From owner-bio-srs@hgmp.mrc.ac.uk Sun Dec 3 20:14:11 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2A2E417AF1; Sun, 3 Dec 2000 20:14:11 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id E156617AEA; Sun, 3 Dec 2000 20:14:09 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 5D9D417AF3; Fri, 1 Dec 2000 19:32:12 +0000 (GMT) To: bionet-software-srs@net.bio.net From: Krishna.Sankhavaram@stjude.org ("Sankhavaram, Krishna ") Newsgroups: bionet.software.srs Subject: SRS and GCG databases Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <83B4CF76D818D111982000805F31CA53030E0756@sjmemexc1.stjude.org> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 8A12517A6E; Fri, 1 Dec 2000 19:32:09 +0000 (GMT) X-Received: from gatekeeper.stjude.org (gatekeeper.stjude.org [192.55.208.10]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 63731415DD for ; Fri, 1 Dec 2000 19:31:59 +0000 (GMT) X-Received: by gatekeeper.stjude.org; (8.8.8/1.3/10May95) id NAA01247; Fri, 1 Dec 2000 13:25:46 -0600 (CST) X-Received: from somewhere by smtpxd X-To: "'bio-srs@net.bio.net'" X-Mailer: Internet Mail Service (5.5.2650.21) Date: Sun, 3 Dec 2000 20:14:09 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Hello, I am a new user/adminstrator of SRS. We have just installed SRS on our Alpha server. I would like to know how to configure SRS so I can use my existing GCG formatted databases. I tried to follow the steps that were recommended, but could not get it to work. SRS does not recognize my gcgdata directory. I also want to know if we can have both GCG formatted datafiles and other public databases, such as HGBASE and dbSNP. Please reply. Thank you for the help. Regards, Krishna. --- From owner-bio-srs@hgmp.mrc.ac.uk Tue Dec 5 14:32:59 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5F42317B70; Tue, 5 Dec 2000 14:32:59 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id F322C17AFB; Tue, 5 Dec 2000 14:32:56 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 8744417B45; Mon, 4 Dec 2000 17:36:41 +0000 (GMT) Received: from moderated.news.pipex.net (moderated.news.pipex.net [158.43.192.79]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id A47EE415E2 for ; Mon, 4 Dec 2000 17:36:22 +0000 (GMT) Received: (qmail 13756 invoked by alias); 4 Dec 2000 17:36:20 -0000 Received: (qmail 13752 invoked from network); 4 Dec 2000 17:36:19 -0000 Received: from resu1.ulb.ac.be (164.15.59.200) by moderated.news.pipex.net with SMTP; 4 Dec 2000 17:36:19 -0000 Received: from snic.vub.ac.be (snic.ulb.ac.be [164.15.128.20]) by resu1.ulb.ac.be (8.8.8/3.17.0.ap (resu)) id SAA26514; Mon, 4 Dec 2000 18:31:57 +0100 (MET) for Received: (news@localhost) by snic.vub.ac.be (8.9.3/%I%.0.ap (snic.test)) id SAA19206; Mon, 4 Dec 2000 18:36:07 +0100 (MET) for bionet-software-srs@moderators.isc.org To: bionet-software-srs@moderators.isc.org From: Guy Bottu Newsgroups: bionet.software.srs Subject: Re: SRS and GCG databases Organization: Belgian EMBnet Node Message-ID: <90gkm7$hiq$1@snic.vub.ac.be> References: <83B4CF76D818D111982000805F31CA53030E0756@sjmemexc1.stjude.org> X-Trace: snic.vub.ac.be 975951367 18010 134.184.15.23 (4 Dec 2000 17:36:07 GMT) X-Complaints-To: usenet@snic.vub.ac.be NNTP-Posting-Date: 4 Dec 2000 17:36:07 GMT User-Agent: tin/1.4.3-20000502 ("Marian") (UNIX) (SunOS/5.7 (sun4u)) Date: Tue, 5 Dec 2000 14:32:56 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Dear Krishna, Using databanks in GCG instead of "native" format is in principle not complicated. Under SRS 6 you must in the file xxx.i change two things : replace : fileType:{$DAT_FILE $SEQ_FILE} #orig format # fileType:{$GCGREF_FILE $GCGSEQ_FILE} #GCG format by : # fileType:{$DAT_FILE $SEQ_FILE} #orig format fileType:{$GCGREF_FILE $GCGSEQ_FILE} #GCG format and replace : # $Field:[$DF_DNASequence token:gcgseq format:embl] #GCG format $Field:[$DF_DNASequence token:sequence format:embl] #orig format by : $Field:[$DF_DNASequence token:gcgseq format:embl] #GCG format #$Field:[$DF_DNASequence token:sequence format:embl] #orig format Under SRS 5 it is similar, except that the distribution files are already configured for GCG databanks. Make of course sure that the path in srsdb.i and the file name in xxx.i are correct. There is however a problem : we are using SRS 6.0.7.2 at the moment and I have noticed that for databanks in GenBank format (GenBank, Genpept, Aidsbase,...) SRS cannot index the GCG version. We'll see what SRS 6.0.7.3 does. Guy Bottu From owner-bio-srs@hgmp.mrc.ac.uk Wed Dec 27 15:10:20 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7ECE217ADC; Wed, 27 Dec 2000 15:10:19 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 03ABB17AAD; Wed, 27 Dec 2000 15:10:14 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6018) id 7886317AC6; Fri, 22 Dec 2000 15:06:03 +0000 (GMT) To: bionet-software-srs@net.bio.net From: Paolo Romano Subject: Corba and XML: Towards a bioinformatics integrated network environment Organization: Biotechnology Dept. IST Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Accept-Language: it,en,fr Newsgroups: bionet.software.srs Message-Id: <20001227151014.03ABB17AAD@mercury.hgmp.mrc.ac.uk> Date: Wed, 27 Dec 2000 15:10:14 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Dear bionetters, I'm glad to announce the following workshop: NETTAB - NETWORK TOOLS AND APPLICATIONS IN BIOLOGY CORBA and