From owner-srs@net.bio.net Tue Oct 01 23:00:00 1996 Path: biosci!agate!howland.erols.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: Re: We want to help you to market your great software (which nobody knows about) Date: 02 Oct 1996 08:32:46 GMT Organization: The Sanger Centre Lines: 20 Distribution: world Message-ID: References: <529ta2$ksr@news.inforamp.net> <52ao2m$irq@arcturus.ciril.fr> <3250FA99.167E@embl-heidelberg.de> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: Thure Etzold's message of Tue, 01 Oct 1996 13:03:53 +0200 In article <3250FA99.167E@embl-heidelberg.de> Thure Etzold writes: > > 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;-) But the beer is better in Heidelberg :-) SRS: the first software in the pub domain ?! -- ------------------------------------------------------------------------ Peter Rice | Informatics Division, E-mail: pmr@sanger.ac.uk | The Sanger Centre, Tel: (44) 1223 494967 | Wellcome Trust Genome Campus, Fax: (44) 1223 494919 | Hinxton, Cambridge, CB10 1SA, URL: http://www.sanger.ac.uk/~pmr/ | England From owner-srs@net.bio.net Tue Oct 01 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!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: Wed, 02 Oct 1996 20:52:00 +0200 Organization: EMBL Lines: 67 Distribution: world Message-ID: <3252B9D0.446B@embl-heidelberg.de> References: <52quc2$15t@lovelace.infobiogen.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: bioinfo@infobiogen.fr Claude Scarpelli wrote: > > 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. > Together with Rob Hooft from the EMBL we have looked at that problem in detail: We found alltogether three more or less practical options to turn off caching: 1) include /cgi-bin/ in the URL 2) adding a 'Pragma:no-cache' header 3) adding a header with an expiry date, eg, "Expires: Thu, 01 Dec 1994 16:00:00 GMT" the first we didn't like since it is quite 'clunky' and forces one to put all cgi's into a single directory (not just the one of SRSWWW). options 2 and 3 both work well ...too well since they turn off cashing by Netscape with the consequence that one has to reload always when going a page back or forward in the client. However, consulting the internet standard RFC 1945 we found this: Applications must not cache responses to a POST request because the application has no way of knowing that the server would return an equivalent response on some future request. Now in SRS5 the pages with user context that are generated by the server are either POST requests - so they are not cashed - or if obtained by GET have the user-ID in the URL which makes them unique from pages retrieved by another user. All other page obtained by GET without the userId, eg, pages with single entries, have no user context and can be safely cached and shared among users. As far as SRS5 is concerned the system should be safe as it is now. The only page in SRS4 that is problematic is the one with the URL http://server/srs/srsc since it contains user context information but the userId is not included in the URL. So the best would be to add an expiry date + no cache pragma to the header of just that page. 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 Tue Oct 01 23:00:00 1996 Path: biosci!agate!howland.erols.net!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!news.sgi.com!esiee.fr!jussieu.fr!univ-lyon1.fr!news.imag.fr!ciril.fr!u-strasbg.fr!news From: Frederic PLEWNIAK Newsgroups: bionet.software.srs Subject: Re: We want to help you to market your great software (which nobody knows about) Date: Wed, 02 Oct 1996 11:12:53 +0200 Organization: IGBMC Lines: 11 Message-ID: <32523215.646A@igbmc.u-strasbg.fr> References: <529ta2$ksr@news.inforamp.net> <52ao2m$irq@arcturus.ciril.fr> <3250FA99.167E@embl-heidelberg.de> NNTP-Posting-Host: didon.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b7 (X11; I; SunOS 5.5 sun4m) Peter Rice wrote: > > SRS: the first software in the pub domain ?! > Er???... I thought it was DARTS (Dynamics Algorithms for Real-Time Simulation)(*). Fred (*) http://robotics.jpl.nasa.gov/tasks/darts/homepage.html From owner-srs@net.bio.net Tue Oct 01 23:00:00 1996 Path: biosci!agate!howland.erols.net!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!enews.sgi.com!news.sgi.com!esiee.fr!jussieu.fr!univ-lyon1.fr!news.imag.fr!ciril.fr!usenet From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software.srs Subject: Re: We want to help you to market your great software (which nobody knows about) Date: 2 Oct 1996 09:03:22 GMT Organization: IGBMC Lines: 23 Message-ID: <52tb4q$tv@arcturus.ciril.fr> References: <529ta2$ksr@news.inforamp.net> <52ao2m$irq@arcturus.ciril.fr> <3250FA99.167E@embl-heidelberg.de> 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 article , pmr@sanger.ac.uk (Peter Rice) writes: >But the beer is better in Heidelberg :-) Perhaps we can try Guiness...Then Des Higgins will come with, perhaps. >SRS: the first software in the pub domain ?! Yep, next bioinformatics meeting in a pub, somewhere... (We all always put our softwares in the /ftp/pub directory, no?) Francois. -- 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 Wed Oct 02 23:00:00 1996 Path: biosci!agate!newsgate.duke.edu!news.duq.edu!newsfeed.pitt.edu!gatech!csulb.edu!news.sgi.com!nntp.coast.net!oleane!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: 3 Oct 1996 12:40:00 +0200 Organization: GIS INFOBIOGEN, 7 rue Guy Moquet BP8, 94801 VILLEJUIF, France Lines: 91 Message-ID: <530560$mih@lovelace.infobiogen.fr> References: <52quc2$15t@lovelace.infobiogen.fr> <3252B9D0.446B@embl-heidelberg.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 <3252B9D0.446B@embl-heidelberg.de>, Thure Etzold wrote: " " Together with Rob Hooft from the EMBL we have looked at that problem in " detail: " " We found alltogether three more or less practical options to turn off " caching: " " 1) include /cgi-bin/ in the URL " 2) adding a 'Pragma:no-cache' header " 3) adding a header with an expiry date, eg, "Expires: Thu, 01 Dec 1994 " 16:00:00 GMT" " " the first we didn't like since it is quite 'clunky' and forces one to " put all cgi's into " a single directory (not just the one of SRSWWW). No. Just create a cgi-bin directory inside the SRS WWW directory. But the URL must contained the (9 characters) string /cgi-bin/ somewhere, not necessarely in the beginning. I consider that storing the documents in one place, the gif images in another one, and the cgi-bin in another is a good practice. " " options 2 and 3 both work well ...too well since they turn off cashing " by Netscape " with the consequence that one has to reload always when going a page " back or forward in the " client. " I have seen that. Sight:-(. This should be the good solution though... Just keep it in mind, and use it as soon as browser will no longer be brain damadged (see below): " However, consulting the internet standard RFC 1945 we found this: " " Applications must not cache responses to a POST request because the " application has no way of knowing that the server would return an " equivalent response on some future request. " I don't think this paragraph applies to the 'BACK' button. However, netscape think the opposite. " Now in SRS5 the pages with user context that are generated by the server " are either POST requests - so they are not cashed - or if obtained by " GET have the user-ID in the URL which makes them unique from pages " retrieved by another user. " " All other page obtained by GET without the userId, eg, pages with single " entries, have no " user context and can be safely cached and shared among users. " " As far as SRS5 is concerned the system should be safe as it is now. I agree. " The only page in SRS4 that is problematic is the one with the URL " http://server/srs/srsc " since it contains user context information but the userId is not " included in the URL. " So the best would be to add an expiry date + no cache pragma to the " header of just " that page. " It should be the best... except that it will break Netscape, from a end-user point of vue (/cgi-bin/ in URL does not break netscape and its 'back' button). Put /cgi-bin/ somewhere in the URL appears to me as the only solution avalaible today. Regards, -- ------------------------------------------------------------------------------ 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) -- ------------------------------------------------------------------------------ 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 Sun Oct 06 23:00:00 