From owner-srs@net.bio.net Sat Aug 08 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsxfer3.itd.umich.edu!news-peer.sprintlink.net!news-peer-europe.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.ecrc.net!newsfeed2.ecrc.net!news.primus-online.de!not-for-mail From: "morm" Newsgroups: bionet.software.srs Subject: britanica serial Date: 9 Aug 1998 23:38:37 GMT Organization: Metronet GmbH Lines: 3 Message-ID: <01bdc3e6$8638b680$48b1a8c1@default> NNTP-Posting-Host: frankfurt3.pop.metronet.de X-Newsreader: Microsoft Internet News 4.70.1160 how can get the serial number of britanica! my e-mail is talmosh@hotmail.com From owner-srs@net.bio.net Mon Aug 10 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!news.maxwell.syr.edu!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news.sprintlink.net!151.201.0.37!world6.bellatlantic.net!news From: jaugust@bellatlantic.net (John Augustine) Newsgroups: bionet.software.srs Subject: MS-Dos Date: Tue, 11 Aug 1998 12:51:51 GMT Organization: Bell Atlantic Internet Solutions Lines: 9 Message-ID: <35d03b70.1495662@news4.bellatlantic.net> NNTP-Posting-Host: client-151-197-124-19.bellatlantic.net X-Newsreader: Forte Free Agent 1.1/16.230 I was surprised to discover that some people don't know where to find MS-Dos Software. One TERRIFIC SOURCE that I know of is Simtel.Net or one of their many distributers ("Mirror" sites). Simtel.Net's MS-Dos Library has well over 12,000 files in about 165 catagories. Note: Simtel.Net also has a Windows Library too. From owner-srs@net.bio.net Wed Aug 12 23:00:00 1998 From: nobody@nowhere33.yet Newsgroups: bionet.software.srs Subject: !!! Free Internet Marketing Tools !!! Message-ID: <13089815.5540@nowhere33.yet> Date: Thursday, 13 Aug 1998 15:55:40 -0600 Reply-To: trial@marketingsuite.com NNTP-Posting-Host: 195.59.0.67 X-Trace: 13 Aug 1998 09:51:58 -0600, 195.59.0.67 Lines: 69 X-Authenticated-User: elvis Organization: Newsfeeds.com http://www.newsfeeds.com The LARGEST News server in the world! Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!news.idt.net!news-peer-east.sprintlink.net!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news.sprintlink.net!209.74.93.229!news.newsfeeds.com!nowhere33.yet New Software and Free Internet Marketing Tools for Webmasters The Internet Marketing Suite - For Fast, Easy & Effective Online Promotion http://www.marketingsuite.com/dl2.html The Internet Marketing Suite is a new, comprehensive suite of utilities for improving, tracking and sustaining your Internet profile. 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Download today for a free 14 day trial 9533676 http://www.marketingsuite.com/dl2.html ------------===www.newsfeeds.com===------------ Join the Largest News Server in the World! 54,000 newsgroups Strong ------------===www.newsfeeds.com===------------ ------------===www.newsfeeds.com===------------ Join the Largest News Server in the World! 54,000 newsgroups Strong ------------===www.newsfeeds.com===------------ From owner-srs@net.bio.net Wed Aug 12 23:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!oleane!jussieu.fr!infobiogen.fr!lovelace.infobiogen.fr!dessen From: dessen@lovelace.infobiogen.fr (Philippe Dessen) Newsgroups: bionet.software.srs Subject: qf option with getz Date: 13 Aug 1998 13:12:20 GMT Organization: GIS INFOBIOGEN, 7 rue Guy Moquet BP8, 94801 VILLEJUIF, France Lines: 25 Message-ID: <6quonk$crr@caroll.infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL2] Thure, Some time ago,you put in your log the reactivation of the qf option of getz which was in SRS4. That whas been programmed for the SRS5.1 .... That is a very efficient option on the contrary of a loop in a shell script. Secondly, in the same area, it would be of interest to have a possibility to input a list of identificators on the WEB page (as qf option in getz). You could introduce some personal selection . Lastly, in Nuc sequence output (ex: embl, genbank) there is no translation of the CDS (in comparison of Pept hypertext access in SRS4). Is it envisaged to put this option in the future ? Regards Philippe -- ------------------------------------------------------- Philippe Dessen GIS INFOBIOGEN 7 rue Guy Moquet BP8, 94801 VILLEJUIF Cedex, France tel : +33 1 45 59 52 41 fax : +33 1 45 59 52 50 e-mail : dessen@infobiogen.fr http://www.infobiogen.fr ------------------------------------------------------- From owner-srs@net.bio.net Wed Aug 12 23:00:00 1998 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.srs Subject: AD: Free 20 Minutes of International Phone Calls to Launch 'Call for Freedom' Movement Date: 13 Aug 1998 08:07:25 +0100 Lines: 54 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6qu3bd$rmn@mserv1.dl.ac.uk> Original-To: This message is sent in compliance of