From owner-srs@net.bio.net Tue Dec 01 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!dca1-hub1.news.digex.net!digex!news2.randori.com!not-for-mail Newsgroups: bionet.software.srs Subject: NetSpy permits to supervise the task on the remote PC. From: fax_na@hotmail.com (A.E.) Organization: private X-Newsreader: WinVN 0.99.5 MIME-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 Lines: 82 Message-ID: Date: Wed, 02 Dec 1998 13:36:50 GMT NNTP-Posting-Host: 207.245.207.204 X-Trace: news2.randori.com 912605810 207.245.207.204 (Wed, 02 Dec 1998 05:36:50 PDT) NNTP-Posting-Date: Wed, 02 Dec 1998 05:36:50 PDT NetSpy permits to supervise the task on the remote PC. It is useful tool for manager to see what the personnel is doing during the work time. NetSpy work in Win NT 4.x or Windows 95 (98) netowrk environment using TCP/IP. NetSpy consistes of 2parts - server (NetSpyS) and client (Raposa). The NetSpyS runs as minimized window. It is Gui application Default TCP/IP port number is 79 for connection with client (Raposa). (In demo version NetSpyS presents advetizing string read fron the host UACT.NET. In this state NetSpyS is Always-on-top window) It ispossible to use other port number,creating specila NetSpy.INI file and put this file into the Windows directory. This file should have the following contents: [Communication] Port = 99 for port number 99 for example. Client Raposa is console Windows application. It should be started from virtual DOS (DOS-PROMT) by typing the following command string: >Raposa network_remote_computer_name/IP__remote_computer [port_number] By default the port number is 79 (Finger TCP/IP port - 79). Port number should be the same as used by NetspyS. Example of Raposa stating: C:\WINNT40>raposa 127.0.0.1 99 or C:\WINNT40>raposa ts1p12.uact.net If connection was succesful the client Raposa would present the list of tasks on the remote compute, for example: E:\DOWN>a:\netspy\raposa 127.0.0.1 80 NetSpy Client Part. Questions: fax_na@hotmail.com Connected to [127.0.0.1:80]. Conneted to the NetSpy Server Host Name: gwork_a The current date and time are: Fri Oct 16 20:15:20 1998 Task Report 1. Mimimized NoZoomed Name: NetSpy Server Part 2. NoMimimized NoZoomed Name: NetDDE Agent 3. NoMimimized NoZoomed Name: Shortcut to cmd - a:\netspy\raposa 127.0.0.1 80 4. NoMimimized NoZoomed Name: Battery Meter 5. NoMimimized NoZoomed Name: OleMainThreadWndName 6. NoMimimized NoZoomed Name: Program Manager Done! E:\DOWN> If you want to receive the sources of NetSpy or not-demo version (without demo string) please write to: fax_na@hotmail.com From owner-srs@net.bio.net Tue Dec 01 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!xmission!nntp.csuchico.edu!cscnews.csc.calpoly.edu!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software.srs Subject: getz syntax question Date: 2 Dec 1998 18:33:20 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 57 Message-ID: <74415g$nla@gap.cco.caltech.edu> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu SRS 5.1 on Linux/Intel. Can somebody please explain to me how to get from the query description language in the html page to the following observed behavior? Yes, this started out as a typo, but since it doesn't throw an error, it is apparently allowed syntax. All of these rapidly return a list of all SWISSPROT entries: % getz 'swissprot-id:ha12_mouse' % getz 'swissprot-id' % getz 'swissprot' but % getz 'swiss' SRSICA:srsquery.i:51: error: unknown set or databank. "swiss" It looks like all databases are predefined as "sets", and also getz will return a "set" even if no operators are present on the query line. However, how the parser handles the first two commands above is very unclear. Also, this doesn't do what I'd expect if the preceding was the full explanation: % getz '{nrl3d swissprot}' since it returns NOTHING, why not both? Elsewhere {database database} can be used anywhere that "database" alone can. % getz 'nrl3d | swissprot' returns both sets, swissprot first. So the logical operators function in this context, but not the {} operator. One interesting side note, the "obvious" methods of listing a database take orders of magnitude longer than the methods described above. On a 400 Mhz PII, all SRS databases on a single 9 Gb U2W scsi disk, no other load on system: % getz 'swissprot' > /dev/null took 3 seconds, but % getz '[swissprot-id:*]' > /dev/null took 423 seconds. (The fastest method of all to get this information was % cat swissprot.seqcat > /dev/null which took lesss than a second, but not all sites will have that GCG file.) Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-srs@net.bio.net Tue Dec 01 22:00:00 1998 From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: New Application in SRS Date: Wed, 02 Dec 1998 13:37:54 +0100 Organization: INFOBIOGEN Lines: 30 Message-ID: <366534A2.DF285885@infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (X11; I; SunOS 5.6 sun4u) X-Accept-Language: en Path: biosci!news.ic.sunysb.edu!news-nysernet-16.sprintlink.net!news-east1.sprintlink.net!news-peer1.sprintlink.net!news.sprintlink.net!howland.erols.net!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!oleane!jussieu.fr!infobiogen.fr!newsmaster Hello, We have an application called b2f that i would like to set in SRS. This application only needs as input a blast output. I defined for B2F_APP a datatype for proteins (dataType:@PROTSEQ_DATA) and I add it in srsgen.i(@B2F_APP in PROTSEQ_DATA). By this way, B2F appears (launch botton) after a query result for proteins and also for blast result. Is there a way to get it only for blast result ? 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 Thu Dec 03 22:00:00 1998 Path: biosci!YAHOO.COM!mri87492 From: mri87492@YAHOO.COM Newsgroups: bionet.software.srs Subject: your site Date: 4 Dec 1998 00:33:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 74 Sender: daemon@net.bio.net Distribution: world Message-ID: <199812040832.AAA28104@net.bio.net> NNTP-Posting-Host: net.bio.net We'll Submit Your Site To Over 900 Search Engines, Directories, & Indices For A "One Time Cost" Of Only $39.95 *** 100% Money Back Guarantee *** *** Immediately Increase Your Sites Exposure *** For Less Than 4 Cents Each We Will Submit Your Web Site To Over 900 Of The Net's Hottest Search Engines, Directories & Indices. 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From owner-srs@net.bio.net Thu Dec 03 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.concentric.net!howland.erols.net!newsfeed.nacamar.de!univ-lyon1.fr!jussieu.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: embl search in SRS Date: Fri, 04 Dec 1998 11:30:40 +0100 Organization: INFOBIOGEN Lines: 26 Message-ID: <3667B9D0.13D13D9C@infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (X11; I; SunOS 5.6 sun4u) X-Accept-Language: en hello all, I find a problem using parentheses for embl search : no entries found, query: "[embl-Description: alpha* & (globin*|hemoglobin*)] " but Query "[embl-Description: alpha* & globin*|hemoglobin*] " found 12032 entries Query "[embl-Description: alpha* & globin*] " found 2144 entries Query "[embl-Description: alpha* & hemoglobin*] " found 5157 entries The query search with lookup is ok. Regards -- --------------------------------------------------- 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 Thu Dec 03 22:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.cwix.com!158.43.192.17!rill.news.pipex.net!pipex!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: embl search in SRS Date: 04 Dec 1998 13:38:10 +0000 Organization: The Sanger Centre Lines: 22 Message-ID: References: <3667B9D0.13D13D9C@infobiogen.fr> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 912778579 5275 193.60.84.160 (4 Dec 1998 13:36:19 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 4 Dec 1998 13:36:19 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 Jean-Marc Plaza writes: > I find a problem using parentheses for embl search : > > no entries found, query: "[embl-Description: alpha* & (globin*|hemoglobin*)] " Seems that parentheses are badly broken: getz '[swissprot-authors:drew* & rice*]' -> 1 entry getz '[swissprot-authors:(drew* & rice*)]' -> nothing But the SRS manual offers as an example: [medline-authors:(wu* & rice*) ! (smith* | jones*)] so we are apparently using the 'correct' syntax. -- ---------------------------------------------------------------------- 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 Sun Dec 06 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!newsfeed1.swip.net!swipnet!rill.news.pipex.net!pipex!uunet!in1.uu.net!news1-gui.server.ntli.net!news-feed.ntli.net!news5-gui.server.ntli.net!news-feed.ntli.net!server4.netnews.ja.net!server2.netnews.ja.net!pegasus.csx.cam.ac.uk!not-for-mail From: timc@chiark.greenend.org.uk (Tim Cutts) Newsgroups: bionet.software.srs Subject: Indexing of RL lines from EMBL Date: 07 Dec 1998 10:14:52 +0000 (GMT) Organization: Linux Unlimited Lines: 9 Message-ID: NNTP-Posting-Host: rrw1000.sel.cam.ac.uk Originator: timc@news.chiark.greenend.org.uk ([127.0.0.1]) The current EMBL parser only indexes the RL field if it conforms to a published reference. It would be useful to be able to search the database for information from other entries, so I could, for example, ask "Give me all the entries submitted by this organisation". Has anyone already done this to the EMBL parser, just so that I can avoid reinventing the wheel... Tim. From owner-srs@net.bio.net Tue Dec 08 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.tli.de!newsfeed.wirehub.nl!news.belnet.be!surfnet.nl!barba.uci.kun.nl!sci.kun.nl!not-for-mail From: "K. Cuelenaere" Newsgroups: bionet.software.srs Subject: Re: embl search in SRS Date: Wed, 09 Dec 1998 11:40:17 +0100 Organization: CAOS/CAMM Center Lines: 34 Message-ID: <366E5391.70A94C3C@caos.kun.nl> References: <3667B9D0.13D13D9C@infobiogen.fr> NNTP-Posting-Host: cammsg11.caos.kun.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX 6.2 IP22) Peter Rice wrote: > > Jean-Marc Plaza writes: > > I find a problem using parentheses for embl search : > > > > no entries found, query: "[embl-Description: alpha* & (globin*|hemoglobin*)] " > > Seems that parentheses are badly broken: > > getz '[swissprot-authors:drew* & rice*]' -> 1 entry > getz '[swissprot-authors:(drew* & rice*)]' -> nothing > > But the SRS manual offers as an example: > > [medline-authors:(wu* & rice*) ! (smith* | jones*)] > > so we are apparently using the 'correct' syntax. Hi, Jack noted the same problem some time ago and mentioned it to Thure. Thure confirmed the parentheses problem and I believe he said it will be back in the next release, Regards, Koen. -------------------------------------------------------------- Koen Cuelenaere Email: koenc@caos.kun.nl CAOS/CAMM Center Phone: +31 24 3653383 University of Nijmegen Fax: +31 24 3652977 Toernooiveld 6525 ED Nijmegen The Netherlands URL: http://www.caos.kun.nl/ -------------------------------------------------------------- From owner-srs@net.bio.net Wed Dec 09 22:00:00 1998 Path: biosci!AOL.COM!Gangst2219 From: Gangst2219@AOL.COM Newsgroups: bionet.software.srs Subject: Publishing Company For Sale Date: 10 Dec 1998 01:13:32 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 222 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net See information about Free Credit Application Below! 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If you have received this message in error, reply with the word unsubscribe in the subject. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * From owner-srs@net.bio.net Wed Dec 09 22:00:00 1998 Message-ID: <366CDFD5.7F1F9CA2@igbm.unil.ch> Date: Tue, 08 Dec 1998 08:14:14 +0000 From: Marco Pagni X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.32 i686) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.software.srs Subject: Re: List of queries with getz References: <365A92E2.C1144E31@igs.cnrs-mrs.fr> <365AAEDF.B5907AFA@ebi.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: pcisrec-c205c.unil.ch X-Trace: 8 Dec 1998 09:14:14 +0100, pcisrec-c205c.unil.ch Lines: 58 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!news-ge.switch.ch!news-zh.switch.ch!cisun5000.unil.ch!pcisrec-c205c.unil.ch Peter Rice wrote: > Heikki Lehvaslaiho writes: > > > Olivier POIROT wrote: > > > Is it possible to use a file containing a list of Ids with getz (SRS > > > version 5.1)? > > Dear Olivier, > > I suppose you mean lists like these: > > % more my.list > > EMBL:AB015259 > > EMBL:AB015260 > > EMBL:AB015261 > > EMBL:AB015262 > > % > > getz needs its input formatted in a slightly different way. Let's > > write a script, in icarus of course, that does what you want and can > > be extended as needed. > > Not really what is needed. That Icarus script just runs getz for each > sequence and writes the results to stdout. > > I have asked Thure several times for the SRS 4 capability to use a list > of entries as a query. Then you can do things like: > > getz '@my.list > swissprot' > getz '@my.list' -f 'id acc des' > getz '@my.list ! (embl < emblnew)' > > So far no sign of this appearing, though Thure promised it was not > difficult. I really miss this capability. The lists can be created by > getz (they are the default output) but cannot be used since SRS 4 went > away. > > -- > ---------------------------------------------------------------------- > 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/ I have exactely the same need, and I am sure that we are more than two SRS users with the same need. The rationale for this is that SRS outputs reflect the databases content which are not free from erroneous annotations. To be fully biologically significant, a few entries must often be added to or removed from result sets. And unfortunately such "manually" corrected cannot be read by SRS as input for further querying databases. Regards, Marco Pagni Swiss Institute of Bioinformatics mpagni@igbm.unil.ch From owner-srs@net.bio.net Thu Dec 10 22:00:00 1998 Path: biosci!daresbury!server5.netnews.ja.net!server6.netnews.ja.net!nntp.news.xara.net!xara.net!news.maxwell.syr.edu!news-peer.gip.net!news-dc.gip.net!news.gsl.net!gip.net!duke.telepac.pt!news.telepac.pt!194.65.24.2!152.205.178.172 From: vvousw@aol.com Newsgroups: bionet.software.srs Subject: 100% FREE XXX SITE 2038 Date: 11 Dec 1998 07:36:07 GMT Lines: 12 Message-ID: <3670cb67.0@194.65.24.2> NNTP-Posting-Host: 194.65.24.2 The sex gallery ! It's all FREE here ! FREE xxx memberships, passwords,pic,thumbnails,and much more ! Now featuring live hott erotic talk ! Cum by today ! WE'RE WAITING ! 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From owner-srs@net.bio.net Wed Dec 16 22:00:00 1998 From: "Thure Etzold" Newsgroups: bionet.software.srs Subject: job opportunities within the SRS project at LION Bioscience, Cambridge Date: Thu, 17 Dec 1998 21:58:05 -0000 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 NNTP-Posting-Host: 193.122.103.27 Message-ID: <36797e7a.0@nnrp1.news.uk.psi.net> Path: biosci!agate!newsfeed.berkeley.edu!news-peer1.sprintlink.net!news.sprintlink.net!news-peer.gip.net!news-lond.gip.net!news.gsl.net!gip.net!dispose.news.demon.net!demon!ayres.ftech.net!news.ftech.net!news.lattis.xara.net!uknet!nnrp1.news.uk.psi.net!193.122.103.27 Lines: 80 LION Bioscience Ltd. is a subsidiary of LION Bioscience AG. LION is unique in the integration of a complete collection of proprietary genomics technologies ranging from experimen- tal biology to information technology. LION's goal is to become the leading provider of biological knowledge to the life science industry. Biological knowledge is the outcome of customised genomics projects, target gene identification, and informatics tools to most rapidly and effectively capital- ise on the results. LION Bioscience Ltd. is based in Cambridge, UK, and focuses on commercial development of the SRS software system. SRS is a data retrieval system that integrates heterogeneous databanks in molecular biology and genome analysis. There are currently several dozen servers world-wide that provide access to over 300 different databanks via the World Wide Web. Additional technology to integrate externally developed applications into the package gives novel and powerful capabilities for biological data analysis. LION offers an exciting start-up environment with a bright and energetic team. Information about LION Bioscience is available on the web at http://www.lion-ag.de. LION is looking for scientists and engineers to join our enthusiastic and fast-moving team in the following areas. Software Engineers (30-40k) Experienced software engineers to work on the SRS project. SRS is evolving and growing rapidly and provides a unique set of networking and data management challenges. This forces us to evaluate and use the latest software technolo- gies and develop novel solutions ourselves. Qualifications include fluency in the C language, and comfort participating in a large software development project. A background in biology or experience in HTML, Java and object-oriented programming would be welcome. Q/A Engineers (30-40k) Software Quality Assurance engineers experienced in developing and implementing Q/A plans, software testing suites, and bug tracking systems. Should be familiar with biological software applications and data, and capable of interacting with software engineers. Documentation Lead (25-35k) Experienced writer to lead the software documentation effort. Responsibilities will include the writing of a user manual, administrator manual, online help, and quick reference guides. Candidates should either have a strong background as a user of bioinformatics software or a strong background in software documentation. The company will train in the other discipline. Customer Service (25-35k) Scientists to provide high-quality technical and scientific support to our installed customer base. Responsibilities will include the establishment of a call centre, case tracking and reporting software as well as responding to and interacting with customers to quickly solve problems. Additional responsibilities include travel to customer sites to install, upgrade, maintain, and customise installations. Strong tech- nical and communications skills are necessary. Please send your resume to CV to jobs@lionbio.co.uk. LION Bioscience Ltd. Sheraton House Castle Park Cambridge CB3 0AX United Kingdom Phone: +44 (0) 1223 224 700 Fax: +44 (0) 1223 224-701 From owner-srs@net.bio.net Thu Dec 17 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!rill.news.pipex.net!pipex!ams.news.uu.net!uunet!in5.uu.net!stalker.oem.net!not-for-mail From: "Sean" Newsgroups: bionet.software.srs Subject: Universal Software Date: Tue, 15 Dec 1998 05:01:40 -0500 Organization: oemnetworks.com Lines: 28 Message-ID: <36758784.0@rboc1.prime-x.net> NNTP-Posting-Host: rboc1.prime-x.net X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Thought this might be of interest-- my name is Sean Hughes and Im with Biostorm. Just making people aware we exist -hope not to offend anyone with this shamelss plug.:) Chemi-16 Gel documentation & Chemiluminescence: With 16-bits cooled integrating digital CCD, lens, UV filter, dark room, 302nm transilluminator, conversion screen………Introductory….$15,995 (Only Biorad has 16-bits priced at $29,950. Other suppliers have 8-bits at $18,000 & upon request Color-Monochrome, (FISH) Automatic Karyotyping of Chromosomes & Cytogenetic Analysis The program performs automatic chromosome analysis of acquired color or monochrome metaphase images from camera installed on microscope (light or fluorescence), scanner, disk, clipboard, files in BMP, .PCX, .GIF, .TIF formats, etc. $8,500.00 Software 18 Windows, 14 Mac, 24 DOS. 1D main program, 1D Advanced 2D advanced DNA sequence reading, PCR, RFLP, RAPD DNA fingerprinting Dots-ELISA Image analysis Color/B&W image analysis Colony count-sort Particle size analysis Similarity dendrograms ---------------------------------------------------------------------------- ----------------------------------------- From owner-srs@net.bio.net Thu Dec 17 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet!nntp.news.xara.net!xara.net!server6.netnews.ja.net!server4.netnews.ja.net!server2.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: job opportunities within the SRS project at LION Bioscience, Cambridge Date: 18 Dec 1998 09:49:29 +0000 Organization: The Sanger Centre Lines: 17 Message-ID: References: <36797e7a.0@nnrp1.news.uk.psi.net> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 913974433 14468 193.60.84.160 (18 Dec 1998 09:47:13 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 18 Dec 1998 09:47:13 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 "Thure Etzold" writes: > LION Bioscience Ltd. is based in Cambridge, UK, and > focuses on commercial development of the SRS software > system Careful Thure - there are restrictions on commercial activities in the BIOSCI/bionet newsgroups. I assume this posting was cleared first. See http://net.bio.net/BIOSCI/biosci.FAQ.html -- ---------------------------------------------------------------------- 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 Dec 18 22:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 Dec 1998 02:00:11 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199812191000.CAA03712@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 Sat Dec 19 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.maxwell.syr.edu!nntp.ntr.net!Supernews60!supernews.com!uunet!in3.uu.net!satlink!ul3.satlink.com!not-for-mail From: File Detect Newsgroups: bionet.software.srs Subject: Useful program Date: Sun, 20 Dec 1998 00:15:08 -0600 Organization: Marsc Lines: 71 Message-ID: <367C95EB.96198BA2@Detect.com> NNTP-Posting-Host: maq033b.advance.com.ar Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="------------15580F8F48C8662D2EF4209C" X-Mailer: Mozilla 4.03 [en] (Win95; I) --------------15580F8F48C8662D2EF4209C Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit File Detect: File Detect is a Windows 95 program. This program detects new, modified or deleted files in your disk. Also detects new or deleted folders (Directories). This is very useful to know what files (As to be *.DLL's, *.OCX's, *.TTF's *.HLP's and many other) are copied to your disk when you install a new program, driver or make a change in the system configuration. As you know, when you install a program or driver in your disk, a lot of files are installed in your system folders, Some times you uninstall a program and these files remain there occupying several MB of space in your disk. Think about it. How many times do you download a program from the Internet?. How many games?. With File Detect you can take control on this situation since all what is copied to your disk is detected. For more information about this program and for downloading it visit the home page: www.angelfire.com/fl/filedetect --------------15580F8F48C8662D2EF4209C Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit File Detect:

File Detect is a Windows 95 program.
This program detects new, modified or deleted files in your disk.
Also detects new or deleted folders (Directories).
This is very useful to know what files (As to be *.DLL's, *.OCX's, *.TTF's
*.HLP's and many other) are copied to your disk when you install a new program,
driver or make a change in the system configuration.

As you know, when you install a program or driver in your disk, a lot of
files are installed in your system folders, Some times you uninstall a program
and these files remain there occupying several MB of space in your disk.

Think about it. How many times do you download a program from the Internet?.
How many games?.
With File Detect you can take control on this situation since all what is
copied to your disk is detected.

For more information about this program and for downloading it visit
the home page: www.angelfire.com/fl/filedetect
 
  --------------15580F8F48C8662D2EF4209C-- From owner-srs@net.bio.net Tue Dec 22 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: stuart@ludwig.ucl.ac.uk (Stuart Rison) Newsgroups: bionet.software.srs Subject: Spanning multiple SRS servers. Date: 23 Dec 1998 13:49:59 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 24 Message-ID: <75qse7$fg7$1@mserv2.dl.ac.uk> NNTP-Posting-Host: mserv2.dl.ac.uk Original-To: bio-soft@dl.ac.uk, bio-srs@dl.ac.uk content-length: 817 Return-Path: Dear all, I would like to query Unigene (the clustred EST database) and dbEST (the EST database) with SRS simultaneously. Unfortnately, I have not yet found an SRS server that provides indexing for BOTH of them (searched using SRS on databanks). Is it possible to 'save' data and pass them from one server to another? For example, could I pull a list of EST accesion numbers from dbEST on one server, save that set of accession numbers and get hold of all the clusters in UniGene that contain these EST accession numbers? I do not have that facilities to index dbEST and UniGene 'in house'. could you please cc your postings to stuart@NO_JUNK.ludwig.ucl.ac.uk (with NO_JUNK removed) as I am currently unable to check on newsgroups regularly. Thanks for any help you may provide. best regards, Stuart Rison. From owner-srs@net.bio.net Tue Dec 22 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!btnet-peer!btnet!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: stuart@ludwig.ucl.ac.uk (Stuart Rison) Newsgroups: bionet.software.srs Subject: Spanning multiple SRS servers... addendum. Date: 23 Dec 1998 14:03:56 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 17 Message-ID: <75qt8c$frp$1@mserv2.dl.ac.uk> NNTP-Posting-Host: mserv2.dl.ac.uk Original-To: bio-soft@dl.ac.uk, bio-srs@dl.ac.uk content-length: 419 Return-Path: Dear All, >Unfortnately, I have not yet found an SRS server that provides indexing for BOTH of them >(searched using SRS on databanks). Must have searched very badly or been very tired! Found plenty of such servers now! All the same, I am curious to know if the passing of data between servers is possible should I ever find myself in such a situation again. best regards, Stuart stuart@NO_JUNK.ludwig.ucl.ac.uk From owner-srs@net.bio.net Mon Dec 28 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.cwix.com!158.43.192.17!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: Spanning multiple SRS servers. Date: 29 Dec 1998 09:38:46 +0000 Organization: The Sanger Centre Lines: 22 Message-ID: References: <75qse7$fg7$1@mserv2.dl.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 914924180 28353 193.60.84.160 (29 Dec 1998 09:36:20 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 29 Dec 1998 09:36:20 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 stuart@ludwig.ucl.ac.uk (Stuart Rison) writes: > I would like to query Unigene (the clustred EST database) and dbEST (the EST > database) with SRS simultaneously. Unfortnately, I have not yet found an > SRS server that provides indexing for BOTH of them (searched using SRS on > databanks). As you found, there are several servers with both. You need to take care over how the databases are linked. At the Sanger Centre we link UNIGENE and DBEST using the CloneID rather than the accession number. SRS only allows one link between databases. You would need to use EMBL to get links by accession number. We also have DBESTSEQ (the dbEST FASTA format sequences file) but that currently has no direct link to UNIGENE. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Wed Dec 30 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: bioinfo@my-dejanews.com Newsgroups: bionet.software.srs Subject: Algorithm for Restriction Enzyme Analysis Date: Thu, 31 Dec 1998 05:05:55 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 14 Message-ID: <76f0nj$la$1@nnrp1.dejanews.com> NNTP-Posting-Host: 202.54.48.86 X-Article-Creation-Date: Thu Dec 31 05:05:55 1998 GMT X-Http-User-Agent: Mozilla/4.0 (compatible; MSIE 4.01; Windows NT) X-Http-Proxy: 1.0 x5.dejanews.com:80 (Squid/1.1.22) for client 202.54.48.86 Hi All, I am in trouble. I am developing an algorithm for restriction enzyme analysis but it is taking too long. The reason is because there are so many degenerate bases in the DNA sequence and thus it takes very long to analyze for all of them considering the possible combiantions they make. All the more the recognition sequence also have degenerate bases. Is there anybody out there to help me optimize the algorithm? Yes, there is. So thanking in advance to all those who respond. Ravi Gupta. Research Scholar DA University, M.P., India. -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own