From jeedward from yahoo.com Sat May 2 07:37:06 2009 From: jeedward from yahoo.com (John Edward) Date: Tue May 5 14:25:07 2009 Subject: [Computational-biology] Extended draft paper submission: BCBGC-09 call for papers Message-ID: <862098.14718.qm@web45916.mail.sp1.yahoo.com> Extended draft paper submission: BCBGC-09 call for papers ? This Extended Call for Papers for the 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) is for those who didn't get a chance to submit the papers for the earlier call for papers. The papers received and accepted in response to this extended call for papers will be included in the final version of the respective conference proceedings. These proceedings will be either ready by the time of the conference (i.e., they will be available during the conference) or soon after the conference (before the end of August 2009), based how fast the proceedings can be prepared. Note: If you have already submitted a paper (whether accepted or rejected or currently under review) for MULTICONF-09, please DO NOT submit that paper again to this extended call for papers. IMPORTANT DATES: Draft paper submission date: May 11, 2009 Acceptance/rejection decision: May 21, 2009 Camera ready paper and copyright and pre-registration due: May 28, 2009 Conference dates: July 13-16, 2009 ? ? BCBGC-09 will be held during July 13-16 2009 in Orlando, FL, USA. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: ????????? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ????????? International Conference on Automation, Robotics and Control Systems (ARCS-09) ????????? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) ????????? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) ????????? International Conference on Information Security and Privacy (ISP-09) ????????? International Conference on Recent Advances in Information Technology and Applications (RAITA-09) ????????? International Conference on Software Engineering Theory and Practice (SETP-09) ????????? International Conference on Theory and Applications of Computational Science (TACS-09) ????????? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) ? The website http://www.PromoteResearch.org contains more details. ? Sincerely John Edward Publicity committee ? ? From mourad12345678 from yahoo.com Tue May 5 20:12:01 2009 From: mourad12345678 from yahoo.com (Mourad Elloumi) Date: Wed May 6 11:59:48 2009 Subject: [Computational-biology] Motif-Finding Problems Complexities Message-ID: <875034.65090.qm@web31505.mail.mud.yahoo.com> Dear All, We are seeking the complexities of the following Motif-Finding Problems : 1. Planted (l,d)-Motif Problem (PMP) 2. Extended (l,d)-Motif Problem (ExMP) 3. Further Extended (l,d)-Motif Problem (FExMP) 4. Edited Motif Search Problem (EdMP) 5. Simple Motifs Search Problem (SMS) Do you know have any references on these complexities? Thanks. Best regards, Mourad. ______________________________________________________ E.Mail:Mourad.Elloumi@fsegt.rnu.tn URL :www.esstt.rnu.tn/utic/english/memb_elloumi.html ______________________________________________________ From congen from popgen.eu Thu May 14 13:57:26 2009 From: congen from popgen.eu (Congen) Date: Thu May 14 14:12:28 2009 Subject: [Computational-biology] Conservation genetics data analysis course Message-ID: <6d941f120905141157n2fb7cb2bxc7c3187252f71b73@mail.gmail.com> 4th ConGen- Population Genetics Data Analysis Course Recent Approaches for Estimation of Population Size, Structure, Gene flow, Selection Detection focusing on conservation and beyond 31-Aug/4-Sep 2009, Flathead Lake Biological Station, Montana, USA Applications for 2009 are open! Objective: To provide training in conceptual and practical aspects of data analysis for the conservation genetics of natural and managed populations. Emphasis will be on interpretation of output from recent novel statistical approaches and software programs. The course also will allow daily discussions among young researchers and top-researchers to help develop the next generation of conservation geneticists, and to identify developments needed to improve data analysis approaches. This course will cover analysis methods including the coalescent, Bayesian, approximate Bayesian, and likelihood-based approaches. Who should apply: Ph.D. students, post-docs, and population biologists with a background of at least one semester university-level course in population genetics and a course in population ecology. Applicants must have a basic background in population genetic data analysis, including testing for Hardy-Weinberg proportions and gametic disequilibrium. Participation will be limited to 20 people allowing efficient instruction with hands-on computer exercises during the course. Priority will be given to persons with their own data to analyze (for example graduate students at the end of their degree program). Deadline for application is 30 June, 2009 Course/Workshop Format: For each subject, we provide 30-45 minutes of background, theory, discussion and introduction to concepts. Immediately following, we will conduct data analyses together for 30-60 minutes using relevant software programs and real data sets. Evening hands-on computer sessions and housing together of instructors and students in the same location will allow for extensive exchange and facilitate learning. For detailed information see http://popgen.eu/congen2009/ congen@popgen.eu From db60 from st-andrews.ac.uk Thu May 14 06:42:04 2009 From: db60 from st-andrews.ac.uk (Daniel Barker) Date: Thu May 14 14:13:07 2009 Subject: [Computational-biology] Conference, Comparative Genomics, University of St Andrews Message-ID: Dear bionet.biology.computational, I would like to draw your attention to these events in St Andrews this August: - One day conference, "Comparative Genomics" - Summer school, "Bioinformatics and Comparative Genomics" - Workshop, "The Role of Behaviour in Speciation" Details are below. ***************************************************************** Comparative Genomics one-day international conference Date: 18th August 2009 Location: Bute Building, University of St Andrews, UK ***************************************************************** The Scottish Bioinformatics Forum and the University of St Andrews are pleased to announce a one-day international conference, "Comparative Genomics", with nine invited speakers and an open poster session. Confirmed speakers: - Prof MARK BLAXTER, University of Edinburgh. "Comparative nematode genomics". - Prof GEOFF BARTON, University of Dundee. "A tale of three small RNAs". - Prof DANNIE DURAND, Carnegie Mellon University. "The evolution of multidomain families". - Prof NEIL HALL, University of Liverpool. "Fast forward genetics using second generation sequencing". - Dr MATTHEW HEGARTY, Aberystwyth University. "Genomic mergers: the consequences of hybridisation and polyploidy in Senecio". - Prof IAN KORF, University of California Davis Genome Center. "Intron mediated enhancement". - Dr DAVID MARTIN, University of Dundee. "Predicting protein function". - Dr ZEMIN NING, Wellcome Trust Sanger Institute. "Cancer genome assemblies and variation detection between normal and tumor human cells". - Prof ZIHENG YANG FRS, University College London. "Population genomics and human-chimpanzee speciation". For more information on the conference, including registration and poster abstract submission, please see: http://www.sbforum.org/events.php?e_id=70 ***************************************************************** Summer School - Bioinformatics and Comparative Genomics Start Date: 15th August 2009, 9:00 am End Date: 18th August 2009 (including one-day conference) Location: University of St Andrews, UK ***************************************************************** The Scottish Bioinformatics Forum and the University of St Andrews are pleased to announce the first Summer School on Bioinformatics and Comparative Genomics. The summer school will address practical bioinformatics for sequence analysis and comparative genomics, for use in biological and biomedical research. The summer school will be held in St Andrews on 15th-17th August 2009. Registration for the summer school also includes attendance at the one-day conference on Comparative Genomics on 18 August (see above). Confirmed tutors: - Prof ZIHENG YANG FRS, University College London - Dr ZEMIN NING, Wellcome Trust Sanger Institute - Dr DAVID MARTIN, University of Dundee - Prof IAN KORF, University of California Davis Genome Center - Dr CHRIS JANSSEN, SBF and University of Glasgow - Prof NEIL HALL and Dr ALISTAIR DARBY, University of Liverpool - Dr DAVID FERRIER, University of St Andrews - Prof DANNIE DURAND, Carnegie Mellon University - Prof GEOFF BARTON and Dr JIM PROCTER, University of Dundee - Dr DANIEL BARKER, University of St Andrews For more information on the summer school and registration details, please see: http://www.genome-bioinformatics.org/index.html ***************************************************************** Workshop - The Role of Behaviour in Speciation Start Date: 19th August 2009 End Date: 22nd August 2009 Location: University of St Andrews, UK ***************************************************************** This is a separate workshop at St Andrews, arranged by the EU Marie Curie Initial Training Network "SPECIATION". Details of this workshop are available from Prof Mike Ritchie: http://biology.st-andrews.ac.uk/staff/mgr.htm and will appear at: http://speciation.group.shef.ac.uk Looking forward to seeing you in St Andrews! Kind Regards Daniel Barker -- Daniel Barker http://bio.st-andrews.ac.uk/staff/db60.htm The University of St Andrews is a charity registered in Scotland : No SC013532 From coss.eps from ceu.es Fri May 15 04:10:26 2009 From: coss.eps from ceu.es (coss.eps@ceu.es) Date: Fri May 15 11:26:57 2009 Subject: [Computational-biology] Fourth Summerschool on Advanced Statistics and Data Mining (Madrid, July 6th-17th, 2009) Message-ID: Dear colleagues, the Polytechnical Univ. of Madrid organizes a summerschool on "Advanced Statistics and Data Mining" in Madrid between July 6th and July 17th. The summerschool comprises 18 courses divided in 2 weeks. Attendees may register in each course independently. Registration will be considered upon strict arrival order.For more information, please, visit http://www.dia.fi.upm.es/index.php?page=presentation&hl=es_ES or http://biocomp.cnb.csic.es/~coss/Docencia/ADAM/ADAM.htm. Best regards, Carlos Oscar *List of courses and brief description* (full description at http://biocomp.cnb.csic.es/~coss/Docencia/ADAM/ADAM.htm) Week 1 (July 6th - July 10th, 2009) Course 1: Bayesian networks (15 h), Practical sessions: Hugin, Elvira, Weka, LibB Bayesian networks basics. Inference in Bayesian networks. Learning Bayesian networks from data Course 2: Multivariate data analysis (15 h), Practical sessions: MATLAB Introduction. Data Examination. Principal component analysis (PCA). Factor Analysis. Multidimensional Scaling (MDS). Correspondence analysis. Multivariate Analysis of Variance (MANOVA). Canonical correlation. Course 3: Dimensionality reduction (15 h), Practical sessions: MATLAB Introduction. Matrix factorization methods. Clustering methods. Projection methods. Applications Course 4: Supervised pattern recognition (Classification) (15 h), Practical sessions: Weka Introduction. Assessing the Performance of Supervised Classification Algorithms. Classification techniques. Combining Classifiers. Comparing Supervised Classification Algorithms Course 5: Introduction to MATLAB (15 h) Overview of the Matlab suite. Data structures and files. Programming in Matlab. Visualization tools. Some applications in pattern recognition. Course 6: Datamining, a practical perspective (15h), Practical sessions: MATLAB, R, Weka Introduction to Data Mining and Knowledge Discovery. Prediction in data mining. Classification. Association studies. Data mining in free-form texts: text mining. Course 7: Time series analysis (15 h), Practical sessions: MATLAB Introduction. Probability models to time series. Regression and Fourier analysis. Forecasting and Data mining. Course 8: Neural networks (15 h), Practical sessions: MATLAB Introduction to the biological models. Nomenclature. Perceptron networks. The Hebb rule. Foundations of multivariate optimization. Numerical optimization. Rule of Widrow-Hoff. Backpropagation algorithm. Practical data modelling with neural networks Course 9: Introduction to SPSS (15 h) Introduction. Describing data. Statistical inference. Time series. Sampling. Classification and regression Week 2 (July 13th - July 17th, 2009) Course 10: Regression (15 h), Practical sessions: SPSS Introduction. Simple Linear Regression Model. Measures of model adequacy. Multiple Linear Regression. Regression Diagnostics and model violations. Polynomial regression. Variable selection. Indicator variables as regressors. Logistic regression. Nonlinear Regression. Course 11: Practical Statistical Questions (15 h), Practical sessions: study of cases (without computer) I would like to know the intuitive definition and use of …: The basics. How do I collect the data? Experimental design. Now I have data, how do I extract information? Parameter estimation. Can I see any interesting association between two variables, two populations, …? How can I know if what I see is “true”? Hypothesis testing How many samples do I need for my test?: Sample size Can I deduce a model for my data? Other questions? Course 12: Missing data and outliers (15 h), Practical sessions: R Missing Data: Typology of missing data; Simple missing-data methods; Imputation Methods; Diagnostics and Overimputing. Outliers and robust statistics: Typology of outliers; Influence measures; Robust methods Course 13: Hidden Markov Models (15 h), Practical sessions:HTK Introduction. Discrete Hidden Markov Models. Basic algorithms for Hidden Markov Models. Semicontinuous Hidden Markov Models. Continuous Hidden Markov Models. Unit selection and clustering. Speaker and Environment Adaptation for HMMs. Other applications of HMMs Course 14: Statistical inference (15 h), Practical sessions: SPSS Introduction. Some basic statistical test. Multiple testing. Introduction to bootstrapping Course 15: Features Subset Selection (15 h), Practical sessions: MATLAB, R, Weka Filter approaches. Wrapper methods. Embedded methods. Course 16: Introduction to R (15 h) An introductory R session. Data in R. Importing/Exporting data. Programming in R. R Graphics. Statistical Functions in R Course 17: Unsupervised pattern recognition (clustering) (15 h), Practical sessions: MATLAB Introduction. Prototype-based clustering. Density-based clustering. Graph-based clustering. Cluster evaluation. Miscellanea Course 18: Evolutionary computation (15 h), Practical sessions: MATLAB Genetic algorithms. Genetic programming. Robust and self-adapting intelligent systems. Introduction to Estimation of Distribution Algorithms. Improvements, extensions and applications of EDAs. Current research in EDAs. From paolo.romano from istge.it Wed May 27 11:18:34 2009 From: paolo.romano from istge.it (Paolo Romano) Date: Wed May 27 11:30:40 2009 Subject: [Computational-biology] NETTAB 2009: Last Call for Participation Message-ID: <200905271633.n4RGXXII038788@ibm43p.biotech.ist.unige.it> Last Call for Participation NETTAB 2009 Workshop on "Technologies, Tools and Applications for Collaborative and Social Bioinformatics Research and Development" with a Special Session on: "Methods and Tools for RNA Structure and Functional Analysis" June 10-13, 2009 Department of Computer Science, University of Catania, Italy http://www.nettab.org/2009/ KEYNOTE TALKS RNA WikiProject: Community annotation of RNA families Alex Bateman, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK. Who are you? Managing collaborative digital identities in bioinformatics with myExperiment Duncan Hull, School of Chemistry, University of Manchester, Manchester, UK. Semantically Integrated eCommunities in Biomedicine: Next-Generation Models of Biomedical Communication Tim Clark, Director of Informatics, MassGeneral Institute for Neurodegenerative Disease Neurology Research Department, Massachusetts General Hospital, Boston, USA. Bacterial Phylogeny and Taxonomy in the High-Throughput Sequencing World Gabriel Valiente, Technical University of Catalonia, Department of Software, Barcelona, Spain. Non coding RNAs (title to be confirmed) Doron Betel, MSKCC - Computational Biology Center, New York, USA . SELECTED ORAL COMMUNICATIONS The DC-THERA Directory: A Knowledge Management System to Support Collaboration on Dendritic Cell and Immunology Research Michaela Guendel, Ciro Scognamiglio, Marco Brandizi and Andrea Splendiani Bioinformatics Experimentation in a New Agent-Based Infrastructure OpenKnowledge Dietlind Gerloff, Xueping Quan, Adrian de Pinninck, Paolo Besana, Siu-wai Leung, Marco Schorlemmer and David Robertson Abstraction based cooperation for the design of bioinformatics workflows Fr?d?ric Cadier and Philippe Picouet Biomedical applications in the EELA-2 Project Leandro N Ciuffo and Rafael Mayo Make Histri: collaborative curation of exchange histories of bacterial and archaeal type strains Bert Verslyppe, Paul De Vos, Bernard De Baets and Peter Dawyndt SBMM Assistant: Social Pathway Annotation Ismael Navas-Delgado, Alejandro del Real-Chicharro, Francisca S?nchez-Jim?nez and Jose F Aldana Montes GePh-CARD: an information exchange application for an Hub & Spoke Network for Skeletal Dysplasias Marina Mordenti and Luca Sangiorgi ProDaMa-C: a collaborative web application to generate specialized protein structure datasets Giuliano Armano and Andrea Manconi RNA tertiary structure prediction with ModeRNA Magdalena Musielak, Kristian Rother, Tomasz Puton and Janusz M. Bujnicki Improved heuristic for pairwise RNA secondary structure prediction Olivier Perriquet and Pedro Barahona Analysing the microRNA-17-92/Myc/E2F/RB Compound Toggle Switch by Theorem Proving Giampaolo Bella and Pietro Li? Mapping miRNA genes on human fragile sites and translocation breakpoints Alfredo Ferro, rosalba giugno, Alessandro Lagan?, Alfredo Pulvirenti and Francesco Russo MicroRNA.gr: A suite of web based tools for elucidating microRNA function Giorgio L. Papadopoulos, Panagiotis Alexiou, Manolis Maragkakis, Martin Reczko and Artemis G. Hatzigeorgiou miRScape: A Cytoscape Plugin to Annotate Biological Networks with microRNAs Alfredo Ferro, rosalba giugno, Alessandro Lagan?, Misael Mongiov?, Giuseppe Pigola, Alfredo Pulvirenti, Gary Bader and Dennis Shasha POSTERS A web site supporting collaborative activities within the Italian Network for Oncology Bioinformatics Silvia Giuliani, Elda Rossi, Stefania Parodi and Paolo Romano Prediction of human targets for viral encoded microRNAs Alessandro Lagan?, Stefano Forte, Rosalba Giugno, Alfredo Pulvirenti and Alfredo Ferro Genome-wide microRNA target gene identification and annotation using multiple prediction algorithms Dario Corrada, Luciano Milanesi and Daniele Catalucci Design of highly specific synthetic miRNAs Alessandro Lagan?, Stefano Forte, Angela Papa, Rosalba Giugno, Alfredo Pulvirenti, Dennis Shasha and Alfredo Ferro NETTAB '09 - Ninth International Workshop on Network Tools and Applications in Biology 10-13 June 2009, Catania, Italy http://www.nettab.org/2009/ Paolo Romano (paolo.romano@istge.it) Bioinformatics National Cancer Research Institute (IST) From tavares from fe.up.pt Thu May 7 08:30:04 2009 From: tavares from fe.up.pt (tavares@fe.up.pt) Date: Wed Sep 30 17:18:23 2009 Subject: [Computational-biology] (no subject) Message-ID: <8eccf9db-dbad-462f-a381-0af541cfe11b@e24g2000vbe.googlegroups.com> ------------------------------------------------------------------------------------------------------------------------------------------------ Special Track “Computational Bioimaging” 5th International Symposium on Visual Computing (ISVC09) Las Vegas, Nevada, USA, November 30 - December 2, 2009 http://www.isvc.net (Apologies for cross-posting. We would appreciate if you could distribute this information by your colleagues and co-workers.) ------------------------------------------------------------------------------------------------------------------------------------------------ Dear Colleague, Within the ISVC09 – 5th International Symposium on Visual Computing (http://www.isvc.net), to be held in Las Vegas, Nevada, USA, in November 30 - December 2, 2009, we are organizing the Special Track “ST6 - Computational Bioimaging” (http://www.isvc.net/ST6.pdf). The main goal of the Special Track “ST6 - Computational Bioimaging” is to bring together researchers working in the related fields of Image Acquisition, Segmentation, Registration, Tracking, Matching, Shape Reconstruction, Motion and Deformation Analysis, Medical Imaging, Software Development, Grid, Parallel and High Performing Computing, to discuss and share ideas that will lead us to set the major lines of development for the near future. Therefore, the Special Track “ST6 - Computational Bioimaging” will gather researchers representing the various fields of Computational Vision, Computational Mechanics, Mathematics, Statistics, and Biomedical Imaging. This track intends to contribute more realistic computational models extracted from images of living organisms and attempts to establish a bridge between practitioners and researchers from these diverse fields. Due to your research activities in those fields, we would like to invite you to submit your work and participate in the Special Track “ST6 - Computational Bioimaging”. TOPICS The topics of interest include but are not limited to the following areas: - Image Processing and Analysis for Computational Bioimaging; - Segmentation, Reconstruction, Tracking and Motion Analyse in Biomedical Images; - Biomedical Signal and Image Acquisition and Processing; - Computer Aided Diagnosis, Surgery, Therapy, Treatment and Telemedicine Systems; - Software Development for Computational Bioimaging; - Grid and High Performance Computing for Computational Bioimaging. SUBMISSION/PROCEEDINGS Instructions for authors are available in the website of ISVC'09 (http://www.isvc.net/author.html). Authors should submit electronically their contributions through the website of ISVC'09 (http://www.isvc.net), selecting the Special Track “ST6 - Computational Bioimaging”. Accepted papers will appear in the symposium proceedings which will be published by Springer-Verlag in the Lecture Notes in Computer Science (LNCS) series. IMPORTANT DATES - Submission deadline: July 10, 2009; - Notification of acceptance: August 31, 2009; - Camera-ready version: September 14, 2009. SCIENTIFIC COMMITTEE - Alberto De Santis, Università degli Studi di Roma "La Sapienza", Italy - Alexandre Cunha, California Institute of Technology, USA - Alexandre Xavier Falcão, University of Campinas, Brazil - Ana Mafalda Reis, University of Porto, Portugal - Arrate Muñoz Barrutia, University of Navarra, Spain - Begoña Calvo, University of Zaragoza, Spain - Constantine Kotropoulos, Aristotle University of Thessaloniki, Greece - Daniela Iacoviello, Università degli Studi di Roma "La Sapienza", Italy - Denilson Laudares Rodrigues, PUC Minas, Brazil - Dinggang Shen, University of Pennsylvania, USA - Djemel Ziou, University of Sherbrooke, Canada - Eduardo Borges Pires, Instituto Superior Técnico, Portugal - Fiorella Sgallari, University of Bologna, Italy - Francisco Perales, Balearic Islands University, Spain - Gustavo Rohde, Carnegie Mellon University, USA - Hanchuan Peng, Howard Hughes Medical Institute, USA - Hélder C. Rodrigues, Instituto Superior Técnico, Portugal - Hemerson Pistori, Dom Bosco Catholic University, Brazil - Huiyu Zhou, Brunel University, UK - Igor Yanovsky, Jet Propulsion Laboratory, USA - Jason Corso, SUNY at Buffalo, USA - João Manuel R. S. Tavares, University of Porto, Portugal - Javier Melenchón Maldonado, Open University of Catalonia, Spain - Jorge M. G. Barbosa, University of Porto, Portugal - Jorge S. Marques, Instituto Superior Técnico, Portugal - Jose M. García Aznar, University of Zaragoza, Spain - Jussi Tohka, Tampere University of Technology, Finland - Luminita Vese, University of California at Los Angeles, USA - Luís Paulo Reis, University of Porto, Portugal - Mahmoud El-Sakka, The University of Western Ontario London, Canada - Manuel González Hidalgo, Balearic Islands University, Spain - Maria Elizete Kunkel, Universität Ulm, Germany - Metin N. Gurcan, Ohio State University, USA - Michael Liebling, University of California at Santa Barbara, USA - Patrick Dubois, Institut de Technologie Médicale, France - Renato M. N. Jorge, University of Porto, Portugal - Reneta P. Barneva, State University of New York, USA - Roberto Bellotti, University of Bari, Italy - Sabina Tangaro, National Institute of Nuclear Physics, Italy - Shawn Newsam, University of California at Merced, USA - Susana Branco Silva, University of Lisbon, Portugal - Todd Pataky, University of Liverpool, UK - Valentin Brimkov, State University of New York, USA - Yongjie Zhan, Carnegie Mellon University, USA With kind regards, João Manuel R. S. Tavares, University of Porto, Portugal, tavares@fe.up.pt Renato Natal Jorge, University of Porto, Portugal, rnatal@fe.up.pt Alexandre Cunha, California Institute of Technology, USA, cunha@caltech.edu (Organizers of the Special Track “ST6 - Computational Bioimaging and Visualization”) PS. For more information about the Special Track “ST6 - Computational Bioimaging”, please download its flyer at: www.fe.up.pt/~tavares/downloads/calls/bima09.pdf