the new e-mail bill: SECTION 301, Paragraph (a)(2)(C) of s. 1618 Sender : Hoek Industries, P.O. Box 130544, St Paul, MN 55113 Phone : 1-612-646-8174 E-mail : cuba@cyber-host.net To be removed from our mailing list, simply reply with "REMOVE" in the subject. Free 20 Minutes of International Phone Calls (Si usted prefiere español, to Launch "Call for Freedom" Movement por favor vea debajo.) The Digital Freedom Network (DFN), which promotes freedom of the press worldwide by publishing the works of imprisoned dissident authors on the net, invites you to make 20 minutes of free international calls from your PC to friends’ or relatives’ normal telephones as part of our worldwide "Call for Freedom" movement. All we ask is that during the call you mention the plight of one of our imprisoned authors to your friends or relatives and ask them to visit or email us their support and then to make a free call on us to one of their friends. If millions and millions of people around the world do this and "call for freedom" the prison doors will surely swing open. Please visit our website at http://www.dfn.org today to download your free calling software and learn about these imprisoned heros. Please do it now. The condition of imprisoned authors worldwide, especially the Havana 4 who are being held in terrible conditions in Cuba, is desperate and being ignored. 20 Minutos Gratis En Llamadas Internacionales Para Lanzar El Movimiento "Llamada Por Libertad" La Digital Freedom Network (FDN), la cúal promociona la libertad de prensa mundialmente publicando trabajos de autores del Web para los disidentes emprisionados le invita a hacer llamadas gratuitas a familiares y amigos desde su PC a teléfonos convencionales por 20 minutos como parte de el movimiento "Llamda Por Libertad". Todo lo que pedimos es que durante su llamada usted mencione a sus amigos y familiares el acontesimiento de uno de los autores emprisionados y que visite o nos envie un correo electrónico para demostrar su apoyo y hacer una llamada a sus amigos. Si millónes y millónes de personas alrededor del mundo hacen esto y "llaman por libertad", las rejas de estas prisiones seguramente abrirán. Por favor visite nuestra página del web "http://www.dfn.org" hoy para bajar su software y aprender de estos emprisioados héroes. Por favor hágalo ahora. Las condiciones de autores emprisionados mundialmente, especialmente estos 4 cubanos son terribles y están desesperadamente siendo ignorados. From owner-srs@net.bio.net Sun Aug 16 23:00:00 1998 Newsgroups: bionet.software.srs Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsxfer3.itd.umich.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!leeds.ac.uk!news From: bmbjmm@bmb.leeds.ac.uk (Jez Murray) Subject: downloading X-Accept-Language: en Message-ID: <35D7F6EE.360E99F6@bmb.leeds.ac.uk> NNTP-Posting-Host: bmbsgi18.leeds.ac.uk X-Mailer: Mozilla 4.5b1 [en] (X11; I; IRIX 6.3 IP32) Content-Type: text/plain; charset=us-ascii Organization: University of Leeds MIME-Version: 1.0 Date: Mon, 17 Aug 1998 10:14:33 +0100 (BST) Lines: 19 Content-Transfer-Encoding: 7bit Hi i was wondering if anyone knows of any software that will download a website and all its links i could use a version that is either win95 or unix compatible l8rz -- . .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .- |\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|| ||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \| -' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' ` Jeremy Murray MAIL: bmbjmm@bmb.leeds.ac.uk-nospam Biochemistry & Molecular Biology TEL: +44 113 233 2591 Leeds University, LEEDS LS2 9JT FAX: +44 113 233 3167 http://www.smb.leeds.ac.uk/wwwsb/jez.html . .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .- |\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|| ||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \| -' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' ` From owner-srs@net.bio.net Tue Aug 18 23:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 Aug 1998 02:00:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199808190900.CAA22793@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-srs@net.bio.net Tue Aug 18 23:00:00 1998 Path: biosci!CYBER-HOST.NET!viewzone From: viewzone@CYBER-HOST.NET Newsgroups: bionet.software.srs Subject: AD: New on-line zine needs YOUR help! Date: 19 Aug 1998 16:40:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: <199808192340.QAA19316@net.bio.net> NNTP-Posting-Host: net.bio.net This message is sent in compliance with the new e-mail bill: SECTION 301, Paragraph (a)(2)(C) of s. 1618 Sender : ViewZone, 1 Phelps Lane, Simsbury, CT 06070 Phone : 1-860-651-7433 E-mail : viewzone@cyber-host.net To be removed from our mailing list, simply reply with "REMOVE" in the subject. ----------------------------------------------------------------------- We'd Like Your Help ViewZone is an on-line magazine that looks at life from different angles. It's hard to describe but we think you'll enjoy it - AND we want your opinion. Viewzone is a little crazy at times, thought provoking, sometimes controversial - but always entertaining. """"We hate spam (except for breakfast) - but we thought you'd want to check out this new on-line magazine. It's FREE and, well, we'd like your opinion on what you see.""""" Weird science, humor, reality(!), interesting personalities and interesting adventures... check us out! (e-mail back from the site) We're at: http://www.viewzone.com Gary Vey CEO, Viewzone Magazine From owner-srs@net.bio.net Tue Aug 18 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-fra.maz.net!news-fra1.dfn.de!news-kar1.dfn.de!news-stu1.dfn.de!news-mue1.dfn.de!rzg.mpg.de!not-for-mail From: Petra Maierl Newsgroups: bionet.software.srs Subject: Re: downloading Date: Wed, 19 Aug 1998 09:00:10 +0200 Organization: MIPS Lines: 53 Message-ID: <35DA77FA.41C6@mips.biochem.mpg.de> References: <35D7F6EE.360E99F6@bmb.leeds.ac.uk> NNTP-Posting-Host: roe.mips.biochem.mpg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.04 (X11; I; OSF1 V3.2 alpha) Jez Murray wrote: > > Hi > i was wondering if anyone knows of any software > that will download a website and all its links > i could use a version that is either win95 or unix compatible > l8rz > > -- > . .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .- > |\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|| > ||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \| > -' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' ` > Jeremy Murray MAIL: bmbjmm@bmb.leeds.ac.uk-nospam > Biochemistry & Molecular Biology TEL: +44 113 233 2591 > Leeds University, LEEDS LS2 9JT FAX: +44 113 233 3167 > http://www.smb.leeds.ac.uk/wwwsb/jez.html > . .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .- > |\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|| > ||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \| > -' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' ` Dear Jez, i dont know if that has anything to do with SRS... Anyway, you can use gnu wget for UNIX: wget -h says: +++++++++++++++++++++++ GNU Wget/1.4.5 by Hrvoje Niksic Options: -o --output-file log messages to logfile -i --input-file read URL-s from file -q --quiet quiet (no output) -t --tries set number of retries per URL (0 to unlimit) -r --recursive recursive web-suck -- use with care! -l --level maximum recursion depth (0 to unlimit) -D --domains comma-separated list of domains to accept -A --accept comma-separated list of extensions to accept -R --reject comma-separated list of extensions to reject -c --continue-ftp restart getting an existing file Refer to the info documentation for a complete list of options. Mail bug reports to . Copyright (C) 1995, 1996, 1997 Free Software Foundation, Inc. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. +++++++++++++++++++++++++++++++ I dont know exactly where to get it from, but its probably mirrored at any software mirror under GNU software. (or just mail to Niksic) CU, Petra From owner-srs@net.bio.net Thu Aug 27 23:00:00 1998 Path: biosci!daresbury!uninett.no!howland.erols.net!newsfeed.internetmci.com!193.190.198.39!news.belnet.be!news.vub.ac.be!bigben!gbottu From: gbottu@bigben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: errors in the Icarus files for prosite and pfam Date: 28 Aug 1998 11:02:27 GMT Organization: Brussels Free Universities VUB/ULB Lines: 32 Message-ID: <6s62o3$fdo$1@mach.vub.ac.be> NNTP-Posting-Host: bigben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] from : the Belgian EMBnet Node Dear fellow SRS server managers, While installing the Pfam databank in our SRS server, I did stumble on two errors. 1. Try to retrieve [prositedoc-id:PDOC00017]. You will see that the entry is truncated. The reason is that the second line of the description begins with a '[' and that the parser erroneously "believes" that the references starts there. The fix : in prositedoc.is replace f_des: ~ {$Wrt:des} ('[' {$Not} ln)* ~ by f_des: ~ {$Wrt:des} ('[ 1]' {$Not} ln)* ~ I just noticed that the EBI server has already fixed the problem, but many other sites have not. 2. srsbuild reports that there are no valid references from Pfam to PROSITE, while there should be. The reason is that Pfam actually contains references to the PROSITEDOC table and not to the PROSITE table with the SWISS-PROT entries. The fix : in pfam.i replace $link:[@PFAM_DB to:@?PROSITE_DB token: 'link|PROSITE' toField:@DF_Accession] by $link:[@PFAM_DB to:@?PROSITEDOC_DB token: 'link|PROSITE' toField:@DF_ID] Regards, Dr. Guy Bottu From owner-srs@net.bio.net Thu Aug 27 23:00:00 1998 Path: biosci!daresbury!uninett.no!news-feed.inet.tele.dk!bofh.vszbr.cz!newspeer.monmouth.com!news.belnet.be!news.vub.ac.be!bigben!gbottu From: gbottu@bigben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: How does SRS jump over links ? Date: 28 Aug 1998 12:22:54 GMT Organization: Brussels Free Universities VUB/ULB Lines: 19 Message-ID: <6s67eu$4nv$1@mach.vub.ac.be> NNTP-Posting-Host: bigben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] from : the Belgian EMBnet Node While preparing a demonstration I searched papain in the Swiss-Prot and asked for the links to the databanks with protein alignments. To my initial surprise no PRINTS entry showed up. The reason was quickly found : since there is no direct link, SRS resolves a link, and in this case it chooses SWISSPROT > PDB > PRINTS and finds nothing because there is no link between the PRINTS entry PAPAIN and the PDB (well, there should, but the file contains PBD in the place of PDB so that the parser does not find it). Since there are PRINTS entries with no link to PDB it would have been better to take SWISSPROT > PROSITE > PRINTS. Now, it is not very realistic to urge our users to look at the Library Network and choose the most appropriate chain of links. Therefore my question : does anybody know how SRS chooses the series of direct links used to resolve a link ? And is there a way to customize the Icarus files in such a way as to mimimize problems of the kind explained above ? Dr. Guy Bottu From owner-srs@net.bio.net Fri Aug 28 23:00:00 1998 Path: biosci!rutgers!gatech!205.252.116.205.MISMATCH!howland.erols.net!news-peer.sprintlink.net!news-nysernet-15.sprintlink.net!news.sprintlink.net!24.129.0.46!newsfeed.se.mediaone.net!news2.jacksonville.net.POSTED!not-for-mail From: JennaJaimeson@FamousChicks.com Newsgroups: bionet.software.srs Subject: RAPE VIDEOS 39489 Message-ID: <29089805.4249@FamousChicks.com> Organization: Distribution: World Lines: 11 Date: Sat, 29 Aug 1998 09:44:31 GMT NNTP-Posting-Host: 24.129.42.110 NNTP-Posting-Date: Sat, 29 Aug 1998 05:44:31 EDT http://cristyshouse.fsn.net WE HAVE A BRAND NEW SITE THAT YOU WILL LOVE. THERE ARE 4 GIRLS LIVING IN A HOUSE WITH CAMERAS IN EVREY ROOM. SEE THEM DO EVERYTHING YOU CAN IMAGINE. IT IS ALL FREE TAKE A PEEK. http://cristyshouse.fsn.net http://cristyshouse.fsn.net Tq2 From owner-srs@net.bio.net Sun Aug 30 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!Cabal.CESspool!bofh.vszbr.cz!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!scarp.sanger.ac.uk!birney From: Ewan Birney Newsgroups: bionet.software.srs Subject: Re: errors in the Icarus files for prosite and pfam Date: Mon, 31 Aug 1998 10:57:27 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 17 Message-ID: References: <6s62o3$fdo$1@mach.vub.ac.be> NNTP-Posting-Host: scarp.sanger.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII To: Guy Bottu In-Reply-To: <6s62o3$fdo$1@mach.vub.ac.be> WRT to Pfam - are you using the old 2.1 release or the 3.0 bbeta release - 3.0 beta release has a different format, and annoyingly we have soem direct links from Pfam to prosite profiles which are considered by prosite/srs as the same thing as prosite patterns. (the problem is that if you put a direct link from prosite to pfam using that you only end up with 6 entires, whereas prosite>prositedoc>pfam is much close to 600!) Just for your info Ewan Birney http://www.sanger.ac.uk/Users/birney/ From owner-srs@net.bio.net Mon Aug 31 23:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!news-ge.switch.ch!news.unige.ch!news From: Alain GATEAU Newsgroups: bionet.software.srs Subject: blastall Date: Tue, 01 Sep 1998 12:21:09 +0200 Organization: University of Geneva Lines: 8 Message-ID: <35EBCA95.6540@cmu.unige.ch> NNTP-Posting-Host: cmusun18.unige.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.6 sun4m) Hi, Doe's anyone have a new blast.i file corresponding to the new command line interface of blast ? blastall -p bpastp -d sprot -i infile ... Thank you Alain From owner-srs@net.bio.net Mon Aug 31 23:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cam-news-feed2.bbnplanet.com!news.bbnplanet.com!ulowell.uml.edu!news-feeder.onramp.net!news.onramp.net!not-for-mail From: "Cynthia S. Smagula" Newsgroups: bionet.software.srs Subject: About the BioToolKit Date: Tue, 01 Sep 1998 14:15:49 -0600 Organization: BIOTA Publications Lines: 3 Message-ID: <35EC55DA.6B45@onramp.net> Reply-To: biota@onramp.net NNTP-Posting-Host: isdn13-54.dllstx.onramp.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC) Over 140 new web databases and analytical resources were recently added to the BioToolKit (http://www.biosupplynet.com) bringing the total to 640 annotated web tools.