XML: Towards a bioinformatics integrated network environment First Announce and Call for contributions May 17th-18th, 2001 Advanced Biotechnology Center, Genova, Italy http://www.cba.unige.it/Events/NETTAB/ SCOPE Internet has become the natural environment for the distribution of bioinformatics information and services. Researchers get access to various remote and/or local services and softwares by switching among them to retrieve the information they need and submit intermediate results. Data is manually analysed and transfered via FTP, HTTP, or by "cut and paste". In the near future, this integration activity will be carried out by purpose softwares that will be able to "understand" the data they are managing, and to search, select and locate remote sites that can process the information and to finally submit it to them, until the desided elaboration has been completely fullfilled. This will be possible by defining and adopting new communication standards purposely designed for the bioinformatics needs. CORBA (Common Object Request Broker Architecture) by OMG (Object Management Group) and XML (eXtensible Markup Language) by W3C (WWW Consortium) are the emerging frames within which a new bioinformatics integrated network environment will most probably be built. This workshop will try to introduce these evolving standardization activities and outline, through the final round table, the most probable scenarios of coming years. TOPICS * Emerging network standards and their application in the integration of distributed environments. Related facilities and services. Role of ontologies in biology standardization. * New standards, servers, clients and applications in the field of molecular biology and biotechnology, with emphasis on bioinformatics. * Use of programming languages for the exploitation of the integration of distributed databases and software: Perl, Java, Python, PHP, other "open source" languages. Libraries for bioinformatics applications. * Integrated systems and software, SRS implementations. INVITED SPEAKERS A preliminar list includes: Alvis Brazma, European Bioinformatics Institute, UK Terence Critchlow, Lawrence Livermore National Laboratory, USA Thure Etzold, Lion Biosciences Ltd, United Kingdom Carole Goble, University Manchester, UK Ralf Hofestaedt, University of Magdeburg, DE Philip Ljinzaad, European Bioinformatics Institute, UK Luciano Milanesi, Advanced Biomedical Technology Institute CNR, IT Matthew Pocock, The Sanger Centre, UK Paolo Romano, National Cancer Research Institute, IT Steffen Schulze-Kremer, RZPD, DE Martin Senger, European Bioinformatics Institute, UK Luca Toldo, Merck KGgA, DE WEB SITE AND ANNOUNCE MAILING LIST All information related to the workshop are now available at the workshop web site: http://www.cba.unige.it/Events/NETTAB/ . A low traffic announce mailing list has also been established. You are all invited to subscribe by filling in the form at the Web site: http://www.cba.unige.it/Events/NETTAB/rform.html . You will be kept informed about all workshop's news and deadlines. CALL FOR CONTRIBUTIONS A call for contributions will soon be open. All related information will be available at the workshop web site: http://www.cba.unige.it/Events/NETTAB/ . All workshop's topics will be addressed (see above for a list). For submitting a contribution, an extended abstract (max 2 A4 pages, PDF format) will have to be submitted via a Submission Form of the Workshop site. The deadline for submitting a contribution will be March 1st, 2001. Notifications of acceptance will be sent within April 1st, 2001. Accepted communications and posters will have to submit a short paper (3 to 5 A4 pages) for the Conference Proceedings within May 1st, 2001. * Communications and posters A limited number of oral communications will be selected and admitted to the Oral Communications Session on Friday 18th. Posters will be displayed in the foyer of the Advanced Biotechnology Center. The poster session will be in the afternoon of the 17th . * Demo of clients/servers applications A demo session will be held on the 18th. A computer room will be available for demonstrating bioinformatics related network applications based on CORBA and XML clients and servers. Researchers wishing to demonstrate their softwares are invited to submit a poster as well. * Communications (companies' session) A session will be devoted to the presentation of softwares developed by companies. Interested companies should get in touch with the Workshop Secretariat (see below). REGISTRATION FEE A small registration fee is required. A reduced rate is foreseen for academic participants and for early registrations. Before May 1st, 2001: Academic: 150 Euro Non-academic: 300 Euro After May 1st, 2001: Academic: 200 Euro Non-academic: 400 Euro Fees include coffee breaks, lunches, social dinner, abstracts' book. CONTACTS NETTAB Workshop, Servizio Biotecnologie, Istituto Nazionale per la Ricerca sul Cancro, c/o Centro Biotecnologie Avanzate, Largo Rosanna Benzi 10, I-16132 Genova, Italy Fax: +39-010-5737295 Email: nettab@ist.unige.it Web site: http://www.cba.unige.it/Events/NETTAB/ -- Paolo Romano (paolo@ist.unige.it) Biotechnology Department, National Cancer Research Institute IST, c/o Advanced Biotechnology Centre Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 - Fax: +39-010-5737-295