From owner-srs@net.bio.net Fri Apr 04 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!news-xfer.netaxs.com!news.maxwell.syr.edu!news.apfel.de!fu-berlin.de!unlisys!blackbush.xlink.net!rz.uni-karlsruhe.de!news.uni-ulm.de!not-for-mail From: Markus Kieninger Newsgroups: bionet.software.srs Subject: Question about C-API of SRS Date: Fri, 04 Apr 1997 13:06:30 +0200 Organization: University of Ulm, Germany Lines: 16 Message-ID: <3344E0B6.215A@faw.uni-ulm.de> NNTP-Posting-Host: merlin.faw.uni-ulm.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.5 sun4c) hallo I have got a problem with the C-API of SRS5. At the moment I am programming a little Modul that takes a string (ex.: "[embl-id ...]"), makes a query out of the string and prints the result to STDOUT. (like in demo "Printing Entries"). My question is: What must I do to get the results of the query in a string-variable (or every field of the result in a different string-variable) ? Markus From owner-srs@net.bio.net Wed Apr 16 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.maxwell.syr.edu!news-peer.sprintlink.net!news.sprintlink.net!sprint!howland.erols.net!univ-lyon1.fr!pasteur.fr!oleane!jussieu.fr!saphir.jouy.inra.fr!usenet From: Daniel Kahn Newsgroups: bionet.software,bionet.software.srs,fr.bio.genome,inra.genome Subject: ProDom34 available with several new features Date: Thu, 17 Apr 1997 23:13:07 +0200 Organization: I.N.R.A. Lines: 57 Message-ID: <33569263.2781@toulouse.inra.fr> NNTP-Posting-Host: saphir.jouy.inra.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX64 6.2 IP28) Xref: biosci bionet.software:18384 bionet.software.srs:469 This is a general annoucement of ProDom release 34 available at: http://protein.toulouse.inra.fr/prodom.html The Protein Domain database, ProDom, release 34, has been constructed by clustering homologous segments derived from 53145 non-fragmentary sequences present in SWISS-PROT 34. It can be retrieved by FTP at: ftp://ftp.toulouse.inra.fr/pub/prodom/prodom34 It provides 18086 mutiple alignments and consensus sequences for homologous domain families. The vast majority of these families have been generated automatically using MKDOM, a much improved version of the DOMAINER program (Sonnhammer & Kahn, 1994, Protein Science, 3:482-492; Gouzy, Eugene, Greene, Kahn & Corpet, in preparation). Several steps have been taken towards improving the quality of ProDom. In particular, all multiple alignments have been recalculated ab initio using the MultAlin program (Corpet, 1988, Nucl. Acids Res. 16:10881-10890; http://www.toulouse.inra.fr/multalin.html). In addition a new expertise procedure has been introduced to validate some domain boundaries. The Web user interface has also been considerably enhanced. Links are provided to and from PROSITE and PDB. They have been calculatedwith the help of the LASSAP program (http://alize.inria.fr/). Domain families can be searched by keyword, and graphical representations of domain arrangements can considerably facilitate the structural interpretation of large protein families. In addition, we now provide a sensitive homology search procedure which scans all domain sequences in ProDom and retrieves matches with only one sequence for each domain family, thus drastically reducing output redundancy. The most significant matches are visualized graphically to assist with interpretation. For long queries the former less sensitive but faster search on consensus sequences is also provided. Choice is given between the classical NCBI BLAST 1.4.9 and the new WU-BLAST 2.0a8 allowing for gapped outputs (http://blast.wustl.edu). For any request please mailto:proquest@toulouse.inra.fr Jerome Gouzy Daniel Kahn Laboratoire de Biologie Moleculaire des Relations Plantes-Microorganismes, CNRS-INRA Florence Corpet Laboratoire de Genetique Cellulaire, INRA BP 27 31326 Castanet-Tolosan Cedex France From owner-srs@net.bio.net Thu Apr 17 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.maxwell.syr.edu!rill.news.pipex.net!pipex!tank.news.pipex.net!pipex!news.hol.gr!not-for-mail From: "Paul Reckas" Newsgroups: bionet.software.srs Subject: Opinions on New Software wanted Date: 18 Apr 1997 07:35:18 GMT Organization: Softrie S.A. Lines: 26 Message-ID: <01bc4bd4$3a718780$1ed01ec2@comp126> NNTP-Posting-Host: port14.ppp10.hol.gr X-Newsreader: Microsoft Internet News 4.70.1155 We are trying to get an honest feedback on our new Business Information Management software we have developed. Please visit us at our site: http://www.softrise.com. There you can find information on our products, Business Coordinator Professional and Light. We have a FULL working demo at http://www.softrise.com/demo_dl.htm for you to download and evaluate. You may send us your opinion from our feedback