From asidhu at biomap.org Sun Oct 1 11:01:29 2006 From: asidhu at biomap.org (Amandeep S. Sidhu) Date: Mon, 2 Oct 2006 01:01:29 +1000 (EST) Subject: [BiO BB] 2nd CFP: IJBRA Special Issue on Ontologies for Bioinformatics Message-ID: <51327.144.136.102.223.1159714889.squirrel@biomap.org> International Journal of Bioinformatics Research and Applications (IJBRA) Special Issue on "Ontologies for Bioinformatics" To be Published as Volume 3, Issue 2 in 2007 https://www.inderscience.com/browse/index.php?journalcode=ijbra Special Issue on Ontologies for Bioinformatics http://ijbra.biomap.org/ Call for Papers Biomedical Ontologies have developed in an uncoordinated way, often reflecting mere relations of 'association' between what are called 'concepts', and serving primarily the purposes of information extraction from on-line biomedical literature and databases. In recent years, we have learned a great deal about the criteria which must be satisfied if ontology is to allow true information integration and automatic reasoning across data and information derived from different sources. The goal of this issue is to survey existing biomedical ontologies and reform them in such a way as to allow true information integration in biomedical domain. Authors are invited to submit original papers to both the sessions exploring the theories, techniques, and applications of biomedical ontologies. Papers are invited (but not limited) to the following themes: * Conceptual Models for Biological and Medical Data. * Semantic Biological Data Modeling. * Use of semantics to manage Interoperation in Biomedical Databases. * Semantic Web technologies and formalisms for Biomedical Data. * OWL and Biomedical Ontologies. * Biomedical Data Engineering using Ontologies. * Biological Data Integration using Ontologies. * Application of Biomedical Ontologies for Heterogeneous Database Access. * Application of Biomedical Ontologies for Issues in Privacy and Security. * Query Optimization Techniques for Biomedical Database using Ontologies. * Support of Ontologies for Biological Information Retrieval and Web Services. * Change Management in Biomedical Ontologies. * Tools for Development and Management of Biomedical Ontologies. Important Dates October 23, 2006 Call for Submissions November 20, 2006 Notification of acceptance December 15, 2006 Final camera-ready paper due January 15, 2006 Issue Deadline Paper Submission Submission and Review Guidelines * No hardcopy submissions are being accepted. * Electronic submissions of original technical research papers will be preferred in PDF format. * Submitted papers should not have been previously published nor be currently under consideration for publication elsewhere. * Include one cover sheet, stating the issue title (Special Issue on Ontologies for Bioinformatics), paper title, authors, keywords, corresponding author's information. * Author names should appear only on the cover sheet, not on the paper. * All papers are refereed through a double blind process. Submission Procedures All submissions will be done electronically via the online submission system for this issue: http://biomap.it.uts.edu.au/ijbra07/ If you have any problems with submission please email: ijbra at biomap.org Templates Please note that the format of submission will be in IJBRA template format. Both MS-Word and Latex format templates are available. Submissions are highly encouraged in this format. A guide for authors, sample copies and other relevant information for submitting papers are available on the Submission Guidelines web-page. Co-Editors * Tharam S. Dillon (University of Technology Sydney, Australia) * Elizabeth Chang (Curtin University of Technology, Australia) * Amandeep S. Sidhu (University of Technology Sydney, Australia) * Jake Chen (Indiana University, USA) Special Issue Review Board * Tharam S. Dillon (University of Technology Sydney, Australia) * Elizabeth Chang (Curtin University of Technology, Australia) * Amandeep S. Sidhu (University of Technology Sydney, Australia) * Philip E. Bourne (University of California San Diego) * Martin Senger (European Bioinformatics Institute) * Midori Harris (European Bioinformatics Institute) * Robert Meersman (Vrije Universiteit Brussel, Belgium) * Mustafa Jarrar (Vrije Universiteit Brussel, Belgium) * Ernesto Damiani (Computer Science Department, Milan University, Italy) * Ling Feng (University of Twente, Netherlands) * Jake Chen (Indiana University, USA) * Suzanna Lewis (Berkeley Drosophila Genome Project) * Mihaela Ulieru (University of New Brunswick, Canada) * Hans-Dieter Ehrich (Technical University of Braunschweig, Germany) * Fabio Porto (Database Laboratory, EPFL, Switzerland) * Rajugan Rajagopalapillai (University of Technology Sydney, Australia) * Manish Bhide (IBM India Research Lab, India) * Paul Kennedy (University of Technology Sydney, Australia) * Wenny Rahayu (La Trobe University, Australia) * Farookh K. Hussain (Curtin University of Technology, Australia) * Pornpit Wongthongtham (Curtin University of Technology, Australia) * Maja Hadzic (Curtin University of Technology, Australia) From iscis06 at sabanciuniv.edu Sun Oct 1 15:35:02 2006 From: iscis06 at sabanciuniv.edu (iscis06) Date: Sun, 01 Oct 2006 22:35:02 +0300 Subject: [BiO BB] ISCIS'06 Call for Participation Message-ID: <45201866.6060102@sabanciuniv.edu> ISCIS'06 Call for Participation The 21st International Symposium on Computer and Information Sciences November 1-2-3, 2006 Istanbul, Turkey Organized by Sabanci University We kindly invite you to participate in the twenty-first of the ISCIS series of conferences that bring together computer scientists and engineers from around the world. This year's conference will be held in Istanbul, Turkey, and co-sponsored by International Federation for Information Processing (IFIP), The Scientific and Technological Research Council of Turkey (TUBITAK) and IEEE Turkey Chapter. The proceedings of ISCIS'06 will be published by Springer-Verlag in LNCS series and the proceedings will be distributed during the symposium. This year, there are various sessions covering several aspects of computer and information sciences: Algorithms and Theory Bioinformatics Computational Intelligence Computer Architecture Computer Graphics Computer Networks Computer Vision Data Mining Databases Embedded Systems Information Retrieval Mobile Computing Parallel and Distributed Computing Performance Evaluation Security and Cryptography Software Engineering There will be five excellent invited talks in ISCIS'06. These talks will be given by Erol Gelenbe of the Imperial College, UK, Daniel Thallman of the EPFL, Switzerland, Jacques Verly of the University of Liege, Belgium and Manfred Broy of the TU- Munich, Germany. Moreover, Eric Badique of the European Commission will give an informative talk on "Information and Communication Technologies in the EU's Seventh Framework Programme". The technical program and the registration details can be reached at http://fens.sabanciuniv.edu/iscis06/ This year, ISCIS will be held in Istanbul, Turkey. Istanbul, which was known as capital of the capital cities, and created huge peace geographies with reigning to first Roma, and then Eastern Roman (Byzantium) Empire and continents, and was the capital city of Ottoman Empire, is going to a modern future with preserving magnificence of history with proud. Variety in Istanbul is really charming the visitors. It is serving infinite nuances with its museums, churches, palaces, mosques, bazaar places and natural beauties. CONTACT INFO ISCIS'06 Sabanci University Faculty of Engineering and Natural Sciences Orhanli Tuzla, 34956 Istanbul, TURKEY E-mail: iscis06 at sabanciuniv.edu Fax: +90 216 4839550 Web: http://fens.sabanciuniv.edu/iscis06/ From barry.hardy at vtxmail.ch Mon Oct 2 18:03:49 2006 From: barry.hardy at vtxmail.ch (Barry Hardy) Date: Tue, 03 Oct 2006 00:03:49 +0200 Subject: [BiO BB] Advances in Drug Discovery & Development Message-ID: <5.0.2.1.0.20061002235731.03080340@pop.vtxmail.ch> The eCheminfo Community of Practice InterAction Meeting "Latest Advances in Drug Discovery & Development" will take place 16-19 October 2006, Bryn Mawr, Philadelphia, USA. The eCheminfo InterAction meeting will discuss the latest developments in virtual screening, structure-based drug design, reaction planning, medicinal chemistry and predictive toxicology supporting decision making in drug discovery & development. The meeting brings together researchers, industry experts and managers, academics and solution providers with a common interest of improving the productivity and effectiveness of modeling and informatics methods in drug discovery, design and development. In addition to meeting presentations, significant time at meetings is reserved for panel discussions, workshops, and evening poster session and networking activities. A parallel InnovationWell Meeting on "Innovation in Life Science & Healthcare Research & Product Development" will also take place at the same location on the same dates. The InnovationWell Program will be concentrating on themes of relevance to FDA's Critical Path initiative including topics in Knowledge Management in Clinical and Translational Research, Decision Support for R&D, Metabolomics, Predictive Toxicology and Biomarkers & Systems Biology approaches. Confirmed Speakers at the Bryn Mawr meeting include: Frank Hollinger (Locus Pharmaceuticals), Erin Duffy (Rib-X), Mike Malams (Wyeth), Debananda Das (NCI), Max Cummings (Johnson & Johnson PR&D), Lance Westerhoff (QuantumBio), Jose Duca (Schering-Plough), Osman Guner (Turquoise Consulting), Hege Beard (Schrodinger), Stan Young (NISS), John Irwin (UCSF), William Douglas Figg (NCI), Daryll Reid (Simbiosys), Gregory Warren (GlaxoSmithKline), Deepak Bandyopadhyay (Johnson & Johnson PR&D), Paul Hawkins (OpenEye), Chris Cooper (BMS), James Arnold (Astra-Zeneca), Phil Edwards (Astra-Zeneca), Pete Connolly (Johnson & Johnson PR&D), Michael Farnum (Johnson & Johnson PRD), Jim Wikel (Coalesix), Tudor Oprea (Univ. New Mexico), Alex Tropsha (UNC), Curt Breneman (RPI), Sanji Bhal (ACD/Labs), Michael Bolger (Simulations Plus), Bob Clark (Tripos), Gilles Klopman (Multicase), Navita Mallalieu (Roche Pharmaceuticals), Deepak Bandyopadhyay (Johnson & Johnson PR&D), Zentam Tsuchihashi (BMS), Peter Henstock (Pfizer), Darius Dziuda (Multivariate bioMarkers Discovery), Keith Elliston (Genstruct), Michael Jones (Novartis), Ansgar J. Pommer (SkinSysTec), Bernd Bonnekoh (Otto-von-Guericke-University), Michael Liebman (Windber Research Institute), Jonathan Sheldon (InforSense), Duane Shugars (Concentia Digital), Jian Wang (Biofortis), Peter Gates (Johnson & Johnson PR&D), Barry Hardy (Douglas Connect), Dennis Underwood (Praxeon), Jeff Spitzner (Rescentris), David Mosenkis (Spotfire), Joel Hoffman (IntraSphere), Delia Wolf (Harvard Medical School), Craig Liddell (Epacris), Joseph Bitran (Enterprizer), Alvin Berger (Metabolon), Gregory Banik (Bio-RAD), George Harrigan (Monsanto), Rick Beger (NCTR, FDA), Don Robertson (Pfizer), Teresa Garret (Duke University), Greg Maguire (SIDMAP), Bruce Kristal (Cornell University), Andrew Lane (JG Brown Cancer Center, U. Louisville), Eric Nemec (Leco Corporation), Oliver Fiehn (UC Davis Genome Center), Susan Connor (Glaxo SmithKline) A poster session will take place on the evening of 18 October. Abstracts should be submitted to eCheminfo [at] douglasconnect.com For those unable to attend the whole meeting special one or two day passes at reduced registration fee rates may be arranged with the conference secretariat. Academic discounts are offered. (Please contact Nicki.Douglas [at] douglasconnect.com) Program (as pdfs): Latest Advances in Drug Discovery & Development Bryn Mawr College, Philadelphia, PA (16-19 October 2006) http://barryhardy.blogs.com/cheminfostream/files/eChemProgramBrynMawr06-web1a4.PDF AND Innovation in Life Science & Healthcare Research & Product Development Bryn Mawr College, Philadelphia, PA (16-19 October 2006) http://barryhardy.blogs.com/theferryman/files/innwprogrambrynmawr06final_web2.pdf The detailed agenda for the meeting with linked abstracts are provided at the following links: http://www.innovationwell.net/COMTY_conferenceprogram/ and http://www.echeminfo.com/COMTY_conferenceprogram/ Updates are provided at the following Blog links: Cheminfostream Blog: http://barryhardy.blogs.com/cheminfostream/ Ferryman Blog http://barryhardy.blogs.com/theferryman/ best regards Barry Hardy Douglas Connect Baermeggenweg 14 Zeiningen, CH-4314 Switzerland Tel: +41 61 851 0170 -------------- next part -------------- An HTML attachment was scrubbed... URL: From xiaowei.jiang at msn.com Tue Oct 3 12:11:16 2006 From: xiaowei.jiang at msn.com (Xiaowei JIANG) Date: Tue, 3 Oct 2006 18:11:16 +0200 Subject: [BiO BB] Looking for PhD positions In-Reply-To: <20061003160154.3591F369161@primary.bioinformatics.org> Message-ID: Dear fellows, I am wrting this letter to ask for information about any PhD positions in the field of Bioinformatics. If you have any news please let me know. Or if you are the supervisor or related personnel please also contact me for further information. I really appreciate your kind help. Kind regards, Xiaowei Jiang ---------------------------------------- Tel: +(00)32-(0)484-926889 University Center for Statistics Faculty of Science Katholieke Universiteit Leuven,Belgium ucs.kuleuven.be ---------------------------------------- MSc Statistics/Mathematics 2005-2007 MSc Bioinformatics, BEng Computer Science ---------------------------------------- Disclaimer:http://www.kuleuven.be/cwis/email_disclaimer.htm From rajkumar.bondugula at gmail.com Thu Oct 5 15:50:57 2006 From: rajkumar.bondugula at gmail.com (Raj) Date: Thu, 5 Oct 2006 14:50:57 -0500 Subject: [BiO BB] protein secondary structure alignment Message-ID: <353b2b10610051250v175c8ec6w9f195e42ec351544@mail.gmail.com> Hello all, Does any one know a nice tool to perfom secondary struture alignment (similar to BLAST multiple sequence alignment on protein sequences). The query to the program is secondary structure sequence. The database contains a bunch of secondary structure sequences (secondary structures corresponding to the proteins in my local database). The reason is I want to retrive structural homolog when the sequence identity between the query protein is too low with any of the proteins in the database. I am aware of SSEA. It is a wonderful program, except that I could not get it to compile that program on Windows (both cygwin and VC++), inspite of spending weeks of time. Ideally, it would be great if I could modify NCBI BLAST (I know I am being greedy, but PSIBLAST) to search for structural homologies (input is a secondary structure sequence, the BLAST databases made up of secondary structures and modify the appropriate scoring matrices). Did any one try this? Regards, Raj From marian.thieme at lycos.de Fri Oct 6 03:54:58 2006 From: marian.thieme at lycos.de (Marian Thieme) Date: Fri, 06 Oct 2006 09:54:58 +0200 Subject: [BiO BB] Consed: combine amplicons of same individual Message-ID: <45260BD2.1050805@lycos.de> Hello, I have a question about the Alignment und Sequence editor Consed, because I want to evaluate and compare some sequence analysis tools to find out which one is best suited for a resequencing project: Is it possible to combine fragments/amplicons so that I get a contiguous sequence. I could imagine, that all fragments of a certain individual are placed in one line, so I can easly browse and edit the sequence for each individual. (Perhaps, overlapping fragments should be merged in some way). (At the moment I havent managed that, so all amplicons are treated seperatly.) Thanks, Marian From tcan at ceng.metu.edu.tr Wed Oct 11 06:47:50 2006 From: tcan at ceng.metu.edu.tr (Tolga Can) Date: Wed, 11 Oct 2006 13:47:50 +0300 Subject: [BiO BB] Call for Papers: International Symposium on Health Informatics and Bioinformatics (HIBIT) 2007 In-Reply-To: <45201866.6060102@sabanciuniv.edu> Message-ID: <20061011104836.E4BC51CD4C8@postman.ceng.metu.edu.tr> HIBIT'07 INTERNATIONAL SYMPOSIUM ON HEALTH INFORMATICS AND BIOINFORMATICS Belek, Antalya, TURKEY April 30 - May 2, 2007 http://hibit.ii.metu.edu.tr/07/index.html Aim of the HIBIT?07 is to bring together academicians from medical, life sciences and IT fields with industry and government for creating synergy and supporting interdisciplinary research and development. It is the second HIBIT conference, with expected participation from all around the world, as in the first one. High Quality Research Submissions are invited for technical papers describing original unpublished results of theoretical, empirical, conceptual, and experimental work. Topics of interest include, but are not limited to: HEALTH INFORMATICS Electronics Health Records and Standards, Clinical Informatics and Hospital Information Systems, Telemedicine and Mobile Applications, Decision Support Systems and Computer Aided Diagnosis, Health Informatics (HI) Education, Security, Ethics and Privacy, Data Mining and Knowledge Discovery in HI, Medical Signal/Image Analysis and Visualization, Medical Imaging and Instrumentation, Virtual Reality and Simulation in HI, Medical Transaction Provision Systems BIOINFORMATICS Biomolecular Sequence Analysis, Comparative Genomics, Biomedical Genome Research, Microarray Informatics, Protein Expression and Modification, Protein Interactions, Protein Structure Prediction, Biomedical Proteome Research, Genetic Networks, Systems Biology, Text mining and Information Extraction, Evolution and Phylogeny, Structural Bioinformatics CONFERENCE CHAIR Nese Yalabik, METU (yalabik at ceng.metu.edu.tr) PROGRAM CHAIRS Nazife Baykal, METU Tolga Can, METU Mesude Iscan, METU Erkan Mumcuoglu, METU ORGANIZING COMMITTEE L. Efe Akman, METU Seref Arikan, Datasel Volkan Atalay, METU Ceren Caner Berkman, METU Didem G?kcay, METU Oya Deniz Kocgil, METU Ismail ?zt?rk, METU ?mer Sinan Sarac, METU Inci Togan, METU ADVISORY BOARD Nihat Akpinar, Ministry of Health, Turkey Ersan Akyildiz, METU Reng?l Atalay, Bilkent U. Song?l Dogan, Ministry of Health, TurkMIA Aydan Erkmen, METU Hakan ?rer, Hacettepe U. Nazmi ?zer, Hacettepe U. Mustafa ?zmen, TurkMIA, Hacettepe U. Zeki Sagay, MNG Bilgisayar Corp. Osman Saka, TurkMIA, Akdeniz U. Ugur Sezerman, Sabanci U. Azmi Telefoncu, Ege U. G. Wilhelm Weber, METU SUBMISSION Papers will be selected on the basis of originality, significance and clarity. Length of submitted full papers is limited to 8 pages. Proceedings will be published before the symposium. Posters reporting on recent research (both theoretical and experimental) are also sought. Abstracts of accepted posters will also be published in the symposium proceedings. A number of tutorials will be given by distinguished Lecturers. CONFERENCE INFORMATION will be available at at the homepage http://hibit.ii.metu.edu.tr/07/index.html, which has been designed to be a living document offering up-to-date news on all conference events, submission instructions and deadlines, hotel information, registration, tourist information, travel, etc.. The continuously updated web pages will help you plan your involvement in the conference. We encourage you to leave your own mark on this important event. IMPORTANT DATES Full paper submission December 1, 2006 Author notification for full papers February 1, 2007 Poster abstract submission February 10, 2007 Author notification for posters February 20, 2007 Camera ready deadline March 1, 2007 The organizers are looking forward to welcoming you to hospitable Turkey! From Bart.Boerjan at student.kuleuven.be Thu Oct 12 15:00:15 2006 From: Bart.Boerjan at student.kuleuven.be (Bart Boerjan) Date: Thu, 12 Oct 2006 21:00:15 +0200 Subject: [BiO BB] max mA in 2D-DIGE Message-ID: <002e01c6ee30$a7636df0$dd245b0a@bartb05c52c91a> dear colleague scientists, I'm a university student in Belgium at the KUL. I'm working on proteomics now and one of the techniques I'm using is 2D-DIGE. I would like to run a strip in second dimension loaded (via IEF) with bacterial cellular peptides. normally we adjust the mA so that the gel runs for about 13 hours. this afternoon we tried for the first time 72mA (instead of 24) for a tank with two gels (so 36mA per gel) and after two hours the tracking dye was already half of the gel, so i wondered could a seperation that goes this fast cauze complications? I found his mailing list via google search, and I hope maybe one of you can answer me, or share an experience sincerely Bart Boerjan Korte Vooruitgangstraat 8 8310 Assebroek-Belgium 0472/53.33.07 Bart.Boerjan at student.kuleuven.Be Barten15 at hotmail.com From codeshepherd at gmail.com Mon Oct 16 12:56:19 2006 From: codeshepherd at gmail.com (Deepan Chakravarthy) Date: Mon, 16 Oct 2006 22:26:19 +0530 Subject: [BiO BB] Smith-Waterman on FPGA In-Reply-To: <20060928065800.15987.qmail@web57007.mail.re3.yahoo.com> References: <20060928065800.15987.qmail@web57007.mail.re3.yahoo.com> Message-ID: <1161017779.19384.10.camel@localhost.localdomain> Hello, I am curious to know if anyone has programmed Smith-Waterman algorithm into FPGA. I guess FPGA is being used to run BLAST. Anyone who is currently playing with FPGA and any of the sequence alignment algorithms please share your experience. Thanks Deepan Chakravarthy N http://www.codeshepherd.com From je64p at yahoo.com Mon Oct 16 16:46:23 2006 From: je64p at yahoo.com (Jean-Etienne Poirrier) Date: Mon, 16 Oct 2006 21:46:23 +0100 (BST) Subject: [BiO BB] Re: max mA in 2D-DIGE In-Reply-To: <20061013160115.EBA57368FCE@primary.bioinformatics.org> Message-ID: <20061016204623.56367.qmail@web54515.mail.yahoo.com> Bart, Are you sure of your solutions? You didn't say anything about your gel concentration. Once, we made a mistake in the gels concentrations and it went (a lot) faster. We are not considering the current when running our 2nd dimension gels but we are considering power ... Here is our protocol: Step 1. 2.5W per gel during 30 minutes (maximum of 600V or 400mA) Step 2. 100W for all gels for a maximum of 5 hours (maximum of 600V or 400mA ; I think it's 5W for all gels for an overnight run but I don't have the protocol here). What are your other parameters? Bart, I'm also a university student in Belgium but at the ULg and working with 2D-DIGE. If you have any other questions, feel free to ask. Yours, Jean-Etienne --- Bart.Boerjan at student.kuleuven.be wrote: > Date: Thu, 12 Oct 2006 21:00:15 +0200 > From: "Bart Boerjan" > > Subject: [BiO BB] max mA in 2D-DIGE > To: > > dear colleague scientists, > > I'm a university student in Belgium at the KUL. I'm > working on proteomics > now and one of the techniques I'm using is 2D-DIGE. > > I would like to run a strip in second dimension > loaded (via IEF) with > bacterial cellular peptides. normally we adjust the > mA so that the gel runs > for about 13 hours. this afternoon we tried for the > first time 72mA (instead > of 24) for a tank with two gels (so 36mA per gel) > and after two hours the > tracking dye was already half of the gel, so i > wondered could a seperation > that goes this fast cauze complications? > > I found his mailing list via google search, and I > hope maybe one of you can > answer me, or share an experience > > sincerely > > Bart Boerjan Jean-Etienne Poirrier, je64p at yahoo.com http://www.poirrier.be/~jean-etienne/ http://www.epot.org/blog/ Send instant messages to your online friends http://uk.messenger.yahoo.com From landman at scalableinformatics.com Tue Oct 17 10:07:53 2006 From: landman at scalableinformatics.com (Joe Landman) Date: Tue, 17 Oct 2006 10:07:53 -0400 Subject: [BiO BB] Smith-Waterman on FPGA In-Reply-To: <1161017779.19384.10.camel@localhost.localdomain> References: <20060928065800.15987.qmail@web57007.mail.re3.yahoo.com> <1161017779.19384.10.camel@localhost.localdomain> Message-ID: <4534E3B9.7070302@scalableinformatics.com> Hi Deepan: Our partner, Progeniq, has this. Deepan Chakravarthy wrote: > Hello, > I am curious to know if anyone has programmed Smith-Waterman algorithm > into FPGA. I guess FPGA is being used to run BLAST. Anyone who is > currently playing with FPGA and any of the sequence alignment > algorithms please share your experience. See http://progeniq.com/product.html for more details. Since they are in Singapore as well, you might contact them directly there. > Thanks > Deepan Chakravarthy N > http://www.codeshepherd.com > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 786 8423 fax : +1 734 786 8452 or +1 866 888 3112 cell : +1 734 612 4615 From xiaowei.jiang at msn.com Wed Oct 18 17:39:46 2006 From: xiaowei.jiang at msn.com (Xiaowei JIANG) Date: Wed, 18 Oct 2006 23:39:46 +0200 Subject: [BiO BB] Using Bioconductor to analyse Microarray data set In-Reply-To: <20061017160132.EDEA3368648@primary.bioinformatics.org> Message-ID: Dear fellows, I would appreciate that if anyone can share your experience using Bioconductor to analysis Microarray data with me. --Do you have any experience with the execution speed and time with specific large Microarray data set (around 30,000 features)? or say with a typical workstation configuration:3GHz Intel P4 CPU, 1GB DDR RAM, 128 DDR RAM Graphic Card GPU 500GHz? --Can Bioconductor handle a extremely large data set? --Any other comments? Kind regards, Xiaowei JIANG ---------------------------------------- University Center for Statistics Faculty of Science Katholieke Universiteit Leuven,Belgium ucs.kuleuven.be ---------------------------------------- From aloraine at gmail.com Wed Oct 18 21:06:39 2006 From: aloraine at gmail.com (Ann Loraine) Date: Wed, 18 Oct 2006 20:06:39 -0500 Subject: [BiO BB] Using Bioconductor to analyse Microarray data set In-Reply-To: References: <20061017160132.EDEA3368648@primary.bioinformatics.org> Message-ID: <83722dde0610181806q3ec1e9eja3a25592226e86dc@mail.gmail.com> Hi, It depends in part on the number of arrays you're dealing with. My Mac laptop (G3, ~ 1 gig memory) can process 20 CEL files (Affy rat 230, RMA, quantile normalization) in a reasonable time. (I did this tonite -- I started the job, ate my dinner, and when I had finished the meal, the job was done :-) -Ann On 10/18/06, Xiaowei JIANG wrote: > Dear fellows, > > I would appreciate that if anyone can share your experience using > Bioconductor to analysis Microarray data with me. > > --Do you have any experience with the execution speed and time with specific > large Microarray data set (around 30,000 features)? > or say with a typical workstation configuration:3GHz Intel P4 CPU, 1GB DDR > RAM, 128 DDR RAM Graphic Card GPU 500GHz? > > --Can Bioconductor handle a extremely large data set? > > --Any other comments? > > Kind regards, > Xiaowei JIANG > ---------------------------------------- > University Center for Statistics > Faculty of Science > Katholieke Universiteit Leuven,Belgium > ucs.kuleuven.be > ---------------------------------------- > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Ann Loraine Assistant Professor Section on Statistical Genetics University of Alabama at Birmingham http://www.ssg.uab.edu http://www.transvar.org From pfern at igc.gulbenkian.pt Tue Oct 17 08:57:58 2006 From: pfern at igc.gulbenkian.pt (Pedro Fernandes) Date: Tue, 17 Oct 2006 13:57:58 +0100 Subject: [BiO BB] Smith-Waterman on FPGA In-Reply-To: <1161017779.19384.10.camel@localhost.localdomain> References: <20060928065800.15987.qmail@web57007.mail.re3.yahoo.com> <1161017779.19384.10.camel@localhost.localdomain> Message-ID: <1161089878.4534d356da2dd@webmail.igc.gulbenkian.pt> I haven't tried, but I guess that http://www.clccube.com/flexible.html has it ready for testing, in a box wuth USB connection. -- Pedro Fernandes Quoting Deepan Chakravarthy : > Hello, > I am curious to know if anyone has programmed Smith-Waterman algorithm > into FPGA. I guess FPGA is being used to run BLAST. Anyone who is > currently playing with FPGA and any of the sequence alignment > algorithms please share your experience. > Thanks > Deepan Chakravarthy N > http://www.codeshepherd.com > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From hershel.safer at weizmann.ac.il Tue Oct 17 10:02:41 2006 From: hershel.safer at weizmann.ac.il (Hershel Safer) Date: Tue, 17 Oct 2006 16:02:41 +0200 Subject: [BiO BB] ECCB 06: Call for Late-Breaking Results Message-ID: <4534E281.40101@weizmann.ac.il> 5th European Conference on Computational Biology - ECCB '06 Eilat, Israel January 21-24, 2007 www.eccb06.org Call for Late-Breaking Results: Oral Presentations and Posters You are invited to submit your latest research results to a special "Late-Breaking Results Session" that will be held at ECCB in Eilat. Short extended abstracts are solicited (up to three pages, not including references and figures and tables containing experimental results). Six (6) submissions will be accepted for oral presentations in a special session, and an additional 30 will be accepted as late-breaking posters. The extended abstract should clearly identify the novel aspects of the contribution and how it relates to existing techniques. Only one submission per author is allowed. Topics of interest are the same as for the regular sessions (see the conference website, http://www.eccb06.org/new_pages/submission/sub_callFor.html) . Submit your manuscript to http://www.easychair.org/ECCB06Ext/ by October 26, 2006, 11 pm GMT. Authors will be notified by November 15, 2006. Each submission will be refereed by at least two members of the special "late-breaking results" session program committee. The late-breaking papers will not be published in the conference proceedings and so can be submitted in parallel to an archival journal. The abstracts will be included in the conference program book and the conference CD. Results should be novel and should not be published or presented at another conference before January 21, 2007. Special-Session Program Committee: Hanah Margalit - Hebrew University of Jerusalem Michal Linial - Hebrew University of Jerusalem Ron Pinter - Technion - Israel Institute of Technology Eytan Ruppin - Tel Aviv University Hershel Safer - Weizmann Institute of Science Ron Shamir - Tel Aviv University Jeffrey Skolnick - Georgia Institute of Technology Martin Vingron - Max Planck Institute for Molecular Genetics Haim Wolfson, Chair - Tel Aviv University -- Hershel M. Safer, Ph.D. Chair, 5th European Conference on Computational Biology (ECCB '06) Head, Bioinformatics Unit, Department of Biological Services Weizmann Institute of Science Levine Building, PO Box 26, Rehovot 76100, Israel v: +972-8-934-3456 | f: +972-8-934-6006 | skype: hsafer e: hershel.safer at weizmann.ac.il | hsafer at alum.mit.edu w: http://bioportal.weizmann.ac.il | http://alum.mit.edu/www/hsafer *************************************************** Plan now for ECCB '06! 5th European Conference on Computational Biology Eilat, Israel, January 21-24, 2007 Visit www.eccb06.org for details -------------- next part -------------- An HTML attachment was scrubbed... URL: From roland at luethy.net Tue Oct 17 11:15:28 2006 From: roland at luethy.net (Roland Luethy) Date: Tue, 17 Oct 2006 08:15:28 -0700 Subject: [BiO BB] Smith-Waterman on FPGA In-Reply-To: <1161017779.19384.10.camel@localhost.localdomain> Message-ID: <200610171515.k9HFFV0r017559@luethy.net> Depaan, TimeLogic has Smith-Waterman using FPGA, as well as BLAST. See www.timelogic.com. Roland ---------------------------------------------------------------------- Roland Luethy mailto:luethy at activemotif.com Director Bioinformatics Research TimeLogic Biocomputing Active Motif Inc. Phone: (805) 386-2158 Fax: (206) 203-2027 ---------------------------------------------------------------------- > -----Original Message----- > From: > bio_bulletin_board-bounces+roland=luethy.net at bioinformatics.or > g > [mailto:bio_bulletin_board-bounces+roland=luethy.net at bioinform > atics.org] On Behalf Of Deepan Chakravarthy > Sent: Monday, October 16, 2006 9:56 AM > To: General Forum at Bioinformatics.Org > Cc: anand at novaglobal.com.sg; henny at novaglobal.com.sg; > ivanho at novaglobal.com.sg > Subject: [BiO BB] Smith-Waterman on FPGA > > Hello, > I am curious to know if anyone has programmed Smith-Waterman > algorithm into FPGA. I guess FPGA is being used to run BLAST. > Anyone who is currently playing with FPGA and any of the > sequence alignment algorithms please share your experience. > Thanks > Deepan Chakravarthy N > http://www.codeshepherd.com > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From wharman at prism.net Tue Oct 17 12:51:06 2006 From: wharman at prism.net (William Harman) Date: Tue, 17 Oct 2006 10:51:06 -0600 Subject: [BiO BB] Smith-Waterman on FPGA In-Reply-To: <1161017779.19384.10.camel@localhost.localdomain> Message-ID: <02a501c6f20c$737c4090$8f662a42@WHARMAN> Star Bridge Systems in Salt Lake City set this up in early 2002 for the US National Cancer Institute. http://www.starbridgesystems.com/news/43/national-cancer-institute-nci-purch ases-starbridge-hypercomputer-to-accelerate-genome-data-research You can find more examples on their web site. Bill Harman, P - (801) 572-9252 F - (801) 571-4927 wharman at prism.net ------ High Performance Computing Solutions ------ -----Original Message----- From: bio_bulletin_board-bounces+wharman=prism.net at bioinformatics.org [mailto:bio_bulletin_board-bounces+wharman=prism.net at bioinformatics.org] On Behalf Of Deepan Chakravarthy Sent: Monday, October 16, 2006 10:56 AM To: General Forum at Bioinformatics.Org Cc: anand at novaglobal.com.sg; henny at novaglobal.com.sg; ivanho at novaglobal.com.sg Subject: [BiO BB] Smith-Waterman on FPGA Hello, I am curious to know if anyone has programmed Smith-Waterman algorithm into FPGA. I guess FPGA is being used to run BLAST. Anyone who is currently playing with FPGA and any of the sequence alignment algorithms please share your experience. Thanks Deepan Chakravarthy N http://www.codeshepherd.com _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From marty.gollery at gmail.com Tue Oct 17 08:57:49 2006 From: marty.gollery at gmail.com (Martin Gollery) Date: Tue, 17 Oct 2006 05:57:49 -0700 Subject: [BiO BB] Smith-Waterman on FPGA In-Reply-To: <1161017779.19384.10.camel@localhost.localdomain> References: <20060928065800.15987.qmail@web57007.mail.re3.yahoo.com> <1161017779.19384.10.camel@localhost.localdomain> Message-ID: Quite a few people have done this, Deepan. It is much easier than BLAST! Compugen, TimeLogic, Progeniq, CLCbiosystems, Adaptive Genomics, Mitrion, and several academic groups have ported it. Cheers, Marty On 10/16/06, Deepan Chakravarthy wrote: > > Hello, > I am curious to know if anyone has programmed Smith-Waterman algorithm > into FPGA. I guess FPGA is being used to run BLAST. Anyone who is > currently playing with FPGA and any of the sequence alignment > algorithms please share your experience. > Thanks > Deepan Chakravarthy N > http://www.codeshepherd.com > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From wharman at prism.net Tue Oct 17 18:11:41 2006 From: wharman at prism.net (William Harman) Date: Tue, 17 Oct 2006 16:11:41 -0600 Subject: [BiO BB] Smith-Waterman on FPGA In-Reply-To: <1161017779.19384.10.camel@localhost.localdomain> Message-ID: <003901c6f239$3cbbdc00$93662a42@WHARMAN> The algorithm Starbridge programmed is Smith-Waterman. We currently can perform ~20 Billion Smith-Waterman steps per second per HC-62 which translates into 1.5 days for the entire x vs y chromosomes (30M X 140M). Any questions let me know Kent Gilson KGilson at starbridgesystems.com Star Bridge Systems in Salt Lake City set this up in early 2002 for the US National Cancer Institute. http://www.starbridgesystems.com/news/43/national-cancer-institute-nci-purch ases-starbridge-hypercomputer-to-accelerate-genome-data-research You can find more examples on their web site. Bill Harman, P - (801) 572-9252 F - (801) 571-4927 wharman at prism.net ------ High Performance Computing Solutions ------ -----Original Message----- From: bio_bulletin_board-bounces+wharman=prism.net at bioinformatics.org [mailto:bio_bulletin_board-bounces+wharman=prism.net at bioinformatics.org] On Behalf Of Deepan Chakravarthy Sent: Monday, October 16, 2006 10:56 AM To: General Forum at Bioinformatics.Org Cc: anand at novaglobal.com.sg; henny at novaglobal.com.sg; ivanho at novaglobal.com.sg Subject: [BiO BB] Smith-Waterman on FPGA Hello, I am curious to know if anyone has programmed Smith-Waterman algorithm into FPGA. I guess FPGA is being used to run BLAST. Anyone who is currently playing with FPGA and any of the sequence alignment algorithms please share your experience. Thanks Deepan Chakravarthy N http://www.codeshepherd.com _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From nuraini at cs.usm.my Tue Oct 17 20:46:26 2006 From: nuraini at cs.usm.my (Nur'Aini Abd.Rashid) Date: Wed, 18 Oct 2006 08:46:26 +0800 (SGT) Subject: [BiO BB] Smith-Waterman on FPGA In-Reply-To: <1161017779.19384.10.camel@localhost.localdomain> References: <20060928065800.15987.qmail@web57007.mail.re3.yahoo.com> <1161017779.19384.10.camel@localhost.localdomain> Message-ID: Look at work by Liao h.Y et. al (2004) On Mon, 16 Oct 2006, Deepan Chakravarthy wrote: > Date: Mon, 16 Oct 2006 22:26:19 +0530 > From: Deepan Chakravarthy > Reply-To: General Forum at Bioinformatics.Org > > To: General Forum at Bioinformatics.Org > > Cc: anand at novaglobal.com.sg, henny at novaglobal.com.sg, ivanho at novaglobal.com.sg > Subject: [BiO BB] Smith-Waterman on FPGA > > Hello, > I am curious to know if anyone has programmed Smith-Waterman algorithm > into FPGA. I guess FPGA is being used to run BLAST. Anyone who is > currently playing with FPGA and any of the sequence alignment > algorithms please share your experience. > Thanks > Deepan Chakravarthy N > http://www.codeshepherd.com > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From xiaowei.jiang at msn.com Thu Oct 19 14:37:46 2006 From: xiaowei.jiang at msn.com (Xiaowei JIANG) Date: Thu, 19 Oct 2006 20:37:46 +0200 Subject: [BiO BB] Re: Using Bioconductor to analyse Microarray data In-Reply-To: <20061019012908.76EA436968A@primary.bioinformatics.org> Message-ID: Dear ANN? That sounds interesting. Thanks. I will try Bioconductor later on. Kind regards, Xiaowei JIANG ---------------------------- UCS, K.U.Leuven, Belgium From bioinfosm at gmail.com Thu Oct 19 11:39:53 2006 From: bioinfosm at gmail.com (Samantha Fox) Date: Thu, 19 Oct 2006 11:39:53 -0400 Subject: [BiO BB] PISE interface for blast Message-ID: <726450810610190839x233db8c4h830a9d24026dfc6d@mail.gmail.com> Hi, any of you familiar with generating PISE interface for a database that I wish to blast. Do we have to write a separate xml for that ? Any help or suggestion would be welcome. Thanks, ~S -------------- next part -------------- An HTML attachment was scrubbed... URL: From skhadar at gmail.com Fri Oct 20 06:53:00 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Fri, 20 Oct 2006 16:23:00 +0530 Subject: [BiO BB] Re: [BioPython] Automated ligand extraction from PDB In-Reply-To: References: <200610200252.34046.tomee@genesilico.pl> Message-ID: I strongly beleive this can be done using a 'grep' and 'substitution' commands in linux. Since the ligand data starts with HETATM, they can be easily grepable. No need any 'parser' - a simple perl script can do this ! Cheers, Shameer Khadar NCBS-TIFR B'lore On 10/20/06, Tomek Jarzynka wrote: > > Hi, > > I would like to create a script that would take a PDB file as input, > try and identify the ligand structures and delete them from the PDB > file. I figured this would be possible with Biopython by looking at > the atom id (whether it contains 'H_') and subclassing Select to > not allow those items to be written to a file. > Is there any more elegant way of doing this, perhaps another PDB parser > framework, or maybe someone has already done similar work? > > Thanks in advance, > -- > Tomasz K. Jarzynka / +48 601 706 601 / tomee(a-t)genesilico(d-o-t)pl > Laboratory of Bioinformatics and Protein Engineering | www.genesilico.pl > International Institute of Molecular and Cell Biology | www.iimcb.gov.pl > > "You can have either freedom of speech or quality of communication. > -- Orson Scott Card" > _______________________________________________ > BioPython mailing list - BioPython at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biopython > -------------- next part -------------- An HTML attachment was scrubbed... URL: From landman at scalableinformatics.com Fri Oct 20 08:48:31 2006 From: landman at scalableinformatics.com (Joe Landman) Date: Fri, 20 Oct 2006 08:48:31 -0400 Subject: [BiO BB] [Fwd: [blast-announce] BLAST-Announce #056] BLAST 2.2.15 released] Message-ID: <4538C59F.7050104@scalableinformatics.com> -------- Original Message -------- Subject: [blast-announce] BLAST-Announce #056] BLAST 2.2.15 released Date: Fri, 20 Oct 2006 08:37:34 -0400 Notes for the 2.2.15 release BLAST 2.2.15 is now available from the BLAST download page. Major changes include: * BLAST now uses a 28-letter protein alphabet supporting the J (leucine or isoleucine) and O (pyrrolysine) residues. * formatrpsdb will now generate RPS blast databases that assume a 28-letter alphabet. These databases are incompatible with rpsblast versions older than 2.2.15. * blastpgp can now combine the e-value from the alignment with a p-value determined by the composition to yield a unified e-value that is ultimately used to evaluate the significance of alignments. This behavior can be enabled with the -t 1u or -t 2u options. * megablast now supports incremental ASN.1 output. This behavior can be enabled with the -D 4 and -D 5 options. * BLAST binaries are now available for Windows XP/2003 x64 edition. * blastx searches are now significantly faster for queries exceeding 10kbp in length. * seedtop can now perform pattern searches even if the pattern is considered too likely to occur. This behavior can be enabled with the -f option. * BLAST now natively supports the BLOSUM50 and BLOSUM90 score matrices. * BLAST now correctly handles databases restricted by gi lists even if no sequences will be searched. * blastall now prints a header for each query even if queries have been concatenated. If you have any questions please write to blast-help at ncbi.nlm.nih.gov Scott D. McGinnis, M.S. DHHS/NIH/NLM/NCBI www.ncbi.nlm.nih.gov -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 786 8423 fax : +1 734 786 8452 or +1 866 888 3112 cell : +1 734 612 4615 From ethan.strauss at promega.com Fri Oct 20 10:44:47 2006 From: ethan.strauss at promega.com (Ethan Strauss) Date: Fri, 20 Oct 2006 09:44:47 -0500 Subject: [BiO BB] PISE interface for blast In-Reply-To: <726450810610190839x233db8c4h830a9d24026dfc6d@mail.gmail.com> Message-ID: Hi, I am working with a PISE interface for BLAST right now. I don't pretend to be know what I am doing, but I am doing something :-) Anyway, I could send you the interface I have and you could at least use it as a starting point. Alternately, you could take a look at http://www.pasteur.fr/recherche/unites/sis/Pise/XML/. There is an example there... Ethan ________________________________ From: bio_bulletin_board-bounces+ethan.strauss=promega.com at bioinformatics.org [mailto:bio_bulletin_board-bounces+ethan.strauss=promega.com at bioinformat ics.org] On Behalf Of Samantha Fox Sent: Thursday, October 19, 2006 10:40 AM To: The general forum at Bioinformatics.Org Subject: [BiO BB] PISE interface for blast Hi, any of you familiar with generating PISE interface for a database that I wish to blast. Do we have to write a separate xml for that ? Any help or suggestion would be welcome. Thanks, ~S -------------- next part -------------- An HTML attachment was scrubbed... URL: From skhadar at gmail.com Fri Oct 20 12:38:24 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Fri, 20 Oct 2006 22:08:24 +0530 Subject: [BiO BB] PISE interface for blast In-Reply-To: References: <726450810610190839x233db8c4h830a9d24026dfc6d@mail.gmail.com> Message-ID: Dear Ethan, I also need to impliment Pise interface for Several bioinfo program to be used internally for a bioinformatics course. It will be nice If you can explain - step-by-step . Cheers, Shameer Khadar On 10/20/06, Ethan Strauss wrote: > > Hi, > I am working with a PISE interface for BLAST right now. I don't > pretend to be know what I am doing, but I am doing something :-) > Anyway, I could send you the interface I have and you could at least > use it as a starting point. Alternately, you could take a look at > http://www.pasteur.fr/recherche/unites/sis/Pise/XML/. There is an example > there... > Ethan > > ------------------------------ > *From:* bio_bulletin_board-bounces+ethan.strauss= > promega.com at bioinformatics.org [mailto: > bio_bulletin_board-bounces+ethan.strauss=promega.com at bioinformatics.org] *On > Behalf Of *Samantha Fox > *Sent:* Thursday, October 19, 2006 10:40 AM > *To:* The general forum at Bioinformatics.Org > *Subject:* [BiO BB] PISE interface for blast > > > Hi, > any of you familiar with generating PISE interface for a database that I > wish to blast. > Do we have to write a separate xml for that ? Any help or suggestion would > be welcome. > > Thanks, > ~S > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From letondal at pasteur.fr Fri Oct 20 05:28:53 2006 From: letondal at pasteur.fr (Catherine Letondal) Date: Fri, 20 Oct 2006 11:28:53 +0200 Subject: [BiO BB] PISE interface for blast In-Reply-To: <726450810610190839x233db8c4h830a9d24026dfc6d@mail.gmail.com> References: <726450810610190839x233db8c4h830a9d24026dfc6d@mail.gmail.com> Message-ID: <5f522e75259be01522ca4286ddd51eff@pasteur.fr> Hi Samantha, On Oct 19, 2006, at 5:39 PM, Samantha Fox wrote: > > Hi, > any of you familiar with generating PISE interface for a database that > I wish to blast. > Do we have to write a separate xml for that ? Any help or suggestion > would be welcome. > > Thanks, > ~S > There are indeed separate XML files for that. It's called protdbs.xml and nucdbs.xml HTH, -- Catherine Letondal -- Institut Pasteur www.pasteur.fr/recherche/unites/sis/Pise From paolo.romano at istge.it Fri Oct 20 05:42:53 2006 From: paolo.romano at istge.it (Paolo Romano) Date: Fri, 20 Oct 2006 11:42:53 +0200 Subject: [BiO BB] NETTAB 2007 on A Semantic Web for Bioinformatics Message-ID: <7.0.1.0.0.20061020113641.01d2e2a8@istge.it> This message will be posted to many mailing lists. Sorry for the duplications. --- Preliminar announcement Workshop NETTAB 2007 focused on A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications June 12-15, 2007, Pisa, Italy http://www.nettab.org/2007/ Scientific Programme Overview NETTAB 2007 workshop intends to focus on the Semantic Web, as it is defined in the action statements of the WorldWideWeb Consortium (W3C) (see http://www.w3.org/2001/sw/) and in its possible uses in bioinformatics. It therefore aims at: - introducing the basic knowledge of related standards and technologies, in a non trivial way through invited lectures - outlining the promising features of the semantic web in bioinformatics through invited lectures and open discussion - showing some valuable examples in bioinformatics through invited lectures, oral communications and posters - allowing for as much discussion as possible through open discussions and a panel discussion - demonstrating "how it works" practically through tutorials For these reasons, the workshop will include: - invited lectures on technological issues, perspectives and examples in bioinformatics - oral communications on applications, tools and examples in bioinformatics - a panel discussion on perspectives of the Semantic Web in bioinformatics - a poster session - tutorials, both on implementation of tools and technologies and on the best practice in bioinformatics Note that, starting from this edition, NETTAB workshops will also include special sessions devoted both to the general theme of the series of workshops, i.e. "Network Tools and Applications in Biology", and on further topics selected by local organizers. This year, you are therefore welcome to submit your work on any of the followings topics: - Main focus theme: Semantic Web applications in bioinformatics - Adjunct focus themes: Algorithms in bioinformatics and Formal Methods for Systems Biology - General theme: Network Tools and Applications in Bioinformatics GOALS Biological information is increasing at an impressive rate. An integrated access to this huge amount of information requires complex searching and retrieval software. In particular, this integration activity is concerned with how to link data, how to select and extract information and how to pipe retrieval and analysis steps. This automated approach requires the adoption of new technologies and tools and their applications in the bioinformatics domain. Some reference points have already been assessed or are now emerging: the adoption of XML schemas for the creation of the models of the information, the definition of XML based languages for data representation and exchange, the implementation of Web Services for the interoperability of software aiming to an automated access to data and analysis tools, the creation of computerised pipelines and workflows for the definition and automated execution of both basic and complex analysis processes of interest to the researchers. Workflow enactment portals can also bring some added value by allowing all researchers, even the non expert ones, access to automated processes. However, while these first steps towards integration of data and automation of real processes have been made, little has been made for supporting semantic integration. What we need are common definitions of knowledge domains, e.g. ontologies, association of biological concepts to existing data, metadata information describing all information sources and searching tools that are able to make the best use of this additional information. The definition of common ontologies and their application to software and database tools may be seen as a first, needed attempt to organize the information, overcoming heterogeneity of data structures, but the problem of associating the huge amount of information included in existing databases and information sources with concepts defined in these ontologies is a big one. Anyway, the addition of semantic contents in current databases would give an essential contribution to the best integration of biological distributed information. At the same time, the development of metadata for biological information, on the basis of Semantic Web standards and tools, and its definition for all information sources, not only databases, can also be seen as a promising approach for a future, semantic based integration of biological information. Text mining is of a fundamental importance in research since literature is still the most relevant information source in biomedical research. It is the most evident example of an unstructured information source whose content should be integrated with structured data in order to achieve the best results. TOPICS Goals of the Semantic Web for Bioinformatics: - Roles and uses of ontologies in knowledge discovery, text analysis and data mining - Expected results of adoption of Semantic Web tools in Bioinformatics Standards, Technologies, Tools: - Semantic Web standards (RDF, OWL, .) - RDF Schemas and Query systems - Biomedical Ontologies and related tools - Formal approaches to large biomedical controlled terminologies and vocabularies Systems: - RDF repositories and query systems for life sciences - Semantically aware biomedical Web Services - Semantic Biological Data Integration Systems Existing and perspective applications: - Case studies, use cases, and scenarios - Semantic Web applications in life sciences CHAIRS P. Romano, Bioinformatics, National Cancer Research Institute, Italy M. Schr?der, Biotechnology Centre, TU Dresden, Germany N. Cannata, Mathematics and Computer Science, University of Camerino, Italy O. Signore, ISTI, National Research Council, Italy PROGRAMME COMMITTEE G. Armano, Electrical and Electronic Engineering Dept, Univ. of Cagliari, IT C. Baker, Institute for Infocomm Research (I2R), SG P. Barahona, Department of Informatics, New University of Lisboa, PT L. Barrio-Alvers, Transinsight GmbH, DE O. Bodenreider, National Library of Medicine, USA A. Burger, Department of Computer Science, Heriot-Watt University, UK M. Cannataro, Experimental and Clinical Medicine Dept, Univ. of Catanzaro "Magna Graecia", IT W. Ceusters, Bioinformatics and Life Sciences, University at Buffalo, USA M. Cockerill, BioMed Central, UK M.-D. Devignes, LORIA, Vandoeuvre les Nancy, FR R. Dieng, INRIA, Sophia Antipolis, FR L. Grivell, European Molecular Biology Organisation, DE M. Harris, European Bioinformatics Institute, UK M. Helmer-Citterich, Biology Dept, University of Rome "Tor Vergata", IT C. M. Keet, Computer Science Faculty, Free University of Bozen-Bolzano, IT J. Koehler, Biomathematics and Bioinformatics, Rothamsted Research, UK M. Krallinger, Spanish National Cancer Research Center (CNIO), ES L. Krippahl, Department of Informatics, New University of Lisboa, PT P. Lambrix, Computer and Information Science Dept, Link?ping University, SE U. Leser, Institute for Computer Science, Humboldt-University of Berlin, DE J. Luciano, Department of Genetics, Harvard Medical School, USA R. Marangoni, Computer Science Department, University of Pisa, IT M. Marchiori, Pure and Applied Mathematics Dept, University of Padua, IT M. Masseroli, Department of BioEngineering, Polytechnic of Milan, IT G. Mauri, Informatics Systems and Communication Dept, Univ. Milan "Bicocca", IT E. Merelli, Mathematics and Computer Science Dept, University of Camerino, IT L. Milanesi, Biomedical Technologies Institute, National Research Council, IT S. Moeller, Institute of Neuro- and Bioinformatics, University of L?beck, DE S. Philippi, Institute for Software Technology, Univ. of Koblenz-Landau, DE D. Quann, IBM Software Group, USA D. Rubin, Stanford Medical Informatics, Stanford University Medical Center, USA S.-A. Sansone, European Bioinformatics Institute, UK M. Senger, International Rice Research Institute, PH D. Turi, School of Computer Science, University of Manchester, UK G. Vetere, IBM Center for Advanced Studies of Rome, IT D. Zaccagnini, Language and Computing, USA Paolo Romano (paolo.romano at istge.it) Bioinformatics and Structural Proteomics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 From rich at thevillas.eclipse.co.uk Fri Oct 20 08:42:54 2006 From: rich at thevillas.eclipse.co.uk (rich) Date: Fri, 20 Oct 2006 13:42:54 +0100 Subject: [BiO BB] predicting promoter regions In-Reply-To: References: Message-ID: <4538C44E.4040204@thevillas.eclipse.co.uk> Hi, can anybody recommend any tools for predicting promoter/regulatory regions? I believe TRANSFAC is one? Any others that people would recommend? Cheers Rich From DGURGUL at PARTNERS.ORG Fri Oct 20 08:58:05 2006 From: DGURGUL at PARTNERS.ORG (Gurgul, Dennis J.) Date: Fri, 20 Oct 2006 08:58:05 -0400 Subject: [BiO BB] PISE interface for blast In-Reply-To: <726450810610190839x233db8c4h830a9d24026dfc6d@mail.gmail.com> Message-ID: <11821FC5155A5A48AB5CF6480C46D86403790FDF@PHSXMB1.partners.org> I'm sure Chris Dwan or Chris Dagdigian at http://web.bioteam.net/metadot/index.pl could tell you all about it. Dennis Gurgul Partners HealthCare Research Computing 617.724.3169 http://www.partners.org/rescomputing/ ________________________________ From: bio_bulletin_board-bounces+dgurgul=partners.org at bioinformatics.org [mailto:bio_bulletin_board-bounces+dgurgul=partners.org at bioinformatics.org] On Behalf Of Samantha Fox Sent: Thursday, October 19, 2006 11:40 AM To: The general forum at Bioinformatics.Org Subject: [BiO BB] PISE interface for blast Hi, any of you familiar with generating PISE interface for a database that I wish to blast. Do we have to write a separate xml for that ? Any help or suggestion would be welcome. Thanks, ~S -------------- next part -------------- An HTML attachment was scrubbed... URL: From ethan.strauss at promega.com Fri Oct 20 15:31:08 2006 From: ethan.strauss at promega.com (Ethan Strauss) Date: Fri, 20 Oct 2006 14:31:08 -0500 Subject: [BiO BB] PISE interface for blast In-Reply-To: Message-ID: Hi Shameer, I really don't understand PISE anywhere near well enough to explain it. When I said I was working with right now I should have added that I am working with it for the first time. Maybe I will actually understand it better in a few months, but not yet. Sorry, Ethan ________________________________ From: bio_bulletin_board-bounces+ethan.strauss=promega.com at bioinformatics.org [mailto:bio_bulletin_board-bounces+ethan.strauss=promega.com at bioinformat ics.org] On Behalf Of Shameer Khadar Sent: Friday, October 20, 2006 11:38 AM To: General Forum at Bioinformatics.Org Subject: Re: [BiO BB] PISE interface for blast Dear Ethan, I also need to impliment Pise interface for Several bioinfo program to be used internally for a bioinformatics course. It will be nice If you can explain - step-by-step . Cheers, Shameer Khadar On 10/20/06, Ethan Strauss wrote: Hi, I am working with a PISE interface for BLAST right now. I don't pretend to be know what I am doing, but I am doing something :-) Anyway, I could send you the interface I have and you could at least use it as a starting point. Alternately, you could take a look at http://www.pasteur.fr/recherche/unites/sis/Pise/XML/. There is an example there... Ethan ________________________________ From: bio_bulletin_board-bounces+ethan.strauss=promega.com at bioinformatics.org [mailto:bio_bulletin_board-bounces+ethan.strauss=promega.com at bioinformat ics.org ] On Behalf Of Samantha Fox Sent: Thursday, October 19, 2006 10:40 AM To: The general forum at Bioinformatics.Org Subject: [BiO BB] PISE interface for blast Hi, any of you familiar with generating PISE interface for a database that I wish to blast. Do we have to write a separate xml for that ? Any help or suggestion would be welcome. Thanks, ~S _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From letondal at pasteur.fr Sat Oct 21 08:29:26 2006 From: letondal at pasteur.fr (Catherine Letondal) Date: Sat, 21 Oct 2006 14:29:26 +0200 Subject: [BiO BB] PISE interface for blast In-Reply-To: References: <726450810610190839x233db8c4h830a9d24026dfc6d@mail.gmail.com> Message-ID: <504220861a29744c269a4c858b72906f@pasteur.fr> On Oct 20, 2006, at 6:38 PM, Shameer Khadar wrote: > Dear Ethan, > > I also need to impliment Pise interface for Several bioinfo program to > be used internally for a bioinformatics course. It will be nice If you > can explain - step-by-step . > > Cheers, > Shameer Khadar > > Dear Shameer, Explanations and examples for defining the XML files can be found there: http://www.pasteur.fr/recherche/unites/sis/Pise/#progdesc Do not hesitate to ask for help (pise at pasteur.fr). Best, -- Catherine Letondal -- Institut Pasteur www.pasteur.fr/recherche/unites/sis/Pise From skhadar at gmail.com Mon Oct 23 03:20:41 2006 From: skhadar at gmail.com (Shameer Khadar) Date: Mon, 23 Oct 2006 12:50:41 +0530 Subject: [BiO BB] predicting promoter regions In-Reply-To: <4538C44E.4040204@thevillas.eclipse.co.uk> References: <4538C44E.4040204@thevillas.eclipse.co.uk> Message-ID: Hi, Try TOUCAN : http://homes.esat.kuleuven.be/~saerts/software/toucan.php -- Shameer On 10/20/06, rich wrote: > > Hi, > > can anybody recommend any tools for predicting promoter/regulatory > regions? > I believe TRANSFAC is one? Any others that people would recommend? > > Cheers > Rich > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jmuralie at gmail.com Sun Oct 22 23:47:55 2006 From: jmuralie at gmail.com (Muralidharan Jayaraman) Date: Sun, 22 Oct 2006 22:47:55 -0500 Subject: [BiO BB] Course for Medical Instrumentation Message-ID: <200610222247.56266.jmuralie@gmail.com> Hi all, I would like to know if anyone can give me some information about a course that would lead to a MS in "Medical Instrumentation". Most of the courses offered are "Biomedical Engineering". Any information regarding this course is appreciated. Thanks, Murali. From ybolo001 at student.ucr.edu Mon Oct 23 03:25:04 2006 From: ybolo001 at student.ucr.edu (Eugene Bolotin) Date: Mon, 23 Oct 2006 00:25:04 -0700 Subject: [BiO BB] predicting promoter regions In-Reply-To: References: <4538C44E.4040204@thevillas.eclipse.co.uk> Message-ID: <941fcc750610230025r56453bb9m23d0b5334d9b9276@mail.gmail.com> MotifScanner/MotifLocaoter are command line stand alone programs which are pretty good. Eugene On 10/23/06, Shameer Khadar wrote: > > Hi, > > Try TOUCAN : http://homes.esat.kuleuven.be/~saerts/software/toucan.php > -- > Shameer > > On 10/20/06, rich wrote: > > > > Hi, > > > > can anybody recommend any tools for predicting promoter/regulatory > > regions? > > I believe TRANSFAC is one? Any others that people would recommend? > > > > Cheers > > Rich > > _______________________________________________ > > General Forum at Bioinformatics.Org - > > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From golharam at umdnj.edu Wed Oct 25 00:21:53 2006 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 25 Oct 2006 00:21:53 -0400 Subject: [BiO BB] BLAST (and others) RPM available Message-ID: <002e01c6f7ed$1a7a4b90$2f01a8c0@GOLHARMOBILE1> I've constructed RPMs for various Open Source tools and just updated the NCBI rpm to incorporate the new version of BLAST 2.2.15. All RPMs are available for download from http://serine.umdnj.edu/~golharam/biorpms. If you have any questions, please feel free to email me. -- Ryan Golhar, PhD - golharam at umdnj.edu The Informatics Institute of UMDNJ From ykalidas at gmail.com Wed Oct 25 23:32:05 2006 From: ykalidas at gmail.com (Kalidas Yeturu) Date: Thu, 26 Oct 2006 09:02:05 +0530 Subject: [BiO BB] Re: [BioPython] Automated ligand extraction from PDB In-Reply-To: References: <200610200252.34046.tomee@genesilico.pl> Message-ID: <5632703b0610252032x6b1b5784wab3b7e009c1103d5@mail.gmail.com> Hi I would like to add to what Mr.Shameer has said. When DNA is a ligand, in many PDB files, it goes with ATOM instead of HETATM -token; in such cases you can "grep" on "A or T or C or G" for residue-name field. Regards Kalidas. Y On 10/20/06, Shameer Khadar wrote: > > I strongly beleive this can be done using a 'grep' and 'substitution' > commands in linux. > Since the ligand data starts with HETATM, they can be easily grepable. > > No need any 'parser' - a simple perl script can do this ! > Cheers, > Shameer Khadar > NCBS-TIFR > B'lore > > On 10/20/06, Tomek Jarzynka wrote: > > > > Hi, > > > > I would like to create a script that would take a PDB file as input, > > try and identify the ligand structures and delete them from the PDB > > file. I figured this would be possible with Biopython by looking at > > the atom id (whether it contains 'H_') and subclassing Select to > > not allow those items to be written to a file. > > Is there any more elegant way of doing this, perhaps another PDB parser > > framework, or maybe someone has already done similar work? > > > > Thanks in advance, > > -- > > Tomasz K. Jarzynka / +48 601 706 601 / tomee(a-t)genesilico(d-o-t)pl > > Laboratory of Bioinformatics and Protein Engineering | www.genesilico.pl > > International Institute of Molecular and Cell Biology | www.iimcb.gov.pl > > > > "You can have either freedom of speech or quality of communication. > > -- Orson Scott Card" > > _______________________________________________ > > BioPython mailing list - BioPython at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biopython > > > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > -- Kalidas Y http://ssl.serc.iisc.ernet.in/~kalidas -------------- next part -------------- An HTML attachment was scrubbed... URL: From tho at ifs.tuwien.ac.at Thu Oct 26 04:43:28 2006 From: tho at ifs.tuwien.ac.at (Nguyen Manh Tho) Date: Thu, 26 Oct 2006 10:43:28 +0200 Subject: [BiO BB] Call for papers - CISIS 2007: First International Conference on Complex, Intelligent and Software Intensive Systems In-Reply-To: <4538C59F.7050104@scalableinformatics.com> Message-ID: <200610260843.k9Q8hch0016601@mr.tuwien.ac.at> (Apologies for multiple copies due to cross postings. Please send to interested colleagues and students) Call for Papers ##################################################################### First International Conference on Complex, Intelligent and Software Intensive Systems (CISIS-2007) http://www.cisis-conference.eu/ April 10 - April 13, 2007 Vienna, Austria ##################################################################### To be held in conjunction with: ARES-2007 International Conference http://www.ares-conference.eu/ Aim ====== The aim of the conference is to deliver a platform of scientific interaction between the three interwoven challenging areas of research and development of future ICT-enabled applications: - Software Intensive Systems - Complex systems - Intelligent Systems Software Intensive Systems are systems which heavily deal with other systems, sensors, actuators, devices, other software systems and users. More and more domains are involved with software intensive systems, i.e. automotive, telecommunication systems, embedded systems in general, industrial automation systems, business applications. The outcome of web services delivers a new platform for enabling software intensive systems. The conference will focus on tools, practically relevant and heoretical foundations for engineering software intensive systems. Complex Systems Research is focused on the overall understanding of systems rather than its components. The ICT-enabling aspect of Complex Systems is the focus of the contributions to be presented at CISIS 2007. Complex Systems are very much characterised by the changing environments in which they act and by their multiple internal and external interactions. They evolve and adapt through internal and external dynamic interactions. The development of Intelligent Systems and agents which is more and more characterised by the use of ontologies and their logical foundations build a fruitful impulse for both Software intensive Systems and Complex Systems. Recent research in the field of intelligent systems ?robotics, neuroscience, artificial intelligence, and cognitive sciences- builds an important factor for the future development and innovation of software intensive and complex systems. CISIS 2007 is aiming at delivering a forum for in-depth scientific discussions amongst the three communities leading to significant contributions in areas such as: - Monitoring and Control of Large Systems or Environments. - Managing the hetrogeneity of knowledge by means of ontologies - Use of Sevice Oriented Architectures for complex applications in business and industries - The consideration of Software Intensive Systems as Complex Systems - Enabling of Systems Biology concepts as software intensive conmplex systems - Knowledge management of complex IT-systems etc. Scope ========= Networks of today are going through a rapid evolution. Different kinds of systems with different characteristics are emerging and they are integrating in heterogeneous networks. For these reasons, there are many interconnection problems which may occur at different levels in the hardware and software design of communicating entities and communication networks. These kinds of networks need to manage an increasing usage demand, provide support for a significant number of services, guarantee their QoS, and optimize the utilization of network resources. Therefore, architectures and algorithms in these networks become very complex and it seems imperative to focus on new models and methods as well as mechanisms, which can enable the network to perform adaptive behaviors. Many new computing technologies have emerged as new paradigms for solving complex problems by enabling large-scale aggregation and sharing of computational, data and other geographically distributed resources. Rapid advances are being reported by many researchers and forums as regards understanding numerous issues in such paradigms, from theoretic to application aspects. Moreover, the continuous development of Internet and the construction of new infrastructures are making possible the development of large scale applications from many fields of science and engineering. To deal with complexity, we should construct physically instantiated systems that can perceive, understand, and interact with their environment ? but also evolve in order to achieve human-like performance in activities requiring context-specific knowledge. This is far beyond the current state of the art and will remain so for many years to come. Therefore, many research efforts are required to make headway towards this vision. The strategic challenges are motivated by recent research in the field of intelligent systems ? robotics, neuroscience, artificial intelligence, and cognitive sciences. In recent years, a large community of researchers has begun to realize the importance of brain-body interaction for understanding intelligence and its central role in a wide range of processes including perception, object manipulation, movement, and high-level cognition. The research challenges include theoretical frameworks based on the notions of embodiment, the dynamical systems metaphor, complete agents rather than individual components, self-reconfiguration and self-repair, morphology and development. Progress in the theoretical underpinnings of embodied intelligence will have strong technological implications in areas including robotics, actuator technology, materials, self-assembling systems. Research in intelligent and cognitive systems is an interdisciplinary field requiring the cooperation of researchers from artificial intelligence, neuroscience (including cognitive and computational), psychology (cognitive and developmental), linguistics, developmental biology, robotics (and engineering in general), biomechanics, and dynamical systems. Software has become a central part of a rapidly growing range of applications, products and services from all sectors of economic activity. Systems in which software interacts with other software, systems, devices, sensors and with people are called software- intensive systems. Examples include large-scale heterogeneous systems, embedded systems for automotive and avionics applications, telecommunications, wireless ad hoc systems, business applications with an emphasis on web services. Our daily activities increasingly depend on complex software-intensive systems that are becoming ever more distributed, heterogeneous, decentralized and inter-dependent, and that are operating more and more in dynamic and often unpredictable environments. There exist different kinds of complexity in the development of software. Software systems grew larger, the focus shifted from the complexity of developing algorithms to the complexity structuring large systems, and then to the additional complexities in building distributed, concurrent systems. In the next ten to fifteen years we will have to face another level of complexity arising from the fact that systems have to operate in large, open and non- deterministic environments: the complexity of knowledge, interaction and adaptation. Instead of developing computer-oriented systems where people have to adapt to the computer we have to develop human- oriented systems into which computers integrate seamlessly. Also, the requirements for software quality will dramatically increase. But our current methods are not sufficient to deal with adaptive software in a dynamic environment, especially not for large systems with complex interactions. We need to develop practically useful and theoretically well founded principles, methods and tools for engineering future software-intensive systems. All the complex systems depend on software that controls the behavior of individual components and the interaction between components, and on software which interacts with other software, systems, devices, sensors and with people. In other words: they depend on software- intensive systems. The CISIS-2007 seeks original contributions in all relevant areas, including but not limited to the following topics. Topics of interest ====================== ? Agent Technology ? Human-Oriented Systems ? Evolving Systems ? Intelligent and Cognitive Systems and Applications ? Genetic Programming and Algorithms ? Fuzzy Logic and Fuzzy Systems ? Neuro-computing and Applications ? Knowledge-based Systems ? Dynamic Systems ? Parallel and Distributed Algorithms ? Databases and Data Mining ? Grid and P2P Infrastructures ? Data Intensive and Computing Intensive Applications ? Scheduling, Resource Discovery and Allocation ? JXTA-based Applications ? Large-scale Collaborative Problem Solving Environments ? Methodology and Practice of Semantic Grid and Web ? Web and Grid Service-based Applications ? Ubiquitous Computing Applications ? Pervasive Computing and Applications ? Multimedia Systems and Applications ? Human-Robots ? Embedded Systems ? Overlay Networks for P2P Systems ? Autonomous Systems ? Autonomic Computing ? Bio-inspired Systems and Applications ? Fault-Tolerant Systems ? Heterogeneous Networks ? Heterogeneous Wireless Networks ? Sensor Networks ? Ad Hoc Networks ? Sensor and Actor Networks ? High-Speed Networks ? Routing Algorithms ? Software QoS ? Adaptive Software-Intensive Systems ? Self-Modifying Software Systems ? Self-Designing and Self-Maintaining software Important Dates ================== ? Submission Deadline: November 30, 2006 ? Author Notification: January 10, 2007 ? Author Registration: January 21, 2007 ? Proceedings Version: January 21, 2007 ? Workshop Dates: April 10-April13, 2007 Submission Guidelines ========================= Authors are invited to submit research and application papers following the IEEE Computer Society Proceedings Manuscripts style: two columns, single-spaced, including figures and references, using 10 fonts, and number each page. You can confirm the IEEE Computer Society Proceedings Author Guidelines at one of the following web pages: * http://www.ieee.org/portal/pages/pubs/transactions/stylesheets.html * or http://www.tinmith.net/tabletop2006/IEEE/Format/instruct.htm Submission papers are classified into 3 categorizes (1) full paper (8 pages), (2) short paper (5 pages), and (3) poster (2 pages) representing original, previously unpublished work. Submitted papers will be carefully evaluated based on originality, significance, technical soundness, and clarity of exposition. Contact author must provide the following information at the CISIS- 2007 web site: paper title, authors' names, affiliations, postal address, phone, fax, and e-mail address of the author(s), about 200- 250 word abstract, and about five keywords. Submission of a paper implies that should the paper be accepted, at least one of the authors will register and present the paper in the conference. Accepted papers will be given guidelines in preparing and submitting the final manuscript(s) together with the notification of acceptance. Proceedings of the CISIS-2007 conference will be published by IEEE Computer Society Press. Based on quality and referee reviews, some papers not suitable for acceptance as full paper will be accepted for presentation at CISIS-2007 in Poster category and will be also included in the IEEE Proceedings. The best papers selected by CISIS- 2007 program committee out of papers accepted for presentation at CISIS-2007 will be further published in some International Journals. The submission site for CISIS-2007 paper is available at http://www.ares-conf.org/confdriver/?q=confdriver/papers/add If you have any difficluty in submitting the papers, please do not hesitate to send them to tho at ifs.tuwien.ac.at. Conference Chairpersons ============================ Leonard Barolli, Fukuoka Institute of Technology, Japan A Min Tjoa, Vienna University of Technology, Austria International Liaison Co-Chairs ================================= Makoto Takizawa, Tokyo Denki University, Japan Arjan Durresi, Louisiana State University, USA Publicity Chairs ===================== Nguyen Manh Tho, Vienna University of Technology, Austria Fatos Xhafa, Polytechnic University of Catalonia, Spain Publication Co-Chairs ======================== Yoshitaka Shibata, Iwate Prefectural University, Japan Roland Wagner, University of Linz, Austria Local Organizing Chairs ========================== Maria Schweikert, Vienna University of Technology, Austria Markus Klemen, Vienna University of Technology, Austria Program Committee ===================== ? Chandra Krintz, University of California, USA ? Mukesh Mohania, IBM India Research Laboratory, India ? Tomoya Enokido, Risho University, Japan ? Joan Manel Marqu?s, Open University of Catalonia, Spain ? Akio Koyama, Yamagata University, Japan ? Nguyen Manh Tho, Vienna University of Technology, Austria ? Fatos Xhafa, Polytechnic University of Catalonia, Spain ? Arjan Durresi, Louisiana State University, USA ? Naohiro Hayashibara, Tokyo Denki University, Japan ? Claudi Paniagua Maci, IBM GTS, Virtualization and Grid Computing EBO, Spain ? Irfan Awan, University of Bradford, UK ? Hui-huang Hsu, Tamkang University, Taiwan ? Jin Hwan Park, State University of New York New Paltz, USA ? Kuo-Ming Chao, Coventry University, UK ? Muhammed Younas, Oxford Brookes University, UK ? Bhed Bahadur Bista, Iwate Prefectural University, Japan ? Minoru Uehara, Toyo University, Japan ? Elhadi Shakshuki, Acadia Univiversity, Canada ? David Taniar, Monash University, Australia ? Nobuyoshi Sato, Toyo University, Japan ? Hiroaki Kikuchi, Tokai University, Japan ? Sajid Hussain, Acadia University, Canada ? Fumiaki Sato, Toho University, Japan ? Kaoru Sugita, Fukuoka Institute of Technology, Japan ? Timothy K. Shih, Tamkang University, Taiwan ? Markus Aleksy, University of Mannheim, Germany ? Takahiro Hara, Osaka University, Japan ? Takuo Suganuma, Tohoku University, Japan ? Wenny Rahayu, La Trobe University, Australia ? Ismail Khalil Ibrahim, Johannes Kepler University Linz, Austria ? Giuseppe De Marco, Fukuoka Institute of Technology, Japan ? G?nther Pernul, University of Regensburg, Germany ? Andrei Doncesku, University Paul Sabatier, France ? Lin Guan, Loughborough University, UK ? Frank Ball, Bournemouth University, UK ? Ahmed Al-Dubai, Napier University, UK ? Qiang Ni, Brunel University, UK ? Juan Jose Alcaraz Espin, Polytechnic University of Cartagena, Spain ? Winston Seah, Institute for Infocomm Research, Singapore ? Antonio Pescape, University of Napoli, Italy ? Leonid Kalinichenko, Russian Academy of Science, Russia ? Lawrence Y. Deng, St. John's and St.Mary's Institute of Technology, Taiwan ? Xiangen Hu, University of Memphis, USA ? Ching-Sheng Wang, Aletheia University, Taiwan ? Kuei-Ping Shih Tamkang University, Taiwan ? Been-Chian Chien, National University of Tainan, Taiwan ? Wen-Yang Lin, National University of Kaohsiung, Taiwan ? Vincent Lee, Monash University, Australia ? Michael Sheng, CSIRO ICT Centre, Australia ? Soraya Kouadri M., Oxford Brookes University, UK ? S.C. Cheung, Hong Kong University of Science and Technology (HKUST), Hong Kong ? Karl R.P.H. Leung, Hong Kong Institute of Vocational Education (Tsing Yi) HKIVE, Hong Kong ? Victor C.S. Lee, City University of Hong Kong, Hong Kong ? Henry Chan, Hong Kong Polytechnic University, Hong Kong ? Hon-Va Leong, Hong Kong Polytechnic University, Hong Kong ? Qing Lu, Hong Kong Polytechnic University, Hong Kong ? Thomas Grill, University of Linz, Austria ? Fabio Postiglione, University of Salerno, Italy ? Said Mirza, Advanced Institute of Science and Technology, Japan ? Ajith Abraham, Yonsei University, Korea ? Takuo Nakashima, Kyushu Tokai University, Japan For any further questions or inquiries please contact Conference Organizers: Conference Organizers: ========================= Leonard Barolli Department of Information and Communication Engineering Faculty of Information Engineering Fukuoka Institute of technology (FIT) 3-30-1 Wajiro-Higashi, Higashi-ku, Fukuoka 811-0295 Japan Email: barolli at fit.ac.jp A Min Tjoa Institute for Software Technology and Interactive Systems Vienna University of Technology, Austria Favoritenstrasse 9-11/188 A-1040 Vienna, Austria E-mail: tjoa at ifs.tuwien.ac.at Nguyen Manh Tho Institute for Software Technology and Interactive Systems Vienna University of Technology, Austria Favoritenstrasse 9-11/188 A-1040 Vienna, Austria E-mail: tho at ifs.tuwien.ac.at From asidhu at biomap.org Sat Oct 28 03:33:50 2006 From: asidhu at biomap.org (Amandeep S. Sidhu) Date: Sat, 28 Oct 2006 17:33:50 +1000 (EST) Subject: [BiO BB] 2nd CFP: IEEE Workshop on Biomedical Applications for Digital Ecosystems (BADE 2007) Message-ID: <3356.144.136.102.183.1162020830.squirrel@biomap.org> 2007 IEEE Workshop on Biomedical Applications for Digital Ecosystems (BADE 2007) with Inaugural IEEE International Digital Ecosystems and Technology Conference 2007 20 February 2007, Cairns, Australia http://bade07.biomap.org/ Scope of the workshop: The primary focus of BADE 2007 workshop is to share research applications using biomedical data and to identify new issues and directions for future research in biomedical applications. Authors are invited to submit original papers to the workshop exploring theories, techniques, and applications for biomedicine. Papers are invited, but not limited to the following themes: * Bioinformatics and Computational Biology * Data Representation and Visualization * Biological Databases & Data Integration * Microarray analysis * Protein and RNA structure prediction * Feature selection and pattern discovery in biological data * System Biology and Pathways * Biomedical Ontologies and taxonomies * Text Mining * Health Care Information Systems * Electronic Health Records * Clinical Assessment and Patient Diagnosis * Disease Control and Prevention * Privacy and Security in Healthcare Important Dates: * Submission of Full Papers: November 10, 2006 * Noification of Acceptance: December 10, 2006 * Camera-ready Copies of papers: December 31, 2006 Paper Submission Procedures: All paper submissions will be handled electronically at: http://bradleyuniversityvolunteer.ieee-ies.org/submit/dest07/ * Authors are Invited to submit electronically, a full paper (6 pages, about 4500 words, PDF file) of their original work. * Select "W01: Biomedical Applications" in Technical Track drop down menu on Author Page. High quality papers in biomedical applications are solicited. Original papers exploring new directions will receive especially careful and supportive reviews. Papers that have already been accepted or are currently under review for other conferences or journals will not be considered for publication at IEEE DEST 2007. Paper submissions should be in the IEEE 2-column format, and will be reviewed by the Program Committee on the basis of technical quality, relevance, originality, significance, and clarity. Accepted IEEE BADE 2007 will be published in the conference proceedings by IEEE Industrial Electronics Society and will be included in EI index and IEEE Xplore. General Chairs: Tharam S. Dillon (University of Technology Sydney, Australia) Elizabeth Chang (Curtin University of Technology, Australia) Program Chairs: Amandeep S. Sidhu (University of Technology Sydney, Australia) Xiaohua Hu (Drexel University, USA) Farookh Hussain (Curtin University of Technology, Australia) Maja Hadzic (Curtin University of Technology, Australia) For further inquiries, please contact bade07 at biomap.org -- Amandeep S. Sidhu, MIEEE, MACM, MAPBioNet Researcher (Bioinformatics) Room CB10.04.130 Faculty of Information Technology University of Technology, Sydney PO Box 123 Broadway, NSW 2007, Australia UTS Email: asidhu"AT SIGN"it.uts.edu.au Personal Email: asidhu"AT SIGN"biomap.org Personal Web: http://www.amandeep.org/ Project Web: http://www.proteinontology.info/ Ph: +61 2 9514 4469 Fax: +61 2 9514 1807 Mobile: +61 448897900 From maximilianh at gmail.com Sun Oct 29 18:08:31 2006 From: maximilianh at gmail.com (Maximilian Haeussler) Date: Mon, 30 Oct 2006 00:08:31 +0100 Subject: [BiO BB] predicting promoter regions In-Reply-To: <4538C44E.4040204@thevillas.eclipse.co.uk> References: <4538C44E.4040204@thevillas.eclipse.co.uk> Message-ID: <76f031ae0610291508r28e9f2cm1363a5b2de80543d@mail.gmail.com> Hi Rich, I don't think that you have a good understanding of the difference between predicting enhancers/promoters on the one and analysing their content on the other hand. transfac isn't a software and cannot predict promoters. In short: a) promotor are assumed to be located to the start of transcription you can use software like FIE or dragon promoter prediction for these. b) enhancers are the other type of cis-regulatory elements. you can use software like phastCons or RP on UCSC (current version is called ESPERR) to predict them. This assumes multiple alignments available for your sequences c) once you have them identified you can apply transfac scanners like those from toucan for them. But you should really know what you are doing here. Try a random sequence to get an impression that toucan can predict anything everywhere. You can have a look at my masters at http://www.stud.uni-potsdam.de/masters or at my transcriptional regulation wiki www.stud.uni-potsdam.de/wiki. for an introduction to promoter prediction / analysis you can try the tutorials at genomatix.de. Any other introductions available that anyone knows of? Cheers, Max On 20/10/06, rich wrote: > Hi, > > can anybody recommend any tools for predicting promoter/regulatory regions? > I believe TRANSFAC is one? Any others that people would recommend? > > Cheers > Rich > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Maximilian Haeussler, skype: maximilianhaeussler From maximilianh at gmail.com Sun Oct 29 18:16:19 2006 From: maximilianh at gmail.com (Maximilian Haeussler) Date: Mon, 30 Oct 2006 00:16:19 +0100 Subject: [BiO BB] Seqio and fmtseq In-Reply-To: References: Message-ID: <76f031ae0610291516p4e48d48ag6949e77282ecffc0@mail.gmail.com> do you have them available for download anywhere? why not post the url to this board and maybe something like nodalpoint.org or the bioperl mailing list so people searching for them one day in google will find them... thanks max On 13/09/06, Li, Alex wrote: > > > > > We have got the fixes for James Knight's legend seqio and fmtseq to get > compiled and work on linux. > > > > Let me know if anyone is still interested in compiling seqio on linux or > newer unix machines. > > > > Alex Li > > Bioinformatics > > 515-334-4736 > > > > Alex.li at pioneer.com > > > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > -- Maximilian Haeussler, skype: maximilianhaeussler From ethan.strauss at promega.com Mon Oct 30 15:53:19 2006 From: ethan.strauss at promega.com (Ethan Strauss) Date: Mon, 30 Oct 2006 14:53:19 -0600 Subject: [BiO BB] RefSeq coverage? In-Reply-To: <76f031ae0610291508r28e9f2cm1363a5b2de80543d@mail.gmail.com> Message-ID: Hi, Does any one know what sort of coverage RefSeq has for various species? If I have an arbitrary human mRNA, I feel pretty sure that it will be represented in the RNA section of RefSeq. I also would feel OK about E. coli, mouse, rat C. elegans and a few others. But, I don't know about dog, cow, rice, soybean and so forth. I would love a listing that had something that listed coverage info for DNA, RNA, and proteins for various species. Does anything like this exist? Thanks! Ethan Ethan Strauss Ph.D. Bioinformatics Scientist Promega Corporation 2800 Woods Hollow Rd. Madison, WI 53711 608-274-4330 800-356-9526 ethan.strauss at promega.com From basu at pharm.sunysb.edu Mon Oct 30 16:00:09 2006 From: basu at pharm.sunysb.edu (Siddhartha Basu) Date: Mon, 30 Oct 2006 16:00:09 -0500 Subject: [BiO BB] RefSeq coverage? In-Reply-To: References: Message-ID: <454667D9.8090606@pharm.sunysb.edu> Ethan Strauss wrote: > Hi, > Does any one know what sort of coverage RefSeq has for various > species? If I have an arbitrary human mRNA, I feel pretty sure that it > will be represented in the RNA section of RefSeq. I also would feel OK > about E. coli, mouse, rat C. elegans and a few others. But, I don't know > about dog, cow, rice, soybean and so forth. I would love a listing that > had something that listed coverage info for DNA, RNA, and proteins for > various species. > Does anything like this exist? > Thanks! > Ethan Hi, Go to the taxonomy browser and search for your species of interest. For example, this page gives the coverage for dog......... http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9615&lvl=3&lin=f&keep=1&srchmode=1&unlock Hope this helps. -siddhartha > > Ethan Strauss Ph.D. > Bioinformatics Scientist > Promega Corporation > 2800 Woods Hollow Rd. > Madison, WI 53711 > 608-274-4330 > 800-356-9526 > ethan.strauss at promega.com > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dafniosn at post.tau.ac.il Tue Oct 31 02:02:43 2006 From: dafniosn at post.tau.ac.il (Osnat Dafni) Date: Tue, 31 Oct 2006 09:02:43 +0200 Subject: [BiO BB] Error messages when running blastpgp (NCBI PSI-BLAST) Message-ID: <1162278163.4546f513af14e@webmail.tau.ac.il> Hi, I'm trying to run the local version of ncbi psi-blast (blastpgp) using a self-generated database and a fasta query file. I get the following error messages repeatedly while the program runs: [NULL_Caption] ERROR: ncbiapi [000.000] BioseqFindFunc: couldn't uncache [NULL_Caption] ERROR: ncbiapi [000.000] ObjMgrNextAvailEntityID failed with idx 2048 I'm using the following command line: blastpgp -d db_file -i query_file -e 1.0 -m 8 -o output_file -I T -a 2 -j 4 -h 0.001 While experimenting I've noticed that when replacing the option "-m 8" (tabular output format) with "-m 0" (default output format), the errors go away. Does any one has any information about what could be causing these errors? Thanks in advance. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From idoerg at burnham.org Tue Oct 31 14:12:16 2006 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue, 31 Oct 2006 11:12:16 -0800 Subject: [BiO BB] Error messages when running blastpgp (NCBI PSI-BLAST) In-Reply-To: <1162278163.4546f513af14e@webmail.tau.ac.il> References: <1162278163.4546f513af14e@webmail.tau.ac.il> Message-ID: <4547A010.60201@burnham.org> Osnat Dafni wrote: need more info.. how did you formatdb your database? Iddo > Hi, > > I'm trying to run the local version of ncbi psi-blast (blastpgp) using a > self-generated database and a fasta query file. I get the following error > messages repeatedly while the program runs: > > [NULL_Caption] ERROR: ncbiapi [000.000] BioseqFindFunc: couldn't uncache > [NULL_Caption] ERROR: ncbiapi [000.000] ObjMgrNextAvailEntityID failed with idx > 2048 > > I'm using the following command line: > > blastpgp -d db_file -i query_file -e 1.0 -m 8 -o output_file -I T -a 2 -j 4 -h > 0.001 > > While experimenting I've noticed that when replacing the option "-m 8" (tabular > output format) with "-m 0" (default output format), the errors go away. > > Does any one has any information about what could be causing these errors? > Thanks in advance. > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037 Tel: (858) 646 3100 x3516 Fax: (858) 795 5249 ** NEW ** http://iddo-friedberg.org http://BioFunctionPrediction.org From bioinfosm at gmail.com Tue Oct 31 16:58:39 2006 From: bioinfosm at gmail.com (Samantha Fox) Date: Tue, 31 Oct 2006 16:58:39 -0500 Subject: [BiO BB] NJ distance matrix error (Phylip) Message-ID: <726450810610311358n11a01346x71f21c8d9e957c52@mail.gmail.com> Hi, I had a very simple question. The distance matrix I input to Neighbor-Joining gives error for incorrect input file ! Here is the matrix dmel 0 13 13 25 29 31 28 34 29 23 22 23 dsim 13 0 6 16 22 28 31 35 30 28 27 24 dsec 13 6 0 18 20 32 33 39 28 28 25 24 dyak 25 16 18 0 20 30 33 37 28 32 27 26 dere 29 22 20 20 0 24 29 33 34 28 27 24 dana 31 28 32 30 24 0 31 31 32 28 29 22 dpse 28 31 33 33 29 31 0 10 37 31 28 29 dper 34 35 39 37 33 31 10 0 39 33 34 27 dwil 29 30 28 28 34 32 37 39 0 32 31 24 dmoj 23 28 28 32 28 28 31 33 32 0 21 20 dvir 22 27 25 27 27 29 28 34 31 21 0 23 dgri 23 24 24 26 24 22 29 27 24 20 23 0 Can someone please point as to what can be the error in this distance matrix ?? Thanks, ~S -------------- next part -------------- An HTML attachment was scrubbed... URL: