From owner-srs@net.bio.net Tue Sep 03 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Sabino Liuni Newsgroups: bionet.software.srs Subject: patch for Tcl/tk interface for SRS4.08 Date: 4 Sep 1996 13:25:30 +0100 Lines: 199 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <50jsfq$d78@mserv1.dl.ac.uk> X-Sender: sabino@area.ba.cnr.it (Unverified) Original-To: bio-srs@dl.ac.uk Hi folks, here I include the patch for TCl/tk interface for SRS 4.08. We have installed the Tcl/tk interface for SRS4.08 on a Alpha running OSF/1 and we have experienced some problems (running Tcl 7.4 and Tk 4.1). We have realized a patch for the following problems: 1) The sequence selection in the main box now works even if there are more than one set displayed. In the original release, when a user selects a set in the list box, the script tries to handle a multiple selection of all the sets included between the previous selected set and the current one, producing a Tcl interpreter error ("Error: expected integer but got 'something wrong..' ") 2) When a user wants to combine multiple sets, the script has now the capability to warn the user if he/she tries to combine identical sets. Attached to this mail, you will find the patch to be applied to srstk.tcl for the above modifications (patch -c srstk.tcl patchfile). For additional info, feel free to contact Massimo Ianigro (e_mail: massimo@area.ba.cnr.it) or Flavio Licciulli (e-mail:flavio@area.ba.cnr.it. Best regards Sabino Liuni ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dr. Sabino LIUNI Area di Ricerca CNR ^ Administrator for the Via Amendola 166/5 ^ Italian EMBnet Node 70126 Bari (Italy) ^ tel. +39-80-5482176/5482130 ^ Fax. +39-80-5484467 ^ ^ E_mail:sabino@area.ba.cnr.it ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ OPEN YOUR EYES TO THE WORLD OF BIOCOMPUTING ^ ---------------------------------------------------------- *** CUT HERE *** CUT HERE *** CUT HERE *** *** srstk.tcl Fri Aug 2 18:55:10 1996 --- srstk.tcl.modified Fri Aug 2 18:54:36 1996 *************** *** 139,146 **** -bd $Bwi -command \ { set setname [SelSet .query.qhist.fr.list] if {$setname != ""} { ! DoComb $setname } } button .query.qhist.butt.del -text "Delete Set" -bg $Bcol -bd $Bwi \ --- 139,147 ---- -bd $Bwi -command \ { set setname [SelSet .query.qhist.fr.list] + set selectedentry [.query.qhist.fr.list curselection] if {$setname != ""} { ! DoComb $setname $selectedentry } } button .query.qhist.butt.del -text "Delete Set" -bg $Bcol -bd $Bwi \ *************** *** 182,188 **** set selcomm "selection set" } bind .query.qhist.fr.list \ ! "%W $selcomm \[%W nearest %y\] ;SelField .mbar.fields.menu \$SetDbs(\[SelSet .query.qhist.fr.list\])" } --- 183,189 ---- set selcomm "selection set" } bind .query.qhist.fr.list \ ! "%W selection clear 0 \[%W size\]; %W $selcomm \[%W nearest %y\] \[%W nearest %y\] ;SelField .mbar.fields.menu \$SetDbs(\[SelSet ..query.qhist.fr.list\])" } *************** *** 1329,1335 **** -command "DoQuery Group $group \[MakeSetName Group $group\]" button $w.query.buts.clear -text "Clear Query Form" -bg $BQFcol \ -command "ClearForm \"$GFLD($group)\"" ! button $w.query.buts.cancel -text "Cancel" -bg $BQFcol \ -command "destroy $w" pack $w.query.buts.submit $w.query.buts.clear $w.query.buts.cancel \ -side left -padx 2m -pady 2m --- 1330,1336 ---- -command "DoQuery Group $group \[MakeSetName Group $group\]" button $w.query.buts.clear -text "Clear Query Form" -bg $BQFcol \ -command "ClearForm \"$GFLD($group)\"" ! button $w.query.buts.cancel -text "Close" -bg $BQFcol \ -command "destroy $w" pack $w.query.buts.submit $w.query.buts.clear $w.query.buts.cancel \ -side left -padx 2m -pady 2m *************** *** 1478,1484 **** # # Combine Sets # ! proc DoComb {setname} { global coperators copsbitmaps srs_bitmaps BQFcol global SetNames Expression --- 1479,1485 ---- # # Combine Sets # ! proc DoComb {setname selectedentry} { global coperators copsbitmaps srs_bitmaps BQFcol global SetNames Expression *************** *** 1495,1501 **** $w.topfr.fr.list insert end $Expression($set) } ! bind $w.topfr.fr.list "AddCombQuery $setname" frame $w.topfr.opfr -width 3c -height 4c -bd 4 -relief groove pack $w.topfr.opfr -side left -padx 2m -pady 2m if {[info exists srs_bitmaps]} { --- 1496,1502 ---- $w.topfr.fr.list insert end $Expression($set) } ! bind $w.topfr.fr.list "AddCombQuery $setname $selectedentry" frame $w.topfr.opfr -width 3c -height 4c -bd 4 -relief groove pack $w.topfr.opfr -side left -padx 2m -pady 2m if {[info exists srs_bitmaps]} { *************** *** 1520,1526 **** frame $w.botfr -width 5c -height 2c -bd 4 -relief groove pack $w.botfr -side bottom -fill x -padx 2m -pady 2m button $w.botfr.accept -text "Accept" -bg $BQFcol \ ! -command "AddCombQuery $setname" pack $w.botfr.accept -side left -fill x -padx 2m -pady 2m button $w.botfr.cancel -text "Cancel" -bg $BQFcol -command \ "destroy $w; .query.qhist.butt.linkset configure -state normal" --- 1521,1527 ---- frame $w.botfr -width 5c -height 2c -bd 4 -relief groove pack $w.botfr -side bottom -fill x -padx 2m -pady 2m button $w.botfr.accept -text "Accept" -bg $BQFcol \ ! -command "AddCombQuery $setname $selectedentry" pack $w.botfr.accept -side left -fill x -padx 2m -pady 2m button $w.botfr.cancel -text "Cancel" -bg $BQFcol -command \ "destroy $w; .query.qhist.butt.linkset configure -state normal" *************** *** 1565,1574 **** RedoQSet $setname } ! proc AddCombQuery {firstset} { global COpSel SetNames Expression Ft SetType SetDbs dogetz set secondset [SelSet .combSet.topfr.fr.list] if {$secondset == ""} {return} set setname [MakeSetName Combine {}] --- 1566,1582 ---- RedoQSet $setname } ! proc AddCombQuery {firstset selectedentry} { global COpSel SetNames Expression Ft SetType SetDbs dogetz + + set secondset [SelSet .combSet.topfr.fr.list] + + if {$firstset == $secondset} { + DoConsole "You have already selected this set ($secondset); Please choose another one" + return + } if {$secondset == ""} {return} set setname [MakeSetName Combine {}] *************** *** 2459,2464 **** --- 2467,2473 ---- listbox $w.fr.list -relief raised -selectmode single \ -yscrollcommand "$w.fr.scrolly set" \ -xscrollcommand "$w.fr.scrollx set" + if {$oldTK} {tk_listboxSingleSelect $w.fr.list} scrollbar $w.fr.scrolly \ -command "$w.fr.list yview" From owner-srs@net.bio.net Sun Sep 08 23:00:00 1996 Path: biosci!CCR.DSI.UANL.MX!pearl From: pearl@CCR.DSI.UANL.MX ("Dr. Paul R.Earl") Newsgroups: bionet.software.srs Subject: Biomx-----Call for papers Date: 9 Sep 1996 07:42:24 -0700 Organization: UANL Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <323449A4.55A9@ccr.dsi.uanl.mx> NNTP-Posting-Host: net.bio.net Please see HomePage by entering Biomx under Yahoo search. It is HTTP://WWW.UANL.MX/BIOMX Very interested in software for teaching and can cooperate to change various into Spanish. Example: VENN (diagram) which includes a game by Univ of Arizona seems a better teacher than I am. Thank you, Paul R Earl From owner-srs@net.bio.net Tue Sep 17 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!lll-winken.llnl.gov!usenet From: Chris Barry Newsgroups: bionet.software.srs Subject: what is srs? Date: Wed, 18 Sep 1996 13:20:39 -0700 Organization: Lawrence Livermore National Lab Lines: 3 Message-ID: <32405997.7203BB56@llnl.gov> NNTP-Posting-Host: mackiller.llnl.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; Linux 1.1.72 i486) what is srs? Thanks in advance. Chris From owner-srs@net.bio.net Wed Sep 18 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 Sep 1996 02:00:40 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199609190900.CAA19673@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-srs@net.bio.net Wed Sep 18 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!news-peer.sprintlink.net!www.nntp.primenet.com!nntp.primenet.com!cam-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!newsfeed.internetmci.com!in3.uu.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: Michele Clamp Newsgroups: bionet.software.srs Subject: embl48 - no go Date: Thu, 19 Sep 1996 14:05:15 +0100 Organization: University of Oxford Lines: 25 Message-ID: <3241450B.41C6@bioch.ox.ac.uk> NNTP-Posting-Host: speed.biop.