page at http://www.softrise.com/feedback.htm or e-mail us directly at feedback@softrise.com. As a courtesy for your time and effort we will enter you on our drawing to win one of 19 Business Coordinator packages that we give away every month (total value of packages $7,150.00). We thank you in advance for your interest and your opinions. -- ________________________________________ Paul Reckas International Marketing Executive Softrise S.A. http://www.softrise.com softrise@softrise.com ---------------------------------------------------------------------------- ---- From owner-srs@net.bio.net Fri Apr 18 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 Apr 1997 02:00:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199704190900.CAA08239@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 Apr 28 23:00:00 1997 From: "Adam Cooper" Subject: LIFETIME REMINDER SERVICE Newsgroups: bionet.software.srs Message-ID: <01bc53fb$3d57eb40$37ef10d0@default> X-Newsreader: Microsoft Internet News 4.70.1161 NNTP-Posting-Host: mo-ken-p05.bootheel.net Date: 29 Apr 97 16:25:57 GMT Organization: Primary Network. http://www.primary.net Lines: 40 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!news-peer.sprintlink.net!sprint!news-pull.sprintlink.net!news.sprintlink.net!cheech.primary.net!mo-ken-p05.bootheel.net Dear Newsgrouper, DO YOU FORGET? -Friends Birthdays -Anniversaries -Any Important Dates that you want to be reminded of? -Or even reminders to call your friend once a year in Alaska FOR THE REST OF YOUR LIFE WE WILL REMIND YOU!!!!!!! One Time Fee of $39.00 and this lasts for the rest of your life. Also, we can even send Gift Paks to anyone you want automatically. (This is optional) Memberships available in USA ONLY Send Check or Money Order TO: Adam Cooper Email: Rt. 1 Box 63-A acooper@mail.bootheel.net Senath, MO 63876 Please allow 2 weeks for clearance on Checks. Thank You, Adam Cooper BE SURE TO INCLUDE MAILING ADRESS From owner-srs@net.bio.net Mon Apr 28 23:00:00 1997 Newsgroups: bionet.software.srs Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!EU.net!chsun!news.eunet.ch!cgchb!news From: "Andreas Krause" Subject: srs db specs - new .i and .is files Message-ID: <01bc53f4$5aa2b6f0$2546a8c0@isw-krausan1> Sender: news@ciba-geigy.ch Nntp-Posting-Host: dhcp-ring-300-192-168-70-37.is.chbs Organization: Ciba-Geigy Ltd.,Basel,Switzerland X-Newsreader: Microsoft Internet News 4.70.1155 Date: Mon, 28 Apr 1997 16:51:01 GMT Lines: 5 Has anyone added some more database specs to srs and is willing to share the .i and .is files ? We should perhaps think of adding them to srs. andreas krause, basel From owner-srs@net.bio.net Mon Apr 28 23:00:00 1997 Path: biosci!agate!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: srs db specs - new .i and .is files Date: 29 Apr 1997 15:41:29 +0100 Organization: The Sanger Centre Lines: 21 Sender: pmr@unst Message-ID: References: <01bc53f4$5aa2b6f0$2546a8c0@isw-krausan1> NNTP-Posting-Host: unst.sanger.ac.uk X-Newsreader: Gnus v5.3/Emacs 19.34 "Andreas Krause" writes: > Has anyone added some more database specs to srs and is willing to share > the .i and .is files ? > We should perhaps think of adding them to srs. We have an SRS 5.04 server at the Sanger Centre. I am still working thrugh databases and adding .i/.is/.it files (and those I have are incomplete), but you are welcome to try them. http://www.sanger.ac.uk/srs5/ SRS 4 will stay as our main SRSWWW server until I have finished playing with the Icarus files, probably for a few more weeks yet. -- ------------------------------------------------------------------------ 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 Apr 29 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: etzold Newsgroups: bionet.software.srs Subject: Re: srs db specs - new .i and .is files Date: Wed, 30 Apr 1997 17:16:53 +0100 Organization: EMBL-EBI Lines: 22 Message-ID: <33677075.6085@ebi.ac.uk> References: <01bc53f4$5aa2b6f0$2546a8c0@isw-krausan1> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.0b2 (Win95; I) To: Andreas Krause X-Priority: 3 (Normal) Andreas Krause wrote: > > Has anyone added some more database specs to srs and is willing to share > the .i and .is files ? > We should perhaps think of adding them to srs. > > andreas krause, basel I think we all are quite busy adding .i and .is files. Problem is that there is still not a central repository of these files. I compiled a list of srs5 servers in http://srs.ebi.ac.uk:5000/srs5list.html you can have a look at all servers and see if there are new databanks. the bottom of the 'databank information page' have links to the corresponding .i and .is files ...if you try these pages on our server you will get even 'colorized' icarus pages regards thure