From owner-srs@net.bio.net Mon Oct 02 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!xlink.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: Retrieving features with SRS : the problem Date: 3 Oct 1995 09:16:24 GMT Organization: EMBL Lines: 25 Distribution: world Message-ID: <44qv18$e6o@lion.embl-heidelberg.de> References: <44b9th$kdv@rc1.vub.ac.be> NNTP-Posting-Host: falcon.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1S (X11; I; IRIX 5.3 IP20) To: gbottu@ben.vub.ac.be X-URL: news:44b9th$kdv@rc1.vub.ac.be gbottu@ben.vub.ac.be (Guy Bottu) wrote: >SRS allows to retrieve parts of sequences corresponding to features >mentioned in the documentation. However, it does not work entirely >satisfactorily : > >- with the WWW interface : if you select "sequenceFeatures" in the > pull-down menu of the QueryForm, SRS does generate separate entries > for each feature, but it contains the complete sequence, not just the > feature. this is true for single entries but not for the option "view complete entries" at the top of the entry listing - this will return only the fragments - we will improved the situation in the new WWW interface which will be available by the begin of next year thure -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany From owner-srs@net.bio.net Tue Oct 03 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!news.sprintlink.net!in2.uu.net!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!biotek11 From: rodrigol@biotek.uio.no (Rodrigo Lopez) Newsgroups: bionet.software.srs Subject: PDB Structures w/ SRS-WWW Date: Wed, 04 Oct 95 23:23:46 GMT Organization: EMBnet-Norway Lines: 78 Message-ID: <44ufol$m9d@hermod.uio.no> NNTP-Posting-Host: biotek11.uio.no X-Newsreader: News Xpress Version 1.0 Beta #3 Hello SRS fans (actaully this message is intented for the SRS-WWW managers), Here follow a suggestion on how to display PDB structures using SRS-WWW. I have used this method for quite sometime now and find it adequate for visualisation purposes. Presently there are two servers using this method and they are: http://bioslave.uio.no:8001/srs/srsc I will not post the name of the second server here as I don't know if the manager allows access to PDB outside of his site. I'm sure he will let us all know if he is an accessible point. ..Errr, and please don't bombard my server (modify yours!). Some PDB entries are very long and choke the networks. The first thing to do is to add the following CSH script, which I call 'showpdb' into your server's cgi-bin directory: ----------------------------------------------------------------------- #!/sbin/csh -f while ("$1" != "") set tst=`echo $argv[1] | tr '[A-Z]' '[a-z]'` shift echo Content-type: chemical/x-pdb; echo # the following contains the absolute path of where you store # the PDB distribution files cat /usr3/PDB/"$tst" end ------------------------------------------------------------------------ The second thing to do is to edit the hyperlink.sdl file in the 'odd' directory of the SRS installation. Look for the line that reads: #linkcall /id=%FETCH_PDB /call="%s" and change/add to: ------------------------------------------------------------------------ #linkcall /id=%FETCH_PDB ! /call="%s" /call="%s" ------------------------------------------------------------------------ Third, make a new call to 'srssection' and you should be setup to 'serve structures' to your users. In this way links to PDB from say, Prosite, PDBFinder, Swiss-prot, etc...will return the PDB entry such that the browser will be able to pass it on to an external application. A direct query to PDB will result in the server returning the actual PDB record. I personally recommend the use of Rasmol/Raswin from R. Sayle. for visualisation purposes. But users may use any PDB viewer they prefer (i.e. Kinemage, GEMM, Whatif, Atoms, depending on what kind of workstation (PC, MAC, UNIX) they have). For PC and MAC users the result of clicking on a PDB link within SRS-WWW should result in the WWW broswers (i.e. Mosaic and Netscape's latest versions) asking for saving the entry or configuring a viewer. This is fairly straght forward here so I won't go into it. On a UNIX box, the users .mailcap and/or mime.types file should contain for example: chemical/x-pdb; xterm -e /u2/RasMol2/rasmol -pdb %s If anyone can come up with suggestions and improvements to this please do so in this list. OKDK - Thats all folks!!! R:) From owner-srs@net.bio.net Wed Oct 04 23:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: Euphoria Tape...Try it with a Lover! Message-ID: <1995Oct4.150010.22596@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <44ts6u$8qk@globe.indirect.com> Date: Wed, 4 Oct 1995 15:00:10 GMT Lines: 15 Estascy@euphoria.com wrote: : The Euphoria Tape. I am astonished to see that audio databases become available. Please forward the sdl file, I want to link certain features into there! :-) Regards Reinhard -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| BioComputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-srs@net.bio.net Wed Oct 04 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!rodrigol From: rodrigol@biomaster.uio.no (Rodrigo Lopez) Newsgroups: bionet.software.srs Subject: Re: PDB Structures w/ SRS-WWW Date: 5 Oct 1995 09:56:44 GMT Organization: University of Oslo Lines: 37 Message-ID: <450a4s$p8@hermod.uio.no> References: <44ufol$m9d@hermod.uio.no> NNTP-Posting-Host: biomaster.uio.no X-Newsreader: TIN [version 1.2 PL2] Here follows a simple modificatiom to the showpdb csh script that should enable managers using the standard PDB distribution directories (i.e. storing entries in various directories) to use the approach I posted yesterday to get SRS-WWW to 'serve' structures to a PDBviewer. The original posting works if you have PDB in a single directory. ----------------------------------------------------------------------- #!/sbin/csh -f while ("$1" != "") set tst=`echo $argv[1] | tr '[A-Z]' '[a-z]'` shift echo Content-type: chemical/x-pdb; echo # The following contains the absolute path of where you store # the PDB distribution files. Uncomment the following line if # you have PDB in a single directory. # cat /usr3/PDB/"$tst" # # For PDB stored in various directories. Replace the period with # the absolute path (where the top PDB distribution directory is) # Could look somethin like this: # find /databases/PDB -name "$tst" -print -exec cat {}\; find . -name "$tst" -print -exec cat {}\; end ------------------------------------------------------------------------ R:) From owner-srs@net.bio.net Sun Oct 08 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!warwick!bham!bhamcs!news.ox.ac.uk!news From: Ewan Birney Newsgroups: bionet.software.srs Subject: Compression or discard? Date: 9 Oct 1995 16:19:47 GMT Organization: Oxford University Lines: 21 Message-ID: <45bi33$r7n@news.ox.ac.uk> NNTP-Posting-Host: nmrd.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP22) X-URL: news:bionet.software.srs Dear SRS-gurus Hmmm I am setting up SRS locally for myself here (good job on the installation instructions). I have swissprot and embl.dat databases here. Its getting quite large, and I wouldn't mind having a more paired down subset of, in particular the EMBL database (ie, I can discard all the author etc information). Is there any way of doing this inside SRS: or should I write a perl script that goes through each .dat file and simply removes the EMBL lines that I don't need? What does SRS need/not need in embl .dat and do I have to change some of the sdl stuff - what happens if SRS expects some line which I have removed from the .dat file? any comments? Pointers? help? thanks alot ewan birney From owner-srs@net.bio.net Sun Oct 08 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: Compression or discard? Date: 9 Oct 1995 19:31:56 GMT Organization: EMBL Lines: 32 Distribution: world Message-ID: <45btbc$a2g@lion.embl-heidelberg.de> References: <45bi33$r7n@news.ox.ac.uk> NNTP-Posting-Host: falcon.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1S (X11; I; IRIX 5.3 IP20) X-URL: news:45bi33$r7n@news.ox.ac.uk ewan, >Its getting quite large, and I wouldn't mind having a more paired >down subset of, in particular the EMBL database (ie, I can discard all >the author etc information). Is there any way of doing this inside SRS: >or should I write a perl script that goes through each .dat file and >simply removes the EMBL lines that I don't need? What does SRS need/not >need in embl .dat and do I have to change some of the sdl stuff - what >happens if SRS expects some line which I have removed from the .dat file? > it is safe to delete anything from embl except the ID line. If you have only SwissProt and EMBL then the link information (as is the default anyway) will be supplied by SwissProt...but this link utilizes the EMBL accession numbers - don't delete them! The SRS indexing system does not complain about missing data-fields but 'srscheck' will try to rebuilt missing indices - so you should outcomment all fields in embl.sdl except the ID field regards Thure ..almost forgot ...better use the Perl script for removing data-fields! -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany From owner-srs@net.bio.net Tue Oct 10 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Retrieving features with SRS : the problem (part 2!) Date: 11 Oct 1995 11:16:44 GMT Organization: Belgian EMBnet Node Lines: 17 Message-ID: <45g92s$51v@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be. X-Newsreader: TIN [version 1.2 PL2] If you use the srscurses or the srstk interface and you do a search in the features INVOLVING MULTPLE ITEMS (e.g. select SWISSPROT and put in the Features field DOMAIN & CYTOPLASMIC) you get a list of entries, but when you try to retrieve an entry, you get an empty page. It is however possible to make a link to another databank and, with srscurses, you can call the querymanager and a query of the type SQ1 > PARENT will retrieve correctly the complete sequences. Without doubt, the interfaces make errors in parsing the getz output, because the command : getz -td '[SWISSPROT-FTS:DOMAIN & CYTOPLASMIC | more does yield the features. There certainly is need for a next release of the srscurses/srstk software. Is it going to come ? Dr. Guy Bottu From owner-srs@net.bio.net Tue Oct 17 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!Norway.EU.net!nntp.uio.no!rodrigol From: rodrigol@bioslave.uio.no (Rodrigo Lopez) Newsgroups: bionet.software.srs Subject: Re: Retrieving features with SRS : the problem (part 2!) Date: 18 Oct 1995 17:41:31 GMT Organization: University of Oslo Lines: 30 Message-ID: <463e8b$5o1@hermod.uio.no> References: <45g92s$51v@rc1.vub.ac.be> NNTP-Posting-Host: bioslave.uio.no X-Newsreader: TIN [version 1.2 PL2] Guy Bottu (gbottu@ben.vub.ac.be) wrote: : If you use the srscurses or the srstk interface and you do a search in : the features INVOLVING MULTPLE ITEMS (e.g. select SWISSPROT and put : in the Features field DOMAIN & CYTOPLASMIC) you get a list of entries, : but when you try to retrieve an entry, you get an empty page. It is : however possible to make a link to another databank and, with srscurses, : you can call the querymanager and a query of the type : SQ1 > PARENT will retrieve correctly the complete sequences. : Without doubt, the interfaces make errors in parsing the getz output, : because the command : : getz -td '[SWISSPROT-FTS:DOMAIN & CYTOPLASMIC | more : does yield the features. : There certainly is need for a next release of the srscurses/srstk : software. Is it going to come ? : Dr. Guy Bottu It is indeed sad that this is happening with the present version of the interface...we are trying to complete excercises during courses in Trondheim and next week in Oslo...sadly, most of these require input of the type described above (ie: leucine & zipper)....and because of this, SRS is letting us down :-( Dear Gijs: Is there any chance of getting this fixed (soon!)? R:) From owner-srs@net.bio.net Wed Oct 18 23:00:00 1995 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: Retrieving features with SRS : the problem (part 2!) Date: 19 Oct 1995 12:37:56 GMT Organization: EMBL Lines: 39 Distribution: world Message-ID: <465gr4$a6j@lion.embl-heidelberg.de> References: <45g92s$51v@rc1.vub.ac.be> <463e8b$5o1@hermod.uio.no> NNTP-Posting-Host: kappa.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; OSF1 V2.0 alpha) To: rodrigol@bioslave.uio.no X-URL: news:463e8b$5o1@hermod.uio.no rodrigol@bioslave.uio.no (Rodrigo Lopez) wrote: >Guy Bottu (gbottu@ben.vub.ac.be) wrote: >: If you use the srscurses or the srstk interface and you do a search in >: the features INVOLVING MULTPLE ITEMS (e.g. select SWISSPROT and put >: in the Features field DOMAIN & CYTOPLASMIC) you get a list of entries, >: but when you try to retrieve an entry, you get an empty page. It is >: however possible to make a link to another databank and, with srscurses, >: you can call the querymanager and a query of the type >: SQ1 > PARENT will retrieve correctly the complete sequences. > >: There certainly is need for a next release of the srscurses/srstk >: software. Is it going to come ? > >It is indeed sad that this is happening with the present version of >the interface...we are trying to complete excercises during courses >in Trondheim and next week in Oslo...sadly, most of these require >input of the type described above (ie: leucine & zipper)....and because of >this, SRS is letting us down :-( > Gijs checked in fixes in yesterday ...and i worked hard to make a new release srs4.08 ...I tested the tcl clients and they seem to work with features now. if you want to get the fixes without installing SRS4.08 (has very few changes otherwise) just copy all *.tcl files from the srs/tcl directory good luck! regards thure -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany From owner-srs@net.bio.net Wed Oct 18 23:00:00 1995 Path: biosci!daresbury!usenet From: "M.P. Hilbers" Newsgroups: bionet.software.srs Subject: nrl_3d rel 20.0 Date: 19 Oct 1995 17:05:41 GMT Organization: SERC Daresbury Lab, Warrington, U.K. Lines: 17 Distribution: bionet Message-ID: <4660h5$kf3@mserv1.dl.ac.uk> NNTP-Posting-Host: s-crim1.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.2 IP17) X-URL: news:bionet.software.srs For those who want to index the new release (20) of nrl_3d: Entry 2AYH contains a species line of 276 characters, which makes srsbuild crash (at least my srsbuild). You may want to edit the database before indexing. I solved it differently by recompiling srsbuild with a new maximum length for the token string: I changed in parser.h #define PRSxXLSYM 132 /* max token string length */ to #define PRSxXLSYM 300 /* max token string length */ and rebuild srsbuild. I must admit that I don't know if this changes further affects SRS, but sofar it seems to work. Martin HIlbers From owner-srs@net.bio.net Wed Oct 18 23:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: IMPORTANT: BIOSCI miniFAQ Date: 19 Oct 1995 03:41:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 196 Sender: daemon@net.bio.net Distribution: world Message-ID: <199510190900.CAA10663@net.bio.net> This is a new "miniFAQ" 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/. Contents: -------- 1) What to do about "spams," i.e., junk mail, ads, etc. 2) Examples of subscribing and unsubscribing to the mailing lists. 3) How to access BIOSCI/bionet newsgroup archives. 4) The BIOSCI user address and research interest directory. 1) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups) and mailing lists. The same postings are distributed on both 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 newsgroups from about 95% of the spams that are being sent to date. This means 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. Unfortunately there are easy ways for determined spammers to override the moderation mechanism. We are working on new systems to provide access to our newsgroups over the WWW. These should be available soon, probably November 1995, and will allow you to use your Web browser to look at the news postings. While this 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. 2) 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. 3) How to access BIOSCI/bionet newsgroup archives. -------------------------------------------------- Back postings of all BIOSCI/bionet newsgroups can be found on the World Wide Web at URL http://www.bio.net/. There are several searchable newsgroup indices at this site. E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank (anything entered on the Subject: line is ignored). 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 Thu Oct 19 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!warwick!bham!bhamcs!news.ox.ac.uk!news From: Ewan Birney Newsgroups: bionet.software.srs Subject: SRS Gurus again Date: 20 Oct 1995 09:06:28 GMT Organization: Oxford University Lines: 21 Message-ID: <467oqk$evj@news.ox.ac.uk> NNTP-Posting-Host: nmrd.