1996 Path: biosci!agate!howland.erols.net!surfnet.nl!swidir.switch.ch!swsbe6.switch.ch!news.belnet.be!news.vub.ac.be!usenet From: pinstall@sga.ulb.ac.be (Patrick Installe) Newsgroups: bionet.software.srs,embnet.general Subject: Re: SRS will soon stop working :-) Date: Mon, 07 Oct 1996 13:18:47 GMT Organization: Université Libre de Bruxelles Lines: 33 Message-ID: <53b0bk$5i0@rc1.vub.ac.be> References: <52quc2$15t@lovelace.infobiogen.fr> <52r5ha$s89@winx03.informatik.uni-wuerzburg.de> Reply-To: pinstall@sga.ulb.ac.be NNTP-Posting-Host: sga-pc11.ulb.ac.be X-Newsreader: Forte Free Agent 1.0.82 krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) wrote: >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. 5) I didn't follow all the technical detail but another way could perhap's be the cookies .. http://www.netscape.com/newsref/std/cookie_spec.html. Have a nice day Patrick Installe (pinstall@sga.ulb.ac.be) From owner-srs@net.bio.net Sun Oct 06 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!metro!metro!inferno.mpx.com.au!news.unimelb.EDU.AU!wehi.edu.au!wehi!janice From: janice@wehi.edu.au (Janice Coventry, Walter and Eliza Hall Institute) Newsgroups: bionet.software.srs Subject: Genbank indexing Date: 7 Oct 96 16:17:31 +1000 Organization: Walter & Eliza Hall Institute Lines: 25 Message-ID: <1996Oct7.161731@wehi> NNTP-Posting-Host: wehiu.wehi.edu.au Hi It came to my attention that my indexing of Genbank was incorrect for the current version, and after some investigation I realized that the problem is when keywords extend over more than one line. For example if you looked for sequence HSU30473 you returned the correct description with the incorrect sequence attached. And searching gave incorrect results for some searches. To fix this problem I have changed keywords definition from: keywords = [keyword { ';' keyword}] ['.']; to keywords = {keyword {';' [keyword]}} ['.']; Janice -- ================================================================================ Janice Coventry The Walter and Eliza Hall Institute of Medical Research, P.O. Royal Melbourne Hospital, Victoria, 3050, Australia. Phone: International +61-3-9345-2586 FAX: International +61-3-9347-0852 National 03-9345-2586 National 03-9347-0852 Email: janice@wehi.edu.au =============================================================================== From owner-srs@net.bio.net Thu Oct 10 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!www.nntp.primenet.com!nntp.primenet.com!news.sgi.com!esiee.fr!jussieu.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: Problem in SRS4 Date: Fri, 11 Oct 1996 15:32:19 +0200 Organization: INFOBIOGEN Lines: 38 Message-ID: <325E4C63.6150@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 2.02 (X11; I; SunOS 5.4 sun4d) CC: ETZOLD@embl-heidelberg.de Hello, I hope someone could help me to resolv my little problem : As we have changed our SRS address in INFOBIOGEN for "..srs/cgi-bin/srsc", I have some trouble with the hyperlink file for the line #linkcall /id=%FETCH_CDS which require 132 car. max. I have an error message when i run srssection: > srssection ............ ............ .............................................................. .......e__parnotok, parameter does not meet constraints Line nr. 58 in file /env/infobiogen/pack/srs/odd/hyperlink.sdl Attribute: call, string: CDS_Pept , maxlen: 132 I increase MSGxXLN in msg.h and SDLxXASSGSTR in sdl.h but nothing happended. If someone have a clue on how to change the max length for the attribut linkCall, please reply me Thanks for your help in advance, -- --------------------------------------------------- Jean-Marc PLAZA INFOBIOGEN - CNRS 7, rue Guy Moquet BP8 94801 VILLEJUIF Cedex, France tel: +33 45 59 52 39 fax: +33 45 59 52 50 e-mail: plaza@infobiogen.fr --------------------------------------------------- From owner-srs@net.bio.net Fri Oct 11 23:00:00 1996 Path: biosci!agate!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!nntp.uio.no!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: srs5.03b ...some more Date: Sat, 12 Oct 1996 14:26:32 +0200 Organization: EMBL Lines: 26 Distribution: world Message-ID: <325F8E78.167E@embl-heidelberg.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) ...forgot to mention that the path for SRS' cgi dir is still /srsbin/ but if you do srsinstall www you will be asked for a path where /srsbin/ is the default. So following the discussion of how to prevent caching you should enter /srs/cgi-bin/ instead and then make a ScriptAlias for /srs/cgi-bin/. I haven't tested it yet but it should work - and of course I would be interested to get feed back on that. 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 Fri Oct 11 23:00:00 1996 Path: biosci!agate!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!nntp.uio.no!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: new release srs5.03 Date: Sat, 12 Oct 1996 14:20:49 +0200 Organization: EMBL Lines: 102 Distribution: world Message-ID: <325F8D21.41C6@embl-heidelberg.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) A new release of srs5 is ready and can be ftp'ed from ftp://felix.embl-heidelberg.de/pub/databases/trembl/srs5_03b.tar.gz I append here the release notes regards Thure -------------------------------------------------------------------- SRS release 5.03b ================= This is the beta release of SRS 5.0 which has been compiled and tested on IRIX 5.x, IRIX 6.x (32-bit binary), OSF1 2.x, 3.x, 4.x, Linux 2.x and ULTRIX 4.x. It could also work on AIX, HP-UX, IRIX 6.x (64-bit binary), Solaris, SunOS. If installing on Linux, you will have no csh and so you should remove the -e flag on the first line of the file srs/srsinstall. First a list of what is still missing: 1) the GCG formatted databanks are still not supported 2) extraction of subentries (eg, sequence features) is not yet possible Both items are being worked on and will be hopefully released in the next version which will then be without the 'b'. Now the new things: =================== 1) The .is files can now run as an independent script and used by SRS without changing the script. So in 'tfsite.is' the 'entry' production must always have $In:[file:text] entry: ~ {$In:[file:text] $Out} ('AC' {$Not} ln)* ('AC ' {$entryFip=$Fip $Wrt} ln {$App} ('AC' {$Not} ln {$App})+)? ~ and the code for testing at the end must use "$TestMode" if:$TestMode { $job = $JobNew:[prod:$rules skip:" " fileName:'/data/transfac/site.dat'] while:$JobTokens:[$job name:id print:1] { $JobNext:$job $print:"-------->entry\n" } } 2) There is now a very simple Icarus debugger. It is by no means ready but even at this stage really useful. It is documented in chapter 6 in the WWW manual. 3) I modified the information pages for databanks and data-fields in SRSWWW. Have a look at .it files in 'SRSDB:' which have the description about the databanks and fields which is placed into these pages. The library information page has the links to the .i, .it, .is files for each databank (btw, our test server is 'http://kappa.embl-heidelberg.de:8000/srs/'). The idea is that every databank should be documented by a .it file. 4) There is an emacs lisp file in 'SRSETC:' which defines an Icarus mode - defines only coloring with fontlock. I don't know enough emacs lisp to wri a proper mode with automatic indentation etc. - any volunteers? 5) The indexing of databank partitions runs stable now. This means that big databanks like genbank and EMBL can be indexed in chunks of eg, 100000 entries and then later merged. srscheck takes care of all necessary commands. Have a look in embl.i: attribute 'partSize' of $library sets the partitioning. With a part size of 100000 the indexing of EMBL on an alpha takes less than 50mbyte memory. -- Thure Etzold, etzold@embl-heidelberg.de Johnathon Weare, weare@embl-heidelberg.de 10. October, 1996 -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany From owner-srs@net.bio.net Fri Oct 11 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!in3.uu.net!news.idt.net!news From: captroy@mail.idt.net (J. Roy Cash) Newsgroups: bionet.software.srs Subject: SBase Data Analyst for PA contract Date: Sat, 12 Oct 1996 21:42:19 GMT Organization: The RED HOOK TECHNOLOGY GROUP...www.rht.com Lines: 11 Message-ID: <53p36h$g2o@News.IDT.NET> Reply-To: captroy@mail.idt.net NNTP-Posting-Host: ppp-43.ts-1.suf.idt.net X-Newsreader: Forte Free Agent 1.0.82 We are staffing a contract position for an Sbase Data Analyst with 5 years of experience for a 3-6 month contract in the Philly area. DSS knowledge and Visual Basic application development are necessary. This is essentially a DBA type of position. Open Immediately. Call or email Roy at 516 724 7300 ext 104 J.Roy Cash The Red Hook Technology Group (516)724 7300 ext 104 (516)724 8587 (Fax) http://www.rht.com From owner-srs@net.bio.net Fri Oct 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 Oct 1996 02:00:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199610190900.CAA12047@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 Mon Oct 21 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!news.mathworks.com!uunet!in1.uu.net!news.u.washington.edu!pogo!evolution From: "Spenser Barlow" Newsgroups: bionet.software.srs,sci.bio.ecology,sci.bio.entomology,sci.bio.entomology.homoptera,sci.bio.entomology.lepidoptera,sci.bio.entomology.misc,sci.bio.ethology,sci.bio.fisheries,sci.bio.food-science,sci.bio.herp,sci.bio.microbiolo Subject: Watson & Crick '96 High School Fund Raiser Date: 22 Oct 96 07:44:32 GMT Organization: University of Washington Lines: 67 Message-ID: <01bbc050$a3815760$263040ce@sbarlow> NNTP-Posting-Host: pogo.cqs.washington.edu X-Newsreader: Microsoft Internet News 4.70.1155 X-Mailedby: NT SMTP/LISTSERVER v2.11 (ntmail@net-shopper.co.uk) Status: R Originator: evolution@pogo Xref: biosci bionet.software.srs:327 sci.bio.ecology:21405 sci.bio.entomology.homoptera:164 sci.bio.entomology.lepidoptera:5160 sci.bio.entomology.misc:3702 sci.bio.ethology:3543 sci.bio.fisheries:2432 sci.bio.food-science:3654 sci.bio.herp:7025 ---WATSON & CRICK in '96--- Note: This is an advertisement for a HILARIOUS and MOCKING T-shirt. The cost is $15, and we have approximately 75 T-shirts left. SO ORDER SOON! The money is being raised to fund a high-school biotechnology class in Centralia, WA, so this is a worthwhile cause. If you are interested read on. If you are not interested, read on - this ad is quite funny. In case you don't trust us to send you a T-shirt after we receive your money, we welcome you to call us at (360) 736-2146 or E-mail us at docdna@localaccess.com. If that still does not satisfy your fears, I have no idea what you can do and, therefore, you should probably not order from us. ATTENTION: All Molecular Biologists w/money, Geneticists w/money, Biochemists w/money, Microbiologists w/money, Biologists w/money, Science Teachers w/money, Teachers w/money, Biology Students w/money, Students w/money, General Public interested in Genetics w/money, General Public w/money, Dogs of the above people w/money, Goldfish of the above people w/money, Small Furry Animals named Ralph w/money, Small Furry Animals not named Ralph w/money, etc. I think you get the picture. We do not care who you are - just that you have money. In otherwords, we want your money. Now, a logical and sane human being might say NO to sending money to complete strangers. However, we know most BIOLOGISTS and CHEMISTS are NOT SANE. Still, just so you don't look like a fool when your friends ask you why you are sending off $15 dollars to people you don't know, we WILL send you a stylish t-shirt so you can gloat in those doubting Thomas' faces. The Shirt features a blue and red field separated by a white double-helix. On the top red field Watson is emblazoned and on the bottom blue field Crick is labeled. A white "96" is positioned on the right side of the double-helix which stops the helix from reaching the far right side of the T-shirt. See .jpg file attachment. HOW TO ORDER: To order, send a SASE w/check or cash to the order of $18.00 ($15 + $3 shipping) to: Henri Weeks 919 W. Reynolds Ave. Centralia, WA 98531 Option #2: We can ship the shirt COD (check or money order). Write, call, or e-mail us to initiate shipping. All checks must be made out to Henri Weeks. You should receive your order just as soon as the US Mail service or UPS can get it to you. Thank-you for you time. By sbarlow@localaccess.com From owner-srs@net.bio.net Tue Oct 29 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news00.sunet.se!sunic!news.sprintlink.net!news-peer.sprintlink.net!howland.erols.net!news3.cac.psu.edu!news.cse.psu.edu!rutgers!mcrcr6!cmcl2!news.nyu.edu!mcrcr1.med.nyu.edu!user Newsgroups: bionet.software.gcg,bionet.software.srs Subject: searching in comment field Message-ID: From: browns02@mcrcr.med.nyu.edu (Stuart M. Brown) Date: Wed, 30 Oct 1996 13:05:56 -0500 Organization: NYU-MC Research Computing Resource NNTP-Posting-Host: mcrcr1.med.nyu.edu Lines: 18 Xref: biosci bionet.software.gcg:2057 bionet.software.srs:329 We are doing a bunch of BLAST searches with the EST database. I just got an idea - since these est's are routinely BLASTed before they are submitted- and these results are generally noted in the comment field, why can't I search the EST database for comments that mention BLAST hits against my sequences of interest? I've tried LOOKUP- but the "All text" field does not appear to include the comment field of the GenBank entry. I also tried ENTREZ with only a bit more success - yet I can see mentions of my sequence in the comments when I do my own BLAST searches and then read the full annotation of the ESTs that we hit. -- Stuart M. Brown, Molecular Biology Consultant NYU-MC Research Computing Resource, Dept. of Cell Biology 550 First Ave, New York, NY 10016 Phone: (212)263-7689 FAX: (212)263-8139 From owner-srs@net.bio.net Tue Oct 29 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!news From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.gcg,bionet.software.srs Subject: Re: searching in comment field Date: 30 Oct 1996 23:40:54 GMT Organization: Biology, Indiana University - Bloomington Lines: 31 Message-ID: <558p26$pgc@dismay.ucs.indiana.edu> References: NNTP-Posting-Host: chipmunk.bio.indiana.edu Xref: biosci bionet.software.gcg:2059 bionet.software.srs:330 Stuart, This may be a function of how SRS (or the GCG variant Lookup) is configured at a particular server. At IUBIo Archive, I revised the indexing for SRS to make sure the Genbank comment fields were searchable. As a test of your question, I just now searched the Genbank EST section at IUBIo, searching "Comment" fields for "BLAST", and found 165 matches. Feel free to use this SRS server for Genbank lookups. http://iubio.bio.indiana.edu:81/srs/srsc - Don In article , Stuart M. Brown wrote: >We are doing a bunch of BLAST searches with the EST database. > >I just got an idea - since these est's are routinely BLASTed >before they are submitted- and these results are generally noted >in the comment field, why can't I search the EST database for >comments that mention BLAST hits against my sequences of interest? > >I've tried LOOKUP- but the "All text" field does not appear to >include the comment field of the GenBank entry. I also >tried ENTREZ with only a bit more success - yet I can see mentions >of my sequence in the comments when I do my own BLAST searches and >then read the full annotation of the ESTs that we hit. > -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-srs@net.bio.net Wed Oct 30 22:00:00 1996 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: indexing Genbank 97 from gcg format Date: Thu, 31 Oct 1996 12:10:16 +0000 Organization: SEQNET Lines: 35 Distribution: bionet Message-ID: <32789728.41C6@dl.ac.uk> NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP12) Hi folks, Has anybody been able to index genbank 97 from gcg formatted files ? - For me indexing keeps falling over on entry HSHLAK1 in the primates section. The error message I get is: e__nammismatch, names are not identical "HSHLAK1" and "C" It does not occur with the plain genbank files. It can't have anything to do with the size of genbank, as it also occurs if I restrict genbank to the primates section. As far as I can tell the gcg seq and ref file are completely normal for this entry. srsbuild is apparently supposed to produce this error message if the names in the ref and seq files are not the same, but as far as I can tell they are the same, and I really don't understand were this "C" in the error message comes from. Any ideas ? -- --------------------------------------------------------------------------- | Martin Hilbers | E-mail: m.p.hilbers@dl.ac.uk | | SEQNET | Tel: +44-1925-603492 | | Daresbury Laboratory | Fax: +44-1925-603100 | | Daresbury, Warrington |----------------------------------------------| | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.dl.ac.uk/SEQNET/home.html | ---------------------------------------------------------------------------