From owner-bio-srs@hgmp.mrc.ac.uk Mon Mar 4 10:49:29 2002 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 3D43E17B7F for ; Mon, 4 Mar 2002 10:49:26 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id BA72B17B8A for ; Mon, 4 Mar 2002 10:49:15 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id DBC3C17BB6; Mon, 4 Mar 2002 10:48:32 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 9F19117AE7 for ; Mon, 4 Mar 2002 08:21:50 +0000 (GMT) Received: from ist.unige.it (ibm43p.biotech.ist.unige.it [130.251.106.7]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 6142917A88 for ; Mon, 4 Mar 2002 08:21:06 +0000 (GMT) Received: (from paolo@localhost) by ist.unige.it (8.9.3/8.9.3) id JAA20336; Mon, 4 Mar 2002 09:31:04 +0100 From: Paolo Romano Message-Id: <200203040831.JAA20336@ist.unige.it> To: bionet-software-srs@net.bio.net, info@nettab.org Subject: Call for Papers - NETTAB 2002 Newsgroups: bionet.software.srs Date: Mon, 4 Mar 2002 10:48:32 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Dear bionetters, I'm glad to announce the launch of the Call for Contributions for the NETTAB 2002 Workshop on "Agents in Bioinformatics". I hope to see many of you in Bologna on next July. Bye. Paolo Romano --- NETTAB - NETWORK TOOLS AND APPLICATIONS IN BIOLOGY Second International Workshop on "AGENTS IN BIOINFORMATICS" Call for contributions (oral communications, posters and software demos) July 12th-14th, 2002 Bologna, Italy http://www.nettab.org/ SCOPE Agents and multi-agent systems are the emerging new way of computing. The integration of biological data resources will deal, in the Semantic Web Generation, with agents and software robots. In the last five years there has been a growing interest in the application of agent-based systems in different fields such as e-commerce, transports and health. Agent based systems and applications are well suited to support bioscientists during the process of genome analysis and annotation, so as to the problems of effectively managing and improving the processes that are involved with protein structure prediction. Some specialized projects in this topic are beginning to appear. It may now be a good time to report on the results achieved in this area, to discuss the benefits (and drawbacks) that agent-based systems may bring to bioinformatics domains, and also to provide a list of the research topics that should be tackled in the near future to make the deployment of bioinformatics agent-based systems a reality. The aim of this workshop is to bring together who are working towards the vision of a genome analysis and annotation using agents-based systems. The workshop will also aim to inspire collaboration between these two communities, to strengthen the relationships within bioinformatics community, to activate an osmosis cooperation between bioinformatics and computer science communities, to collect the latest ideas, achievements and proposals in the application of agents and multi-agent systems to the bioinformatics area. The worshop is organized in sessions where invited speakers present the state of art of relevant ongoing projects, sessions for oral communications and a tutorial day. The scientific programme is available at http://www.nettab.org/2002/progr.html . TOPICS OF INTEREST - Co-operation between intelligent agents to improve information retrieval in bioinformatics. - Multi-agent systems to support eScientists during their daily research. - Agents applications in bioinformatics. - Multi-agent systems that improve the data resources integration. - Bioinfomatics agent-based decision support systems. - Information agents that gather, compile and organise biological knowledge available on Internet. - Biological data and knowledge modeling tools - Ontologies, Databases and Applications of Semantics in Bioinformatics PROGRAMME COMMITTEE - Kevin Bryson, Institut National de la Recherche Agronomique (INRA), France - Rita Casadio, Centro per le Ricerche Biotecnologiche, University of Bologna, Italy - Paolo Ciancarini, Department of Computer Science, University of Bologna, Italy - Keith Decker, Department of Computer and Information Sciences, University of Delaware, USA - Angelo Facchiano, Istituto Scienze dell'Alimentazione, CNR, Italy - Vasant Honavar, Department of Computer Science, Iowa State University, USA - Ian Horrocks, Department of Computer Science, University of Manchester, UK - Michael Luck, Department of Electronics and Computer Sciences, University of Southampton, UK - Robin McEntire, GlaxoSmithKline, USA - Emanuela Merelli, Department of Mathematics and Computer Science, University of Camerino, Italy - Luciano Milanesi, Istituto Tecnologie Biomediche, CNR, Milano, Italy - Steffen Möller Proteom-Zentrum Rostock, Germany - Luc Moreau, Department of Electronics and Computer Sciences, University of Southampton, UK - Andrea Omicini Dipartimento di Elettronica, Informatica e Sistemistica, University of Bologna, Italy - Paolo Romano Biotechnology Department, National Cancer Research Institute, Genova, Italy - V. S. Subrahmanian, Computer Science Department, University of Maryland, USA - Luca Toldo, Merck KGaA, Germany SUBMISSION Authors are encouraged to: 1. submit a full paper (max 6 A4 pages in length, size 12pt, in pdf or ps format) as an oral communication 2. submit a research statement by poster (max 2 A4 pages, size 12pt, in pdf or ps format) Full papers (category 1) will be reviewed by the programme committee for relevance, clarity and the novelty of results. After the event, a second round of more extensive reviews is planned which is to lead to the publication of extended versions of selected contributions in an edited collection. Accepted full papers and posters (category 2) will be published in the conference proceedings. Posters and informal research demonstrations provide an opportunity to exhibit late-breaking results and to discuss these results with conference participants in an informal setting. We encourage submissions that are based on new work, including work that is in progress. Informal research demos can take place during poster presentation. Presenters need to bring whatever equipment they need for their demonstration; Internet connectivity can be made available upon request. Proposals should consist of a 1-2 page summary of the work to be presented. Please upload the contributions through the online form available at at http://www.nettab.org/2002/rform.html DEADLINES AND IMPORTANT DATES - Paper due for oral ciommunications: April 30, 2002. - Notifications of acceptance to authors: May 20, 2002. - Final version of accepted communications: May 31, 2002 - Research statements and Posters due: May 31, 2002 - Early registration (at discounted rates): May 31, 2002 ORGANIZATIONAL DETAILS The worksop is jointly organized by: - Biotechnology Department, National Cancer Research Institute - Genova, Italy - Department of Mathematics and Computer Science, University of Camerino, Italy - Department of Computer Science and Biotechnological Center, University of Bologna, Italy STEERING COMMITTEE Chair: Paolo Romano (paolo.romano@istge.it) Co-Chairs: Emanuela Merelli (emanuela.merelli@unicam.it), Luca Toldo (luca.toldo@merck.de) Local Chair: Paolo Ciancarini (cianca@cs.unibo.it) WORKSHOP PLACE The workshop will be held at at: Ex scuola Ercolani, Mura Anteo Zamboni, 2b, Bologna RELATED EVENTS AUTONOMOUS AGENTS & MULTI-AGENT SYSTEMS (AAMAS 2002) Palazzo Re Enzo, Bologna, Italy, July 15-19, 2002, http://lia.deis.unibo.it/aamas2002/ http://www.autonomousagents.org/2002/ THE FOURTH EUROPEAN AGENT SYSTEMS SUMMER SCHOOL 2002 Bologna, 8-12 July, 2002 http://www.agentlink.org/happenings/easss/2002/index.html ABOUT BOLOGNA Although not as famous as Venice and Florence, Bologna is indeed one of the most beautiful towns of Italy, being its medieval historical center one of the biggest and better preserved in Europe. Bologna hosts the most ancient university of the world, which is also one of the biggest in Italy. As everybody knows, Bologna has both the best food and the best nightlife in Italy. In addition, Bologna is the ideal place where to stay to visit other wonderful places: Venice, Florence, Ravenna, and Rimini can all be reached in 1 hour by train, Rome in 3 hours. The airport of Bologna (BLQ) has frequent direct connections to all major European Hubs. -- Paolo Romano (paolo.romano@istge.it) National Cancer Research Institute Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 From owner-bio-srs@hgmp.mrc.ac.uk Fri Mar 8 15:23:57 2002 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 273DD17BCB for ; Fri, 8 Mar 2002 15:23:49 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B118817BAE for ; Fri, 8 Mar 2002 15:23:24 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id AE88617BC9; Fri, 8 Mar 2002 15:23:00 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 43C3017BA5 for ; Fri, 8 Mar 2002 12:26:02 +0000 (GMT) Received: from mailbox4.ucsd.edu (mailbox4.ucsd.edu [132.239.1.56]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 3CC0817B53 for ; Fri, 8 Mar 2002 12:25:58 +0000 (GMT) Received: from smtp3.google.com (smtp3.google.com [216.239.33.28]) by mailbox4.ucsd.edu (8.12.1/8.12.1) with ESMTP id g28CPvrP004505 for ; Fri, 8 Mar 2002 04:25:57 -0800 (PST) Received: from sjins2.sj.google.com (proxy.google.com [216.239.35.5]) by smtp3.google.com with ESMTP id EAA11593 for ; Fri, 8 Mar 2002 04:25:56 -0800 Received: from sjmm36.sj.google.com (sjmm36.prod.google.com [10.6.39.36]) by sjins2.sj.google.com (8.9.3/8.9.3) with ESMTP id EAA08412 for ; Fri, 8 Mar 2002 04:25:55 -0800 Received: (from news@localhost) by sjmm36.sj.google.com (8.9.3/8.9.3) id EAA24099 for bionet-software-srs@moderators.isc.org; Fri, 8 Mar 2002 04:25:55 -0800 To: bionet-software-srs@moderators.isc.org From: Bent.Terp@cgb.ki.se (Bent Terp) Newsgroups: bionet.software.srs Subject: [SwissEntry] file could not be opened "" Organization: http://groups.google.com/ Message-ID: <28c22826.0203080425.64206f3d@posting.google.com> Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Trace: posting.google.com 1015590355 24098 127.0.0.1 (8 Mar 2002 12:25:55 GMT) X-Complaints-To: groups-abuse@google.com NNTP-Posting-Date: 8 Mar 2002 12:25:55 GMT Date: Fri, 8 Mar 2002 15:23:00 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Hi! I'm getting a strange error when retrieving protein sequences. The default view, "SwissEntry" just shows the error icon and the message 'file could not be opened "" '. (I think the two doublequotes are significant here.) When I then press the link for a "TextEntry", everything shows up as you'd expect. The same problem does NOT occur with dna sequences, i.e. "EmblEntry" displays as expected. Any suggestions? with kind regards, Bent Nagstrup Terp Systemadministrator Center for Genomics and Bioinformatics Karolinska Instituttet Berzelius Väg 35 171 77 Stockholm, Sweden PS If anybody wants to view it online, the "SwissEntry" can be seen (or rather, NOT seen...) at , which obviously has links to first the "TextEntry" and then onwards to EMBL PPS Apologies to Don Gilbert, I have some indication that you replied to my previous posting regarding NFS indices, but our newsserver here at Karolinska has been misbehaving, so I never got to read your reply. Could you please email me with it? Tnx From owner-bio-srs@hgmp.mrc.ac.uk Tue Mar 12 09:05:59 2002 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D4AE117B76 for ; Tue, 12 Mar 2002 09:05:58 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 59ED117B77 for ; Tue, 12 Mar 2002 09:05:55 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 1878017A7D; Tue, 12 Mar 2002 09:05:49 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 1114517ACC for ; Mon, 11 Mar 2002 11:55:06 +0000 (GMT) Received: from desdemone.pasteur.fr (desdemone.pasteur.fr [157.99.64.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 8155C17AF0 for ; Mon, 11 Mar 2002 11:54:57 +0000 (GMT) Received: (from news@localhost) by desdemone.pasteur.fr (8.9.3/8.9.3/Debian 8.9.3-21) id MAA11592 for bionet-software-srs@net.bio.net; Mon, 11 Mar 2002 12:54:55 +0100 To: bionet-software-srs@net.bio.net From: lmj@pasteur.fr () Newsgroups: bionet.software.srs Subject: Re: [SwissEntry] file could not be opened "" Organization: Institut Pasteur, Paris, France Message-ID: References: <28c22826.0203080425.64206f3d@posting.google.com> X-Trace: desdemone.pasteur.fr 1015847694 11589 157.99.60.135 (11 Mar 2002 11:54:54 GMT) X-Complaints-To: usenet@pasteur.fr NNTP-Posting-Date: 11 Mar 2002 11:54:54 GMT X-Newsreader: trn 4.0-test76 (Apr 2, 2001) Date: Tue, 12 Mar 2002 09:05:49 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk In article <28c22826.0203080425.64206f3d@posting.google.com>, Bent Terp wrote: >Hi! > >I'm getting a strange error when retrieving protein sequences. The >default view, "SwissEntry" just shows the error icon and the message >'file could not be opened "" '. (I think the two doublequotes are >significant here.) There is a directory tmp in the images directory that needs write permission for the web server userid. This was missed by the installer. Basically, set the permissions for ${SRSWWW}/images/tmp to be the same as ${SRSTMP}. --Louis > >When I then press the link for a "TextEntry", everything shows up as >you'd expect. > >The same problem does NOT occur with dna sequences, i.e. "EmblEntry" >displays as expected. > >Any suggestions? > >with kind regards, > Bent Nagstrup Terp > Systemadministrator > Center for Genomics and Bioinformatics > Karolinska Instituttet > Berzelius Väg 35 > 171 77 Stockholm, Sweden > > >PS If anybody wants to view it online, the "SwissEntry" can be seen >(or rather, NOT seen...) at >, >which obviously has links to first the "TextEntry" and then onwards to >EMBL > >PPS Apologies to Don Gilbert, I have some indication that you replied >to my previous posting regarding NFS indices, but our newsserver here >at Karolinska has been misbehaving, so I never got to read your reply. >Could you please email me with it? Tnx > -- -- Louis Jones /\ Institut Pasteur o / \ 28, rue du Dr. Roux /<(*)/\/ \