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP22) X-URL: news:bionet.software.srs After a mammoth srsbuild session on embl it died just before it finished (for reasons not due to srsbuild). Now - what do I do - I can't get it to srsbuild -c embl 'cause it can't find embl_id although the embl_id.ids and embl_id.idx exist in /index (these mean nothing to me... I am a SRS novice) What should you do when you have a half built index??? help appreciated - ;) ewan From owner-srs@net.bio.net Thu Oct 19 23:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: TRANSFAC format change Date: 20 Oct 1995 09:41:53 GMT Organization: The Sanger Centre Lines: 28 Message-ID: NNTP-Posting-Host: unst.sanger.ac.uk The format of the TRANSFAC database (file factor.dat) has changed slightly in release 2.4. The database cross-reference lines now are: DR EMBL: M55619; SCACE2; g. DR SwissProt: P21192; ACE2_YEAST. DR PIR: TWBYA2; TWBYA2. so the transfac.sdl file had to parse these as: linkseq = ('EMBL' ':' accno ) | ('PIR' ':' accno ) | ('SWISSPROT' ':' accno ); (note: ';' changed to ':' and "-" removed from "SWISS-PROT") -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr/ | England From owner-srs@net.bio.net Fri Oct 20 23:00:00 1995 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!news From: Frederic Achard Newsgroups: bionet.software.srs Subject: #function Date: 21 Oct 1995 17:16:31 GMT Organization: Infobiogen Lines: 19 Message-ID: <46b9tf$qv0@lovelace.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 1.1N (X11; I; SunOS 5.4 sun4d) X-URL: news:bionet.software.srs > #function /id=%F_SAVEDATEGB /name="BldSaveDateGenbank" > /args="(PRSoST *st, FILo *file)" /module=BUILD This part is taken from genbank.sdl and I cannot figure out how it works. The parser 'locus' extracts the locus and the date from the LOCUS field: > locus = name ~0-9~ ~a-zA-Z ~ ~0-9A-Z\-~ ; So what is the use (meaning) of /name= and /args= and /module= ? I try to mimic it. I srsssection'it but it fails when srsbuild'ing it I'd appreciate any help Thanx. Frederic. I am new to srs ebnf programs so pardon me if the question is dumb. Can't find any doc in srs to #function..... From owner-srs@net.bio.net Sun Oct 22 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!news From: Scott Rose Newsgroups: bionet.software.srs Subject: Re: SRS Gurus again Date: 23 Oct 1995 20:53:58 GMT Organization: Genetics Computer Group Lines: 16 Message-ID: <46gvd6$140s@news.doit.wisc.edu> References: <467oqk$evj@news.ox.ac.uk> NNTP-Posting-Host: 128.104.224.64 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; OSF1 V3.0 alpha) To: birney@molbiol.ox.ac.uk X-URL: news:467oqk$evj@news.ox.ac.uk Ewan Birney wrote: >After a mammoth srsbuild session on embl it died just before it >finished (for reasons not due to srsbuild). > >Now - what do I do - I can't get it to > > srsbuild -c embl > just run srscheck again ...it will recognize that some indices need to be compressed or rebuild and issue the appropriate srsbuild commands in the script thure From owner-srs@net.bio.net Tue Oct 24 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!tank.news.pipex.net!pipex!dispatch.news.demon.net!demon!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!infobiogen.fr!news From: Frederic Achard Newsgroups: bionet.software.srs Subject: (no subject) Date: 24 Oct 1995 18:56:26 GMT Organization: Infobiogen Lines: 63 Message-ID: <46jcsq$2ao@lovelace.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 1.1N (X11; I; SunOS 5.4 sun4d) To: fred X-URL: news:bionet.software.srs Hi, I am trying to index a new data bank for our srs server and I am not sure about the proper way to do so. My bank is a bank of links and an entry looks like " LNK vgl: 1 gdb-gbk link GDB_gene and Genbank_sequence " GO1 gdb: 118727 NPPA natriuretic peptide precursor A " GO2 gbk: M54951 HUMANFZ2 Human atrial natriuretic factor gene, 3' flank. " COM /score=0.56 /author=genXref v0.9 /date=24-Oct-1995 " // LNK is the link field GO1 and GO2 are genomic objects 1 and 2 COM are comments on that field And the identifier of a data bank object is made of a mnemonic (-3 letters, eg. gbk is Genbank,) a ':', a space and an unique id (uid). The main index should be on the number following "LNK vgl:" I want to have the following stuffs indexed: - the database-ids which are taken from LNK, GO1 and GO2 fields ('vgl: 1', 'gdb: 118727' and 'gbk: M54951') - keywords taken from GO1 and GO2 (but excluding the previous database-id) In genbank, I saw that two tokens are taken from the LOCUS field (locus name and date) but couldn't really figure out how this works. Does it work because \find="" on the #libformat of date or (and) because a function (f=@F_SAVEDATEGB) is called to transmogrify the date in the locus parser. By the way, how do I create my function. Just add the code in srsbuild.c and compile, section and update everything ??? I'd REALLY appreciate any help. A pointer on anything similar will do. I thank you in advance. Frederic. PS: we have a srs for development on our site. You can check what I have done so far at http://www.infobiogen.fr/srsdev/srsc/ in virgil. PS 2: sorry but the of my previous post was wrong. Hope it did not bother any of you. Does it explain why I got no response ;-) From owner-srs@net.bio.net Tue Oct 24 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!daresbury!bioftp.unibas.ch!infobiogen.fr!news From: Frederic Achard Newsgroups: bionet.software.srs Subject: splitting a field Date: 24 Oct 1995 19:00:40 GMT Organization: Infobiogen Lines: 66 Message-ID: <46jd4o$2ao@lovelace.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 1.1N (X11; I; SunOS 5.4 sun4d) To: fred X-URL: news:bionet.software.srs Hi, I am trying to index a new data bank for our srs server and I am not sure about the proper way to do so. My bank is a bank of links and an entry looks like " LNK vgl: 1 gdb-gbk link GDB_gene and Genbank_sequence " GO1 gdb: 118727 NPPA natriuretic peptide precursor A " GO2 gbk: M54951 HUMANFZ2 Human atrial natriuretic factor gene, 3' flank. " COM /score=0.56 /author=genXref v0.9 /date=24-Oct-1995 " // LNK is the link field GO1 and GO2 are genomic objects 1 and 2 COM are comments on that field And the identifier of a data bank object is made of a mnemonic (-3 letters, eg. gbk is Genbank,) a ':', a space and an unique id (uid). The main index should be on the number following "LNK vgl:" I want to have the following stuffs indexed: - the database-ids which are taken from LNK, GO1 and GO2 fields ('vgl: 1', 'gdb: 118727' and 'gbk: M54951') - keywords taken from GO1 and GO2 (but excluding the previous database-id) In genbank, I saw that two tokens are taken from the LOCUS field (locus name and date) but couldn't really figure out how this works. Does it work because \find="" on the #libformat of date or (and) because a function (f=@F_SAVEDATEGB) is called to transmogrify the date in the locus parser. By the way, how do I create my function. Just add the code in srsbuild.c and compile, section and update everything ??? I'd REALLY appreciate any help. A pointer on anything similar will do. I thank you in advance. Frederic. PS: we have a srs for development on our site. You can check what I have done so far at http://www.infobiogen.fr/srsdev/srsc/ in virgil. PS 2: sorry but the of my previous post was wrong. Hope it did not bother any of you. Does it explain why I got no response ;-) PS3: I forgot the subject on the previous one. So I repost it. Not sure if this is good Internet usage . From owner-srs@net.bio.net Tue Oct 24 22:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!EU.net!sun4nl!sci.kun.nl!caos.kun.nl!schaft From: schaft@caos.kun.nl (Gijs Schaftenaar) Subject: Re: Retrieving features with SRS : the problem (part 2!) Message-ID: <1995Oct25.160829.24801@caos.kun.nl> Sender: root@caos.kun.nl (System PRIVILEGED Account) Nntp-Posting-Host: cammsg4.caos.kun.nl Organization: CAOS/CAMM References: <45g92s$51v@rc1.vub.ac.be> <463e8b$5o1@hermod.uio.no> Date: Wed, 25 Oct 1995 16:08:29 GMT Lines: 41 I already posted this message a few days ago on bionet.software.srs, but I am not sure this got through, so here it is again. About a bug in the srscurs/srstk/srsctk interfaces. The bug occurs when using multiple words in the feature field like: swissprot-features:domain & cytoplasmic To fix this bug, change in the files srscurs.tcl, srstk.tcl and srsctk.tcl: In proc DoQuery: old: set Ft($SetName) "$Features" new: set Ft($SetName) "$Features" regsub -all {\ } $Ft($SetName) {} Ft($SetName) regsub -all {\&} $Ft($SetName) {\\&} Ft($SetName) Regards Gijs +----------------------------+-----------------------------------+ Gijs Schaftenaar, Drs. | CAOS/CAMM Center Email: schaft@caos.kun.nl | University of Nijmegen URL : http://www.caos.kun.nl/staff/schaft.html Tel. : +31 80 65 33 69 | Toernooiveld 1 Fax : +31 80 65 29 77 | 6525 ED Nijmegen, The Netherlands +-------- CAOS/CAMM is the Dutch National Node in EMBnet --------+ -- +----------------------------+-----------------------------------+ Gijs Schaftenaar, Drs. | CAOS/CAMM Center Email: schaft@caos.kun.nl | University of Nijmegen URL : http://www.caos.kun.nl/staff/schaft.html From owner-srs@net.bio.net Wed Oct 25 22:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: srs and gcg 8.1 