From hershel.safer at weizmann.ac.il Mon May 2 06:57:29 2005 From: hershel.safer at weizmann.ac.il (Hershel Safer) Date: Mon, 02 May 2005 13:57:29 +0300 Subject: [BiO BB] Only 2 weeks left for ISMB registration discount! Message-ID: <42760799.8070106@weizmann.ac.il> REGISTER NOW for ISMB 2005: June 25-29, 2005 BIG SAVINGS for registration before May 16! The world's largest and longest-running bioinformatics conference! Held in the USA for the first time in 5 years. http://www.iscb.org/ismb2005/ See below for more detailed information or visit the URLs listed. Don't miss out! Register today and save! - Over 100 scientific paper presentations! - Over 600 posters! - Prominent Keynote Speakers - Over 70 abstract presentations from select posters! - Over 70 software demonstrations! - New special interest workshops and panel sessions - 14 Half day tutorial sessions - 10 one and two-day Special Interest Group Meetings (SIG?s) - Over 40 exhibitors! Join us for ISMB 2005, back in the US in one of the most convenient locations in recent years -- hosted by the University of Michigan. ISMB is the single best resource to hear about the newest developments in bioinformatics for genomics, proteomics, biotechnology, and medicine. And for those with an affinity for stochastic processes, Detroit's luxury casinos will provide an interesting diversion. Organizers: David J. States (University of Michigan) and Brian D. Athey (Michigan Center for Biological Information and the University of Michigan) Panel discussions and workshops: - Bioterrorism/Biosecurity - Getting the Grant: Tips on writing grant applications to Federal Agencies - NIH Funding Initiatives and Future Directions Tutorials: http://www.iscb.org/ismb2005/tutorials.html - Integration and Analysis of Diverse Genomic Data; Olga Troyanskaya, Princeton University - Optimal Design and Analysis of Microarray Experiments; Ernst Wit and John McClure, University of Glasgow - RNA: Algorithms for Structure Prediction and Gene-finders; Peter Clote, Boston College - Developing and Using Special Purpose Hidden Markov Model Databases; Martin Gollery, University of Nevada, Reno - Weighted Finite-State Transducers in Computational Biology; Corinna Cortes, Google, Inc., and Mehryar Mohri, New York University - Semantic Aggregation, Integration and Inference of Pathway Data; Joanne Luciano and Jeremy Zucker, Harvard Medical School - Attacking Performance Bottlenecks; Ruud van der Pas, Sun Microsystems, and Karl V. Steiner, University of Delaware - Principles of Ontology Construction; Suzanna Lewis, University of California, Berkeley - Introduction to Phylogenetic Networks; Daniel Huson, Tuebingen University - Mining the Biomedical Literature: State of the Art, Challenges and Evaluation Issues; Hagit Shatkay, Queen's University, Kingston, Ontario - Gene Expression Levels as Traits in Genetic Linkage Analysis; Steffen Muller, University of Rostock, and Robert Hoffman, EBI - A Bioinformatics Introduction to Cluster Computing; Andrew Boyd and Abhijit Bose, University of Michigan - Computational Geometry of Protein Structure and Function; Iosif Vaisman, George Mason University - A Massively Parallel High Performance Computing Environment for Computational Biology; Gyan Bhanot and Bob Germain, IBM T. J. Watson Research Center Pre-Conference Special Interest Groups (SIGs): http://www.iscb.org/ismb2005/sigs.html - Alternative Splicing - Automated Function Prediction - Bioinformatics and Disease - Bioinformatics Open Source Conference (BOSC) - BioLINK - Bio-Ontologies - BioPathways / SigSim Keynote Speakers: http://www.iscb.org/ismb2005/keynotes.html - Howard Cash, CEO of Gene Codes - Peter Hunter, Computational Physiology and IUPS Physiome Project, University of Auckland - Jill Mesirov, The Broad Institute -- MIT - Satoru Miyano, Gene networks play a central role in systems biology. Human Genome Center University of Tokyo - Pavel Pevzner, Transforming Mice into Men: Fragile versus Random Breakage Models of Chromosome Evolution. Department of Computer Science and Engineering -- University of California at San Diego - Gunnar von Heijne, Membrane Proteins in vivo and in silico -- Getting the Best of Two Worlds, Department of Biochemistry & Biophysics, Stockholm Bioinformatics Center - ISCB Overton Prize Winner: Ewan Birney, EMBL-EBI - ISCB Senior Scientist Award Winner: Janet Thornton, EMBL-EBI Scientific Paper Presentations: http://www.iscb.org/ismb2005/papers.html This year the paper presentations are organized into ten tracks representing the diversity of research that constitutes computational biology. This is your opportunity learn about the latest research on computational methods, their application to biological problems, and the insights gained from this work. - Databases and Ontologies; Area Chairs: Susan Davidson and Carol Goble - Sequence Analysis; Area Chair: Des Higgins - Text Mining; Area Chair: Dietrich Rebholz-Schuhmann - Pathways, Networks and Systems; Area Chairs: Alfonso Valencia and Vincent Schachter - Evolution and Phylogeny; Area Chairs: Olivier Gascuel and Dannie Durand - Proteomics; Area Chair: Michal Linial - Transcriptome; Area Chair: Martin Vingron - Genomes; Area Chairs: Ying Xu and Steven Salzberg - Structural Bioinformatics; Area Chairs: Nir Ben-Tal and R. Sowdhamini - Bioinformatics Applications; Area Chair: Phil Bourne Elevated Abstract Presentations: http://www.iscb.org/ismb2005/posters.html New this year: exemplary poster submissions have been selected for oral presentation! - RNA and Protein Structural Biology; Session Chair: Michael Zuker - Sequence Analysis, Phylogeny and Evolution; Session Chair: Serafim Batzoglou - Genomics and Gene Expression; Session Chair: Michael Eisen - Pathways, Networks and Proteomics; Session Chair: Trey Ideker - Ontologies and Natural Language Processing; Session Chair: Mark Musen - Gene Regulation, microRNAs; Session Chair: Chris Burge Software Demonstrations: http://www.iscb.org/ismb2005/demos.html Talk with the designers and developers of the newest software applications! A small sampling of the software demos: - Visualizing and Analyzing Biological Network Data in Cytoscape 2.1 - Reactome - A Knowledgebase of Biological Processes - The Protege Suite of Tools: Accessing, Managing, and Visualizing Biomedical Ontologies - The myGrid/Taverna Toolkit for Workflow Based Bioinformatics - STING - A Web Server for Comprehensive Analysis of Protein Structure and Sequence - PUMA2 - a Grid Technology Based Computational Environment for High-throughput Genetic Sequence Analysis and Evolutionary Analysis of Metabolism - PIR: A Comprehensive Resource for Functional Analysis of Protein Sequences and Families - The Pathway Tools Software - EMBOSS - UCSF Chimera: Molecular Graphics for Research and Analysis - Apple Computer, Inc.: The Apple Workgroup Cluster - Apple Computer, Inc.: Mac OS X v10.4 'Tiger' for the Life Sciences - Biobase Corporation: Pathway Analysis with Curated Protein Databases - CSIRO: GeneRave and New Statistical Algorithms for p>n Data - IBM: From Biological Networks to Web Services: The Latest IBM Technologies for Querying Biological Data - Sun Microsystems: Discovery to Development Demos: How to Save Time, Money & Hassles With 6 Solutions -- Hershel M. Safer, Ph.D. Head, Bioinformatics Core Facility Weizmann Institute of Science PO Box 26, Rehovot 76100, Israel tel: +972-8-934-3456 | fax: +972-8-934-6006 email: hershel.safer at weizmann.ac.il | hsafer at alum.mit.edu url: http://bioportal.weizmann.ac.il *************************************************** Mark your calendar now for ISMB 2005! Detroit, Michigan, USA, June 25--29 Visit www.iscb.org/ismb2005/ for conference details From johncumbers at gmail.com Sun May 1 20:17:39 2005 From: johncumbers at gmail.com (john cumbers) Date: Mon, 2 May 2005 01:17:39 +0100 Subject: [BiO BB] www.BioSysBio.com, Bioinformatics and Systems Biology Conference, July 14/15 Edinburgh UK Message-ID: We are now calling for abstracts for the following conference: _______________________________________________________________ www.BioSysBio.com - Conference in Bioinformatics and Systems Biology Chancellors Building, New Royal Infirmary, Edinburgh, UK July 14th & 15th 2005, Free registration. BioSysBio 2005 is a conference designed to bring together people in bioinformatics and systems biology to meet and exchange ideas at the cutting edge of biotechnology. The conference will give an opportunity for postgraduate students and post-docs from across Europe to present their work, and will feature a number of excellent keynote speakers. The meeting will take place in the new Medical School facilities at the New Royal Infirmary of Edinburgh, provided with the support of the Scottish Centre for Genomic Technology and Informatics. We look forward to welcoming you to Edinburgh. Speakers and session chairs Prof Igor Goryanin - Edinburgh Centre For Bioinformatics Author of DBSolve and previous head of the Cell simulations and Pathway modelling group at GlaxoSmithKline, Igor recently joined Edinburgh University as the Director of the Edinburgh Centre for Bioinformatics. At GSK his group worked on designing anti-microbial drug target identification, target prioritisation and reconstructing cellular networks for cancer and metabolic disorders. Dr Nicholas Luscombe - European Bioinformatics Institute After a PhD at UCL with Janet Thornton, Nick went on to do a post-doc at Yale. His most recent project examined the dynamic usage of the yeast regulatory network under distinct cellular conditions. He has since returned from the USA and is leading a new group of researchers at the European Bioinformatics Institute. Prof Andrew J Millar - Biological Sciences, Edinburgh University Andrew trained as a molecular geneticist at Cambridge and Rockefeller Universities and has recently been appointed to a chair of Systems Biology at Edinburgh University. He is the co-ordinator of the Genomic Arabidopsis Resource Network (GARNet) and a member of the Interdisciplinary Programme for Cellular Regulation (IPCR), based at Warwick University. His group works on the circadian clock in the model plant, Arabidopsis thaliana. We are calling for abstracts in the following 4 areas: # Bioinformatics Novel Applications, Genetic Variation, Comparative Genomics, Gene Expression and Regulation, Microarray Data Analysis , Gene Regulatory Networks, Biological Databases, Text and Data mining, Proteomics, Algorithm Development (e.g Sequence Alignment), Protein Structures, Open Source Bio-Projects, Visualization of Biological Processes and Data, Ontologies. # Computational Systems Biology Modelling and Simulation of Biological Processes, Pathways, Networks, Pipelines, Mathematical and Quantitative Models of Cellular and Multicellular Systems, Statistical Modelling of Biological Data, Prediction and Validation. # Data Generation for Systems Biology (Wet-lab) Genome, Transcriptome, Proteome, Metabalome, Functional Genomics, MicroRNA and RNAi, Evolution and Molecular Phylogenetics, Complexes, Population studies. # Integrative Biology Protein-Protein interactions, Human genetics variability, Biomedical Applications, SNP analysis, Non-Silicon Computation, DNA computing, Synthetic Biological Systems, High Performance Bio-computing. Please check the website www.BioSysBio.com for more details _____________________________________________________________________ John Cumbers - MSc Bioinformatics, Postgraduate Student Edinburgh University UK +44(0)7916 327422 From christoph.gille at charite.de Mon May 2 12:09:10 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Mon, 2 May 2005 18:09:10 +0200 (CEST) Subject: [BiO BB] name standards echemical compounds Message-ID: <49140.192.168.220.201.1115050150.squirrel@webmail.charite.de> I know that there exists somewhere a list of standard names for biochem compounds and abbreviations. Something like glycerinaldehydphospate and GraP does anybody know the address of this resource? Many thanks Christoph Gille From m.liebman at wriwindber.org Mon May 2 12:46:54 2005 From: m.liebman at wriwindber.org (Michael Liebman) Date: Mon, 2 May 2005 12:46:54 -0400 Subject: [BiO BB] name standards echemical compounds In-Reply-To: <49140.192.168.220.201.1115050150.squirrel@webmail.charite.de> Message-ID: <200505021648.j42GmejS031339@host12.websitesource.com> IUPAC www.iupac.org Michael N. Liebman, PhD Chief Scientific Officer Windber Research Institute 600 Somerset Ave Windber, PA 15963 (814) 467 9844 office (814) 467 6334 fax (814) 659 5450 cell -----Original Message----- From: bio_bulletin_board-bounces+m.liebman=wriwindber.org at bioinformatics.org [mailto:bio_bulletin_board-bounces+m.liebman=wriwindber.org at bioinformatics.o rg] On Behalf Of Dr. Christoph Gille Sent: Monday, May 02, 2005 12:09 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] name standards echemical compounds I know that there exists somewhere a list of standard names for biochem compounds and abbreviations. Something like glycerinaldehydphospate and GraP does anybody know the address of this resource? Many thanks Christoph Gille _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dmb at mrc-dunn.cam.ac.uk Mon May 2 12:49:10 2005 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Mon, 2 May 2005 17:49:10 +0100 (BST) Subject: [BiO BB] name standards echemical compounds In-Reply-To: <49140.192.168.220.201.1115050150.squirrel@webmail.charite.de> Message-ID: On Mon, 2 May 2005, Dr. Christoph Gille wrote: >I know that there exists somewhere a list of standard names for biochem >compounds and abbreviations. >Something like >glycerinaldehydphospate and GraP > >does anybody know the address of this resource? I tried to make an archive of such links here; http://bioinformatics.org/scol/links.html Although it is woefully incomplete and disorganised, perhaps it will get you started (see 'Compound Databases' section). Please consider adding anything you turn up to that list :) Dan. > >Many thanks > >Christoph Gille > > > >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From willy_valdivia at orionbiosciences.com Mon May 2 12:40:31 2005 From: willy_valdivia at orionbiosciences.com (willy_valdivia at orionbiosciences.com) Date: Mon, 2 May 2005 09:40:31 -0700 Subject: [BiO BB] name standards echemical compounds Message-ID: <20050502164031.16661.qmail@gem-wbe04> Christoph I hope this helps http://wwmm.ch.cam.ac.uk/nesc2004/webintro/openweb.php > -------- Original Message -------- > Subject: [BiO BB] name standards echemical compounds > From: "Dr. Christoph Gille" > Date: Mon, May 02, 2005 12:09 pm > To: bio_bulletin_board at bioinformatics.org > > I know that there exists somewhere a list of standard names for biochem > compounds and abbreviations. > Something like > glycerinaldehydphospate and GraP > > does anybody know the address of this resource? > > Many thanks > > Christoph Gille > > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From christoph.gille at charite.de Tue May 3 07:43:22 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Tue, 3 May 2005 13:43:22 +0200 (CEST) Subject: [BiO BB] reverse complement need name for method. Message-ID: <37105.192.168.220.201.1115120602.squirrel@webmail.charite.de> Please help me to find a suitable name for a method: My protein model has a method getNucleoteides() and a direction of translation like reverse complement or forward. I have a related method which returns the nucleotide sequence either in the original form or as the revers complement depending on the direction. Currently I have getTransformedNucleotides(); but this is not very descriptive. What is an appropriate name? Many Thanks Christoph From mike.fursov at gmail.com Tue May 3 08:00:16 2005 From: mike.fursov at gmail.com (Mikhail Fursov) Date: Tue, 3 May 2005 19:00:16 +0700 Subject: [BiO BB] reverse complement need name for method. In-Reply-To: <37105.192.168.220.201.1115120602.squirrel@webmail.charite.de> References: <37105.192.168.220.201.1115120602.squirrel@webmail.charite.de> Message-ID: add optional parameter to function : bool revCompl ? On 5/3/05, Dr. Christoph Gille wrote: > Please help me to find a suitable name for a method: > > My protein model has > a method getNucleoteides() and a direction of translation like > reverse complement or forward. > > I have a related method which returns the nucleotide > sequence either in the original form or as the revers complement > depending on the direction. > > Currently I have getTransformedNucleotides(); but this is not very > descriptive. > > What is an appropriate name? > > Many Thanks Christoph > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From marty.gollery at gmail.com Tue May 3 17:41:46 2005 From: marty.gollery at gmail.com (Martin Gollery) Date: Tue, 3 May 2005 14:41:46 -0700 Subject: [BiO BB] reverse complement need name for method. In-Reply-To: <37105.192.168.220.201.1115120602.squirrel@webmail.charite.de> References: <37105.192.168.220.201.1115120602.squirrel@webmail.charite.de> Message-ID: Christoph, How about getNucleotideEither, since it is retrieving the nucleotide sequence in either direction? Marty On 5/3/05, Dr. Christoph Gille wrote: > Please help me to find a suitable name for a method: > > My protein model has > a method getNucleoteides() and a direction of translation like > reverse complement or forward. > > I have a related method which returns the nucleotide > sequence either in the original form or as the revers complement > depending on the direction. > > Currently I have getTransformedNucleotides(); but this is not very > descriptive. > > What is an appropriate name? > > Many Thanks Christoph > > _______________________________________________ > Bioinformatics.Org general forum - 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 ----------- From phoebe.chen at deakin.edu.au Wed May 4 00:57:07 2005 From: phoebe.chen at deakin.edu.au (Phoebe Chen) Date: Wed, 04 May 2005 14:57:07 +1000 Subject: [BiO BB] 1st CFP for APBC2006, Taipei, Taiwan Message-ID: <5.1.1.5.2.20050504145030.048d1b60@mail.deakin.edu.au> **************************************************************** FIRST CALL FOR PAPERS The Fourth Asia-Pacific Bioinformatics Conference Taipei, Taiwan 13-16 February 2006 http://binfo.ym.edu.tw/apbc2006/ **************************************************************** The Asia-Pacific Bioinformatics Conference series is an annual forum for exploring research, development, and applications in bioinformatics. The 4th Asia-Pacific Bioinformatics Conference, APBC2006, will be held in Taipei, Taiwan. High-throughput sequencing and functional genomics technologies have given us a human genome sequence and have enabled large-scale genotyping and gene expression profiling of human populations. Databases containing large numbers of sequences, polymorphisms, and gene expression profiles of normal and diseased tissues in different clinical states are rapidly being generated for human and model organisms. Bioinformatics is thus rapidly growing in importance in the understanding of the interplay between genes and proteins, in the analysis the genetic variability of species, etc. The aim of this conference is to bring together researchers, professionals, and industrial practitioners for interaction and exchange of knowledge and ideas. We invite submissions that address conceptual and practical issues of bioinformatics. Topics of Interest Papers are solicited on, but not limited to, the following topics: ? Novel Methods and Applications in Bioinformatics ? Data Mining & Statistical Modeling of Biological Data ? Computational Analysis of Biological Data ? Modeling and Simulation of Biological Processes ? Visualization of Biological Processes and Data ? Management, Migration, and Integration of Biological Databases ? Access, Indexing, and Search in Biological Databases ? Pathways and Systems Biology ? Structural Bioinformatics ? Statistical Genetics and Genomics ? Comparative Genomics and Evolutionary Biology IMPORTANT DATES Full Paper Submission Deadline Jul 15, 2005 Notification of Paper Acceptance Aug 20, 2005 Tutorial proposals Aug 25, 2005 Camera Ready Papers Due Sep 10, 2005 Author Registration Sep 10, 2005 Poster & demo proposals Sep 20 2005 Conference Feb 13 2006 ~ Feb 16 2006 GENERAL CO-CHAIRS Yi-Ping Phoebe Chen (Deakin University) Wen-Hsiung Li (The University of Chicago) Limsoon Wong (Institute for Infocomm Research) PROGRAM COMMITTEE CO-CHAIRS Tao Jiang, University of California ? Riverside Ueng-Cheng Yang, National Yang-Ming University PROGRAM COMMITTEE Tatsuya Akutsu (Kyoto University) Vineet Bafna (University of California ? San Diego) Paola Bonnizoni (Universita' degli Studi di Milano) David Bryant (McGill University/Niversity of Auckland) Kun-Mao Chao (National Taiwan University) Francis Chin (Hong-Kong University) Ross Coppel (Monash University) Michael Cummings (University of Maryland) Bhaskar DasGupta (University of Illinois ? Chicago) Nadia El-Mabrouk (University of Montreal) Janice Glasgow (Queens University) Sridhar Hannenhalli (University of Pennsylvania) Wen-Lian Hsu (Academia Sinica) Haiyan Huang (University of California ? Berkeley) Ming-Jing Hwang (Academia Sinica) John Kececioglu (University of Arizona) Chris Langmead (Carnegie Mellon University) Sang-Yup Lee (Korea Adv. Institute of Sci. & Technology) Jinyan Li (Institute for Infocomm Research) Jing Li (Case Western Reserve University) Guohui Lin (University of Alberta) Stefano Lonardi (University of California ? Riverside) Horng-Shing Lu (National Chao-Tung University) Bin Ma (University of Western Ontario) Shinichi Morishita (University of Tokyo) Laxmi Parida ( IBM, T.J. Watson Research Center) Kunsoo Park (Seoul National University) Christian Pedersen (University of Aarhus) Alexander Schliep (Max Planck Institute for Mol. Genetics) Shoba Ranganathan (Macquarie University) Christian Schoenbach (RIKEN) Larry Ruzzo (University of Washington) Lusheng Wang (City University of Hong-Kong) Wei Wang (University of North Carolina ? Chapel Hill) Eric Xing (Carnegie Mellon University) Michael Zhang (Cold Spring Harbor Laboratory) Yang Zhong (Fudan University) Xianghong Zhou (University of Southern California) ORGANIZATION COMMITTEE CO-CHAIRS Jorng-Tzong Horng (National Central University) Cheng-Yan Kao (National Taiwan University) SUBMISSION GUIDELINES APBC2006 invites high-quality original papers on any topic related to Bioinformatics. Papers should be no more than 10 pages in length conforming to the formatting instructions for the series Advances in Bioinformatics & Computational Biology (instructions available at the APBC2006 website). Each paper will be fully refereed by an international program committee. Papers will be judged on originality, significance, correctness, and clarity. Authors should submit one copy of a PDF or PS file to APBC2006 Paper Submission Website. The full paper must be submitted by 15 July 2005. The proceedings will be published as a volume in the series Advances in Bioinformatics & Computational Biology by Imperial College Press. Expanded version of the best papers will be invited for publication in the Journal of Bioinformatics and Computational Biology. To publish the paper in the conference, one of the authors needs to register for and present at the conference. -------------- next part -------------- An HTML attachment was scrubbed... URL: From x.sole at ico.scs.es Fri May 6 05:40:18 2005 From: x.sole at ico.scs.es (Sole Acha, Xavi) Date: Fri, 6 May 2005 11:40:18 +0200 Subject: [BiO BB] Anounce: Course on statistical analysis of proteomics data Message-ID: <5FF3F11444E3A9439191AA1EDCB69A1712330E@icosrvmail01.ICO.SCS.local> Course on STATISTICAL ANALYSIS OF MASS SPECTROMETRY DATA: finding proteomic biomarkers for diagnosis and prognosis. Barcelona, September 14th-16th 2005 Organizer Dr. Victor Moreno Bioinformatics and Biostatistics Unit Cancer Epidemiology and Registry Department Catalan Institute of Oncology. Aim Advances in mass spectrometry over the last few years have led to a revolution in the field of proteomics. This course will cover all the issues involved in mass spectrometry data analysis, from raw data to final discovery of protein biomarkers and classification of samples according to their protein pattern. Lecturer All the lectures will be given in English by: Prof. Yukata Yasui Department of Public Health Sciences Faculty of Medicine and Dentistry University of Alberta Short preliminary program: 1. Brief introduction to biology, genomics and proteomics. 2. Introduction to mass spectrometry (MS). 3. MS data preprocessing and experimental design. 4. Analysis of single peaks as biomarkers. 5. Defining proteomic patterns: building and testing predictors with MS data. Course details http://lbe.uab.es/proteomics -------------- next part -------------- An HTML attachment was scrubbed... URL: From dobbo at thevillas.eclipse.co.uk Fri May 6 04:45:42 2005 From: dobbo at thevillas.eclipse.co.uk (rich) Date: Fri, 06 May 2005 09:45:42 +0100 (BST) Subject: [BiO BB] trimming clustalw In-Reply-To: <42694C93.3080103@unr.edu> References: <42694C93.3080103@unr.edu> Message-ID: <1115369142.427b2eb6a3565@webmail.eclipse.net.uk> Hi, I seem to remember reading somewhere that it was possible to trim clustalw output to one of the sequences in the alignment. I can't see it as an option in the option list though. Did I imagine this? cheers Rich From jstroud at mbi.ucla.edu Fri May 6 12:56:41 2005 From: jstroud at mbi.ucla.edu (James Stroud) Date: Fri, 6 May 2005 09:56:41 -0700 Subject: [BiO BB] trimming clustalw In-Reply-To: <1115369142.427b2eb6a3565@webmail.eclipse.net.uk> References: <42694C93.3080103@unr.edu> <1115369142.427b2eb6a3565@webmail.eclipse.net.uk> Message-ID: <200505060956.41697.jstroud@mbi.ucla.edu> I think boxshade has this option. It looks like there are dozens of servers on the net. If you want the source and can't find it on the web, I can email it to you. It is a completely open program. James On Friday 06 May 2005 01:45 am, so sayeth rich: > Hi, > > I seem to remember reading somewhere that it was possible to trim > clustalw output to one of the sequences in the alignment. I can't see it > as an option in the option list though. Did I imagine this? > > cheers > Rich > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com/ From lifei03 at gmail.com Fri May 6 13:26:57 2005 From: lifei03 at gmail.com (Frank) Date: Sat, 07 May 2005 01:26:57 +0800 Subject: [BiO BB] trimming clustalw In-Reply-To: <200505060956.41697.jstroud@mbi.ucla.edu> References: <42694C93.3080103@unr.edu> <1115369142.427b2eb6a3565@webmail.eclipse.net.uk> <200505060956.41697.jstroud@mbi.ucla.edu> Message-ID: <427BA8E1.20004@gmail.com> Block www server, available at http://blocks.fhcrc.org/blocks/ Have a look. It seems it can trim alignment. Frank James Stroud wrote: >I think boxshade has this option. It looks like there are dozens of servers on >the net. If you want the source and can't find it on the web, I can email it >to you. It is a completely open program. > >James > > > >On Friday 06 May 2005 01:45 am, so sayeth rich: > > >>Hi, >> >>I seem to remember reading somewhere that it was possible to trim >>clustalw output to one of the sequences in the alignment. I can't see it >>as an option in the option list though. Did I imagine this? >> >>cheers >>Rich >>_______________________________________________ >>Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> > > > From christoph.gille at charite.de Wed May 11 06:00:54 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Wed, 11 May 2005 12:00:54 +0200 (CEST) Subject: [BiO BB] gene names 2 protein names Message-ID: <33037.192.168.220.201.1115805654.squirrel@webmail.charite.de> Hi everybody, does somebody know a list to map bacterial gene names like ThrC, talB, dnaK to protein- or enzyme names ? Many thanks Christoph From dmb at mrc-dunn.cam.ac.uk Wed May 11 07:19:48 2005 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 11 May 2005 12:19:48 +0100 (BST) Subject: [BiO BB] gene names 2 protein names In-Reply-To: <33037.192.168.220.201.1115805654.squirrel@webmail.charite.de> Message-ID: On Wed, 11 May 2005, Dr. Christoph Gille wrote: >Hi everybody, > >does somebody know a list to map >bacterial gene names like ThrC, talB, dnaK to protein- or enzyme names ? SwissProt has well organised synonym information for its proteins (protein id to gene name). Also seqhound has good interface to NCBI synonym data. You can find both by googling. You may get better replies from others on the list, especially if you can give more detailed information about your problem (i.e. do you have 10 or 10,000 genes to map? / What do you want to retreive for each gene name?) Dan. > >Many thanks > >Christoph > > >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From discover.sunny at gmail.com Wed May 11 07:43:47 2005 From: discover.sunny at gmail.com (sandeep sharma) Date: Wed, 11 May 2005 17:13:47 +0530 Subject: [BiO BB] (no subject) Message-ID: Hi All , I need to ask that What is the difference between C Aplha Trace of Protein and Protein Backbone..... Also if we had a C Alpha Trace how can we approach to find the full protein backbone coordinates...There should be no side chains but only Protein Backbone coordinates ..please tell me all this with relevant to PDB files. Reply Back ASAP Sandeep From boris.steipe at utoronto.ca Wed May 11 08:44:32 2005 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Wed, 11 May 2005 08:44:32 -0400 Subject: [BiO BB] (no subject) In-Reply-To: Message-ID: <6C644D25-C21A-11D9-AADC-000A9577512E@utoronto.ca> The CA trace is a sequence of lines connecting CA-atom coordinates in a graphic. Sometimes this is also drawn as a curve that passes through these coordinates, with various degrees of smoothing. It provides a useful view of overall folding topology. A protein backbone contains minimally 3 (N,CA,C) or usually 4 (including O) covalently bonded atoms of the polypeptide chain. In terms of information this looks very similar to a CA trace, but if the carbonyl oxygens are included you can see backbone hydrogen bonding patterns. MaxSprout will generate full coordinates from CA coordinates. http://www.ebi.ac.uk/maxsprout/ You can simply remove the sidechains afterwards but I can't begin to imagine what that would be useful for :-) Boris On Wednesday, May 11, 2005, at 07:43 Canada/Eastern, sandeep sharma wrote: > Hi All , > > I need to ask that What is the difference between C > Aplha Trace of Protein and Protein Backbone..... Also > if we had a C Alpha Trace how can we approach to find > the full protein backbone coordinates...There should > be no side chains but only Protein Backbone > coordinates ..please tell me all this with relevant to > PDB files. > > Reply Back ASAP > Sandeep > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From stefanielager at fastmail.ca Wed May 11 09:47:40 2005 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Wed, 11 May 2005 13:47:40 +0000 (UTC) Subject: [BiO BB] gene names 2 protein names In-Reply-To: <33037.192.168.220.201.1115805654.squirrel@webmail.charite.de> Message-ID: <20050511134740.0EBE5861891@mail.interchange.ca> You can try the BioMinT - Gene and Protein Name Synonyms Database http://biomint.oefai.at/cgi-bin/bmsynonyms.pl?s= Pillet V, Zehnder M, Seewald AK, Veuthey AL, Petrak J. GPSDB: a new database for synonyms expansion of gene and protein names. Bioinformatics. 2005 Apr 15;21(8):1743-4. Epub 2004 Dec 21. PMID: 15613390 Stefanie > Hi everybody, > > does somebody know a list to map > bacterial gene names like ThrC, talB, dnaK to protein- or enzyme names > ? > > Many thanks > > Christoph > > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From vxg189 at bham.ac.uk Wed May 11 10:30:34 2005 From: vxg189 at bham.ac.uk (Vibhor Gupta) Date: Wed, 11 May 2005 15:30:34 +0100 Subject: [BiO BB] Finding genes over-expressed in lymphoblastoids Message-ID: <1B4C5BA3CB5F2849B0C8DB99156046A43AC516@med-ex1.bham.ac.uk> Hello all, Does anyone know about a resource that can provide information about various cell lines. My idea is to determine the genes that are characteristic of lymphoblastoids that is specifically show increase or decrease in expression in these cell lines in comparison to other cell lines. I am also interested in genes that are characteristic of this cell line and are present on chromosome 19. I will be very grateful to anyone who provide some help regarding this. Thanking you. Mr. Vibhor Gupta Research Associate (Chromatin and Gene Expression Group) Division of Immunity and Infection - Anatomy Institute of Biomedical Research University of Birmingham Birmingham - B15 2TT Email: v.gupta.1 at bham.ac.uk Telephone number: 0121-4158684 From discover.sunny at gmail.com Thu May 12 02:53:32 2005 From: discover.sunny at gmail.com (sandeep sharma) Date: Thu, 12 May 2005 12:23:32 +0530 Subject: [BiO BB] Re: (no subject) In-Reply-To: <6C644D25-C21A-11D9-AADC-000A9577512E@utoronto.ca> References: <6C644D25-C21A-11D9-AADC-000A9577512E@utoronto.ca> Message-ID: Hi Boris.. Thanxxx... I did just had a clue that if we can include the O atom also ......Also can u let me know that if MaxSprout paper soft copy is with me .. if u do have mail me ..... I am basicallly workin on that only .. Sandeep On 5/11/05, Boris Steipe wrote: > The CA trace is a sequence of lines connecting CA-atom coordinates in a > graphic. Sometimes this is also drawn as a curve that passes through > these coordinates, with various degrees of smoothing. It provides a > useful view of overall folding topology. A protein backbone contains > minimally 3 (N,CA,C) or usually 4 (including O) covalently bonded atoms > of the polypeptide chain. In terms of information this looks very > similar to a CA trace, but if the carbonyl oxygens are included you can > see backbone hydrogen bonding patterns. > > MaxSprout will generate full coordinates from CA coordinates. > http://www.ebi.ac.uk/maxsprout/ > You can simply remove the sidechains afterwards but I can't begin to > imagine what that would be useful for :-) > > > Boris > > > > > On Wednesday, May 11, 2005, at 07:43 Canada/Eastern, sandeep sharma > wrote: > > > Hi All , > > > > I need to ask that What is the difference between C > > Aplha Trace of Protein and Protein Backbone..... Also > > if we had a C Alpha Trace how can we approach to find > > the full protein backbone coordinates...There should > > be no side chains but only Protein Backbone > > coordinates ..please tell me all this with relevant to > > PDB files. > > > > Reply Back ASAP > > Sandeep > > _______________________________________________ > > Bioinformatics.Org general forum - > > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From christoph.gille at charite.de Thu May 12 16:04:16 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Thu, 12 May 2005 22:04:16 +0200 (CEST) Subject: [BiO BB] please help to find name for new project Message-ID: <51494.192.168.220.201.1115928256.squirrel@webmail.charite.de> I have started a new project. http://www.charite.de/bioinf/strap/Scripting.html It provides a convenient Bioinformatics toolbox written in Java and works together with Biojava and other Java-projects. It is allmost ready. But I still need a good name for it. Is SCRAP a good name ? Many thanks Christoph From mmckay at tusd.net Thu May 12 16:52:10 2005 From: mmckay at tusd.net (McKay, Mark) Date: Thu, 12 May 2005 13:52:10 -0700 Subject: [BiO BB] please help to find name for new project Message-ID: Hate to tell you this but SCRAP is a derogatory term for a member of the Sureno street gang. Fyi Mark McKay -----Original Message----- From: bio_bulletin_board-bounces+mmckay=tusd.net at bioinformatics.org [mailto:bio_bulletin_board-bounces+mmckay=tusd.net at bioinformatics.org] On Behalf Of Dr. Christoph Gille Sent: Thursday, May 12, 2005 1:04 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] please help to find name for new project I have started a new project. http://www.charite.de/bioinf/strap/Scripting.html It provides a convenient Bioinformatics toolbox written in Java and works together with Biojava and other Java-projects. It is allmost ready. But I still need a good name for it. Is SCRAP a good name ? Many thanks Christoph _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jakechen at iupui.edu Sun May 15 02:45:09 2005 From: jakechen at iupui.edu (Chen, Jake) Date: Sun, 15 May 2005 01:45:09 -0500 Subject: [BiO BB] Call for Book Chapters: Database Modeling in Biology to be Published by Springer 2006 Message-ID: <9BA28484EAC4B843B4EA7834449D6FFE0270DEF3@iu-mssg-mbx05.exchange.iu.edu> Call for Book Chapters [Please help distribute as widely as possible. Thank you!] ========== Book Title ========== Database Modeling in Biology: Practices and Challenges (to be published by Springer in early 2006) ======== We site ======== http://bio.informatics.iupui.edu/book05/ ============ Introduction ============ Database management systems are designed to support large volumes of data storage, data processing, data querying, and most recently, data mining and knowledge discovery activities. Rapid increase in computing power and advances in data management techniques in recent decades have led many researchers to pursue knowledge discovery with databases and database management systems as their primary computing platform. A recent trend of general database research in this direction has been the incorporation of domain semantics into the representation and management of data. Compared with data from general application domains, modern biological data has many unique characteristics. Biological data are often characterized as having large volumes, complex structures, high dimensionality, evolving biological concepts, and insufficient data modeling practices. These characteristics require database researchers and developers to make many special considerations while developing biological databases and database systems. They also have made biological data management and knowledge discovery in databases challenging. Database modeling in the biological domain has received increasing attention both as a research topic and as a practice in biological computings. By carefully representing the structure, semantics, and querying requirements of large volumes of biological data, researchers and developers can help biologists track, query, analyze, and data-mine data from high-throughput genomics, gene expression profiling, proteomics, metabolomics, genotyping, text ming, and chemical screening projects. In this book, we invite papers that cover the fast-growing topic of biological database modeling with an emphasis on both computational techniques and real-world applications. The book will become a useful guide for researchers, practitioners, and graduate-level students interested in learning state-of-the-art development in biological/biomedical data management, data-intensive bioinformatics systems, and other miscellaneous biological database applications. ================== Recommended Topics ================== Specific topics of interest of this book include, but are not limited to A. Conceptual Models of Emerging Large-scale Biological Data * Conceptual/semantic biological data modeling principles and common practices * Current biological data modeling challenges * Modeling Data Uncertainty and Imprecision in Biology * Modeling large-scale motifs, genotypes, pathways, molecular networks, and protein complexes. * Modeling data from high-throughput gene expression, proteomics, and chemical screening pipelines * Evolution and integration of the biological data models * Biological standard data exchange formats, XML biological data models * Gene ontology, unified medical language systems * Conceptual design of biological databases using biological data models * Software systems supporting biological data modeling B. Data and Query Processing Models in Biological Database Systems * Algebraic Operations of the Biological Data * Biological Data Operators and web services * Special biological data Indexing techniques * Query Processing and Query Optimization Techniques for Manipulating Biological Data * Integration of Biological Data and Queries * Interoperation Among Multiple Biological Database Queries * Biological workflow modeling and data processing systems * Dissemination of biological data and query results C. Model-based Biological Knowledge Discovery Systems * System-scale biological discovery challenges and opportunities * Model-driven Knowledge Discovery Software Systems for Biology * General Data-rich Biological Information System Development * Integrated Systems for Comparative Genomics, Proteomics, Functional Genomics, Pharmacogenomics, and Systomics studies. =============== Target Audience =============== The intended target audience of this book are readers who wish to learn about the current research topics and trends in biological database technologies. Specifically, the book will provide a theoretical perspective and practical solutions to graduate students , researchers and practitioners working in the areas of advanced database systems, biological data management, and biological information systems. =============== Important Dates =============== June 15, 2005 Email Letter of intent Due (to the editors). July 31, 2005 Deadline to submit a full book chapter paper. September 30, 2005 Notification of acceptance with referee comments and revision comments. November 30, 2005 Deadline to submit final version of the accepted chapters in camera-ready Springer format ========== Submission ========== Papers should be original and should not be submitted for publication or published elsewhere. All paper are to be submitted electronically (PDF or MS word format preferred) to both the editors by email (listed below) . For details on how to prepare the manuscripts and style files refer to the instruction page for authors, go to http://www.springeronline.com/sgw/cda/frontpage/0,11855,4-40492-0-0-0,00 .htm. This page also includes the latex macro packages and further instructions. ========= Publisher ========= SPRINGER SCIENCE+BUSINESS MEDIA, INC. 233 Spring Street, New York, NY 10013, USA =================== Contact the Editors =================== All contacts and paper submissions should be made to both editors by email: Zongmin Ma College of Information Science and Engineering Northeastern University Shengyang, Liaoning 110004 China Email: edited_book at yahoo.com Jake Y. Chen Indiana University School of Informatics Indianapolis, IN 46202 USA Tel: (317)278-7604 Email: jakechen at iupui.edu Web site: http://bio.informatics.iupui.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From pfern at igc.gulbenkian.pt Mon May 16 11:50:18 2005 From: pfern at igc.gulbenkian.pt (Pedro Fernandes) Date: Mon, 16 May 2005 16:50:18 +0100 (WEST) Subject: [BiO BB] PGBIOINF The FCUL/IGC Post Graduate Programme in Bioinformatics Message-ID: <52921.192.168.50.3.1116258618.squirrel@webmail.igc.gulbenkian.pt> PGBIOINF The FCUL/IGC Post Graduate Programme in Bioinformatics Deadline for the call for applications for the 4th edition starting in September 2005: June 15th 2005 Key features of PGBIOINF ?Students of mixed nationalities ?teaching in English ?Students of two main profiles, BIO and INFO, brought to the level of being able to attend intensive seminars in 15 weeks ?Series of 14 intensive thematic seminars in the next 15 weeks ?Courses fully taught and documented in English ?Marks standarized in ECTS to ensure mobility ?Small number of students: individual attention ?Problem driven teaching methods ?Literature based presentations and discussions by the students (Journal Clubs). __________________________________________________________ PGBIOINF ?total duration: 30 weeks, 60 ECTS Part A (Minimum of 30 ECTS) All courses are mandatory Lectures, Lab Practicals -For ALL students Introduction to Bioinformatics 60h Biostatistics 60h Machine Learning in Biology 30h Introd. to Evolutionary Biology 30h -For students of the BIO profile Program Development 60h Intro to Databases 45h -For students of the INFO profile Molecular Genetics 30h Genetic Engineering 30h Biomolecules Structure & Function 30h Chem. and Biochem. Lab. 15h ________________________________________________ Part B (Minimum of 30 ECTS) Mandatory & optional seminars 35h each Lectures, Lab Practicals, Journal Clubs Mandatory: Statistical Methods in Bioinformatics Biologically Inspired Algorithms Data Warehousing and Mining Protein Str& Fun Prediction Funct& Comparative Genomics Gene Prediction & Identification Limits & Expectations in Bioinformatics Gene Ontology Optional: Population Genetics Phylogenetics and Molecular Evolution Population Dynamics and Epidemiology Proteomics, Transcript & Metabolomics Genetic Expression and Microarrays Quantitative Human Genetics For details including information for new applicants visit http://bioinformatics.fc.ul.pt Pedro Fernandes From magda_mansour at yahoo.fr Mon May 16 13:21:22 2005 From: magda_mansour at yahoo.fr (Magda Mansour) Date: Mon, 16 May 2005 19:21:22 +0200 (CEST) Subject: [BiO BB] (no subject) In-Reply-To: <9BA28484EAC4B843B4EA7834449D6FFE0270DEF3@iu-mssg-mbx05.exchange.iu.edu> Message-ID: <20050516172123.65855.qmail@web25703.mail.ukl.yahoo.com> Hello, I'm trying to start working with the NCBI C++ Toolkit. I have already downloaded the files by FTP, run the "configure" command successfully, run the "make" command unsuccessfully :( { make[3]: Entering directory `/home/mansour/NCBI/toolbox/GCC342-Debug/build/bdb' bdb_file.cpp: In member function `void ncbi::CBDB_RawFile::PrintStat(ncbi::CNcbiOstream&)': /bdb_file.cpp:491: error: 'struct __db_bt_stat' has no member named 'bt_empty_pg' make[3]: *** [bdb_file.o] Error 1 } Forgetting about this error for a while and following The NCBI C++ Toolkit Book: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit It talks about CVS as an alternative to the FTP download, so I thought I could skip this part but the tutorial continuously refers to CVS and as I'm not friendly with CVS, I failed in making the parallelism between the commands with CVS and without. So, now I'm trying to work with CVS in order to understand it better. Starting with defining the $CVSROOT, I finally succeeded in running the command "cvs login" and entered the password ?allowed? but I got an "Unknown host cvsvault" message... It has been many days that I am working on these problems, if somebody can help me in any of these, I would be very grateful. Magda Mansour _____________________________________________________________________________ D?couvrez le nouveau Yahoo! Mail : 1 Go d'espace de stockage pour vos mails, photos et vid?os ! Cr?ez votre Yahoo! Mail sur http://fr.mail.yahoo.com From dmb at mrc-dunn.cam.ac.uk Mon May 16 14:17:27 2005 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Mon, 16 May 2005 19:17:27 +0100 (BST) Subject: [BiO BB] (no subject) In-Reply-To: <20050516172123.65855.qmail@web25703.mail.ukl.yahoo.com> Message-ID: On Mon, 16 May 2005, Magda Mansour wrote: >Hello, > >I'm trying to start working with the NCBI C++ Toolkit. > >I have already downloaded the files by FTP, run the >"configure" command successfully, run the "make" >command unsuccessfully :( >{ >make[3]: Entering directory >`/home/mansour/NCBI/toolbox/GCC342-Debug/build/bdb' >bdb_file.cpp: >In member function `void >ncbi::CBDB_RawFile::PrintStat(ncbi::CNcbiOstream&)': >/bdb_file.cpp:491: error: 'struct __db_bt_stat' has no >member named 'bt_empty_pg' >make[3]: *** [bdb_file.o] Error 1 >} > >Forgetting about this error for a while and following >The NCBI C++ Toolkit Book: >http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit >It talks about CVS as an alternative to the FTP >download, so I thought I could skip this part but the >tutorial continuously refers to CVS and as I'm not >friendly with CVS, I failed in making the parallelism >between the commands with CVS and without. > >So, now I'm trying to work with CVS in order to >understand it better. Starting with defining the >$CVSROOT, I finally succeeded in running the command >"cvs login" and entered the password ?allowed? but I >got an "Unknown host cvsvault" message... > >It has been many days that I am working on these >problems, if somebody can help me in any of these, I >would be very grateful. > >Magda Mansour If you have an IRC (chatting) client you can get help in 'real time' from people who use and develop CVS all the time... open IRC and type "/server irc.freenode.net", then "/join #cvs" '#cvs' is the chat channel where they talk about CVS. If you are nice and polite they may help you with all your problems, although I found it depends a lot on the particular chat room on how much they are willing to help a beginner. mailinglists are so yesterday ;) Else find the CVS manual and begin at the beginning :( Hey! I just found '#bioinformatics' on irc.freenode.net! > > > > > > >_____________________________________________________________________________ >D?couvrez le nouveau Yahoo! Mail : 1 Go d'espace de stockage pour vos mails, photos et vid?os ! >Cr?ez votre Yahoo! Mail sur http://fr.mail.yahoo.com >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From magda_mansour at yahoo.fr Tue May 17 03:37:31 2005 From: magda_mansour at yahoo.fr (Magda Mansour) Date: Tue, 17 May 2005 09:37:31 +0200 (CEST) Subject: [BiO BB] cancelling my last email with 'no subject' Message-ID: <20050517073731.19498.qmail@web25708.mail.ukl.yahoo.com> Hello, I'm sorry for encumbering your email inbox. I finally succeeded accessing the NCBI toolbox via CVS and I hope I won't need to send you other dazed emails. Sincerely, Magda _____________________________________________________________________________ D?couvrez le nouveau Yahoo! Mail : 1 Go d'espace de stockage pour vos mails, photos et vid?os ! Cr?ez votre Yahoo! Mail sur http://fr.mail.yahoo.com From areed at imdc.org Tue May 17 15:35:21 2005 From: areed at imdc.org (Ann Reed) Date: Tue, 17 May 2005 14:35:21 -0500 Subject: [BiO BB] PRESS RELEASE--BiTmaP: Midwest Bioinformatics Training Program appoints training partner for tuition-free program Message-ID: <7BDF6464945AB045B845C2AB588B9B4006D0B9@tachyon.imdc.org> Contact: Ann Reed 312-243-1289 areed at bitmapchicago.com BITMAP APPOINTS UNIVERSITY OF ILLINOIS AT CHICAGO AS ACADEMIC PARTNER FOR THE BIOINFORMATICS TRAINING PROGRAM Chicago, Ill. (May 16, 2005) - BiTmaP, a Chicago Technology Park-sponsored initiative that offers tuition-free bioinformatics training, announced today that it has chosen the University of Illinois at Chicago (UIC), the only accredited bioinformatics program in Illinois, as its academic training partner. UIC will develop and administer the curriculum for the certificate program, which is designed to retrain unemployed and underemployed information technology (IT) workers in the fast-growing field of bioinformatics. Bioinformatics is the use of IT to acquire, store, manage and analyze biological data. For example, genomic research generates a large amount of complex data that involves millions of individual DNA building blocks. Skilled IT workers with the ability to create software and hardware solutions to help scientists understand this data are in great demand in the life and health science industries. "The creative force behind many technological advancements in the life sciences is the utilization of genomic data through bioinformatics tools," said Sam Pruett, executive director of the Illinois Medical District. "We want to create a pool of highly-skilled bioinformatics professionals to drive innovation in a broad range of life science industry sectors. With UIC's focused expertise and industry experience, the BiTmaP program will help to bridge the gap between the surplus of unemployed and underemployed IT professionals and the fast-growing Midwest life science community." The BiTmaP training will utilize distance learning, work-site learning, and industry internships and seminars to provide IT professionals with the science knowledge and specific skills required to obtain and maintain employment as bioinformatics professionals. BiTmaP students will increase earning potential, learn new skills, expand existing skills and earn twelve college-level credits and a certificate in bioinformatics from UIC. The BiTmaP program will also serve as a workforce development program for qualified industry participants. "Our goal is to create a sustainable and flexible retraining program that will help transition IT professionals to the fast-growing field of bioinformatics," said Ann Reed, program director for BiTmaP. "BiTmaP partnerships with local businesses, learning institutions, industrial organizations and workforce development agencies help create a community focused on building the future life science workforce in the Midwest." Dr. Hui Lu, professor of bioengineering at UIC, will serve as Academic Director for BiTmaP. Dr. Lu and his team have more than ten years of experience in bioinformatics. Dr. Lu has published more than thirty peer-reviewed papers on bioinformatics and computational biophysics, and he has been invited to speak at numerous industry events. The BiTmaP program will consist of three courses and an industry internship. The total certification process is projected to take students up to one year to complete. Classes are scheduled to begin in August 2005. Interested students and industry participants should contact Ann Reed at areed at bitmapchicago.com or 312-243-1289. About BiTmaP: BiTmaP is a tuition-free bioinformatics training program, designed to bridge the gap between the surplus of unemployed or underemployed information technology (IT) professionals and the fast-growing life science community in the Midwest. BiTmaP is sponsored by a $3 million grant awarded to the Chicago Technology Park by the U.S. Department of Labor. BiTmaP has appointed the University of Illinois at Chicago to provide IT professionals with the science knowledge and specific IT skills required to obtain and maintain employment as bioinformatics professionals. For more information, please visit www.bitmapchicago.com or call 312-243-1289. From sravan at www.cdfd.org.in Wed May 18 10:41:37 2005 From: sravan at www.cdfd.org.in (P Sravan Kumar. PAsst) Date: Wed, 18 May 2005 07:41:37 -0700 Subject: [BiO BB] mpiblast error. Message-ID: We need assistance from the users of mpiblast regarding the execution on AMD64 grid environment. 1.System Configuration: --------------------- Operating System: Red Hat Enterprise Linux 3.0 for AMD 64 Architecture Sun Fire v20z machine Bio Clusture Grid Engine 2. We have downloaded the NCBI-2.2.10-1.x86_64.rpm and mpiblast-1.3.0-1.x86_64.rpm from scalableinformatics.com. When we installed NCBI: all the binaries like blastall are loaded onto /usr/bin. and mpiblast: all the binaries are loaded onto /usr/local/bin ex: mpiblast, mpiformatdb. 3. We have created one common blastdb in /apps/Databases/blastdb/ using mpiformatdb -i scaffolds --nfrags=250 N 250 -p F. ( 250 fragments have been created). 4. Lamboot and lamnodes are also working fine as we checked by running clustalmpi.sh through mpirun command. 5. But we are unable to run mpiblast through mpirun script as it gives the follwing error: ( I am attaching a file containing the script and the error message ). Our query: --------- 1. Why is this happening? 2. Is there an NCBI.TAR.GZ pacakge that supports AMD64(X86_64) for RH Enterprise WS 3.0? 3. While installing NCBI rpms we were able to find only binary files. We did not find the data files of NCBI ex: blosum, pam etc in any path in Is there any specific path they may be located? Please assist us in proper integration and running of mpiblast tool. We appreciate your early suggestions. Regards. Sravan. -------------- next part -------------- script: ----- #! /bin/sh date /usr/local/lam/bin/mpirun -np 5 /usr/local/bin/mpiblast -p blastn -d /apps/Databases/blastdb/scaff olds -i /home/sravan/demorun/blast/SW_ge2k_BGF.cds -o /home/sravan/demorun/blast/mpiblast.out date lamnodes: execution: ------------------- n0 silk-node7:2:origin,this_node n1 silk-node6:2: n2 silk-node5:2: n3 silk-node4:2: n4 silk-node3:2: n5 silk-node2:2: n6 silk-node1:2: error message: ------------- execution: ./mpiblast.sh on the masternode (silk-node 7 n0) Wed May 18 14:29:55 IST 2005 Sorry, mpiBLAST must be run on 3 or more nodes [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_15547: p4_error: : 0 Sorry, mpiBLAST must be run on 3 or more nodes [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_15548: p4_error: : 0 Sorry, mpiBLAST must be run on 3 or more nodes [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_5535: p4_error: : 0 Sorry, mpiBLAST must be run on 3 or more nodes [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_5536: p4_error: : 0 ----------------------------------------------------------------------------- It seems that [at least] one of the processes that was started with mpirun did not invoke MPI_INIT before quitting (it is possible that more than one process did not invoke MPI_INIT -- mpirun was only notified of the first one, which was on node n0). mpirun can *only* be used with MPI programs (i.e., programs that invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program to run non-MPI programs over the lambooted nodes. ----------------------------------------------------------------------------- Wed May 18 14:29:58 IST 2005 ================================================================================ From landman at scalableinformatics.com Wed May 18 10:24:23 2005 From: landman at scalableinformatics.com (Joe Landman) Date: Wed, 18 May 2005 10:24:23 -0400 Subject: [BiO BB] mpiblast error. In-Reply-To: References: Message-ID: <428B5017.8020801@scalableinformatics.com> Hi Sravan: Since you are using the RPMs we built, maybe I can help. P Sravan Kumar. PAsst wrote: > We need assistance from the users of mpiblast regarding the execution on > AMD64 grid environment. > > 1.System Configuration: > --------------------- > Operating System: > Red Hat Enterprise Linux 3.0 for AMD 64 Architecture > Sun Fire v20z machine > Bio Clusture Grid Engine > 2. We have downloaded the NCBI-2.2.10-1.x86_64.rpm and > mpiblast-1.3.0-1.x86_64.rpm from scalableinformatics.com. When we > installed NCBI: all the binaries like blastall are loaded onto /usr/bin. > and mpiblast: all the binaries are loaded onto /usr/local/bin ex: > mpiblast, mpiformatdb. Good. These binaries are built against mpich-1.2.6. I have not done a build against LAM yet, though I would like to. This is relevant a little later on in the error message portion. > 3. We have created one common blastdb in /apps/Databases/blastdb/ using > mpiformatdb -i scaffolds --nfrags=250 N 250 -p F. ( 250 fragments have > been created). Good. > 4. Lamboot and lamnodes are also working fine as we checked by running > clustalmpi.sh through mpirun command. Since mpiblast (from the RPM) is not using LAM, this is going to be an issue when you try to run it. > > 5. But we are unable to run mpiblast through mpirun script as it gives the > follwing error: > ( I am attaching a file containing the script and the error message ). execution: ./mpiblast.sh on the masternode (silk-node 7 n0) Wed May 18 14:29:55 IST 2005 Sorry, mpiBLAST must be run on 3 or more nodes [0] MPI Abort by user Aborting program ! [0] Aborting program! Yes. Makes sense (oddly enough), as this version of the mpiblast RPM was built against mpich-1.2.6. I would be happy to build against LAM (I have 7.0.3, 7.0.6, and 7.1.1 installed on my build machine), though it might take a little while. Unfortunately, MPI != MPI. I cannot take a LAM compiled binary and run it on an MPICH system, nor can I take an MPICH compiled binary and run it on an LAM system. I would like us to get there, but this requires an MPI ABI, and a few other bits (agreement on how MPI processes are started, etc). > Our query: > --------- > 1. Why is this happening? See above. > 2. Is there an NCBI.TAR.GZ pacakge that supports AMD64(X86_64) for RH > Enterprise WS 3.0? ??? > 3. While installing NCBI rpms we were able to find only binary files. We > did not find the data files of NCBI ex: blosum, pam etc in any path in > Is there any specific path they may be located? I did not include them in the RPM. Would you like a separate RPM with the data files? > Please assist us in proper integration and running of mpiblast > tool. We appreciate your early suggestions. Joe > > Regards. > Sravan. > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Bioinformatics.Org general forum - 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 cell : +1 734 612 4615 From landman at scalableinformatics.com Wed May 18 10:29:07 2005 From: landman at scalableinformatics.com (Joe Landman) Date: Wed, 18 May 2005 10:29:07 -0400 Subject: [BiO BB] mpiblast error. In-Reply-To: References: Message-ID: <428B5133.6000303@scalableinformatics.com> Hi Sravan: Since you are using the RPMs we built, maybe I can help. P Sravan Kumar. PAsst wrote: > We need assistance from the users of mpiblast regarding the execution on > AMD64 grid environment. > > 1.System Configuration: > --------------------- > Operating System: > Red Hat Enterprise Linux 3.0 for AMD 64 Architecture > Sun Fire v20z machine > Bio Clusture Grid Engine > 2. We have downloaded the NCBI-2.2.10-1.x86_64.rpm and > mpiblast-1.3.0-1.x86_64.rpm from scalableinformatics.com. When we > installed NCBI: all the binaries like blastall are loaded onto /usr/bin. > and mpiblast: all the binaries are loaded onto /usr/local/bin ex: > mpiblast, mpiformatdb. Good. These binaries are built against mpich-1.2.6. I have not done a build against LAM yet, though I would like to. This is relevant a little later on in the error message portion. > 3. We have created one common blastdb in /apps/Databases/blastdb/ using > mpiformatdb -i scaffolds --nfrags=250 N 250 -p F. ( 250 fragments have > been created). Good. > 4. Lamboot and lamnodes are also working fine as we checked by running > clustalmpi.sh through mpirun command. Since mpiblast (from the RPM) is not using LAM, this is going to be an issue when you try to run it. > > 5. But we are unable to run mpiblast through mpirun script as it gives the > follwing error: > ( I am attaching a file containing the script and the error message ). execution: ./mpiblast.sh on the masternode (silk-node 7 n0) Wed May 18 14:29:55 IST 2005 Sorry, mpiBLAST must be run on 3 or more nodes [0] MPI Abort by user Aborting program ! [0] Aborting program! Yes. Makes sense (oddly enough), as this version of the mpiblast RPM was built against mpich-1.2.6. I would be happy to build against LAM (I have 7.0.3, 7.0.6, and 7.1.1 installed on my build machine), though it might take a little while. Unfortunately, MPI != MPI. I cannot take a LAM compiled binary and run it on an MPICH system, nor can I take an MPICH compiled binary and run it on an LAM system. I would like us to get there, but this requires an MPI ABI, and a few other bits (agreement on how MPI processes are started, etc). > Our query: > --------- > 1. Why is this happening? See above. > 2. Is there an NCBI.TAR.GZ pacakge that supports AMD64(X86_64) for RH > Enterprise WS 3.0? ??? > 3. While installing NCBI rpms we were able to find only binary files. We > did not find the data files of NCBI ex: blosum, pam etc in any path in > Is there any specific path they may be located? I did not include them in the RPM. Would you like a separate RPM with the data files? > Please assist us in proper integration and running of mpiblast > tool. We appreciate your early suggestions. Joe > > Regards. > Sravan. > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Bioinformatics.Org general forum - 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 cell : +1 734 612 4615 From landman at scalableinformatics.com Wed May 18 11:35:12 2005 From: landman at scalableinformatics.com (Joe Landman) Date: Wed, 18 May 2005 11:35:12 -0400 Subject: [BiO BB] mpiblast error. In-Reply-To: <428B5017.8020801@scalableinformatics.com> References: <428B5017.8020801@scalableinformatics.com> Message-ID: <428B60B0.209@scalableinformatics.com> Hi Sravan: I just rebuilt the RPM for LAM. Have a look at http://downloads.scalableinformatics.com/downloads/mpiblast/mpiblast-1.3.0-2LAM.x86_64.rpm though I haven't had a chance to test it in any great depth. Looks like new ncbi bits are out, so I will build some RPMs of this soon as well. Joe Joe Landman wrote: > Hi Sravan: > > Since you are using the RPMs we built, maybe I can help. > > P Sravan Kumar. PAsst wrote: > >> We need assistance from the users of mpiblast regarding the execution on >> AMD64 grid environment. >> >> 1.System Configuration: >> --------------------- >> Operating System: >> Red Hat Enterprise Linux 3.0 for AMD 64 Architecture >> Sun Fire v20z machine >> Bio Clusture Grid Engine >> 2. We have downloaded the NCBI-2.2.10-1.x86_64.rpm and >> mpiblast-1.3.0-1.x86_64.rpm from scalableinformatics.com. When we >> installed NCBI: all the binaries like blastall are loaded onto /usr/bin. >> and mpiblast: all the binaries are loaded onto /usr/local/bin ex: >> mpiblast, mpiformatdb. > > > Good. These binaries are built against mpich-1.2.6. I have not done a > build against LAM yet, though I would like to. This is relevant a > little later on in the error message portion. > >> 3. We have created one common blastdb in /apps/Databases/blastdb/ using >> mpiformatdb -i scaffolds --nfrags=250 N 250 -p F. ( 250 fragments have >> been created). > > > Good. > >> 4. Lamboot and lamnodes are also working fine as we checked by running >> clustalmpi.sh through mpirun command. > > > Since mpiblast (from the RPM) is not using LAM, this is going to be an > issue when you try to run it. > >> >> 5. But we are unable to run mpiblast through mpirun script as it gives >> the >> follwing error: >> ( I am attaching a file containing the script and the error message ). > > > execution: ./mpiblast.sh on the masternode (silk-node 7 n0) > Wed May 18 14:29:55 IST 2005 > Sorry, mpiBLAST must be run on 3 or more nodes > [0] MPI Abort by user Aborting program ! > [0] Aborting program! > > Yes. Makes sense (oddly enough), as this version of the mpiblast RPM > was built against mpich-1.2.6. I would be happy to build against LAM (I > have 7.0.3, 7.0.6, and 7.1.1 installed on my build machine), though it > might take a little while. > > Unfortunately, MPI != MPI. I cannot take a LAM compiled binary and run > it on an MPICH system, nor can I take an MPICH compiled binary and run > it on an LAM system. I would like us to get there, but this requires an > MPI ABI, and a few other bits (agreement on how MPI processes are > started, etc). > >> Our query: >> --------- >> 1. Why is this happening? > > > See above. > >> 2. Is there an NCBI.TAR.GZ pacakge that supports AMD64(X86_64) for RH >> Enterprise WS 3.0? > > > ??? > >> 3. While installing NCBI rpms we were able to find only binary files. We >> did not find the data files of NCBI ex: blosum, pam etc in any path in >> Is there any specific path they may be located? > > > I did not include them in the RPM. Would you like a separate RPM with > the data files? > >> Please assist us in proper integration and running of mpiblast >> tool. We appreciate your early suggestions. > > > Joe > >> >> Regards. >> Sravan. >> >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Bioinformatics.Org general forum - >> 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 cell : +1 734 612 4615 From moyc at mail.med.upenn.edu Fri May 20 11:04:11 2005 From: moyc at mail.med.upenn.edu (Chris Moy) Date: Fri, 20 May 2005 11:04:11 -0400 Subject: [BiO BB] Hapmap question Message-ID: <6C7B9F9F-C940-11D9-BB39-000A9599E70C@mail.med.upenn.edu> Hello All, I am a little new on working with Hapmaps and I was wondering if someone could explain to me how the D prime (D') measurement on HapMaps are evaluated. Why are their scores significantly different from the r squared measurement? Chris Chris Moy Sr. Programmer/Analyst University of Pennsylvania - Department of Ophthalmology/Genetics 215-898-9838 moyc at mail.med.upenn.edu From sravan_111 at rediffmail.com Fri May 20 13:49:44 2005 From: sravan_111 at rediffmail.com (sravan sravan) Date: 20 May 2005 17:49:44 -0000 Subject: [BiO BB] mpiblast Message-ID: <20050520174944.29965.qmail@webmail50.rediffmail.com> ?Dear Sir, Thanks for the suggestions. I have installed the tool on all the nodes and set up .ncbirc. .ncbirc -------- [NCBI] Data=/apps/Databases/ncbi/data [BLAST] BLASTDB=/apps/Databases/blastdb BLASTMAT=/apps/Databases/ncbi/data [mpiBLAST] Shared=/apps/Databases/blastdb ( full permission) Local=/tmp/mpiblast( full permission) Ncbi:NCBI-2.2.10-5.x86_64.rpm| mpiblast: mpiblast-1.3.0-2LAM.x86_64.rpm As a user I have done mpiformatdb -i silkcds -N 20 -p F which generated database in /apps/Databases/blastdb/ but : with rw-r--r-- permission. Then I have executed mpiblast.sh ( /usr/local/bin/mpiblast -p blastn -d /apps/Databases/blastdb/silkcds -i /home/sravan/demorun/blast/SW_ge2k_BGF.cds -o /home/sravan/demorun/blast/mpiblast.out). I have got the following error message: (0) Error opening: /apps/Databases/blastdb///apps/Databases/blastdb/silkcds.dbs Fatal Error: db_spec.cpp(DbSpecFile): Unable to open file ----------------------------------------------------------------------------- One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a "return 0" or "exit(0)" in your C code before exiting the application. PID 11355 failed on node n0 (172.16.0.17) with exit status 1. ----------------------------------------------------------------------------- So in this case how do I proceed? I strongly appreciate your early reply. Thank you very much. Regards. Sravan. -------------- next part -------------- An HTML attachment was scrubbed... URL: From marty.gollery at gmail.com Fri May 20 14:45:39 2005 From: marty.gollery at gmail.com (Martin Gollery) Date: Fri, 20 May 2005 11:45:39 -0700 Subject: [BiO BB] GEO help Message-ID: Has anyone come across a good book or online resource on NCBI's GEO? I have a colleague that has gone through the tutorial and the FAQ's, but still has some unanswered questions. Thanks, Marty -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- From sravan_111 at rediffmail.com Sat May 21 01:56:13 2005 From: sravan_111 at rediffmail.com (sravan sravan) Date: 21 May 2005 05:56:13 -0000 Subject: [BiO BB] (no subject) Message-ID: <20050521055613.10300.qmail@webmail8.rediffmail.com> Dear Sir, Thanks for your asisstance. During the compilation of lam version I have got this error message. Kindly let me know the solution. ----------------------------------------------------------------------- Process: 1. Compilation of NCBI-2.2.10-5.x86_64.rpm: creates: /usr/share/ncbi/data. and /usr/bin/exes. 2. Compilation of mpiblast-1.3.0-2LAM.x86_64.rpm : created exes in /usr/local/bin. 3. .ncbirc file has been set up in each node at ~sravan/.ncbirc: [NCBI] Data=/apps/Databases/ncbi/data [BLAST] BLASTDB=/apps/Databases/blastdb BLASTMAT=/apps/Databases/ncbi/data [mpiBLAST] Shared=/apps/Databases/blastdb ( full permission) Local=/tmp/mpiblast(full permission) 4. formatdb -N 20 -i /home/sravan/demorun/blast/silkcds -p F : has created a shared blastable parsed dataset fragments in /apps/Databases/blastdb(drwxrwxrwx): but the files are created as user. So their permissions are: -rw-r--r--. 5. script: /usr/local/lam/bin/mpirun -np 5 /usr/local/bin/mpiblast -p blastn -i /home/sravan/demorun/blast/SWseq -d /apps/Databases/blastdb/silkcds -e 10 -v 5 -b 5 -o /home/sravan/demorun/blast/mpiblast.out --debug=mpiblastlog. Error Message I got: ------------- Sat May 21 11:09:14 IST 2005 (0) Error opening: /apps/Databases/blastdb///apps/Databases/blastdb/silkcds.dbs Fatal Error: db_spec.cpp(DbSpecFile): Unable to open file ----------------------------------------------------------------------------- One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a "return 0" or "exit(0)" in your C code before exiting the application. PID 15092 failed on node n0 (172.16.0.17) with exit status 1. ----------------------------------------------------------------------------- MPI_Recv: process in local group is dead (rank 1, SSI:coll:smp:local comm for CID 0) Rank (3, MPI_COMM_WORLD): Call stack within LAM: Rank (3, MPI_COMM_WORLD): - MPI_Recv() Rank (3, MPI_COMM_WORLD): - MPI_Recv() Sat May 21 11:09:16 IST 2005 Thank you very much. Regards. Sravan. -------------- next part -------------- An HTML attachment was scrubbed... URL: From landman at scalableinformatics.com Sat May 21 09:00:28 2005 From: landman at scalableinformatics.com (Joe Landman) Date: Sat, 21 May 2005 09:00:28 -0400 (EDT) Subject: [BiO BB] Re: your mail In-Reply-To: <20050521055613.10300.qmail@webmail8.rediffmail.com> References: <20050521055613.10300.qmail@webmail8.rediffmail.com> Message-ID: Hi Sravan: Dont use an absolute or relative path for the directory entry. mpiblast handles this for you (e.g. your -d /full/path/to/database should be -d database). Joe On Sat, 21 May 2005, sravan sravan wrote: > Dear Sir, Thanks for your asisstance. During the compilation of lam version I have got this error message. Kindly let me know the solution. ----------------------------------------------------------------------- Process: 1. Compilation of NCBI-2.2.10-5.x86_64.rpm: creates: /usr/share/ncbi/data. and /usr/bin/exes. 2. Compilation of mpiblast-1.3.0-2LAM.x86_64.rpm : created exes in /usr/local/bin. 3. .ncbirc file has been set up in each node at ~sravan/.ncbirc: [NCBI] Data=/apps/Databases/ncbi/data [BLAST] BLASTDB=/apps/Databases/blastdb BLASTMAT=/apps/Databases/ncbi/data [mpiBLAST] Shared=/apps/Databases/blastdb ( full permission) Local=/tmp/mpiblast(full permission) 4. formatdb -N 20 -i /home/sravan/demorun/blast/silkcds -p F : has created a shared blastable parsed dataset fragments in /apps/Databases/blastdb(drwxrwxrwx): but the files are created as user. So their permissions are: -rw-r--r--. 5. script: /usr/local/lam/bin/mpirun -np 5 /usr/local/bin/mpiblast -p blastn -i /home/sravan/demorun/blast/SWseq -d /apps/Databases/blastdb/silkcds -e 10 -v 5 -b 5 -o /home/sravan/demorun/blast/mpiblast.out --debug=mpiblastlog. Error Message I got: ------------- Sat May 21 11:09:14 IST 2005 (0) Error opening: /apps/Databases/blastdb///apps/Databases/blastdb/silkcds.dbs Fatal Error: db_spec.cpp(DbSpecFile): Unable to open file ----------------------------------------------------------------------------- One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a "return 0" or "exit(0)" in your C code before exiting the application. PID 15092 failed on node n0 (172.16.0.17) with exit status 1. ----------------------------------------------------------------------------- MPI_Recv: process in local group is dead (rank 1, SSI:coll:smp:local comm for CID 0) Rank (3, MPI_COMM_WORLD): Call stack within LAM: Rank (3, MPI_COMM_WORLD): - MPI_Recv() Rank (3, MPI_COMM_WORLD): - MPI_Recv() Sat May 21 11:09:16 IST 2005 Thank you very much. Regards. Sravan. From massimo.ubaldi at unicam.it Tue May 24 07:03:21 2005 From: massimo.ubaldi at unicam.it (Massimo Ubaldi) Date: Tue, 24 May 2005 13:03:21 +0200 Subject: [BiO BB] Summer School: Microarray and Bioinformatics Message-ID: Dear All, the University of Camerino (UNICAM) is pleased to announce the Summer School: "Microarray Technology and Bioinformatics", that will be held in Camerino from August 29 to September 2, 2005. The Course is aimed at training researchers to a multidisciplinary approach to microrray data analysis. Particular attention is devoted to the design of Microarray experiments, to data normalization and quality control as well as to statistical analysis and data mining techniques. For details and registration, please check the web site: http://web.unicam.it/microarray The event is supported by the European Community : To Spread Bioinformatic Knowledge applied to Functional Genomics. Program MTKD-CT-2004-509242. Best regards Dr. Massimo Ubaldi (Member of the Scientific Committee) Massimo Ubaldi PhD Department of Experimental Medicine and Public Health University of Camerino (UNICAM) Via Scalzino 3 62032 Camerino (MC) Italy phone: +39 0737 40332 fax: +39 0737 630618 -------------- next part -------------- A non-text attachment was scrubbed... Name: SummerSchool.pdf Type: application/pdf Size: 235826 bytes Desc: not available URL: From rcamacho at fe.up.pt Wed May 25 13:39:36 2005 From: rcamacho at fe.up.pt (rcamacho at fe.up.pt) Date: Wed, 25 May 2005 18:39:36 +0100 Subject: [BiO BB] Workshop on Computational Methods in Bioinformatics Message-ID: <20050525183936.hs52i72dh4wwokok@webmail.fe.up.pt> **************************************** *** We apologise for multiple copies *** **************************************** *** Deadline extended *** ** Paper submission June 3rd, 2005 ** Workshop on Computational Methods in Bioinformatics cmb.epia05 at di.ubi.pt as part of the 12th Portuguese Conference on Artificial Intelligence Covilha, Portugal, 5-8 December 2005 http://epia05.di.ubi.pt email: epia05 at di.ubi.pt =============== Call for Papers =============== The success of bioinformatics in recent years has been prompted by research in molecular biology and molecular medicine in initiatives like the human genome project. These initiatives gave rise to an exponential increase in the volume and diversification of data, including protein and gene data, nucleotide sequences and biomedical literature. The accumulation and exploitation of large-scale data bases prompts for new computational technology and for research into these issues. In this context, many widely successful computational models and tools used by biologists in these initiatives, such as clustering and classification methods for gene expression data, are based on artificial intelligence (AI) techniques. Hence, this workshop brings the opportunity to discuss applications of AI with an interdisciplinary character, exploring the interactions between sub-areas of AI and Bioinformatics. Topics and Technical issues --------------------------- Papers should deal with bio-medical data sets. Computer science and mathematical modelling papers must contain a concise description of the biological problem being solved, and biology papers should show how computation or analysis improves the results. Biological areas of interest include, but are not limited to: - sequence analysis, - comparison and alignment methods; - motif, gene and signal recognition; - molecular evolution; - phylogenetics and phylogenomics; - determination or prediction of the structure of RNA and protein in two and three dimensions; - DNA twisting and folding; - gene expression and gene regulatory networks; - deduction of metabolic pathways; - microarray design and analysis; - proteomics; - functional genomics; - molecular docking and drug design; - computational problems in genetics such as linkage and QTL analysis, linkage disequilibrium analysis in populations, and haplotype determination; - systems biology. Computational areas of interest include, but are not limited to: - Knowledge Discovering techniques and Data Mining; - Text Mining and Language Processing; - Machine Learning and Pattern Recognition; - Rough, Fuzzy and Hybrid Techniques; - Hidden Markov Models; - Bayesian Approaches; - Artificial Neural Networks; - Support Vector Machines; - Evolutionary Computing; - Non-linear dynamical analysis methods and Intelligent signal processing Sponsors -------- The 12th Portuguese Conference on Artificial Intelligence is sponsored by APPIA, the Portuguese Association of AI (http://www.appia.pt/). Goals and Intended Audience --------------------------- The workshop's aim is to discuss computational aspects and challenges of important biological problems and, in doing so, identify new research opportunities. A second goal is to establish a forum that will bring together researchers in Artificial Intelligence face to face with researchers in bioinformatics. The hope is that this workshop will provide a forum where people from the two communities can come together to exchange ideas and discuss different approaches. Proceedings ___________ Authors may submit full papers with a maximum of 12 pages or short papers with a maximum of 4 pages. Both kinds of papers may report on innovative work, work reported elsewhere, ongoing research or student projects. Only innovative full papers are candidate to publications in the Springer proceedings as specified below. All papers must follow the Springer instructions for authors as indicated in http://www.springer.de/comp/lncs/authors.html/ A selection of the workshop accepted full papers will be published by Springer in the Lecture Notes in Artificial Intelligence sub-series of LNCS. All accepted papers not published in the Springer proceedings will be published by UBI in the Local Workshop Proceedings, in hard copy, in CD-ROM and in the web. To be a candidate for publication in the main proceedings the following rules must be met: * Submissions must be full technical papers on substantial, original, and previously unpublished research. * Submissions must be formatted according to the Springer LNCS Series guidelines, and must not exceed 12 pages. Each selected paper will be allowed 12 pages in the Proceedings. Up to two additional pages may be purchased by the authors. At least one of the authors must be registered at the conference for the paper to be published in the proceedings. Posters ------- The workshop will have a poster session running during the coffee breaks. Posters are intended to report on work in progress, student projects, open problems and research issues, as well as new application challenges. Important Dates _______________ Here are some important dates: Conference begins December 5th, 2005 Paper submission June 3rd, 2005 Author notification July 15th, 2005 Camera-ready copies July 28th, 2005 Submission and reviewing Information ----------------------------------------------- The workshop will follow a blind reviewing policy. In order to make blind reviewing possible, submissions must be anonymous. This requires that authors exercise some care not to identify themselves in their contributions. Authors should omit their names and affiliations from the paper. Also, while the references should include all published literature relevant to the paper, including previous works of the authors, it should not include unpublished works. When referring to one's own work, authors must use the third person rather than the first person. To submit a paper the author fills in an electronic form with author's and papers information and them upload the paper in PDF format. All papers (short or full papers) will follow the same reviewing process. Submission is made through the submission page available in the EPIA 2005 website http://epia05.di.ubi.pt . Organization ____________ Program Chairs Rui Camacho Alexessander Alves LIACC and FEUP, LIACC Universidade do Porto, Portugal Universidade do Porto, Portugal rcamacho at fe.up.pt alves at ieee.org Joaquim Pinto da Costa Paulo Azevedo LIACC and FCUP Departamento de Informatica Universidade do Porto, Portugal Universidade do Minho, Portugal jpcosta at fc.up.pt pja at di.uminho.pt Program Committee P. Alexandrino (Portugal) T. Freitas (Portugal) A. Alves (Portugal) H. M. Jamil (USA) P. Azevedo (Portugal) A. Jorge (Portugal) P. Bourne (USA) R. King (Wales, UK) V. Brusic (Singapore) I. C. Lerman (France) C. Bystroff (USA) M. P. Monteiro (Portugal) R. Camacho (Portugal) M. Sagot (France) E. Costa (Portugal) T. Scheffer (Germany) A. Carvalho (Brasil) S. Schulze-Kremer (Germany) J. P. Costa (Portugal) A. Srinivasan (India) V. Costa (Brasil) A. Valencia (Spain) I. Dutra (Brasil) J. Vieira (Portugal) L. Dehaspe (Belgium) M. Zaki (USA) D. Gilbert (Scotland, UK) From magda_mansour at yahoo.fr Fri May 27 10:51:28 2005 From: magda_mansour at yahoo.fr (Magda Mansour) Date: Fri, 27 May 2005 16:51:28 +0200 (CEST) Subject: [BiO BB] NCBI: rpsblast segmentation fault In-Reply-To: <20050525183936.hs52i72dh4wwokok@webmail.fe.up.pt> Message-ID: <20050527145128.30991.qmail@web26804.mail.ukl.yahoo.com> Hello, When I run rpsblast with the CDD (conserved domain database) downloaded from the NCBI, I have no problems. When I run it on a custom database made from 2 profiles using formatrpsdb, I get a segmentation fault amd NOTE: [000.000] RDBTaxInfoInit: Unable to open in the rpsblast.log file Here are the commands I use to make my small DB: toolbox-C/ncbi/build/blastpgp -d DB/pdb90 -i trial_db_3/CAA64315.fasta -o trial_db_3/CAA64315.out -C trial_db_3/matric_C.chk -Q trial_db_3/matrix_Q -u1 -J T -j 4 for 2 different sequences. toolbox-C/ncbi/build/formatrpsdb -i trial_db_3/DB_formatrps.pn -o trial_db_3/index -t trial_db_3/DB_formatrps -n trial_db_3/DB_formatrps -l trial_db_3/formatrpsdb.log The output files seem very similar to those of the NCBI DB. (but I can't access all of them). toolbox-C/ncbi/build/rpsblast -i trial_db_3/P00179.fasta -d trial_db_3/DB_formatrps -o trial_db_3/P00179_rps.out -l trial_db_3/rpsblast.log => Segmentation fault!!! NOTE: [000.000] RDBTaxInfoInit: Unable to open Did I forget any important parameter in any step? Isn't it possible to make a database from 2 profiles only? Is there anything wrong with the extensions? Another question, is it possible to create a profile from the output of rpsblast?? Thank you, Yours, Magda. _____________________________________________________________________________ D?couvrez le nouveau Yahoo! Mail : 1 Go d'espace de stockage pour vos mails, photos et vid?os ! Cr?ez votre Yahoo! Mail sur http://fr.mail.yahoo.com From trobalo at mrna.ist.utl.pt Mon May 30 17:29:19 2005 From: trobalo at mrna.ist.utl.pt (=?ISO-8859-1?Q?Tiago_Andr=E9_Robalo?=) Date: Mon, 30 May 2005 22:29:19 +0100 Subject: [BiO BB] Some Help! In-Reply-To: <9ADB6198-81B7-11D9-A931-000D93712582@poulet.org> References: <9ADB6198-81B7-11D9-A931-000D93712582@poulet.org> Message-ID: <429B85AF.6030302@mrna.ist.utl.pt> Hi all, I need an software (free) like CINEMA 5 (http://aig.cs.man.ac.uk/research/utopia/utopia.php) to find the position of a structured or simple motif in many sequences. The CINEMA crashs every time :( and the colour scheme doesnt work! I have try diferents OS (windows and macosx) but the problem persist. Thanks! From operon at cbiot.ufrgs.br Mon May 30 17:38:38 2005 From: operon at cbiot.ufrgs.br (Marcos Oliveira de Carvalho) Date: Mon, 30 May 2005 18:38:38 -0300 Subject: [BiO BB] Some Help! In-Reply-To: <429B85AF.6030302@mrna.ist.utl.pt> References: <9ADB6198-81B7-11D9-A931-000D93712582@poulet.org> <429B85AF.6030302@mrna.ist.utl.pt> Message-ID: Try Genedoc: http://www.psc.edu/biomed/genedoc/ It can search/colour according to ProSite syntax. Also, use a computer with "lots" of RAM (> 512) cheers Marcos On Mon, 30 May 2005 18:29:19 -0300, Tiago Andr? Robalo wrote: > Hi all, > > I need an software (free) like CINEMA 5 > (http://aig.cs.man.ac.uk/research/utopia/utopia.php) to find the > position of a structured or simple motif in many sequences. The CINEMA > crashs every time :( and the colour scheme doesnt work! > > I have try diferents OS (windows and macosx) but the problem persist. > > Thanks! > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From lifei03 at gmail.com Mon May 30 21:47:57 2005 From: lifei03 at gmail.com (Fei Li) Date: Tue, 31 May 2005 09:47:57 +0800 Subject: [BiO BB] B, Z, N, X in refseq Message-ID: <1e3d81a1050530184735522d9e@mail.gmail.com> I am using the refseq from Genbank. There are some strange characteristic such as B, Z, N, X in the protein sequence. Can anybody tell me what these "bad " characteristics means? What should I do if my program compain these bad characteristics. Remove them or replace them with some specific amino acid? Thanks Frank -- Do not guess who I am. I am not Bush in BlackHouse From boris.steipe at utoronto.ca Mon May 30 22:46:20 2005 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Mon, 30 May 2005 22:46:20 -0400 Subject: [Bioperl-l] [BiO BB] B, Z, N, X in refseq In-Reply-To: <1e3d81a1050530185010d15e6e@mail.gmail.com> Message-ID: <2AEBE3A0-D17E-11D9-BD2C-000A9577512E@utoronto.ca> > I am using the refseq from Genbank. There are some strange > characteristic such as B, Z, N, X in the protein sequence. These are standard ambiguity codes, see for example < http://www.ncbi.nlm.nih.gov/blast/html/search.html > (except for "N", which is simply asparagine) > Can anybody tell me what these "bad " characteristics means? This most likely means that particular sequence was derived by chemical sequencing of polypeptides, not by translation of nucleic acids; thus it may be hard to distinguish between N/D or Q/E. > What > should I do if my program compain these bad characteristics. Remove > them or replace them with some specific amino acid? That depends on what you want to do. For database sequence search the BLAST server accepts these codes and they are correctly represented in standard mutation-data matrices for alignment scores, so you don't need to worry. For molecular weight calculations you could use an average or randomly choose one or the other. I can't imagine an application where this level of detail would make much of a difference. However: removing them is always a bad choice, e.g. for sequence alignments you would be introducing a gap (bad!). Hope this helps, it's pretty standard textbook knowledge though, and maybe it would be worthwhile to read up on the Net before you post to several groups at once :-) B. > > Thanks > > Frank > > > -- > Do not guess who I am. I am not Bush in BlackHouse > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From vmalhotra21 at rediffmail.com Tue May 31 03:06:27 2005 From: vmalhotra21 at rediffmail.com (v m) Date: 31 May 2005 07:06:27 -0000 Subject: [BiO BB] help me plzz Message-ID: <20050531070627.1355.qmail@webmail45.rediffmail.com> hi to all members im a new member of this grp. im doin msc bioinformaitcs,india. can any one plzz tel me that whether any drug/s has ben discovered usin bioinformatis tools. i fyes then tel me the company name n the name of the drug too. thank u varun On Tue, 31 May 2005 bio_bulletin_board-request at bioinformatics.org wrote : >Welcome to the BiO_Bulletin_Board at bioinformatics.org mailing list! > >To post to this list, send your email to: > > bio_bulletin_board at bioinformatics.org > >General information about the mailing list is at: > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > >If you ever want to unsubscribe or change your options (eg, switch to >or from digest mode, change your password, etc.), visit your >subscription page at: > > https://bioinformatics.org/mailman/options/bio_bulletin_board/vmalhotra21%40rediffmail.com > > >You can also make such adjustments via email by sending a message to: > > BiO_Bulletin_Board-request at bioinformatics.org > >with the word `help' in the subject or body (don't include the >quotes), and you will get back a message with instructions. > >You must know your password to change your options (including changing >the password, itself) or to unsubscribe. It is: > > 9999999 > >Normally, Mailman will remind you of your bioinformatics.org mailing >list passwords once every month, although you can disable this if you >prefer. This reminder will also include instructions on how to >unsubscribe or change your account options. There is also a button on >your options page that will email your current password to you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.gopee at utm.intnet.mu Tue May 31 05:39:26 2005 From: a.gopee at utm.intnet.mu (Ajit Gopee) Date: Tue, 31 May 2005 13:39:26 +0400 Subject: [BiO BB] PhD Titles? Message-ID: <00bf01c565c4$a51af590$1b4110ac@Gopee> Hello all I'm new to the group. I hold a MSc IT (Bioinformatics). Now I would like to go a PhD in Computer Science but something related to Bioinformatics. However I'm a bit short of ideas for PhD Titles which I can ponder over. Can any one please send me some propable titles for such a PhD? Thanks a lot. Regards Ajit -------------- next part -------------- An HTML attachment was scrubbed... URL: From brunomiguel at dequim.ist.utl.pt Tue May 31 07:05:03 2005 From: brunomiguel at dequim.ist.utl.pt (Bruno Afonso) Date: Tue, 31 May 2005 12:05:03 +0100 Subject: [BiO BB] Some Help! In-Reply-To: <429B85AF.6030302@mrna.ist.utl.pt> References: <9ADB6198-81B7-11D9-A931-000D93712582@poulet.org> <429B85AF.6030302@mrna.ist.utl.pt> Message-ID: <429C44DF.5080706@dequim.ist.utl.pt> You might want to have a look at MEME: http://meme.sdsc.edu/meme/website/intro.html BA Tiago Andr? Robalo wrote: > Hi all, > > I need an software (free) like CINEMA 5 > (http://aig.cs.man.ac.uk/research/utopia/utopia.php) to find the > position of a structured or simple motif in many sequences. The CINEMA > crashs every time :( and the colour scheme doesnt work! > > I have try diferents OS (windows and macosx) but the problem persist. > > Thanks! > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Bruno Afonso, Biological Engineer GABBA Graduate Student Porto, Portugal http://brunoafonso.net/ http://dequim.ist.utl.pt/~bruno/sciTocs/ - Bruno's SciTocs! http://freebsd-pt.org/forum/ - Portuguese FreeBSD forum From magda_mansour at yahoo.fr Tue May 31 09:08:00 2005 From: magda_mansour at yahoo.fr (Magda Mansour) Date: Tue, 31 May 2005 15:08:00 +0200 (CEST) Subject: [BiO BB] NCBI-toolbox. From where should I start? RPS-profile In-Reply-To: 6667 Message-ID: <20050531130800.73166.qmail@web26810.mail.ukl.yahoo.com> Hello, I am trying to work with the NCBI toolbox. I started using the NCBI-C++, but I was told that using the NCBI-C is more stable for an initial use. So I switched to NCBI-C. But I don't know from where should I start. In many pages, it talks about starting with the demo, should I create a new makefile in this folder...?? Creating my own makefile seems to be quite complicated because of the huge number of imbrications in the files. I had also another question. How can I get the chosen profiles from RPS-BLAST? Thank you for your help, Magda Mansour _____________________________________________________________________________ D?couvrez le nouveau Yahoo! Mail : 1 Go d'espace de stockage pour vos mails, photos et vid?os ! Cr?ez votre Yahoo! Mail sur http://fr.mail.yahoo.com From christoph.gille at charite.de Tue May 31 11:06:10 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Tue, 31 May 2005 17:06:10 +0200 (CEST) Subject: [BiO BB] help me plzz drugs virt. drug design In-Reply-To: <20050531070627.1355.qmail@webmail45.rediffmail.com> References: <20050531070627.1355.qmail@webmail45.rediffmail.com> Message-ID: <49521.192.168.220.204.1117551970.squirrel@webmail.charite.de> As far as I know: omeprazole (proton pump inhibitor) The HIV drugs > hi to all members > > im a new member of this grp. > > im doin msc bioinformaitcs,india. > > can any one plzz tel me that whether any drug/s has ben discovered usin > bioinformatis tools. > > i fyes then tel me the company name n the name of the drug too. thank u > varun > > > On Tue, 31 May 2005 bio_bulletin_board-request at bioinformatics.org wrote : > >> Welcome to the BiO_Bulletin_Board at bioinformatics.org mailing list! >> >> >> To post to this list, send your email to: >> >> >> bio_bulletin_board at bioinformatics.org >> >> General information about the mailing list is at: >> >> >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> >> If you ever want to unsubscribe or change your options (eg, switch to >> or from digest mode, change your password, etc.), visit your subscription >> page at: >> >> https://bioinformatics.org/mailman/options/bio_bulletin_board/vmalhotra >> 21%40rediffmail.com >> >> >> >> You can also make such adjustments via email by sending a message to: >> >> >> BiO_Bulletin_Board-request at bioinformatics.org >> >> >> with the word `help' in the subject or body (don't include the quotes), >> and you will get back a message with instructions. >> >> You must know your password to change your options (including changing >> the password, itself) or to unsubscribe. It is: >> >> 9999999 >> >> >> Normally, Mailman will remind you of your bioinformatics.org mailing >> list passwords once every month, although you can disable this if you >> prefer. This reminder will also include instructions on how to >> unsubscribe or change your account options. There is also a button on >> your options page that will email your current password to you. > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > >