtMykg KFNFUk9UT05JTi1HQVRFRA0KSU9ODQpERSAgIENIQU5ORUwgUkVDRVBUT1IpLg0KbW9yb3pv dkBjcnVuY2gxLmxpb24tYWcuZGU+IGdldHoNCiJbc3dpc3Nwcm90LWlkOjVIVDNfSFVNQU5d Jltzd2lzc3Byb3QtZGVzOmNoYW5uZWwqXSIgLWYgZGVzDQptb3Jvem92QGNydW5jaDEubGlv bi1hZy5kZT4NCg0KDQoNCi0tDQpTaW5jZXJlbHksDQoNClZsYWRpbWlyIE1vcm96b3YNCj09 PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09 PT09PT09PT09PT09PT09PT0NClZsYWRpbWlyIE0uIE1vcm96b3YsIFBoRA0KQmlvaW5mb3Jt YXRpY3MgRXhwZXJ0ICAgICAgICAgICAgICAgICB8IG1vcm96b3ZAbGlvbi1hZy5kZQ0KUm9v bSAyMTAsIExJT04gQmlvc2NpZW5jZSBBRyAgICAgICAgICB8IFZvaWNlICs0OS0oMCk2MjIx LTQwMzgxNDMNCldhbGRob2ZlciBTdHIuIDk4LCBELTY5MTIzIEhlaWRlbGJlcmcgfCBGYXgg KzQ5LSgwKTYyMjEtNDAzODIwMQ0KR2VybWFueQ0KaHR0cDovL3d3dy5saW9uLWFnLmRlDQo9 PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09 PT09PT09PT09PT09PT09PT09DQoiV2hlcmUgaXMgdGhlIGtub3dsZWRnZSB3ZSBoYXZlIGxv c3QgaW4gaW5mb3JtYXRpb24iIFQuIFMuIEVsaW90LA0KICAgICAgICAgIENob3J1c2VzIGZy b20gIlRoZSBSb2NrIg0KDQoNCg== From owner-srs@net.bio.net Wed Jul 21 10:24:00 1999 Path: biosci!MAIL.CIC.TSINGHUA.EDU.CN!leroy_qiao From: leroy_qiao@MAIL.CIC.TSINGHUA.EDU.CN (Qiao Li-An) Newsgroups: bionet.software.srs Subject: Quick Download PDB Files Date: 21 Jul 1999 04:24:36 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 26 Sender: daemon@net.bio.net Distribution: world Message-ID: <17806.990721@mail.cic.tsinghua.edu.cn> Reply-To: Qiao Li-An NNTP-Posting-Host: net.bio.net Hello All, We can use SRS method to download a few PDB files, just click the search results one by one. But when we want to download thousands of protein structure PDB files, the task seems tedious. Now I have a list of PDB Entry ID Code. How can I get these PDB files from www directly? Could I use ftp to get all of them? Best regards, Qiao Li-An ----------------------------------------------------------- - Qiao Li-An - - Department of Biological Sciences and Technology, - - Tsinghua University, P.R.China , 100084 - - - - Tel: (86) 10-62784766(Office) - - (86) 10-62785049(Office) - - (86) 10-62775313(Dormitory) - - E-mail: leroy_qiao@mail.cic.tsinghua.edu.cn (default) - - leroy_qiao@263.net - ----------------------------------------------------------- From owner-srs@net.bio.net Wed Jul 21 14:38:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!colt.net!newspeer.clara.net!news.clara.net!remarQ-uK!remarQ.com!supernews.com!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Heikki Lehvaslaiho Newsgroups: bionet.software,bionet.software.srs Subject: Re: Quick Download PDB Files Date: Wed, 21 Jul 1999 16:32:12 +0100 Organization: EMBL - EBI Message-ID: <3795E7FC.A200395@ebi.ac.uk> References: <19806.990721@mail.cic.tsinghua.edu.cn> NNTP-Posting-Host: cetus.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 932571132 29569 193.62.196.199 (21 Jul 1999 15:32:12 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 21 Jul 1999 15:32:12 GMT To: Qiao Li-An X-Mailer: Mozilla 4.6 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en Lines: 45 Xref: biosci bionet.software:23830 bionet.software.srs:1544 Qiao Li-An wrote: > > Hello All, > > We can use SRS method to download a few PDB files, just click the > search results one by one. But when we want to download thousands of > protein structure PDB files, the task seems tedious. > > Now I have a list of PDB Entry ID Code. How can I get these PDB files > from www directly? Could I use ftp to get all of them? Since you are using SRS to find the interesting entries in the first place, the easiest thing to do would be to directly save the results from SRS. Here is how to do it: 0. You probably need relatively new Netscape or IE for this. Versions 4 something should work. The server I use is SRS 5.1.0.at EBI. 1. Before doing the query, set the chunk size to a conveniently large number (e.g. 5000) 2. Do your query and press button 'Save' near the top of the "QueryResult" page. 3. At the next page ("SRS:Download query"), Select view 'Complete entries' and mime type 'binary' before pressing 'Save' button. You will be presented a standard file save window for naming the file. That is all there is to it. Yours, -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ http://www2.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From owner-srs@net.bio.net Wed Jul 21 22:14:00 1999 Path: biosci!pravda.ucr.edu!ihnp4.ucsd.edu!newsfeed.berkeley.edu!howland.erols.net!hub1.ispnews.com!news3.ispnews.com.POSTED!not-for-mail From: "Kal Fawzi" Newsgroups: bionet.software.srs Subject: FREE SALES SOFTWARE Lines: 5 X-Newsreader: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Message-ID: NNTP-Posting-Host: 209.144.27.109 X-Trace: news3.ispnews.com 932598508 209.144.27.109 (Wed, 21 Jul 1999 19:08:28 EDT) NNTP-Posting-Date: Wed, 21 Jul 1999 19:08:28 EDT Date: Wed, 21 Jul 1999 16:31:30 -0500 CHECK OUT THIS SITE FOR FREE SALES AUTOMATION SOFTWARE WWW.AKNAF.COM From owner-srs@net.bio.net Thu Jul 22 00:59:00 1999 Path: biosci!RTEX.NET!Ss5C1WofF From: Ss5C1WofF@RTEX.NET Newsgroups: bionet.software.srs Subject: CAN BULK E-MAIL WORK FOR YOU?? Date: 21 Jul 1999 18:59:34 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 21 Sender: daemon@net.bio.net Distribution: world Message-ID: <199907220159.SAA20811@net.bio.net> Reply-To: gtew655@rtex.net NNTP-Posting-Host: net.bio.net This is Cybernet Enterprise and we are sending you this e-mail to let you in on some of the best prices in Bulk E-Mailing. If you are interested in more information . Just call anytime 209-699-3628 or voice mail 209-548-2585 or e-mail cybernet2@china.com Prices: $200.00 For 1 Million E-Mails Sent. $400.00 For 3 Million E-Mails Sent. $600.00 For 5 Million E-Mails Sent. $800.00 For 7 Million E-Mails Sent. $1000.00 For 10 Million E-Mails Sent. We also have target lists..Just call and ask! P.S. I am able to send you proof of your mailings. I will send you via e-mail, uploaded mail-log files of the actual sendings so you can know first-hand exactly what i'm doing for you. 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