sequence databases Date: 26 Oct 1995 20:05:50 GMT Organization: University of Oslo Lines: 16 Message-ID: <46opmu$5lo@hermod.uio.no> NNTP-Posting-Host: bioslave.uio.no Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP22) X-URL: news:bionet.software.srs for all who wish to run the native srs with sequence databases of gcg 8.1: edit the file odd/srsgeneral.sdl and modify the definition of "GCGSEQ_FILE" to the following #filetype /ID=%GCGSEQ_FILE /typename=seq /maxline=20000 /begstr=">>>>" /advance=0 /exitstr=">>>>" /seqtype=gcg8_1 the seqtype "gcg8_1" makes sure that the split sequences (>350000bp) are treated correctly. regards thure etzold From owner-srs@net.bio.net Thu Oct 26 22:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!jecop From: jecop@ebi.ac.uk (Jeroen Coppieters) Subject: patent references in EMBL Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Fri, 27 Oct 1995 15:21:37 GMT Organization: European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 52 We have been adding sequences from patents to EMBL over the last year. These have a reference of the form: RN [1] RP 1-51 RA ; RT "DNA EXPRESSION SYSTEMS BASED ON ALPHAVIRUSES"; RL Patent number WO9210578-A/26, 25-JUN-1992. XX ... Which was not parsed and terefor not searchable. I corrected the parser in embl.sdl old: ---- reference = ? ref | {~ ~ }; ref = ~A-Za-z .\-_~ ~0-9~ ':' ~0-9~ '-' ~0-9~ '(' ~0-9~ ')'; ----- new: ----- reference = ? patent | ref | {~ ~ }; ref = ~A-Za-z .\-_~ ~0-9~ ':' ~0-9~ '-' ~0-9~ '(' ~0-9~ ')'; patent = 'PATENT NUMBER' ~A-Z0-9\-/~ ',' ~0-9A-Z\-~ '.'; ----- This now allows queries like getz '[embl-ref: patent*]' getz '[embl-ref: patent*] and [embl-ref: wo921*]' Similar queries can be performed in our WWW and SRS-FTP interfaces Jeroen Jeroen -- ============================================================== . O . Jeroen Coppieters . O O o O . Software Support O O O O *o O O Jeroen.Coppieters@embl-ebi.ac.uk O O O O( *o )O O (or jecop@ebi.ac.uk) )O O O O o* O O( ++44 1223 494422 O O O O( o* )O O )O O O O *o O O( EMBL Outstation EBI O O O O( *o )O O (European Bioinformatics Institute) )O @ O O o* O O( Hinxton Hall O O O( o* )O(' Hinxton ` O( *o O ' Cambridge CB10 1RQ ` O ' UK http://www.ebi.ac.uk ============================================================== From owner-srs@net.bio.net Sun Oct 29 22:00:00 1995 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!chi-news.cic.net!simtel!swidir.switch.ch!scsing.switch.ch!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: NRSub Release 6 (from Guy Perriere) Date: 30 Oct 1995 15:08:47 GMT Organization: EMBL Lines: 58 Distribution: world Message-ID: <472ppv$4fd@lion.embl-heidelberg.de> NNTP-Posting-Host: falcon.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1S (X11; I; IRIX 5.3 IP20) X-URL: news:bionet.software.srs NRSub Release 6 (October 1995) The release 6 of NRSub (the Non-Redundant Bacillus subtilis data base) is now available through anonymous FTP at URLs: ftp://biom3.univ-lyon1.fr/pub/nrsub/ or ftp://ftp.nig.ac.jp/pub/db/nrsub/ It is also possible to access NRSub through two World-Wide Web servers located at URLs: http://acnuc.univ-lyon1.fr/nrsub/nrsub.html or http://ddbjs4h.genes.nig.ac.jp/ The distribution includes: - The flat version of NRSub in EMBL format (file NRSub.dat or NRSub.dat.Z). - The NRSub database under ACNUC and the sources of the query program for line mode use (file NRSub.r6.tar.Z). - The binaries of the graphical interface for browsing an ACNUC database (files query_win.*.Z). Query_win.SUN file is for Sun under SunOS, query_win.SOL is for Sun under Solaris, query_win.RS6000 is for IBM RISC, query_win.ALPHA is for DEC Alpha, and query_win.SGI is for Silicon Graphics. NRSub release 6 contains a total of 245 contigs (62 composite) All these sequences are chromosomal (plasmidic sequences are removed) and totalize 1,483,324 bp. This represents approxi- matively 35.6% of the entire Bacillus subtilis chromosome consisting of about 4,165 kbp. These sequences contain 1334 CDS (534 ORFs), 72 tRNAs and 27 rRNAs. Also, 483 bibliographic references can be accessed. Guy Perriere Laboratoire de Biometrie, Genetique et Biologie des Populations, URA CNRS 2055 Universite Claude Bernard - Lyon 1 43, bd. du 11 Novembre 1918 69622 Villeurbanne Cedex France Email: perriere@biomserv.univ-lyon1.fr -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany