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If you have received this message in error,hitl Reply with the word unsubscribe in the subject. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * From owner-srs@net.bio.net Wed Sep 01 20:05:00 1999 Path: biosci!SOL.BIOL.UNLP.EDU.AR!martin From: martin@SOL.BIOL.UNLP.EDU.AR (Martin Sarachu) Newsgroups: bionet.software.srs Subject: Compiling problem with SRS 5.1 Date: 1 Sep 1999 14:05:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <37CD4027.8440A5F7@sol.biol.unlp.edu.ar> NNTP-Posting-Host: net.bio.net Hi im getting this error when i try to compile SRS 5.1 in a Sun Ultrasparc with gcc make for Solaris with parameters: msgdef gcc -Xa -I/export/home/martin/temp/srs/bin/solaris -O2 -D__ODD -DSRSINCLUDE=\"srs5.h\" -c -o /export/home/martin/temp/srs/bin/solaris/msgdef.o msgdef.c gcc: unrecognized option `-Xa' gcc -Xa -I/export/home/martin/temp/srs/bin/solaris -o /export/home/martin/temp/srs/bin/solaris/msgdef /export/home/martin/temp/srs/bin/solaris/msgdef.o gcc: unrecognized option `-Xa' srsmake: end Segmentation Fault - core dumped srsinstall: Stopping due to Error 139 Any idea what's happening? Martin. -- Martin Sarachu E-mail: martin@sol.biol.unlp.edu.ar Red Latinoamericana de Ciencias Biologicas (RELAB) http://prbgrau.biol.unlp.edu.ar EMBnet Argentina http://sol.biol.unlp.edu.ar/embnet From owner-srs@net.bio.net Thu Sep 02 11:53:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!not-for-mail From: Tim Cutts Newsgroups: bionet.software.srs Subject: Re: Compiling problem with SRS 5.1 Date: 02 Sep 1999 13:43:28 +0100 (BST) Organization: Linux Unlimited Lines: 28 Message-ID: References: <37CD4027.8440A5F7@sol.biol.unlp.edu.ar> NNTP-Posting-Host: rrw1000.sel.cam.ac.uk X-Newsreader: trn 4.0-test70 (17 January 1999) Originator: timc@news.chiark.greenend.org.uk ([127.0.0.1]) In article <37CD4027.8440A5F7@sol.biol.unlp.edu.ar>, Martin Sarachu wrote: >Hi > >im getting this error when i try to compile SRS 5.1 in a Sun Ultrasparc with gcc > >make for Solaris with parameters: msgdef >gcc -Xa -I/export/home/martin/temp/srs/bin/solaris -O2 -D__ODD >-DSRSINCLUDE=\"srs5.h\" -c -o >/export/home/martin/temp/srs/bin/solaris/msgdef.o msgdef.c >gcc: unrecognized option `-Xa' >gcc -Xa -I/export/home/martin/temp/srs/bin/solaris -o >/export/home/martin/temp/srs/bin/solaris/msgdef >/export/home/martin/temp/srs/bin/solaris/msgdef.o >gcc: unrecognized option `-Xa' >srsmake: end >Segmentation Fault - core dumped >srsinstall: Stopping due to Error 139 > -Xa is an option for the Sun cc compiler. I think the automatic scripts for SRS assume you are using sun's compiler, even if you are using gcc. You will need to find the place in the srsinstall stuff where the compiler options are set, and remove the -Xa option. Tim. From owner-srs@net.bio.net Thu Sep 02 13:55:00 1999 Path: biosci!SOL.BIOL.UNLP.EDU.AR!martin From: martin@SOL.BIOL.UNLP.EDU.AR (Martin Sarachu) Newsgroups: bionet.software.srs Subject: Compiling problems with SRS 5.1 Date: 2 Sep 1999 07:55:49 -0700 Organization: IBBM, Fac. Cs. Exactas, UNLP Lines: 54 Sender: daemon@net.bio.net Distribution: world Message-ID: <37CE3AF3.3493FC61@sol.biol.unlp.edu.ar> Reply-To: martin@sol.biol.unlp.edu.ar NNTP-Posting-Host: net.bio.net > In article <37CD4027.8440A5F7@sol.biol.unlp.edu.ar>, > Martin Sarachu wrote: > >Hi > > > >im getting this error when i try to compile SRS 5.1 in a Sun Ultrasparc with gcc > > > >make for Solaris with parameters: msgdef > >gcc -Xa -I/export/home/martin/temp/srs/bin/solaris -O2 -D__ODD > >-DSRSINCLUDE=\"srs5.h\" -c -o > >/export/home/martin/temp/srs/bin/solaris/msgdef.o msgdef.c > >gcc: unrecognized option `-Xa' > >gcc -Xa -I/export/home/martin/temp/srs/bin/solaris -o > >/export/home/martin/temp/srs/bin/solaris/msgdef > >/export/home/martin/temp/srs/bin/solaris/msgdef.o > >gcc: unrecognized option `-Xa' > >srsmake: end > >Segmentation Fault - core dumped > >srsinstall: Stopping due to Error 139 > > > > -Xa is an option for the Sun cc compiler. I think the automatic scripts > for SRS assume you are using sun's compiler, even if you are using gcc. > You will need to find the place in the srsinstall stuff where the > compiler options are set, and remove the -Xa option. > > Tim. > Hi Tim I removed -Xa option and still getting the same error, could it be a problem with gcc? This was the output > make for Solaris with