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX64 6.2 IP28) Hi, I'm using SRS4.04 on IRIX6.2 and am having problems with indexing embl 48. It seems to go through the motions of building the indices but when I do a srscheck I get: e__indexwrongversion, invalid index can't open index "SRSINX:embl_id.idx" with version 0 ...should be 1001... Any ideas? What's this version 0 and 1001? version of what? Do I have to change a maximum ID parameter somewhere? embl_id.idx is empty by the way. Many thanks M. -- Michele Clamp email: michele@bioch.ox.ac.uk Lab. of Molecular Biophysics phone: 01865 275 369 University of Oxford Fax: 01865 275 182 Oxford, UK. From owner-srs@net.bio.net Thu Sep 19 23:00:00 1996 Path: biosci!news.Stanford.EDU!nntp-hub2.barrnet.net!cpk-news-feed2.bbnplanet.com!cpk-news-hub1.bbnplanet.com!www.nntp.primenet.com!nntp.primenet.com!news.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!demos!Gamma.RU!srcc!Radio-MSU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: Re: what is srs? Date: 20 Sep 1996 11:01:38 GMT Organization: EMBL Heidelberg Lines: 19 Distribution: world Message-ID: <51ttii$n5@lion.embl-heidelberg.de> References: <32405997.7203BB56@llnl.gov> NNTP-Posting-Host: shag.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12IS (X11; I; IRIX 5.3 IP22) X-URL: news:32405997.7203BB56@llnl.gov SRS stands for Sequence Retrieval System. Basically it is an indexing and retrieval system for biological sequence databanks. It can be used for any databank which are in ascii format. You can find more doc in the new release... Yes it needs an introduction page.... http://kappa.embl-heidelberg.de:8000/srs/man/srsman.html Chenna Ramu =============================================================== Ramu C | EMBL E-mail: chenna@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 356229 (Res) | 69012 Heidelberg Fax: (49) 6221 387517 | Germany http://www.embl-heidelberg.de/~chenna/ ------------------------------------------------------------- From owner-srs@net.bio.net Tue Sep 24 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!nntp.primenet.com!news.sgi.com!esiee.fr!jussieu.fr!univ-angers.fr!ciril.fr!usenet From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software.srs Subject: Re: We want to help you to market your great software (which nobody knows about) Date: 25 Sep 1996 07:47:34 GMT Organization: IGBMC Lines: 29 Message-ID: <52ao2m$irq@arcturus.ciril.fr> References: <529ta2$ksr@news.inforamp.net> NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.6 In-Reply-To: <529ta2$ksr@news.inforamp.net> To: smi@inforamp.net (Software Matchmakers Inc) In article <529ta2$ksr@news.inforamp.net>, smi@inforamp.net (Software Matchmakers Inc) writes: >We want to help you to market your great software >(which nobody knows about) > >We would like to hear from anyone who thinks they have produced really >good, useful software (for any system, application type) and needs help >to market it. > >If interested, please e-mail smi@inforamp.net Of course, only one guy knows something about SRS, and there is a bionet newsgroup only to make jokes about a programme that noone uses... What kind of company can send such posts? They really don't know anything about Internet, so they are completely incompetent in extending a market. Hey Thure, keep SRS free, I will pay you a beer next time we are in Heidelberg! Francois. P.S.: Of course, one for Peter too... -- Francois Jeanmougin Service de bioinformatique / bioinformatics service IGBMC BP 163 67404 Illkirch France tel : (33) 88 65 32 71 e-mail : jeanmougin@igbmc.u-strasbg.fr "Tout ca m'est tergal, qu'il laine ou qu'il chandail" (STTELLLA) From owner-srs@net.bio.net Tue Sep 24 23:00:00 1996 Path: biosci!rutgers!news.sgi.com!www.nntp.primenet.com!nntp.primenet.com!cpk-news-hub1.bbnplanet.com!newsfeed.internetmci.com!in1.uu.net!ott.istar!istar.net!tor.istar!east.istar!news.inforamp.net!news From: smi@inforamp.net (Software Matchmakers Inc) Newsgroups: bionet.software.srs Subject: We want to help you to market your great software (which nobody knows about) Date: 25 Sep 1996 00:10:42 GMT Organization: Software Matchmakers Inc Lines: 9 Message-ID: <529ta2$ksr@news.inforamp.net> NNTP-Posting-Host: ts45-15.tor.istar.ca X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] We want to help you to market your great software (which nobody knows about) We would like to hear from anyone who thinks they have produced really good, useful software (for any system, application type) and needs help to market it. If interested, please e-mail smi@inforamp.net Thank You. ! From owner-srs@net.bio.net Wed Sep 25 23:00:00 1996 Path: biosci!agate!howland.erols.net!news-peer.gsl.net!news.gsl.net!portc01.blue.aol.com!newsstand.cit.cornell.edu!news.acsu.buffalo.edu!dsinc!lebanet!alpha.comsource.net!news.atw.fullfeed.com!online.dct.com!usenet From: "Tim McNicoll" Newsgroups: bionet.software.srs Subject: Proximity Software? Date: 25 Sep 1996 23:02:10 GMT Organization: Tim Lines: 11 Message-ID: <01bbab35$4bcf16e0$46b91dcc@Pmcnic> NNTP-Posting-Host: gbol40.dct.com Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Internet News 4.70.1155 Has anyone ever heard of "Proximity"? It's supposed to be some sort of Sales Person tracking package. One of it's features is that you can bring up an map of the United States and color-code each state according to which Sales Person is assigned to it. That is only one of it's features. It may not even be called Proximity. The manufacturer may have "Proximity" in it's name. I would appreciate any help anyone can give. Tim From owner-srs@net.bio.net Thu Sep 26 23:00:00 1996 Path: biosci!CSB0.IPC.PKU.EDU.CN!owner From: owner@CSB0.IPC.PKU.EDU.CN (Lists Owner) Newsgroups: bionet.software.srs Subject: welcome to sbl Date: 27 Sep 1996 03:56:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 49 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net ********** Welcome to the Structural Biology List! ********** Structural biology has already drawn much attention: it opens the door to a new era of biology. We announce here that a mailing list for structural biologists has been created. It will bring biologists/chemists/pharmacists all across the globe together to a new electronic frontier. The list server locates at the Institute of Physical Chemistry, Peking University, Beijing, China. We send this mail to invite your membership. The suggested topics of this mailing list include: o Macromolecular crystallography o NMR and other spectroscopies o Molecular modeling and design o Structure-based drug design and QSAR o Bioinformatics o Theoretical and computational biology To subscribe, you only need to send a short mail to owner@ipc.pku.edu.cn like this, "please add me to the SBL ..." while stating your name, title, e-mail, address, country and academic interests. Or you can save your time by filling out the following form and send it back to owner@ipc.pku.edu.cn. No fee and no restriction to subscribe. --------------- Structural Biology Mailing List -------------- ---------------------- Membership Form ---------------------- Name: Title: Address: Country: E-mail: Academic interests: -------------------------------------------------------------- Please forward this message to your friends as many as possible. Thank you for concern. Prof. Luhua Lai Institute of Physical Chemistry Peking University, Beijing, P.R.China From owner-srs@net.bio.net Mon Sep 30 23:00:00 1996 Path: biosci!agate!howland.erols.net!news-peer.gsl.net!news.gsl.net!nntp.coast.net!fu-berlin.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: embl48 - no go Date: Tue, 01 Oct 1996 12:57:35 +0200 Organization: EMBL Lines: 43 Distribution: world Message-ID: <3250F91F.41C6@embl-heidelberg.de> References: <3241450B.41C6@bioch.ox.ac.uk> 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 3.0 (X11; I; OSF1 V2.0 alpha) To: Michele Clamp Michele Clamp wrote: > > Hi, > > I'm using SRS4.04 on IRIX6.2 and am having problems with indexing embl > 48. It seems to go through the motions of building the indices but when > I do a srscheck I get: > > e__indexwrongversion, invalid index > can't open index "SRSINX:embl_id.idx" with version 0 ...should be > 1001... > > Any ideas? What's this version 0 and 1001? version of what? Do I have > to change a maximum ID parameter somewhere? > > embl_id.idx is empty by the way. > this error message you get when the index is an empty file. So something must have happened during the index building - either a crash or the input files were empty. You can use the -d flag for embl to see if the parser finds any strings in the input to put into the index so try srsbuild -d embl or srsbuild -d embl -f id to specifically test the ID field since it is the one that remained empty 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 Mon Sep 30 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!not-for-mail From: claude@lovelace.infobiogen.fr (Claude Scarpelli) Newsgroups: bionet.software.srs,embnet.general Subject: SRS will soon stop working :-) Date: 1 Oct 1996 13:13:06 +0200 Organization: GIS INFOBIOGEN, 7 rue Guy Moquet BP8, 94801 VILLEJUIF, France Lines: 85 Message-ID: <52quc2$15t@lovelace.infobiogen.fr> Reply-To: bioinfo@infobiogen.fr NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit We have noticed that most (all ?) SRS WWW sites around the world are configured such in a way that they are not compatible with the emergence of WWW cache. When the browser's client is configured to use a WWW cache, the SRS queries issued by the user may be processed with another client parameters. Here is an example: an SRS session usually begin with (BEN site is used as an example): GET http://ben.vub.ac.be/srs/srsc which retrieve the main SRS page. On the server side, the wgetz program has been run. To keep the session context, it creates a temporary file whose name contains the time and the IP address of the client. This filename is propagated to the form sent to the user as a hidden field. Therefore it is critical that a different file is created for each different user. Unfortunately, this may not be the case a WWW cache is used. The former URL does not contain any magic information (neither explicit) to tell the cache to NOT cache the document. So there is a strong probability (we have easily reproduced it) that the document received (http://ben.vub.ac.be/srs/srsc) by the user has been cached by the WWW cache, resulting in: 1) the document (the hidden field used to retrieve the context) contains context information relevant to another user (actually the one for which a cache miss occurred) 2) wgetz has not been run on the server, so no context for this particular user has been created. Therefore, in case the SRS WWW sites remain configured as they are currently, users are going to face more and more difficulties to access SRS services. How can it be fixed ? 1) configure the WWW cache to NOT cache URL containing srs/srsc. Not practicable, since user may not have enough authority to modify the configuration of the cache they are using. 2) Configure the SRS site in such a way that the magic strings /cgi-bin/ appear in each URL. WWW cache never caches a document when the URL contains this magic string. 3) Have wgetz send a protocol element (Pragma: no-cache) with each documents (especially the very first one). Cache will honor this information by not caching the document. Of course, it requires modification on the wgetz source code. We will ask the author to proceed this way, since it is the best way to communicate with a WWW cache At our site we could only apply the second solution, with the help of the SRS documentation which gives you all the information to modify the SRS WWW URL. This is why the SRS WWW server at INFOBIOGEN can be reached at the following URL: http://www.infobiogen.fr/srs/cgi-bin/srsc We strongly encourage the SRS source maintainer to implement the solution 3 discussed above, at least in the next release. In the maeantime, we urge every SRS WWW site to consider modifying their configuration. Claude Scarpelli -- Jean-Marc Plaza -- INFOBIOGEN claude@infobiogen.fr plaza@infobiogen.fr bioinfo@infobiogen.fr -- ------------------------------------------------------------------------------ Claude Scarpelli | Defenestrate: to exit a window INFOBIOGEN ::= INFOrmatique appliquée à | onscreen. (Time International l'étude des BIOmolécules et des GÉNomes | Vol 146, No. 20, Nov 13, 1995) From owner-srs@net.bio.net Mon Sep 30 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!EU.net!Norway.EU.net!nntp.uio.no!nntp.zit.th-darmstadt.de!voskovec.radio.cz!univ-angers.fr!jussieu.fr!infobiogen.fr!not-for-mail From: claude@lovelace.infobiogen.fr (Claude Scarpelli) Newsgroups: bionet.software.srs,embnet.general Subject: Re: SRS will soon stop working :-) Date: 1 Oct 1996 22:48:12 +0200 Organization: GIS INFOBIOGEN, 7 rue Guy Moquet BP8, 94801 VILLEJUIF, France Lines: 16 Message-ID: <52s02c$37t@lovelace.infobiogen.fr> References: <52quc2$15t@lovelace.infobiogen.fr> <52r5ha$s89@winx03.informatik.uni-wuerzburg.de> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit In article <52r5ha$s89@winx03.informatik.uni-wuerzburg.de>, Cornelius Krasel wrote: > >4) Let the http server in question add a Last-Modified-Since: header > to its information. > Probably better: let the server add an Expires: Jan 1 1970 header. -- ------------------------------------------------------------------------------ Claude Scarpelli | Defenestrate: to exit a window INFOBIOGEN ::= INFOrmatique appliquée à | onscreen. (Time International l'étude des BIOmolécules et des GÉNomes | Vol 146, No. 20, Nov 13, 1995) From owner-srs@net.bio.net Mon Sep 30 23:00:00 1996 Path: biosci!agate!howland.erols.net!EU.net!Norway.EU.net!nntp.uio.no!nntp.zit.th-darmstadt.de!fu-berlin.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs,embnet.general Subject: Re: SRS will soon stop working :-) Date: Tue, 01 Oct 1996 21:30:58 +0200 Organization: EMBL Lines: 24 Distribution: world Message-ID: <32517172.2781@embl-heidelberg.de> References: <52quc2$15t@lovelace.infobiogen.fr> <52r5ha$s89@winx03.informatik.uni-wuerzburg.de> 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 3.0 (X11; I; OSF1 V2.0 alpha) To: Cornelius Krasel Cornelius Krasel wrote: > > Claude Scarpelli (claude@lovelace.infobiogen.fr) wrote: > [snip] > > > How can it be fixed ? > > 4) Let the http server in question add a Last-Modified-Since: header > to its information. > I don't quite get it - could you please send more details. I think Claude's solution with the /cgi-bin/ in the URL can be realized for version 5 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 Mon Sep 30 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!harbinger.cc.monash.edu.au!nntp.coast.net!howland.erols.net!EU.net!Norway.EU.net!nntp.uio.no!nntp.zit.th-darmstadt.de!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!uni-erlangen.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software.srs,embnet.general Subject: Re: SRS will soon stop working :-) Followup-To: bionet.software.srs,embnet.general Date: 1 Oct 1996 13:15:21 GMT Organization: University of Wuerzburg, Germany Lines: 29 Message-ID: <52r5ha$s89@winx03.informatik.uni-wuerzburg.de> References: <52quc2$15t@lovelace.infobiogen.fr> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Claude Scarpelli (claude@lovelace.infobiogen.fr) wrote: [snip] > How can it be fixed ? > > 1) configure the WWW cache to NOT cache URL containing srs/srsc. Not > practicable, since user may not have enough authority to modify > the configuration of the cache they are using. > > 2) Configure the SRS site in such a way that the magic strings > /cgi-bin/ appear in each URL. WWW cache never caches a document > when the URL contains this magic string. > > 3) Have wgetz send a protocol element (Pragma: no-cache) with each > documents (especially the very first one). Cache will honor this > information by not caching the document. Of course, it requires > modification on the wgetz source code. We will ask the author to > proceed this way, since it is the best way to communicate with a > WWW cache 4) Let the http server in question add a Last-Modified-Since: header to its information. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-srs@net.bio.net Mon Sep 30 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!news-in2.uu.net!news.nacamar.de!nntp.zit.th-darmstadt.de!fu-berlin.de!zrz.TU-Berlin.DE!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: We want to help you to market your great software (which nobody knows about) Date: Tue, 01 Oct 1996 13:03:53 +0200 Organization: EMBL Lines: 23 Distribution: world Message-ID: <3250FA99.167E@embl-heidelberg.de> References: <529ta2$ksr@news.inforamp.net> <52ao2m$irq@arcturus.ciril.fr> 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 3.0 (X11; I; OSF1 V2.0 alpha) To: Francois Jeanmougin Francois Jeanmougin wrote: > > What kind of company can send such posts? They really don't > know anything about Internet, so they are completely incompetent in > extending a market. > Hey Thure, keep SRS free, I will pay you a beer next time > we are in Heidelberg! > Francois. > P.S.: Of course, one for Peter too... no plans for commercialization yet - so i take your offer! you could come to Hinxton next year - great chances to find me AND Peter there;-) Thure -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany