From owner-srs@net.bio.net Mon Mar 03 22:00:00 1997 Newsgroups: bionet.software.srs Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!news From: Tao Jiang Subject: a question Sender: news@ebi.ac.uk (usenet news) Message-ID: <331B67F9.5FE0@pku.edu.cn> Date: Tue, 4 Mar 1997 00:08:25 GMT Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5.1 sun4u) Organization: Network Center, Peking University Lines: 14 Hi there, We plan to use the Directory (X.500 or the like) to do the similar work as SRS, and does anyone have any experience with that? (I am specialized in computing and don't know too much about biology) regards, -- Tao Jiang Fax: 86-10-62751982 Network Center Homepage: http://jiangt.pku.edu.cn/~jiangt/ Peking University Email: jiangt@pku.edu.cn From owner-srs@net.bio.net Thu Mar 13 22:00:00 1997 From: (DogZ Software Center) Newsgroups: bionet.software.srs Subject: MS Office 97 only costs US$45?! Shopping Paradise Date: Sat, 15 Mar 1997 10:25:10 GMT Organization: Netvigator Lines: 60 Message-ID: <5gc5rr$6lt@imsp009a.netvigator.com> NNTP-Posting-Host: dialh01043.netvigator.com X-Newsreader: Forte Agent .99b.112 Path: biosci!ihnp4.ucsd.edu!swrinde!cs.utexas.edu!news.sprintlink.net!news-peer.sprintlink.net!news-peer.gsl.net!news-hk.gsl.net!news.gsl.net!newsgate.cuhk.edu.hk!news2.hkt.net!news.hkt.net!imsp009a.netvigator.com!locker Windows 95, Visual Foxpro, MS Office 7.0, Visual Basic, Visual C++, Borland C++, Lotus cc:Mail Release 6, Lotus SmartSuite 97, ...... only costs US$45 for all? MS Office 97 only costs US$45! Hong Kong is the paradise in shopping. You can buy anything you want by an reasonable price. Today, by this chance, we would like to introduce to those who are interest in computing. In Hong Kong, there are five famous spots inclues: Golden Center - Sham Shui Po ; Mongkok Computer Center - Mongkok ; Sino Center - Mongkok ; 298 Computer Center - Wan Chai and Tsuen Fung Center -Tsuen Wan . In which, you can always find the most update warez includes all PC Warez, PC games, CD-Title, Shareware, Video-CD and Playstation game, etc. For Example, Inside a Installer (one CD only, Product No.: IN96112) , it contains MS Visual Foxpro 5.0, MS Windows 95 OEM Service Release, MS Money97, Lotus SmartSuite 97, Lotus cc:Mail Release 6, Symantec Cafe 1.5, Norton Your Eyes Only, Norton Smart Doctor 1.0, Quartdeck SpeedyROM 1.1, KPT BrayceAlpha 2.0, Visual dBASE Professional 4.4a, MacroMedia Animator Designer, Solitaire Antics, Almost Reality, CakeWalk Express 3.01, ClockMan95, Demo-It!2.0, MicroLogic EMAGIC, EXTRA! Version 6.2, MacroMedia Icon Designer, Infinite Disk, InfoSpy Pro, Fractal Deign Ray Dream Studio 4.1, Janna Conract Manager, Kurzweil Voice release 2.0, PC Maclan verion 6.0, NetWizard Plus Version 3.1, Organic Art, Microsoft Edition, PhotoWorks, RandoMedia, Real Oschestra, Reflection 4, RichWin, SoundForge 4.0, SignLab Pro+, Spectrum Pro CD Player, Starfish Internet Sidekick, TeleMagic, TurboCAD 3.0, MS-Visual SourceSafe 5.0, WinBye 32, Xing 3.02 Release, Zydeco Management Desktop. Good news to you today, that is, we would like to introduce all wares in VERY attractive price to you. Not only to provide over 50 warez for you to choose, but also to introduce the most suitable warez to you. We would provide a very attractive price not more than US$50. The more you buy, the more money you can save. Right? Hurry up! Don't miss this chance! Just ask what you want to know OR just decide and place your order to us. If you want some more details , you can go http://www.hkstar.com/~dogz now. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ DogZ Software Center From owner-srs@net.bio.net Thu Mar 13 22:00:00 1997 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs,bionet.software Subject: Re: release of SRS5.0.3 Date: Fri, 14 Mar 1997 18:16:47 +0000 Organization: SEQNET Lines: 68 Distribution: bionet Message-ID: <3329960F.41C6@dl.ac.uk> References: <32F71DAE.6358@computer.at> <33288272.5560@ebi.ac.uk> NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP12) Xref: biosci bionet.software.srs:450 bionet.software:18133 etzold wrote: > > Dear all, > > after versions 5.0.1 and 5.0.2 which still had lots of problems we consider > this to be the first stable version of SRS5. The distribution is now available > on the ftp server at the EBI in Hinxton UK. Hooray ! > 7) in SRSWWW each single entry display contains an additional 'toolbar' > for linking the entry to other databanks, viewing the entry and launching > applications. > 8) The applications BLAST, FASTA, SW (Smith & Waterman search with > Bioccelerator) and CLUSTALW have been added to SRS and can be called from > a the page containing a list of entries and a single entry. Well - at SEQNET we offer world access to the database searches with srs, but the launching of programs, which now features prominently in srs, is something we would rather restrict to our own users. I suppose others have similar thought, so a quick kludge to restrict program launches: ( I suppose it could be done more neatly, but so far it works ) First create a subdirectory of your cgi-bin directory, to which you restrict access in whatever way is appropriate for your httpd server. (You can also use any other script-directory for which you have restricted access). copy wgetz into here (or create a symvolic link). Now edit icarus/util/srswww.i, add a line like $parStr:[cgiappdir set:'/cgi-bin/srs5app'] to the block of $parStr definitions at the beginning of the file. (replace /cgi-bin/srs5app with whatever you have used.) Then near the end of the file, "the form to launch an application", replace line 2551 (or therabout) |
with | And them do a srssection to update things. This way, the system will use the "restricted" wgetz to launch a program. Cheers, Martin -- ----------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/People/m.p.hilbers/ | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.dl.ac.uk/SEQNET/home.html | ----------------------------------------------------------------- From owner-srs@net.bio.net Thu Mar 13 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!cs.utexas.edu!news.sprintlink.net!news-peer.sprintlink.net!news.maxwell.syr.edu!newsfeed.nacamar.de!news-kar1.dfn.de!news-stu1.dfn.de!news-mue1.dfn.de!news-nue1.dfn.de!news-lei1.dfn.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.dfn.de!news.embl-heidelberg.de!usenet From: etzold Newsgroups: bionet.software.srs,bionet.software Subject: release of SRS5.0.3 Date: Thu, 13 Mar 1997 23:40:50 +0100 Organization: EMBL-EBI Lines: 97 Distribution: world Message-ID: <33288272.5560@ebi.ac.uk> References: <32F71DAE.6358@computer.at> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.0b2 (Win95; I) X-Priority: 3 (Normal) Xref: biosci bionet.software.srs:449 bionet.software:18123 Dear all, after versions 5.0.1 and 5.0.2 which still had lots of problems we consider this to be the first stable version of SRS5. The distribution is now available on the ftp server at the EBI in Hinxton UK. If you have problems accessing it please let us know. The file is at ftp://ftp.ebi.ac.uk/pub/software/unix/srs/srs5.0.3.tar.gz Release notes: SRS version 5.0.3 ================= SRS 5.0.3 has been compiled and tested on IRIX 5.x, 6.x (32-bit binary), OSF1 4.x, Solaris. It should work on SunOS, Ultrix and could work on AIX, HP-UX. The numerous problems of version 5.0.2 concerning indexing and entry access should all be fixed. The main differences to the previous release are the addition of an 'option bar' in the entry display and the incorporation of analysis tools (BLAST, FASTA, Smith and Waterman search with the Bioccelerator and Clustalw). The way the applications are defined is still new and needs to be documented. Differences in detail: 1) Many bugs concerning indexing and access to entries have been removed. Indexing of GCG formatted databanks is now stable. 2) The databank descriptions for many databanks, esp. the Transfacs and Genbank has improved. 3) A few Icarus bugs have been fixed and also the error messages are more informative. Both nodd and icarus should not dump core anymore. 4) The example C programs in SRSDEMO have been revised and should all work. 5) The regular expressions have been reintroduced into the SRS query language. (the documentation for the query language is still for version 4 but has been extended for version 5 considerably). 6) The chapter "SRS Server Maintenance" has been added to the online documentation system. It describes in detail how to set up a separate WWW server that runs wgetz under its own account. 7) in SRSWWW each single entry display contains an additional 'tool bar' for linking the entry to other databanks, viewing the entry and launching applications. 8) The applications BLAST, FASTA, SW (Smith & Waterman search with Bioccelerator) and CLUSTALW have been added to SRS and can be called from a the page containing a list of entries and a single entry. Documentation of how to customize these applications and how to add more is still lacking but please have a look into SRSDB/genes.i. Every application is described by an object $application. It has an Icarus command to build the command line and one for launching the application. All the customization happens there. 10) The "SRS group" has moved to the EBI in Hinxton!;-) Known problems with this release: 1) The "Save" option in SRSWWW does still not work properly. 2) Customization of the applications is easy but still not documented. 4) The $application objects in appl.i for the four applications BLAST, FASTA, CLUSTALW and SW have been rewritten several times. It is possible that some default values don't make much sense or are missing - please check and let us know if you find bugs. 3) getz and wgetz can extract feature sequences but it is still not possible to modify their begin and end positions as in SRS4. -- Thure Etzold, etzold@ebi.ac.uk Giorgio Verde, verde@ebi.ac.uk 13. March, 1997 From owner-srs@net.bio.net Sun Mar 16 22:00:00 1997 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs,bionet.software Subject: SRS5.0.3 - GCG format problems Date: Mon, 17 Mar 1997 11:09:31 +0000 Organization: SEQNET Lines: 59 Distribution: bionet Message-ID: <332D266B.41C6@dl.ac.uk> References: <32F71DAE.6358@computer.at> <33288272.5560@ebi.ac.uk> NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP12) Xref: biosci bionet.software.srs:453 bionet.software:18151 Hi folks, I had a few problems when indexing GCG formatted embl and genbank databases with srs5.03. This all happened without modifications of the software and embl/genbank icarus files. (Well, for genbank I had to change the file definitions to GCG - bot otherwise it was all "out of the box") srsbuild crashed on em_fun:scchrix - yeast chromosome IX, a 450 Kb sequence. This happened with DEC/OSF1 3.2 and SGI/Irix 5.3 There was no problem with using the same sequence in the original EMBL file, nor with the same sequence in a GCG formatted GenBank database. With the whole of EMBL indexing crashed after about 860000 entries with the message: SRSDB:embl.is:42: error: insufficient memory - error during malloc, could not allocate "sequence" It could hardly be "insufficient memory" - I monitored memory usage by srsbuild, and it was using about 115 Mb when it crashed, and the system I used (DEC Alpha/ OSF1 3.2) has 190 Mb + 660 Mb swapspace. It occurred during the indexing of em_fun, but well before it got to the scchrix entry. In another try, without the section in which the above problem occurred (em_fun) it ended after about 890000 entries with: 31419 Memory fault - core dumped So there seems to be some kind of memory problem with gcg formatted embl. With Genbank (GCG formatted) I got a bit further, but after about 1048800 entries, it suddenly created the section "11" subindices (I was using chunks of 100000), and proceeded creating sections 12,13,14 etc, without reading any data. I managed to stop it when it was at section 35 ! Any suggestions ? Cheers, Martin -- ----------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/People/m.p.hilbers/ | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.dl.ac.uk/SEQNET/home.html | ----------------------------------------------------------------- From owner-srs@net.bio.net Sun Mar 16 22:00:00 1997 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: SRS5.0.3 - GCG format problems Date: Mon, 17 Mar 1997 14:57:49 +0000 Organization: SEQNET Lines: 33 Distribution: bionet Message-ID: <332D5BED.167E@dl.ac.uk> References: <32F71DAE.6358@computer.at> <33288272.5560@ebi.ac.uk> <332D266B.41C6@dl.ac.uk> <332D439A.2BA0@ebi.ac.uk> NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP12) To: etzold etzold wrote: > > but it looks if some file is truncated so that the last line is > incomplete (without line feed). A fix for that is already in > swissprot.is: > > add the production lnT > > lnT: ~ /[\n]+\n?/~ > > and replace all occurences of "ln" in the production "entry" with "lnT" > > regards > thure I suppose that the production lnT should read: lnT: ~ /[^\n]+\n?/~ Cheers, Martin -- ----------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/People/m.p.hilbers/ | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.dl.ac.uk/SEQNET/home.html | ----------------------------------------------------------------- From owner-srs@net.bio.net Sun Mar 16 22:00:00 1997 Path: biosci!agate!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: etzold Newsgroups: bionet.software.srs Subject: Re: SRS5.0.3 - GCG format problems Date: Mon, 17 Mar 1997 14:14:02 +0100 Organization: EMBL-EBI Lines: 23 Message-ID: <332D439A.2BA0@ebi.ac.uk> References: <32F71DAE.6358@computer.at> <33288272.5560@ebi.ac.uk> <332D266B.41C6@dl.ac.uk> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.0b2 (Win95; I) To: Martin Hilbers X-Priority: 3 (Normal) Martin Hilbers wrote: > With Genbank (GCG formatted) I got a bit further, but after > about 1048800 entries, it suddenly created the section "11" > subindices (I was using chunks of 100000), and proceeded > creating sections 12,13,14 etc, without reading any data. > I managed to stop it when it was at section 35 ! > > Any suggestions ? the "ll" subsection? is that new in genbank or an invention of srs? but it looks if some file is truncated so that the last line is incomplete (without line feed). A fix for that is already in swissprot.is: add the production lnT lnT: ~ /[\n]+\n?/~ and replace all occurences of "ln" in the production "entry" with "lnT" regards thure From owner-srs@net.bio.net Tue Mar 18 22:00:00 1997 Newsgroups: bionet.software.srs Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!news-xfer.netaxs.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!warwick!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!uranus.ebi.ac.uk!malik From: malik@uranus.ebi.ac.uk (Ansar Malik) Subject: ANNOUNCEMENT: Immunogenetics IMGT database - update Sender: news@ebi.ac.uk (usenet news) Message-ID: Date: Tue, 18 Mar 1997 15:39:32 GMT Lines: 60 Reply-To: malik@uranus.ebi.ac.uk (Ansar Malik) Organization: European Bioinformatics Institute (EMBL) - UK X-Newsreader: mxrn 6.18-31 Keywords: database, immunogenetics, immunoglobulin, T cell receptor cell,sequences annotation, DNA sequence IMMUNOGENETICS IMGT DATABASE =================================== Professor Marie-Paule LEFRANC Laboratoire d'ImmunoGenetique Moleculaire, LIGM UMR CNRS 9942, Institut de Genetique Moleculaire BP 5051, 1919 route de Mende, 34033 MONTPELLIER Cedex 1 FRANCE Telephone: (33) 67 61 36 34 FAX : (33) 67 04 02 31/67 04 02 45 e-mail : lefranc@ligm.crbm.cnrs-mop.fr INTRODUCTION ============ The ImMunoGeneTics database, IMGT, is an integrated specialised database containing nucleotide sequence information of genes important in the function of the immune system. It collects and annotates sequences belonging to the immunoglobulin superfamily which are involved in immune recognition, these are the B cell antigen receptor (Immunoglobulin or Ig), the T cell antigen receptor (TCR) (LIGM-database) and the class I and class II molecules of the Human Leucocyte Antigens (HLA) system (HLA-database). IMGT/LIGM DATABASE ================== An integrated immumogenetics database (IMGT/LIGM) specialising in Ig and TcR is under development through collaboration between LIGM, IFG and EMBL oustation EBI. This database consists of the Ig and TcR sequence entries. Collaborators: Release 97.03 contains 8287 fully annotated sequence entries. LIGM Montpellier :Marie-Paule Lefranc (coordinator) Veronique Giudicelli,Denys Chaume EMBL-EBI :Ansar Malik IFG :Werner Mueller ACCESS/DATA DISTRIBUTION ======================== SRS server: http://www.ebi/srs/srsc NOTE: Selecting this option will bring you to the SRS qerry interface page, where you have to select "search Sequence Libraries" WWW server: http://www.ebi.ac.uk/imgt/ FTP server: ftp.ebi.ac.uk/pub/databases/imgt E_MAIL server: email netserv@ebi.ac.uk -- send "help IMGT" in the mail body. This database is available on CD-ROM as an acompanying database to the EMBL Nucleotide Sequence Database at nominal cost. ======================================================================= Ansar Malik Ph.D | Email:Malik@ebi.ac.uk EBI - European Bioinformatics Institute | URL: http://www.ebi.ac.uk Hinxton Hall, Hinxton | Tel: +44 (1223) 494417 Cambridge CB10 1RQ, UK | Fax: +44 (1223) 494968 ======================================================================== From owner-srs@net.bio.net Tue Mar 18 22:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 Mar 1997 02:00:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199703191000.CAA12787@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. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-srs@net.bio.net Tue Mar 18 22:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!rill.news.pipex.net!pipex!warwick!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: etzold Newsgroups: bionet.software.srs Subject: release SRS5.0.4 Date: Wed, 19 Mar 1997 22:28:54 +0100 Organization: EMBL-EBI Lines: 24 Message-ID: <33305A96.6946@ebi.ac.uk> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.0b2 (Win95; I) X-Priority: 3 (Normal) Version 5.0.3 had still problems with EMBL in flat file format. This problem is hopefully fixed now. We added also an improved set of files for DSSP and IMGT done by Peter Rice. The file is at ftp://ftp.ebi.ac.uk/pub/software/unix/srs/srs5.0.4.tar.gz Release notes: SRS version 5.0.4 ================= 1) Fixed a memory leak in srsbuild, EMBL should index without problems 2) SRS supports compressed files again, in particular PDB. pdb.i contains 2 alternatives of PDB_FILE for compressed and uncompressed files 3) Some internal changes should make srsbuild slightly faster 4) Improved descriptions for IMGT and DSSP -- Thure Etzold, etzold@ebi.ac.uk Giorgio Verde, verde@ebi.ac.uk 19. March, 1997 From owner-srs@net.bio.net Tue Mar 25 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!cs.utexas.edu!howland.erols.net!europa.clark.net!news.maxwell.syr.edu!news.apfel.de!news-fra1.dfn.de!news-koe1.dfn.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: Bugs and Fixes : Date: 26 Mar 1997 13:44:55 GMT Organization: EMBL Heidelberg Lines: 38 Distribution: world Message-ID: <5hb98n$d4g@lion.embl-heidelberg.de> NNTP-Posting-Host: shag.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12IS (X11; I; IRIX 5.3 IP22) X-URL: news:bionet.software.srs?ALL A search for [PROSITEDOC-ID:'PDOC00702'] gives truncated entry because of the icarus parsing problem. change the line f_des: ~ {$Wrt:des} ('[' {$Not} ln)* ~ to f_des: ~ {$Wrt:des} (/\\[[0-9 ][0-9 ]\\] / {$Not} ln)* ~ in prositedoc.is file. PDBFINDER does not have compound field include in the AllText. change DF_Compound:$srsfield:[Compound short:com] to DF_Compound:$srsfield:[Compound short:com group:@DF_ALL] in srsgen.is file. Chenna Ramu =============================================================== Chenna Ramu | EMBL E-mail: chenna@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 356229 (Res) | 69012 Heidelberg (49) 6221 387398 (Off) | Germany Fax: (49) 6221 387517 URL: http://www.embl-heidelberg.de/~chenna/ ===============================================================