parameters: msgdef > gcc -I/export/home/martin/temp/srs/bin/solaris -O2 -D__ODD -DSRSINCLUDE=\"srs5.h\" -c -o /export/home/martin/temp/srs/bin/solaris/msgdef.o msgdef.c > gcc -I/export/home/martin/temp/srs/bin/solaris -o /export/home/martin/temp/srs/bin/solaris/msgdef /export/home/martin/temp/srs/bin/solaris/msgdef.o > srsmake: end > Segmentation Fault - core dumped > srsinstall: Stopping due to Error 139 > Martin. -- Martin Sarachu E-mail: martin@sol.biol.unlp.edu.ar Red Latinoamericana de Ciencias Biologicas (RELAB) http://prbgrau.biol.unlp.edu.ar EMBnet Argentina http://sol.biol.unlp.edu.ar/embnet From owner-srs@net.bio.net Thu Sep 02 15:14:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!newsfeed.gamma.ru!Gamma.RU!any.msu.ru!news.msu.ru!not-for-mail From: Yuriy Kotlyarov Newsgroups: bionet.software.srs Subject: Icarus syntax Date: Thu, 02 Sep 1999 20:15:33 +0400 Organization: Moscow State University Lines: 10 Message-ID: <37CEA2A4.335B44EC@hist.msu.ru> NNTP-Posting-Host: geshkin.hist.msu.ru Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.msu.ru 936288505 18192 195.208.218.19 (2 Sep 1999 16:08:25 GMT) X-Complaints-To: usenet@news.msu.ru NNTP-Posting-Date: 2 Sep 1999 16:08:25 GMT X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en Hi all i'd like to find syntax of the Icarus in EBNF. Does anyone know URL or, please, send me the file thanks Yury Kolyarov cotlyarov@hist.msu.ru From owner-srs@net.bio.net Mon Sep 06 08:03:00 1999 Path: biosci!BWORLD.COM.PH!listserver09 From: listserver09@BWORLD.COM.PH Newsgroups: bionet.software.srs Subject: Don't Get Ripped Off With A $15 or $22 Program... Date: 6 Sep 1999 02:03:31 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 211 Sender: daemon@net.bio.net Distribution: world Message-ID: <199909060850.EAA15292@husky5> Reply-To: listserver09@bworld.com.ph NNTP-Posting-Host: net.bio.net Net Spy Exchange Volume 4 - Issue 8 Subscriber Count: 29,081 ------------------------------------------------------------------------------------------------------------ WARNING!!! There are some dishonest people who have copied this advertisement in an attempt to sell their own "cheap imitation" of the Internet Spy & You program. 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DISCLAIMER: The seller of this powerful software resource will not be held responsible for how the purchaser chooses to use its resources. ----------------------------------------------------------------------------------------------------------------- To UNSUBSCRIBE and be removed from this mailing, please leave us your complete email address on our toll-free voicemail server: 1-800-595-2001 HP400 From owner-srs@net.bio.net Tue Sep 07 22:38:00 1999 Path: biosci!bloom-beacon.mit.edu!panix!howland.erols.net!vixen.cso.uiuc.edu!newsfeed.acns.nwu.edu!news.cc.uic.edu!not-for-mail From: Mohyeddin Kassar Newsgroups: bionet.software.srs Subject: Jobs: Statistics/Bio Date: Tue, 07 Sep 1999 17:47:06 -0500 Organization: Energy Resources Center Lines: 35 Message-ID: <37D595E8.8B5638A2@uic.edu> NNTP-Posting-Host: mcgrath.erc.uic.edu Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------5B723A0B332B82076E83A6E8" X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en This is a multi-part message in MIME format. --------------5B723A0B332B82076E83A6E8 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Several positions for PH.D. Statistics or Biostatistics available, If Interested send resume to: jobs@penet-careers.com http://www.penet-careers.com/ --------------5B723A0B332B82076E83A6E8 Content-Type: text/x-vcard; charset=us-ascii; name="mkassar.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Mohyeddin Kassar Content-Disposition: attachment; filename="mkassar.vcf" begin:vcard n:Kassar;Mohyeddin tel;fax:312-996-5620 tel;home:312-829-1485 tel;work:312-413-3615 x-mozilla-html:FALSE org:University Of Illinois at Chicago;Energy Resources Center version:2.1 email;internet:mkassar@uic.edu title:Research Economist adr;quoted-printable:;;(MC156)=0D=0A851 S. Morgan Street, 12th Floor SEO;Chicago;IL;60607-7054;USA fn:Mohyeddin Kassar end:vcard --------------5B723A0B332B82076E83A6E8-- From owner-srs@net.bio.net Wed Sep 08 09:25:00 1999 Message-ID: <37D6381F.28AC@cmu.unige.ch> Date: Wed, 08 Sep 1999 12:19:11 +0200 From: Alain GATEAU X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.6 sun4m) MIME-Version: 1.0 Newsgroups: bionet.software.srs Subject: add features to all text searches Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: cmusun18.unige.ch X-Trace: 8 Sep 1999 12:19:12 +0100, cmusun18.unige.ch Lines: 12 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newsfeed.icl.net!newsfeed.nacamar.de!rz.uni-karlsruhe.de!news.uni-stuttgart.de!news.belwue.de!news-zh.switch.ch!news.unige.ch!cmusun18.unige.ch Hello, I'm running 5.1 and I'd like to have Swiss-prot feature descriptions added to the AllText searches. I edited srsgen.i and added the following line: DF_FtDescription:$SrsField:[FtDescription short:ftd group:@DF_ALL] and then srssection. It just doesn't do it (for a test I look for PYRROLIDONE: in FtDescription -> 588 matches in Alltext -> 18 matches ) any idea ? thank's for helping, alain Gateau From owner-srs@net.bio.net Thu Sep 09 11:30:00 1999 Path: biosci!newsfeed.stanford.edu!cyclone.bc.net!news.maxwell.syr.edu!newspeer.monmouth.com!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!not-for-mail From: Tim Cutts Newsgroups: bionet.software.srs Subject: Bugfix for SRS 5.1 Date: 09 Sep 1999 13:17:01 +0100 (BST) Organization: Linux Unlimited Lines: 93 Message-ID: NNTP-Posting-Host: rrw1000.sel.cam.ac.uk X-Newsreader: trn 4.0-test70 (17 January 1999) Originator: timc@news.chiark.greenend.org.uk ([127.0.0.1]) For those of you still using SRS 5.1, I have found and fixed a bug in its handling of $Library objects. Hope this is of help to those who can't or don't wish to upgrade to SRS 6. SYMPTOMS: If your .i and .it files do not have the same name as databases generated within them, $Library objects have .iFile and .itFile attributes to tell SRS where these files are. Unfortunately, these attributes are then ignored in two common cases: a) Trying to retrieve the Structure or Info links from the library description page returns an empty page. For an example of how this is broken, try looking at the information for dbSNP_SNP on the EBI SRS5 server (http://srs.ebi.ac.uk/) b) The .it file for your database is ignored if you pull up field info pages. The bug does *NOT* seem to exist in SRS 6, as far as I can tell from the EBI SRS 6 server. PATCH: The following patch to $SRSSOU/library.c fixes the bug in SRS 5.1: --- library.c.orig Thu Sep 9 12:58:31 1999 +++ library.c Thu Sep 9 12:52:50 1999 @@ -1,11 +1,11 @@ /*****************************************************************************/ -char library_ID[] = "$Id: library.c,v 1.39 1998/01/08 12:50:36 srs Exp $"; +char library_ID[] = "$Id: library.c,v 1.1 1999/09/09 11:01:39 pubseq Exp pubseq $"; /* ** ** $RCSfile: library.c,v $ -** $Revision: 1.39 $ -** $Date: 1998/01/08 12:50:36 $ -** $Author: srs $ +** $Revision: 1.1 $ +** $Date: 1999/09/09 11:01:39 $ +** $Author: pubseq $ ** ** ** @@ -312,6 +312,38 @@ +/**API* LibIcaFileName ******************************************************** +** +** Returns the library file name. +** +** INPUT: library object [R] +** option: "info", "syntax", "structure" +** IMPLICIT: +** +** RETURNS: library file name stub if found +** NULL if the library name is unknown +*/ + +char *LibIcaFileName (SLBo *lib, char* option) +{ + char *r = lib->nam; + switch (tolower(option[1])) { + case 'n': { /* info */ + if (lib->itFile[0] != '\0') { + r = lib->itFile; + } + break; + } + case 't': { /* structure */ + if (lib->iFile[0] != '\0') { + r = lib->iFile; + } + break; + } + } + return r; +} + /**API* LibName *************************************************************** ** ** Returns the library name. @@ -434,7 +466,7 @@ else StrClear (&name); - strcpy (tmp, LibName (lib)); + strcpy (tmp, LibIcaFileName (lib, option)); SmEdit (tmp, SMxLOWCASE); StrSetS (&name, "SRSDB:"); StrAppS (&name, tmp); From owner-srs@net.bio.net Thu Sep 09 11:30:00 1999 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!netnews.com!newspeer.monmouth.com!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!not-for-mail From: Tim Cutts Newsgroups: bionet.software.srs Subject: Re: Bugfix for SRS 5.1 Date: 09 Sep 1999 13:19:23 +0100 (BST) Organization: Linux Unlimited Lines: 10 Message-ID: References: NNTP-Posting-Host: rrw1000.sel.cam.ac.uk X-Newsreader: trn 4.0-test70 (17 January 1999) Originator: timc@news.chiark.greenend.org.uk ([127.0.0.1]) I forgot to mention: After you apply the patch you need to run 'srsmake' to rebuild all your executables. 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Thank you From owner-srs@net.bio.net Sun Sep 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 Sep 1999 02:00:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199909190900.CAA22384@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 14-AUG-99) 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. -------------------------------------------------------- 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 -------------------------------------------------------------------- the UK-HGMP-Resource Centre (known as hgmp.mrc.ac.uk): ----------------------------------------------------- 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@hgmp.mrc.ac.uk. 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 majordomo@hgmp.mrc.ac.uk. 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 Please ask for help at biosci@hgmp.mrc.ac.uk 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. 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 Sep 20 01:10:00 1999 Path: biosci!sprint.ca!suehan From: suehan@sprint.ca ("Hong Qian") Newsgroups: bionet.software.srs Subject: protein expression Date: 19 Sep 1999 19:10:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 92 Sender: daemon@net.bio.net Distribution: world Message-ID: <007b01bd7fbe$f74eeae0$039294d1@hqian> NNTP-Posting-Host: net.bio.net This is a multi-part message in MIME format. ------=_NextPart_000_0078_01BD7F84.47F52260 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Do you have too many projects and limited time? If high level protein = expression is one of your goals, C&P Biotech is ready to help you with = sub-cloning and protein purification in E. coli. 1.. Sub-cloning, site-directed mutagenesis, large deletion and = insertion mutation. PRICE: US$ 500.00 per sample. 2.. Protein expression and purification based on GST or = histidine-tag fusion. 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------=_NextPart_000_0078_01BD7F84.47F52260-- From owner-srs@net.bio.net Tue Sep 21 15:33:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!join.news.pipex.net!pipex!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: tdeboer@hgmp.mrc.ac.uk Newsgroups: bionet.software.srs Subject: How to get around changing .i files while indexing offline Date: Tue, 21 Sep 1999 17:25:53 GMT Organization: MRC Human Genome Mapping Project Resource Centre Lines: 21 Message-ID: <19990921.17255300@lutetium.hgmp.mrc.ac.uk> NNTP-Posting-Host: lutetium.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable X-Trace: niobium.hgmp.mrc.ac.uk 937931208 17232 193.62.192.71 (21 Sep 1999 16:26:48 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 21 Sep 1999 16:26:48 GMT X-Priority: 3 (Normal) X-Newsreader: Mozilla/3.0 (compatible; StarOffice/5.1; Solaris Sparc) Hi, I'm having trouble with the indexing of my EMBL database. I would like to index the EMBL database offline, and would have to=20 change the embl.i files to reflect the adding of a few new .dat files.=20 But it looks like that screws up the retrieval process of the old=20 'live' EMBL database, since that now can't find the new files=20 offcourse. How do I get around changing and recompiling the .i files when I want=20 to both index the new database offline and still be able to retrieve=20 entries from the former release, without having to revert to using two=20 completely seperate macines ? Thanks, Thon de Boer HGMP From owner-srs@net.bio.net Wed Sep 22 08:27:00 1999 Path: biosci!newshost.lanl.gov!arclight.uoregon.edu!hammer.uoregon.edu!nntp.news.xara.net!xara.net!gxn.net!tank.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: How to get around changing .i files while indexing offline Date: 22 Sep 1999 10:20:38 +0100 Organization: The Sanger Centre Lines: 32 Message-ID: References: <19990921.17255300@lutetium.hgmp.mrc.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 937992031 7409 193.60.84.160 (22 Sep 1999 09:20:31 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 22 Sep 1999 09:20:31 GMT X-Newsreader: Gnus v5.5/Emacs 20.3 tdeboer@hgmp.mrc.ac.uk writes: > How do I get around changing and recompiling the .i files when I want=20 > to both index the new database offline and still be able to retrieve=20 > entries from the former release, without having to revert to using two=20 > completely seperate macines ? In general it is a problem, but for EMBL there is a solution. The SRS index files are on the FTP server at the EBI. You can simply FTP them over and make them live with the new embl.i. The instructions are a little out of date (these are the index files for the flat file version, but it still has a reference to 'GCG formatted files'). The README says they cannot be reallocated for GCG formatted databases. Not sure why - the EBI files used to be for GCG databases and I could reallocate them for flat files with "srsbuild -r embl" given a little care in updating the file names in embl.i. The accession number index has a long-standing bug that misses secondary accession numbers. I have a fixed embl.is file at Sanger but you would need to be careful about rebuilding the links if you reindex the accession numbers. srscheck misses the change and I had to relink by hand. -- ---------------------------------------------------------------------- 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 Thu Sep 23 07:49:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!easynet-tele!easynet.net!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: "Rodrigo Lopez" Newsgroups: bionet.software.srs Subject: Re: How to get around changing .i files while indexing offline Date: Thu, 23 Sep 1999 09:42:10 +0100 Organization: EBI- European Bioinformatics Institute Lines: 75 Message-ID: References: <19990921.17255300@lutetium.hgmp.mrc.ac.uk> NNTP-Posting-Host: pointy-haired-boss.ebi.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 938076131 3107 193.62.196.237 (23 Sep 1999 08:42:11 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 23 Sep 1999 08:42:11 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Hi, The instructions for using the SRS indices at the EBI have been updated. Peter is quite right in pointing out that they should work with the GCG formatted EMBL but EBI cannot take any responsibility if these don't work with your particular flavour of GCG, UNIX and most importantly, SRS. When doing the reallocating you can follow it's progress by doing: % getz -stat embl and you will see the action taken is 'reallocating' rather than 'indexing'. There is another way of achieving what you want: 1. Start a new UNIX session 2. If you know how to use $SRSOFFINX you simply use it. OR: Check you srsdb.i for or add/edit something like this: $libloc:[@EMBL_DB dir:"$dataRootF/embl/"] indexDir:"$dataRootS/srsindex/" offDir:"/ebi/services/ext/data/embl/"] offDir is the location of the new embl files you want to index. $SRSOFFINX is the location where you will store temporarily the index files. 3. Do an srscheck embl. 4. check the content of $SRSETC/srsupdate If everything is to your satisfaction you can start the indexing and continue to query the old embl database in the meantime. FYI: We will be providing indices for SRS6 in the near future. R:) Peter Rice wrote in message news:subaeqfxpy1.fsf@sanger.ac.uk... > tdeboer@hgmp.mrc.ac.uk writes: > > How do I get around changing and recompiling the .i files when I want=20 > > to both index the new database offline and still be able to retrieve=20 > > entries from the former release, without having to revert to using two=20 > > completely seperate macines ? > > In general it is a problem, but for EMBL there is a solution. > > The SRS index files are on the FTP server at the EBI. You can simply > FTP them over and make them live with the new embl.i. The instructions > are a little out of date (these are the index files for the flat file > version, but it still has a reference to 'GCG formatted files'). > > The README says they cannot be reallocated for GCG formatted databases. > Not sure why - the EBI files used to be for GCG databases and I could > reallocate them for flat files with "srsbuild -r embl" given a little > care in updating the file names in embl.i. > > The accession number index has a long-standing bug that misses > secondary accession numbers. I have a fixed embl.is file at Sanger but > you would need to be careful about rebuilding the links if you reindex > the accession numbers. srscheck misses the change and I had to relink > by hand. > > > > -- > ---------------------------------------------------------------------- > 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 Sep 24 08:14:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newsfeed.icl.net!newspeer.clara.net!news.clara.net!remarQ-uK!remarQ.com!supernews.com!tank.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!not-for-mail From: Tim Cutts Newsgroups: bionet.software.srs Subject: Re: How to get around changing .i files while indexing offline Date: 24 Sep 1999 10:06:19 +0100 (BST) Organization: Linux Unlimited Lines: 46 Message-ID: References: <19990921.17255300@lutetium.hgmp.mrc.ac.uk> NNTP-Posting-Host: rrw1000.sel.cam.ac.uk X-Newsreader: trn 4.0-test70 (17 January 1999) Originator: timc@news.chiark.greenend.org.uk ([127.0.0.1]) In article , Rodrigo Lopez wrote: >Hi, > >There is another way of achieving what you want: > >1. Start a new UNIX session >2. If you know how to use $SRSOFFINX you simply use it. >OR: Check you srsdb.i for or add/edit something like this: > > $libloc:[@EMBL_DB dir:"$dataRootF/embl/"] > indexDir:"$dataRootS/srsindex/" > offDir:"/ebi/services/ext/data/embl/"] > >offDir is the location of the new embl files you want to index. >$SRSOFFINX is the location where you will store temporarily the index files. > >3. Do an srscheck embl. > >4. check the content of $SRSETC/srsupdate > >If everything is to your satisfaction you can start the indexing and >continue to query the old embl database in the meantime. No, Rodrigo, that doesn't work, as he said in his initial posting, because the embl.i file has to be edited for the new divisions. This then means that even though you're building offline, the old inices will start returning the wrong entries, because the embl.i file has changed. You need to have an offline version o the database definition as well, and SRS does not have that. There are two solutions: 1) Have a parallel installation of SRS on the same machine which you use only for index building. You can then copy the index files across once its done, update the embl.i file in your online SRS, run srssection and hey presto. You do need to be very careful that the .i files are exactly the same on both installations. 2) Use the same scheme, but with completely separate machines. I believe this is supposed to be fixed in SRS 6, but for commercial sites like mine, buying a new faster machine is more cost-effective than upgrading SRS. Tim. From owner-srs@net.bio.net Fri Sep 24 14:08:00 1999 Path: biosci!newshost.lanl.gov!logbridge.uoregon.edu!newsfeed.icl.net!easynet-tele!easynet.net!tank.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: "Rodrigo Lopez" Newsgroups: bionet.software.srs Subject: Re: How to get around changing .i files while indexing offline Date: Fri, 24 Sep 1999 16:00:54 +0100 Organization: EBI- European Bioinformatics Institute Lines: 64 Message-ID: References: <19990921.17255300@lutetium.hgmp.mrc.ac.uk> NNTP-Posting-Host: pointy-haired-boss.ebi.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 938185255 6765 193.62.196.237 (24 Sep 1999 15:00:55 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 24 Sep 1999 15:00:55 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Oh Dear! The joys of working late. If was talking about SRS6.x. I'm sorry for the previous posting. However, a judicious use of the environment variable that determine where the index and icarus files are as well as building the srs section somewhere else can do the trick with SRS5.x. Thure and I did it here a while back during an emergency and it worked. It required quite a lot of cool (real sweat!) from my part to go through it :-) It can get quite complicated and this is indeed what has appeared 'transparently' in SRS6.x R:) Tim Cutts wrote in message news:xCy*c-S+n@news.chiark.greenend.org.uk... > In article , > Rodrigo Lopez wrote: > >Hi, > > > >There is another way of achieving what you want: > > > >1. Start a new UNIX session > >2. If you know how to use $SRSOFFINX you simply use it. > >OR: Check you srsdb.i for or add/edit something like this: > > > > $libloc:[@EMBL_DB dir:"$dataRootF/embl/"] > > indexDir:"$dataRootS/srsindex/" > > offDir:"/ebi/services/ext/data/embl/"] > > > >offDir is the location of the new embl files you want to index. > >$SRSOFFINX is the location where you will store temporarily the index files. > > > >3. Do an srscheck embl. > > > >4. check the content of $SRSETC/srsupdate > > > >If everything is to your satisfaction you can start the indexing and > >continue to query the old embl database in the meantime. > > No, Rodrigo, that doesn't work, as he said in his initial posting, > because the embl.i file has to be edited for the new divisions. 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