From owner-bio-srs@hgmp.mrc.ac.uk Mon Sep 4 13:01:18 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9692517A99; Mon, 4 Sep 2000 13:01:17 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 1CF6C17A96; Mon, 4 Sep 2000 13:01:16 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 679E117AB8; Sat, 2 Sep 2000 17:52:34 +0100 (BST) To: bionet-software-srs@net.bio.net From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: euGenes, Genomic Information for Eukaryotic Organisms Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200009021652.LAA00289@cricket.bio.indiana.edu> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id C82E717AB5; Sat, 2 Sep 2000 17:52:32 +0100 (BST) X-Received: from cricket.bio.indiana.edu (cricket.bio.indiana.edu [129.79.225.189]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B6529415DC for ; Sat, 2 Sep 2000 17:52:31 +0100 (BST) X-Received: (from gilbertd@localhost) by cricket.bio.indiana.edu (8.9.3+Sun/8.9.1) id LAA00289 for bio-srs@net.bio.net; Sat, 2 Sep 2000 11:52:32 -0500 (EST) X-To: bio-srs@net.bio.net Date: Mon, 4 Sep 2000 13:01:16 +0100 (BST) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Dear SRS maintainers, You can find current flat-file data for euGenes files at ftp://iubio.bio.indiana.edu/eugenes/ See the tools/srs folder for srs indexing files. Work remains to be done to improve euGenes links to other databanks in SRS. euGenes Genomic Information for Eukaryotic Organisms http://iubio.bio.indiana.edu/eugenes/ euGenes provides a common summary of gene and genomic information for eukaryotic organisms. This includes Gene symbol, name, and synonyms Chromosome, genetic and molecular map information Gene product information (function, structure, and homologies) Links to extended gene information. The organisms covered are fruitfly, human, mouse, weed (Arabidopsis), worm (C. elegans), yeast and zebrafish. This summary is automatically maintained from primary databases, along the lines of the GeneCards project. Some aspects of interest in euGenes include - an integrated search across organisms for genes of related function. - identified homologs or similar genes. BLAST summaries among all representative proteins of these genes are provided. - an easy-to-use genome map display for fully sequenced organisms, which lets you locate genes and other sequence features from chromosome to detailed region. This is a beta-release of this summary database. Please send your comments and suggestions to improve this service -- mailto:eugenes@iubio.bio.indiana.edu [ Dear readers: I apologize of this is old news to you. The original post of this in early August did not make it to many readers of this newsgroup. -- Don ] -- -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu --- From owner-bio-srs@hgmp.mrc.ac.uk Thu Sep 7 17:13:38 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A6B2517B18; Thu, 7 Sep 2000 17:13:37 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 0C8F317A9D; Thu, 7 Sep 2000 17:13:35 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 2760917B49; Wed, 6 Sep 2000 19:09:10 +0100 (BST) To: bionet-software-srs@net.bio.net From: ramjam@SDSC.EDU (Ramanujam Raman) Newsgroups: bionet.software.srs Subject: Multiple queries Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <39B6883F.98E23F03@sdsc.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id B7D9817B45; Wed, 6 Sep 2000 19:09:07 +0100 (BST) X-Received: from postal.sdsc.edu (postal.sdsc.edu [132.249.20.114]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id ADA17415D5; Wed, 6 Sep 2000 19:09:05 +0100 (BST) X-Received: from yerkes.sdsc.edu (IDENT:duQpUqP3la2WU6chdUI1WvTrx1c8gZTw@yerkes.sdsc.edu [132.249.40.94]) by postal.sdsc.edu (8.9.3/8.9.3/SDSCserver-16) with ESMTP id LAA00505; Wed, 6 Sep 2000 11:09:04 -0700 (PDT) X-Received: from sdsc.edu by yerkes.sdsc.edu (980427.SGI.8.8.8/1.11-IRIXclient) with ESMTP id LAA91642; Wed, 6 Sep 2000 11:09:04 -0700 (PDT) X-Mailer: Mozilla 4.74 [en] (X11; U; IRIX64 6.5 IP30) X-Accept-Language: en X-To: bio-srs@net.bio.net, bio-www@net.bio.net Date: Thu, 7 Sep 2000 17:13:35 +0100 (BST) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Hi, Could anyone let me know how to query the SRS to retrieve a whole bunch of SWALL entries? I have all the accession number for all the entries in a file. Is it possible to send the file as such by email server or so and get back the sequence information. Appreciate any help I can get. Thanks, Ram. --- From owner-bio-srs@hgmp.mrc.ac.uk Fri Sep 8 10:16:44 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 3624E17B1C; Fri, 8 Sep 2000 10:16:44 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id B8CD117AC4; Fri, 8 Sep 2000 10:16:42 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 19EB017AC4; Fri, 8 Sep 2000 10:06:43 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 03C72415E0 for ; Fri, 8 Sep 2000 10:06:42 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA19248 for bionet-software-srs@net.bio.net; Fri, 8 Sep 2000 10:06:42 +0100 (BST) To: bionet-software-srs@net.bio.net From: Peter Stoehr Newsgroups: bionet.software.srs Subject: Re: Multiple queries Organization: EMBL-EBI Message-ID: <39B8AC21.27BB216A@ebi.ac.uk> References: <39B6883F.98E23F03@sdsc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 968404002 19246 193.62.196.237 (8 Sep 2000 09:06:42 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 8 Sep 2000 09:06:42 GMT X-Mailer: Mozilla 4.75 [en] (WinNT; U) X-Accept-Language: en Date: Fri, 8 Sep 2000 10:16:42 +0100 (BST) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Ram You can send an email such as below to netserv@ebi.ac.uk to get sequences, the server actually does an SRS call to SWALL. Its a very old email server, since 1986, but still going strong ! Regards, Peter Stoehr EMBL-EBI ======== get swall:P01174 get swall:wap_mouse etc Ramanujam Raman wrote: > > Hi, > > Could anyone let me know how to query the SRS to retrieve a whole bunch > of SWALL entries? I have all the accession number for all the entries > in a file. Is it possible to send the file as such by email server or so > and get back the sequence information. Appreciate any help I can get. > Thanks, > > Ram. > > --- From owner-bio-srs@hgmp.mrc.ac.uk Mon Sep 18 11:41:06 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A374B17AB5; Mon, 18 Sep 2000 11:41:05 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 8276C17A59; Mon, 18 Sep 2000 11:41:02 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id D298E17B45; Sat, 16 Sep 2000 17:29:39 +0100 (BST) To: bionet-software-srs@net.bio.net From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: SRS hardware question [this is a repost of lost message to bio-srs] Organization: Biology, Indiana University - Bloomington Message-ID: <200009161629.LAA20550@cricket.bio.indiana.edu> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 1AA9017B44; Sat, 16 Sep 2000 17:29:37 +0100 (BST) X-Received: from cricket.bio.indiana.edu (cricket.bio.indiana.edu [129.79.225.189]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D4824415DE for ; Sat, 16 Sep 2000 17:29:36 +0100 (BST) X-Received: (from gilbertd@localhost) by cricket.bio.indiana.edu (8.9.3+Sun/8.9.1) id LAA20550; Sat, 16 Sep 2000 11:29:35 -0500 (EST) X-To: bio-srs@net.bio.net, mummi@decode.is X-Newsgroups: bionet.software.srs Date: Mon, 18 Sep 2000 11:41:02 +0100 (BST) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk [Note: this is one of the posts to this newsgroup that was lost recently due to automoderation. If you want all readers of this group to see posts, use email to bio-srs@net.bio.net and/or get your local news server admin to update the moderation list from the bionet.announce checkgroup message. -- don gilbert] Date: Thu, 10 Aug 2000 12:39:52 +0000 From: Gudmundur Arni Thorisson Reply-To: mummi@decode.is Organization: Decode X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.14-15mdk i686) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.software.srs Subject: SRS hardware question Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: 213.167.128.100 X-Trace: 10 Aug 2000 12:39:08 -0800, 213.167.128.100 Lines: 25 Path: news.indiana.edu!vixen.cso.uiuc.edu!howland.erols.net!nntp.abs.net!uunet!ffx.uu.net!news.isholf.is!213.167.128.100 Xref: news.indiana.edu bionet.software.srs:1315 I have read the hardware requirements for SRS6 on Lion's homepages, but I need a bit more information