From owner-srs@net.bio.net Tue Jul 07 23:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!news-nysernet-5.sprintlink.net!news-dc-2.sprintlink.net!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!news2.ais.net!jamie!ais.net!portc01.blue.aol.com!audrey01.news.aol.com!not-for-mail From: erdna@aol.com (Erdna) Newsgroups: bionet.software.srs Subject: Software Inventories Lines: 19 Message-ID: <1998070800374000.UAA22726@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Date: 8 Jul 1998 00:37:40 GMT Organization: AOL http://www.aol.com Our company, Caissa Software, is offeriing two inventories at your price. They are the following: 1. "Active Office" Software. A new Graphics Companion for MS Office Applications. Instantly adds great looking graphics to Word, Excel, and Powerpoint. $49.95 . For a demo go to: http://www.spco.com/DEMO/Aodemo1.htm 2. Pre-Paid MCI Web Sites. $99.99 Web Sites from MCI. Includes a home page, all design work, and all hosting fees included for one year. Everything is brand new, and current. Make me an offer. For detail, call Andre at: (714) 246-1960 Or send an e-mail to: erdna@aol.com From owner-srs@net.bio.net Thu Jul 16 23:00:00 1998 Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!howland.erols.net!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: wgetz Date: 17 Jul 1998 13:50:28 GMT Organization: GIS INFOBIOGEN, 7 rue Guy Moquet BP8, 94801 VILLEJUIF, France Lines: 30 Message-ID: <6onkr4$3f@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] Usage of wgetz -------------- We have searched information about the syntax of fields in the wgetz command (nothing in documentation in http://www.infobiogen.fr/srs5/man/srsman.html. After some trials I give a result probably interesting for who want to directly access to parts of entries. 1) With getz you have : getz "[libs={genbank genbanknew}-id:humtpa]" -sf fasta -f 'id des org ftKey' 2) With wgetz : a solution is : http://www.infobiogen.fr/srs5bin/cgi-bin/wgetz?-f+dat%20des%20org%20seq+-sf+fasta+[{genbank%20genbanknew}-id:humtpa] Philippe Dessen -- ------------------------------------------------------- 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 Thu Jul 16 23:00:00 1998 Path: biosci!protana.com!blandfort From: blandfort@protana.com (Jon Sund Blandfort) Newsgroups: bionet.software.srs Subject: What's hot and what's not? Date: 17 Jul 1998 05:13:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <3.0.5.32.19980717141248.008fd420@mail.protana.com> NNTP-Posting-Host: net.bio.net Dear all, I am setting up a Redhat Linux server to run some bioinformatic tools on. I would be grateful if you would share your feelings with me on some of the major packages (e.g. SEALS) academic as well as commercial. What's the best and why? Regards, Jon ------------------------------------------------ Jon Sund Blandfort, Center for Experimental Bioinformatics (CEBI), Odense University, Institute of Molecular Biology, St=E6rmosegaardsvej 16, DK-5230 Odense M. Phone: +45 6315 2031 Fax: +45 6315 2040 email: blandfort@protana.com www: http://www.protana.com/~blandfort/ From owner-srs@net.bio.net Thu Jul 16 23:00:00 1998 Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!newsfeed.nyu.edu!btnet-peer!btnet!dispose.news.demon.net!demon!delos!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!gwilliam From: gwilliam@hgmp.mrc.ac.uk (Gary Williams) Newsgroups: bionet.software.srs Subject: Re: Using Perl's LWP to access SRS? Date: 17 Jul 1998 10:52:52 GMT Organization: UK HGMP Resource Centre Message-ID: <6onae4$rs8$1@niobium.hgmp.mrc.ac.uk> References: <35903363.21AD@fhcrc.org> <6mpk80$kum$1@jetsam.uits.indiana.edu> NNTP-Posting-Host: neptunium.hgmp.mrc.ac.uk Lines: 73 In article <6mpk80$kum$1@jetsam.uits.indiana.edu>, Don Gilbert wrote: >You may have better success with GET instead of POST, if >you suitably url-encode the somewhat messy url's that can >result: > >http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?[libs%3D%7Bembl_SP_emblnew%7D-all:esterase*]+-e > >For instance this pulls all the reports from two libraries >for a term using the -all field. You can also use compound queries, >joining [term]&[term]. > >Knowing the 'getz' syntax for srs will help. Knowing >that _SP_ is a hidden SRS key for joining library names >will help. It is not hard to hack together a simpler interface >that wgetz for automated queries, if you are running your >own SRS server. IUBio has one such (see the iubio.bio.indiana.edu/Genbank >section). I've got a slightly different problem to the one that has been discussed in this thread, 1) The program has been passed either an ID or an AccNumber - it don't know which. 2) I want to search EMBLNEW and EMBL. 3) I want to extract just one sequence from the databases - the latest one from EMBLNEW or failing that, the one from EMBL. The URL: http://srs5.hgmp.mrc.ac.uk/srs5bin/cgi-bin/wgetz?-sf+embl+-e+[libs={EMBLNEW_SP_EMBL}-id:$entry|libs={EMBLNEW_SP_EMBL}-acc:$entry] looks as if it ought to work, but... http://srs5.hgmp.mrc.ac.uk/srs5bin/cgi-bin/wgetz?-sf+embl+-e+[libs={EMBLNEW_SP_EMBL}-id:hsfau|libs={EMBLNEW_SP_EMBL}-acc:hsfau] gives "arguments missing" http://srs5.hgmp.mrc.ac.uk/srs5bin/cgi-bin/wgetz?-sf+embl+-e+[{EMBLNEW_SP_EMBL}-id:hsfau|{EMBLNEW_SP_EMBL}-acc:hsfau] pulls out the sequence OK. http://srs5.hgmp.mrc.ac.uk/srs5bin/cgi-bin/wgetz?-sf+embl+-e+[{EMBLNEW_SP_EMBL}-id:X65923|{EMBLNEW_SP_EMBL}-acc:X65923] gives: Information: no entries found, query: "[{EMBLNEW EMBL}-id:X65923|{EMBLNEW EMBL}-acc:X65923]" http://srs5.hgmp.mrc.ac.uk/srs5bin/cgi-bin/wgetz?-sf+embl+-e+[{EMBLNEW_SP_EMBL}-acc:X65923|{EMBLNEW_SP_EMBL}-id:X65923] pulls out the sequence OK. i.e. it only works if it searches for an id first and finds a match to an ID or it searches for a match to an AccNumber first and finds a match to an AccNumber http://srs5.hgmp.mrc.ac.uk/srs5bin/cgi-bin/wgetz?-sf+embl+-e+[{EMBLNEW_SP_EMBL}-id:AC003034|{EMBLNEW_SP_EMBL}-acc:AC003034] pulls out the sequence twice because AC003034 is in both EMBL and EMBLNEW and it pulls out the two versions. Can anyone suggest an alternative to doing multiple SRS searches, stopping when a sequence has been found? I'm sure it ought to be possible; I must confess a woeful ignorance of SRS syntax. Gary Williams Tel: +44 1223 494522 mailto:G.Williams@hgmp.mrc.ac.uk http://www.hgmp.mrc.ac.uk/ Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK From owner-srs@net.bio.net Thu Jul 16 23:00:00 1998 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.srs Subject: AD: NET-VEST PICKS HOT STOCK Date: 17 Jul 1998 04:05:27 +0100 Lines: 73 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6omf1n$9t5@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 : Net-Vest, P.O. Box 70037, Los Angeles, CA 90070-0037 Phone : 1-888-619-8468 E-mail : net-vest@net-vest.net To be removed from our mailing list, simply reply with "REMOVE" in the subject. Will JT's Restaurants, Inc. 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The information contained herein is based on material which NET-VEST, based on its best efforts, believes to be reliable, but as to which no representation is made as to its completeness or accuracy. From owner-srs@net.bio.net Fri Jul 17 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news-peer.gip.net!news-lond.gip.net!news.gsl.net!gip.net!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Heikki Lehvaslaiho Newsgroups: bionet.software.srs Subject: [TIPS] adding hypertext links Date: Sat, 18 Jul 1998 20:31:19 +0100 Organization: EMBL - EBI Lines: 66 Message-ID: <35B0F807.AF45AB0D@ebi.ac.uk> NNTP-Posting-Host: cetus.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX64 6.2 IP28) A couple of tips for you writing parsers. 1. Hypertext links are usually added into documents by writing a $href into srsdb.i file and invoked from icarus productions using the $Rep function. Instead of writing a new $href for every a new database link and cluttering the srsdb.i file, you could use a generic one which is already defined (in v. 5.1.0.): $href:[entryR link:"%s"] and call that from SRS e.g. h_pt: ~ {$In:[fields c:pt t:html]} 'PT' (word {$Rep:{$ParStr:entryR 'rebase' 'id' $Ct $Ct}} |noword)* ~ to parse line like PT HindIII 2. Whenever you have a literature reference containing the name or standardized abbreviation of the journal, volume and first page of the article, you can create a link PubMed using a predefined link. $href:[pubmedR link: |%s\ ] h_ref: ~ {$In:[fields c:rl t:html] $Out } # journal vol first page /..[ ]+/ (/([^0-9]+)([0-9]+): ?([0-9]+)[^\n]+/ {$j=$StrRep:[$1 from:'.' to:'+'] $j=$StrRep:[$j from:'&' to:''] $j=$StrRep:[$j from:' ' to:'+'] $j=$StrRep:[$j from:'++' to:'+'] $j=$Trim:[$j skip:'+'] $Rep:{$ParStr:pubmedR $j $2 $3 $Ct}} |/./)* ~ to add hypertext link to a line like: RL J. Mol. Biol. 132:133-139(1979). More information and other options of the NCBI Citation Matcher page at http://www.ncbi.nlm.nih.gov/PubMed/citmatch.html Have fun, -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ http://www2.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From owner-srs@net.bio.net Sat Jul 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 Jul 1998 02:00:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199807190900.CAA17449@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 Sat Jul 18 23:00:00 1998 Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!news.maxwell.syr.edu!Supernews60!supernews.com!Supernews69!not-for-mail From: Kelley Williams Newsgroups: bionet.software.srs Subject: Free Advertisment For Your Software Date: Sun, 19 Jul 1998 12:58:50 -0500 Organization: Ye 'Ol Disorganized NNTPCache groupie Lines: 53 Message-ID: <35B233D9.229BD725@imsday.com> Reply-To: kwilliams@imsday.com NNTP-Posting-Host: 209.42.203.46 Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="------------6367E8EE596D8F8BF192BEE1" X-Trace: 900871060 ZF/2VA9KICB2ED12AC usenet54.supernews.com X-Complaints-To: newsabuse@supernews.com X-Mailer: Mozilla 4.05 [en] (Win95; I) Cache-Post-Path: news.imsday.com!unknown@d2052192143.imsday.com X-Cache: nntpcache 2.3.2.1 (see http://www.nntpcache.org/) Cache-Post-Path: station1.firehouse.net!news@news.imsday.com X-Cache: nntpcache 2.3.2 (see http://www.nntpcache.org/) --------------6367E8EE596D8F8BF192BEE1 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Developer, I am offering to advertise your software on my newest site. If you wish to be included, please send a summary of your software, including the price and location where the software can be purchased and downloaded. If there is a trial version, please indicate this. I am only accepting adds for software that can be downloaded from the internet at this time. At this time, all advertising is free, and your advertisement will be narrowed to 100 words. In the future, K. Williams Resources will be offering prime advertising space on the site at a reasonable cost. K. Williams Resources will also be publishing an ezine that will introduce new software to our subscribers, and include a section where software is rated. You will be notified by email when your link has been added to the site. Send information to : K. Williams Resources --------------6367E8EE596D8F8BF192BEE1 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Developer,

I am offering to advertise your software on my newest site. If you wish to be included, please send a summary of your software, including the price and location where the software can be purchased and downloaded. If there is a trial version, please indicate this. I am only accepting adds for software that can be downloaded from the internet at this time.

At this time, all advertising is free, and your advertisement will be narrowed to 100 words. In the future, K. Williams Resources will be offering prime advertising space on the site at a reasonable cost.

K. Williams Resources will also be publishing an ezine that will introduce new software to our subscribers, and include  a section where software is rated.

You will be notified by email when your link has been added to the site.

Send information to :  K. Williams Resources --------------6367E8EE596D8F8BF192BEE1-- From owner-srs@net.bio.net Sun Jul 19 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.corridex.com!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: chenna@embl-heidelberg.de Newsgroups: bionet.software.srs Subject: Re: wgetz Date: Mon, 20 Jul 1998 12:09:25 GMT Organization: Deja News - The Leader in Internet Discussion Lines: 49 Message-ID: <6ovc1l$bbp$1@nnrp1.dejanews.com> References: <6onkr4$3f@caroll.infobiogen.fr> NNTP-Posting-Host: 192.54.41.195 X-Article-Creation-Date: Mon Jul 20 12:09:25 1998 GMT X-Http-User-Agent: Mozilla/4.05 [en] (X11; I; IRIX 5.3 IP22; Nav) You can also use multiple -f flag .... http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?-id+1ujxs19Uv9f+[SWISSPROT-ID:'BENA_ACICA']+-f+id+-f+seq+-f+des Ramu _______________________________________________________________ Chenna Ramu; EMBL; Postfach 10.2209; 69012 Heidelberg; Germany. Email: chenna@embl-heidelberg.de Url: http://www.embl-heidelberg.de/~chenna/ Tel: (49) 6221 387530 (Off) ; Fax: (49) 6221 387517 _______________________________________________________________ In article <6onkr4$3f@caroll.infobiogen.fr>, dessen@lovelace.infobiogen.fr (Philippe Dessen) wrote: > Usage of wgetz > -------------- > We have searched information about the syntax of fields in the > wgetz command > (nothing in documentation in http://www.infobiogen.fr/srs5/man/srsman.html. > > After some trials I give a result probably interesting for who want > to directly access to parts of entries. > > 1) With getz you have : > > getz "[libs={genbank genbanknew}-id:humtpa]" -sf fasta -f 'id des org ftKey' > > 2) With wgetz : > > a solution is : > http://www.infobiogen.fr/srs5bin/cgi-bin/wgetz?-f+dat%20des%20org%20seq+-sf+fasta+[{genbank%20genbanknew}-id:humtpa] > > Philippe Dessen > > -- > ------------------------------------------------------- > Philippe Dessen GIS INFOBIOGEN > 7 rue Guy Moquet BP8, 94801 VILLEJUIF Cedex, France > tel : +33 1 45 59 52 41 fax : +33 1 45 59 52 50 > e-mail : dessen@infobiogen.fr http://www.infobiogen.fr > ------------------------------------------------------- > -----== Posted via Deja News, The Leader in Internet Discussion ==----- http://www.dejanews.com/rg_mkgrp.xp Create Your Own Free Member Forum From owner-srs@net.bio.net Mon Jul 20 23:00:00 1998 Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!news.maxwell.syr.edu!news-was.dfn.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: pdbfinder parser error, a possible fix. Date: 21 Jul 1998 08:44:57 GMT Organization: EMBL Heidelberg Lines: 31 Distribution: world Message-ID: <6p1kea$rco@lion.embl-heidelberg.de> NNTP-Posting-Host: shag.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12IS (X11; I; IRIX 5.3 IP22) To: chenna@embl-heidelberg.de X-URL: news:bionet.software.srs Hi All You might have noticed that when you try '[pdbfinder-id:1AC0]' -e you get part of the entry and the error message invalid token access Token is not of type "object". Quick way to solve this is to change the line in $fn={ 'Sequence': sequence to 'Sequence': sequenc (or something May be the right way of solving will follow this :-) Ramu _______________________________________________________________ Chenna Ramu; EMBL; Postfach 10.2209; 69012 Heidelberg; Germany. Email: chenna@embl-heidelberg.de Url: http://www.embl-heidelberg.de/~chenna/ Tel: (49) 6221 387530 (Off) ; Fax: (49) 6221 387517 _______________________________________________________________ 'Organised people just have limited horizons' From owner-srs@net.bio.net Mon Jul 20 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news.maxwell.syr.edu!news-was.dfn.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: pdbfinder parser error, a possible fix. Date: 21 Jul 1998 08:46:07 GMT Organization: EMBL Heidelberg Lines: 31 Distribution: world Message-ID: <6p1kgf$rco@lion.embl-heidelberg.de> NNTP-Posting-Host: shag.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12IS (X11; I; IRIX 5.3 IP22) To: chenna@embl-heidelberg.de X-URL: news:bionet.software.srs Hi All You might have noticed that when you try '[pdbfinder-id:1AC0]' -e you get part of the entry and the error message invalid token access Token is not of type "object". Quick way to solve this is to change the line in $fn={ 'Sequence': sequence to 'Sequence': sequenc (or something May be the right way of solving will follow this :-) Ramu _______________________________________________________________ Chenna Ramu; EMBL; Postfach 10.2209; 69012 Heidelberg; Germany. Email: chenna@embl-heidelberg.de Url: http://www.embl-heidelberg.de/~chenna/ Tel: (49) 6221 387530 (Off) ; Fax: (49) 6221 387517 _______________________________________________________________ 'Organised people just have limited horizons' From owner-srs@net.bio.net Tue Jul 21 23:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!199.0.154.208!news2.ais.net!jamie!ais.net!uunet!in4.uu.net!news.winternet.com!news.cinenet.net!not-for-mail From: 'v;cglk Newsgroups: bionet.software.srs Subject: "Pam Lee & Bret Michaels Sex Video ! Date: Wed, 22 Jul 1998 07:38:31 PST Organization: asdlfjas Lines: 64 Message-ID: <07221998073831joeuroieuro@lajlfjasldfa.org> NNTP-Posting-Host: ppp06.labridge.com content-length: 1783 HOLY SHIT BATMAN!!!!!!!! http://www.pamporn.com - ANNOUNCING YET ANOTHER- PAMELA ANDERSON HARDCORE SEX TAPE!!!!!!!! -Pamela Anderson & Bret Michaels Sex Tape- UN-FUCKING BELIEVABLE Could it be true? YES! 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So get your credit card ready and order today. http://www.pamporn.com YYHKUUWLIIZCXJXPSCLXCIWQEPZQMWRMKAQLEDIP From owner-srs@net.bio.net Sun Jul 26 23:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!newsfeed.nacamar.de!blackbush.xlink.net!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: srsbuild -i doesnt work on OSF 4.0 Date: Mon, 27 Jul 1998 11:38:50 +0200 Organization: MIPS Lines: 12 Message-ID: <35BC4AA9.41C6@mips.biochem.mpg.de> 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) I have problems with srsbuild -i on Alpha DEC 4.0 (formerly OSF1). Installing/Compiling srs5.1 is fine, but i get a "segmentation fault" when calling srsbuild -i -s unix. We have installed a yet local version of srs5.05 at MIPS. I have indexed some databases with srsbuild -w/-c/-m, but couldnt index with srsbuild -i (this doesnt work on srs5.1 either). Is it a problem to leave out indices created with srsbuild -i? Our local version seems to work without these indices as we mainly do searches on single databases (views seem to make problemss...., and i didnt install applications yet). CU, Petra Maierl @ MIPS (Martinsrieder Information center for Protein Sequences)