on that. My situation will likely be the following: -Intel multi-CPU setup with RedHat's Enterprise Linux (for 64bit file system functionality), -At least 1Gb of RAM, more if necessary -One or more 80Gb EIDE disk drives -Probably no more than 10-20 users connnected via browser concurrently, plus non-human connections from the various scripts The main concern is regarding the disk drives: are we talking performance sacrificing by using EIDE- instead SCSI-drives in the server? Is there a way to complement for this by increasing RAM and changing parameters for the software? Are there any RAM-optimizations in general? User stories would be appreciated, to get an idea of what people are running out there. Thanks Gudmundur, Bioinformatics -- -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu --- From owner-bio-srs@hgmp.mrc.ac.uk Mon Sep 18 11:41:10 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id EBC0617A59; Mon, 18 Sep 2000 11:41:08 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 048A117AB6; Mon, 18 Sep 2000 11:41:03 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 289CB17B43; Sat, 16 Sep 2000 17:17:22 +0100 (BST) To: bionet-software-srs@net.bio.net From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: Re: Newsgroup for SRS-discussions or not? Organization: Biology, Indiana University - Bloomington Message-ID: <200009161617.LAA20500@cricket.bio.indiana.edu> References: <39C37301.99EB9AFC@li.is> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 11AA917B42; Sat, 16 Sep 2000 17:17:19 +0100 (BST) X-Received: from cricket.bio.indiana.edu (cricket.bio.indiana.edu [129.79.225.189]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C7634415E1 for ; Sat, 16 Sep 2000 17:17:14 +0100 (BST) X-Received: (from gilbertd@localhost) by cricket.bio.indiana.edu (8.9.3+Sun/8.9.1) id LAA20500; Sat, 16 Sep 2000 11:17:14 -0500 (EST) X-To: bio-srs@net.bio.net X-Newsgroups: bionet.software.srs Date: Mon, 18 Sep 2000 11:41:03 +0100 (BST) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Gudmundur, 'extremely inactive' is the term for many bionet newsgroups, as commercial spam of the last several years has driven many bioscientists away. But bionet.software.srs is now moderated, which is why you find many fewer posts (no spam :). It is still used; find archives of it at http://iubio.bio.indiana.edu/news/bionet/ and http://www.bio.net/hypermail/bio-srs/ Most news servers expire articles older than a few weeks at most, so you need to check these archives for older articles. Note that this news posting of mine may not reach many readers, as my local news server hasn't updated its list of moderated bionet newsgrps for a while, and the change in admin apparently has started enforcing moderation and loss of such non-compliant news postings. This may also be the case for your news server, as I recall seeing posts from '.is' domain were also being lost (compare above archives). So ask your SRS questions, you likely will get answers. But if you want all readers of this group to see them, use email to bio-srs@net.bio.net and/or get your local news server admin to update the moderation list from the bionet.announce checkgroup message. -- Don In article <39C37301.99EB9AFC@li.is>, =?iso-8859-1?Q?Gu=F0mundur=20=C1rni=20=DE=F3risson?= wrote: > Hi. I am a new SRS-user looking for discussion forums. This >newgroup is named "bionet.software.srs", but it seems to be extremely >inactive. So, I was wondering if any longtime user could tell me if this >list has been abandoned .? > Besides, how come I can only see messages since the middle of >August, no older? > > Gudmundur > -- -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu --- From owner-bio-srs@hgmp.mrc.ac.uk Mon Sep 18 11:41:18 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8A3A117A59; Mon, 18 Sep 2000 11:41:17 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id C670417A59; Mon, 18 Sep 2000 11:41:15 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 3279517B45; Sat, 16 Sep 2000 17:33:11 +0100 (BST) To: bionet-software-srs@net.bio.net From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: Re: parser for PIR-CODATA format ? [repost of lost message] Organization: Biology, Indiana University - Bloomington Message-ID: <200009161633.LAA20594@cricket.bio.indiana.edu> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id A17D317B44; Sat, 16 Sep 2000 17:33:09 +0100 (BST) X-Received: from cricket.bio.indiana.edu (cricket.bio.indiana.edu [129.79.225.189]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 57E23415DF for ; Sat, 16 Sep 2000 17:33:08 +0100 (BST) X-Received: (from gilbertd@localhost) by cricket.bio.indiana.edu (8.9.3+Sun/8.9.1) id LAA20594; Sat, 16 Sep 2000 11:33:08 -0500 (EST) X-To: bio-srs@net.bio.net X-Newsgroups: bionet.software.srs Date: Mon, 18 Sep 2000 11:41:15 +0100 (BST) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk [Note: this is one of the posts to this newsgroup that was lost recently due to automoderation. If you want all readers of this group to see posts, use email to bio-srs@net.bio.net and/or get your local news server admin to update the moderation list from the bionet.announce checkgroup message. -- don gilbert] >From news.indiana.edu!not-for-mail Sat Aug 12 22:49:51 2000 From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: Re: parser for PIR-CODATA format ? Date: 12 Aug 2000 22:49:51 GMT Organization: Biology, Indiana University - Bloomington Lines: 22 Message-ID: <8n4kaf$3a9$1@jetsam.uits.indiana.edu> References: <8mu8h1$b13$1@snic.vub.ac.be> NNTP-Posting-Host: chipmunk.bio.indiana.edu Xref: news.indiana.edu bionet.software.srs:1317 Guy, IUBio archive has always served PIR in its CODATA format (me thinking that is more appealing to users). I have SRS v5 and v6 icarus files for it, though I'm not sure if the v6 ones are great yet, as I'm still in process of implementing v6. For v5, see http://iubio.bio.indiana.edu/srs5bin/cgi-bin/wgetz?-fun+pagelibinfo+-info+PIR For v6, see http://iubio.bio.indiana.edu/srs6bin/cgi-bin/wgetz?-page+LibInfo+-lib+PIR -- Don PS, PIR @ Georgetown source that I use offers weekly updates but only in NBRF format currently. PIR developers say a CODATA version will be forthcoming. -- -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@bio.indiana.edu --- From owner-bio-srs@hgmp.mrc.ac.uk Sun Sep 24 15:28:11 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id F2A3917AB6; Sun, 24 Sep 2000 15:28:10 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id CA50817A5D; Sun, 24 Sep 2000 15:28:09 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id B1DDA17B07; Fri, 22 Sep 2000 14:31:20 +0100 (BST) To: bionet-software-srs@net.bio.net From: bjohnson@got.wedgie.org (Brad Johnson) Newsgroups: bionet.software.srs Subject: SRS 5.1.0 and EMBL Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id CAD4C17B05; Fri, 22 Sep 2000 14:31:18 +0100 (BST) X-Received: from got.wedgie.org (got.wedgie.org [216.181.169.146]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A212A415DD for ; Fri, 22 Sep 2000 14:31:17 +0100 (BST) X-Received: by got.wedgie.org (Postfix, from userid 1010) id D910DD908; Fri, 22 Sep 2000 09:31:03 -0400 (EDT) X-Received: from localhost (localhost [127.0.0.1]) by got.wedgie.org (Postfix) with ESMTP id CA39D9B19 for ; Fri, 22 Sep 2000 09:31:03 -0400 (EDT) X-To: bio-srs@net.bio.net Date: Sun, 24 Sep 2000 15:28:09 +0100 (BST) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Hello all... I recently grabbed the current EMBL data files off ftp.expasy.ch and tried to index them using SRS 5.1.0. Needless to say it took quite a bit of time! Once I was finished, however, this was the output of srscheck: ++++++> must build index "FtKey" for EMBL, does not exist ++++++> must build index "FtQualifier" for EMBL, does not exist Segmentation fault (core dumped) I'm using the default embl.* icarus files that come with SRS 5.1.0 set up to use standard EMBL and not GCG Embl. I built indexes for EMBLNEW just fine. If I try to run srsupdate to finish building the indexes, I get no output back whatsoever (as if nothing else needs to be done). If I attempt to run any getz's on the EMBL database, I get a seg fault. Has anyone else run into this problem? Should I just upgrade to SRS6? Any good way around this? I'm running on a Sun E250 with 2 GB of RAM, 4 16 GB hard drives and 2 72 gig hard drives. Thanks for any help you can provide... Sincerely, Brad Johnson ---