From biplabbose from gmail.com Fri May 2 16:13:23 2008 From: biplabbose from gmail.com (biplabbose@gmail.com) Date: Fri May 2 18:52:54 2008 Subject: [Computational-biology] Kinetic Monte Carlo Message-ID: <1e4cb5a2-a6ed-4d75-b520-3aee1292e093@x19g2000prg.googlegroups.com> Hi, Does any one here work on lattice based kinetic Monte Carlo of Biochemical systems? Particularly on the subject of Receptor ligand interaction, biological membranes. I need some help in understanding certain aspects of this technique. Thanks in advance With regards Biplab From coss.eps from ceu.es Sun May 4 15:43:19 2008 From: coss.eps from ceu.es (coss.eps@ceu.es) Date: Sun May 4 21:03:25 2008 Subject: [Computational-biology] Third CEU Summerschool on Advanced Statistics and Data Mining (June 30th-July 11th, 2008) Message-ID: <820e2a66-7331-4eb2-b2ab-90b425a2f72d@k37g2000hsf.googlegroups.com> Dear colleagues, San Pablo - CEU University in collaboration with other five universities (Málaga, Politécnica de Madrid, País Vasco, Complutense, and Castilla La Mancha), Unión Fenosa, CSIC and IEEE organizes a summerschool on "Advanced Statistics and Data Mining" in Madrid between June 30th and July 11th. The summerschool comprises 12 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://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 (June 30th - July 4th, 2008) 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: 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 4: Association rules (15 h), Practical sessions: Bioinformatic tools Introduction. Association rule discovering. Rule Induction. KDD in biological data. Applications. Hands-on exercises. Course 5: 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 6: Time series analysis (15 h), Practical sessions: MATLAB Introduction. Probability models to time series. Regression and Fourier analysis. Forecasting and Data mining. Week 2 (July 7th - July 11th, 2008) Course 7: 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 8: 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 9: 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 10: Statistical inference (15 h), Practical sessions: SPSS Introduction. Some basic statistical test. Multiple testing. Introduction to bootstrapping Course 11: Dimensionality reduction (15 h), Practical sessions: MATLAB Introduction. Matrix factorization methods. Clustering methods. Projection methods. Applications Course 12: Unsupervised pattern recognition (clustering) (15 h), Practical sessions: MATLAB Introduction. Prototype-based clustering. Density-based clustering. Graph-based clustering. Cluster evaluation. Miscellanea From xqzhu from cse.fau.edu Mon May 5 08:47:47 2008 From: xqzhu from cse.fau.edu (Xingquan Zhu) Date: Mon May 5 10:23:53 2008 Subject: [Computational-biology] CFP: The 2nd KDD workshop on on Mining Multiple Information Sources (MMIS-08) Message-ID: <1209995267.667@cse.fau.edu> We apologize if you received multiple copies of this Call for Papers. Please disseminate the following announcement to those who may be interested ***************************************************************************** The 2nd ACM KDD Workshop on Mining Multiple Information Sources (MMIS-08) In conjunction with ACM SIGKDD-08, August 24, 2008 http://www.cse.fau.edu/~xqzhu/mmis/kdd08_mmis.html Deadline of Paper Submission: May 30, 2008 Acceptance Notification: June 15, 2008 Camera-ready Paper Submission: June 20, 2008 ------------------------------------------------------------------- The aim of this workshop is to bring together data mining experts to revisit the problem of pattern discovery from multiple information sources, and identify and synthesize current needs for such purposes. Representative questions to be addressed include but are not limited to: 1. Harnessing Complex Data Relationship a. Database similarity assessment b. Automatic schema mapping and relationship discovery c. New mapping framework for multiple information sources d. Data source classification and clustering e. Data cleansing, data preparation, conflict and inconsistency resolution 2. Integrative and Cooperative Mining a. Model integration for heterogeneous information sources b. Mode transferring across different data domains c. Incremental and scalable data mining algorithms d. Multi-tasks multi-sources co-learning for multiple information sources 3. Differentiation and Correlation a. Local pattern analysis and fusion b. Global pattern synthesizing and assessment c. Merging local rules for global pattern discovery d. Pattern summarization from multiple datasets e. Multi-dimensional pattern search and comparison f. Pattern comparison across multiple data sources g. Inter pattern discovery from complex data sources 4. Stream data mining algorithms a. Clustering and classification of data of changing distributions b. Data stream processing, storage, and retrieval systems c. Sensor networking 5. Security and privacy issues in multiple information sources 6. Interactive data mining systems a. Query languages for mining multiple information sources b. Query optimization for distributed data mining c.Distributed data mining operators in supporting interactive data mining ------------------------------------------------------------------- For submission of the paper, please use Easychair system at http://www.easychair.org/conferences/?conf=mmis08 ------------------------------------------------------------------- Organizing Committee Workshop Co-chairs Xingquan Zhu, Florida Atlantic University Ruoming Jin, Kent State University Yuri Breitbart, Kent State University Program Committee Walid G. Aref, Purdue University, USA Philip Chan, Florida Institute of Technology, USA Dejing Dou, University of Oregon, USA Christopher Jermaine, University of Florida, USA Taghi M. Khoshgoftaar, Florida Atlantic University, USA Tao Li, Florida International University, USA Huan Liu, Arizona State University, USA Prem Melville, IBM T.J. Watson, USA Xintao Wu, UNC Charlotte, USA Jieping Ye, Arizona State University, USA Shichao Zhang, University of Technology, Sydney Aoying Zhou, Fudan University, China Zhi-hua Zhou, Nanjing University, China From frist from cc.umanitoba.ca Mon May 5 17:41:47 2008 From: frist from cc.umanitoba.ca (Brian Fristensky) Date: Mon May 5 19:11:21 2008 Subject: [Computational-biology] Bioinformatics Course: Vancouver area Message-ID: <200805052241.m45MflZO025047@mira.cc.umanitoba.ca> --------------------------------------------------- Genome Canada APPLIED COMPUTATIONAL GENOMICS COURSE Simon Fraser University, Burnaby, BC, Canada July 24 - 30, 2008 --------------------------------------------------- The ACGC introduces biologists to some of the latest methods in bioinformatics, including DNA and protein sequence analysis, automation of data analysis, web services and workflows, and high-throughput genome annotation. The course is led by researchers from the Genome Canada Bioinformatics Platform. Both lectures and extensive hands-on tutorial sessions are included. For full details see: For more information visit the website: http://www.gcbioinformatics.ca/training ________________________________________________________________________________ The project is supported by Genome Alberta and Genome Canada, a not-for-profit organization which is leading Canada's national strategy on genomics with $ 600 million in funding from the federal government. From aao from fe.up.pt Tue May 6 09:00:43 2008 From: aao from fe.up.pt (alexandra) Date: Tue May 6 10:31:24 2008 Subject: [Computational-biology] 2nd annoucement of NN2008 Message-ID: <000501c8af81$939f9410$a56aa8c0@ineb.fe.up.pt> Apologies for multiple copies. We appreciate if you can forward this Announcement to potential candidates. ============================================================= SUMMER SCHOOL NN2008 NEURAL NETWORKS in CLASSIFICATION, REGRESSION and DATA MINING July 7-11, 2008, Porto, Portugal ============================================================= http://www.nn.isep.ipp.pt email: nn-2008@isep.ipp.pt GENERAL INFORMATION The Summer School will be held at Porto, Portugal, jointly organized by the Polytechnic School of Engineering of Porto (ISEP) and the Faculty of Engineering, Porto University (FEUP). Following last year experience, this year's edition also includes a POSTER/WORKSHOP SESSION providing a discussion forum where the participants can obtain peer guidance for their projects. PROGRAMME COMMITTEE ? Alexander Zien (Research Scientist at the Friedrich Miescher Laboratory, Germany) ? Carlos Soares (Assistant Professor, Faculty of Economy, University of Porto, Portugal) ? Christopher Bishop (Deputy Managing Director at Microsoft Research Laboratory in Cambridge and Chair of Computer Science at the University of Edinburgh, UK) ? Igor Aizenberg (Assistant Professor at the Department of Computer and Information Sciences, Texas A&M University-Texarkana, USA) ? Joaquim Marques de S? (Full Professor, Dept. Electr. and Comp. Engineering, Fac. of Engineering, University of Porto, Portugal) ? Jorge Santos(Assistant Professor, Engineering Polythecnic Institute, Porto, Portugal) ? Mark Embrecht (Associate Professor, Rensselaer Polytechnic Institute, RPI Troy, New York, U.S.A.) ? Noelia S?nchez Maro?o (Assistant Professor, Coruna University, Spain) ? Paulo Cortez (Assistant Professor, University of Minho, Portugal) ? Petia Georgieva (Assistant Professor, University of Aveiro, Portugal) ? Yann Guermeur (Scientific Director of the Laboratoire Lorrain de Recherche en Informatique et ses Applications, France) COURSE CONTENTS Neural networks (NN) have become a very important tool in classification and regression tasks. The applications are nowadays abundant, e.g. in the engineering, economy and biology areas. The Summer School on NN is dedicated to explain relevant NN paradigms, namely multilayer perceptrons (MLP), radial basis function networks (RBF) and support vector machines (SVM) used for classification and regression tasks, illustrated with applications to real data. Specific topics are also presented, namely Multi-Valued and UB Neurons , Functional Networks , MLP's with Entropic Criteria and Data Mining using NN. Classes include practical sessions with appropriate software tools. The trainee has, therefore, the opportunity to apply the taught concepts and become conversant with a broad range of NN topics and applications. A special workshop session will provide a discussion forum where the participants can obtain peer guidance for their projects. PRELIMINARY PROGRAMME A preliminary programme and further information about the classes are available at the school webpage (http://www.nn.isep.ipp.pt) IMPORTANT DEADLINES Early Registration: 18 May 2008 Poster Submission: 15 June 2008 Hotel booking : 15 June 2008 Summer School: 7-11 July 2008 All participants are required to register prior to the start of the School - until the June 15 - even if you choose to pay the late registration fee at the registration desk. Please note that only a LIMITED number of participants can be accepted. REGISTRATION In order to attend the School you must fill in the registration form, available at the School web page. Please note that if you have any guests who would like to take part in the social programme, you must register them as well, by filling in the corresponding field in the registration form. SCHOOL FEES The registration fee for participants amounts to: - Early registration fee (paid before the 18th of May) * 350 Euro (students, ISEP and FEUP staff) * 400 Euro (all other participants) - Late registration fee (paid after the 18th of May) * 400 Euro (students, ISEP and FEUP staff) * 450 Euro (all other participants) The registration fee includes: * school package (manuscripts, lecture's notes, CD) * coffee breaks * daily lunch * welcome reception * school banquet NOTE: The registration fee for those who attended previous editions amounts to 25/30 euro per lecture and includes the school package and coffee-breaks. Please, contact the LOC for further details. LOCAL ORGANIZING COMMITTEE (LOC) - Helena Br?s Silva ? Assistant Professor, Dept. Mathematics, ISEP, Portugal - Jorge M. Santos - Assistant Professor, Dept. Mathematics, ISEP, Portugal - Rui Chibante - Assistant Professor, Dept. Mathematics, ISEP, Portugal CONTACT ADDRESS Local Organizing Committee (LOC) - Summer School NN2008 A/C Jorge M. Santos Departamento de Matem?tica Instituto Superior de Engenharia do Porto Rua Dr. Ant?nio Bernardino de Almeida 431 4200-072 PORTO / PORTUGAL Email: nn-2008@isep.ipp.pt NN2008 Secretariat Ms. Gabriela Afonso Email: gafonso@fe.up.pt Programme Chair: Prof. Joaquim Marques de S? Tel. +351 225081828 - Email: jmsa@fe.up.pt ======================================== From barry.hardy from vtxmail.ch Tue May 6 08:50:27 2008 From: barry.hardy from vtxmail.ch (Barry) Date: Tue May 6 10:33:36 2008 Subject: [Computational-biology] Program for eCheminfo Drug Discovery Workshop Week (Oxford, 21-25 July 2008) Message-ID: <0cd15ef0-317f-4fb2-86b2-c7524e7a374d@x35g2000hsb.googlegroups.com> The program, abstracts and schedule for the 5 Day eCheminfo Hands-on Drug Discovery Workshop Week (21-25 July 2008) at the Medical Sciences Teaching Center, Oxford University, Oxford, UK is now available at: http://barryhardy.blogs.com/cheminfostream/2008/05/program-schedul.html Topics to be covered: Virtual Screening & Docking; Structure-based Drug Design; Ligand Optimisation & Library Design; Structure Search, Similarity and Property Estimation; Data Mining, Analysis & Visualisation; Pharmacophore Modelling for Lead Identification; Fragment-based Drug Design; QSAR-based Predictive Toxicology; and Quantitative Spectrometric Data-Activity Relationship Modelling. To complete registration arrangements for the workshop, please contact Nicki.Douglas –(at)- douglasconnect.com, +41 61 851 0461 best regards Barry Hardy eCheminfo Community of Practice Douglas Connect +41 61 851 0170 From juffi from ke.informatik.tu-darmstadt.de Wed May 7 13:08:33 2008 From: juffi from ke.informatik.tu-darmstadt.de (Johannes Fuernkranz) Date: Wed May 7 13:55:47 2008 Subject: [Computational-biology] ECML-PKDD-08 WS: From Local Patterns to Global Models Message-ID: [ please distribute - apologies for multiple postings ] ------------------------------------------------------------------------ LeGo-08 From Local Patterns to Global Models ECML/PKDD-08 Workshop 15 September 2008, Antwerp, Belgium http://www.ke.informatik.tu-darmstadt.de/events/LeGo-08/ ------------------------------------------------------------------------ The topic of this workshop is the induction of actionable global models from local patterns. The different elements of this subject can be organised in the following three steps: Pattern Discovery, Pattern Set Selection, and Global Modeling. We call for papers concerning these three steps with a particular focus on the interaction of these phases. The workshop's goal is to bring people that work on various aspects of this subject into a fruitful dicussion about the state-of-the-art and the remaining open problems, about commonalities and differences in their respective works. Research areas that are of interest to this workshop include: * Associative Classification * Combination Strategies * Compression-based Pattern Selection * Constraint-based Pattern Set Mining * Efficient Pattern Set Discovery * Ensembles of Patterns * Feature Construction and Selection * Generalilty of Local Pattern Constraints * Global Modeling with Patterns * Iterative Local Pattern Discovery * KDD Process-models for Building Global Models from Local Patterns * Metrics for Pattern Set Selection * Pattern Ordering * Patterns and Information Theory * Pattern Set Selection * Pattern Teams * Propagation of Global Modeling Constraints to Local Pattern Discovery * Propositionalisation * Quality Measures for Pattern Sets * Resolution of Conflicting Predictions * Subgroup Discovery We will also admit position statements or interesting incomplete or immature work into the program, which will hopefully stimulate discussions, in order to further the main goal of the workshop, namely to increase the awareness of different approaches to this general problem. Thus, we welcome various types of papers that deal with the topics of this workshop, including papers that present new results, ongoing research projects, completed work (even previously published), position statements, surveys, open problems and challenges. There is no minimum or maximum length of papers. However, presentation times for accepted contributions may vary. Given sufficient high-quality submissions, a post-workshop special issue in a journal will be considered. Paper submissions should be sent by E-mail (in PDF format) to . Final versions must be formatted according to Springer's LNCS-style (as for the main conference). Important Dates * Dates Paper deadline: June 16 * Notifications of Acceptance: August 4 * Final versions: August 14 Organizers * Johannes Fürnkranz (TU Darmstadt) * Arno Knobbe (Utrecht University and Kiminkii) From shandar from nibio.go.jp Fri May 9 00:10:48 2008 From: shandar from nibio.go.jp (Shandar Ahmad) Date: Fri May 9 10:44:03 2008 Subject: [Computational-biology] PRIB 2008: Call for short papers/ posters Message-ID: <20080509051048.7E0B1928087@intnewmail.nibio.go.jp> ** Our apologies if you receive multiple copies of this announcement * IAPR PRIB 2008 CALL FOR SHORT PAPERS AND EXTENDED ABSTRACTS ____________________________________________________________________________________________________________________________ Third IAPR International Conference on Pattern Recognition in Bioinformatics October 15-17, 2008 Novotel St. Kilda, Melbourne, Australia Conference Web Site: www.infotech.monash.edu.au/prib08 _____________________________________________________________________________________________________________________________ Important Deadlines: Paper submission: 25 May 2008 Author notification: 25 June 2008 _____________________________________________________________________________________________________________________________ PRIB 2008 is aimed at bringing together top researchers, practitioners, and students from around the world to discuss the applications of pattern recognition methods in the field of bioinformatics to solve problems in life sciences. Pattern recognition techniques of interest include: statistical, syntactic, and structural approaches, Bayesian, hidden Markov and graphical models, neural networks, fuzzy and genetic algorithms, data mining, and their hybrids. Short papers are solicited for poster presentation at PRIB 2008. Short papers in areas of (but not limited to) bio-sequence analysis, gene and protein expression analysis, structure prediction, protein folding, docking, metabolic pathway analysis and regulatory networks, system biology, drug design, and bioimaging, are solicited for presentation at the conference. A few selected papers may also be considered for oral presentation. The short papers will be published in the Supplementary Proceedings of the PRIB 2008 conference. The papers should follow the IEEE two-column format and be limited to four pages. If you need more pages, you should email the general chair in this regard. Submission of papers will be electronic and through the conference website. The details and the template for short paper preparation as well as the latest information on PRIB 2008 conference are available at: www.infotech.monash.edu.au/prib08 Apart from oral and poster paper presentation, we are also inviting bioinformatics 'gurus' to come forth and be the keynote speakers. Location: Melbourne is a sophisticated city in the south-east corner of mainland Australia. It is known for its attractive site seeing places, great events, passion for food and wine and fabulous scenery. Boasting as a style-setter, Melbourne is home to continuous program of festivals, art exhibitions and musical extravaganzas. Warning: you might never want to go home. For latest information on PRIB 2008, visit the conference web site or email the secretariat at prib2008.melb@infotech.monash.edu.au ________________________________________________________________________________________________________________________________ General Chair: Madhu Chetty (Monash University, Australia) General Co-Chair: Raj Acharya (Pennsylvania State University, USA) Program Chair: Jagath Rajapakse (NTU, Singapore) Technical Chairs: Elena Marchiori (Vrije University, The Netherlands) Bertil Schmidt (NICTA, Australia) Special Session Chair: Alioune Ngom (University of Windsor, Canada) Short Paper Chairs: Shandar Ahmed (Inst. of Biomedical Innovation, Japan) Ponraj Prabhakaran (Duke University, USA) Michael Grominha (Comp Biol. Res. Center, Japan) Local Organization Chair: Shyh Wei Teng (Monash University, Australia) Publicity Chairs: Shandar Ahmed (Inst. of Biomedical Innovation, Japan) Phoebe Chen (Deakin University, Australia) Mariofanna Milanova (University of Arkansas at LR, USA) Md. Tamjidul Hoque (Griffith University, Australia) Publication Chairs: Sy Loi Ho (NTU, Singapore) Girija Chetty (University of Canberra, Australia) Sponsorship Chair: Dieter Bulach (CSIRO, Australia) Finance Manager: Narelle Wilkins (Monash University, Australia) Secretariat: Tina Bradshaw (Monash University, Australia) Web Master: Margot Schuhmacher (Monash University, Australia) ________________________________________________________________________________________________________________________________ Contact: PRIB 2008 Secretariat Gippsland School of Information Technology Monash University Churchill, Victoria - 3842, Australia Tel: +61 3 9902 6566 Fax: +61 3 9902 7137 Email: prib2008.melb@infotech.monash.edu.au ________________________________________________________________________________________________________________________________ ***************************************************************************** We are sending the call in anticipation of your interest in such conferences and because previous emails to these addresses did not result in receipt of an unsubscription request. We aplogize if there is an error here. If you do not want to receive PRIB email on this addess, please write to us at prib2008.melb@infotech.monash.edu.au and CC to: shandar@nibio.go.jp ***************************************************************************** From masulli from disi.unige.it Tue May 13 10:14:05 2008 From: masulli from disi.unige.it (Francesco Masulli) Date: Tue May 13 16:54:52 2008 Subject: [Computational-biology] 2nd CPF: CIBB 2008 3-4 October, 2008 Vietri sul Mare, Salerno (Italy) Message-ID: <200805131714.06238.masulli@disi.unige.it> Please, accept our apologies for multiple postings. 2nd Call for Papers and for Special Sessions ========================================================================================= CIBB 2008 FIFTH INTERNATIONAL MEETING ON COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS IIASS - Vietri sul Mare, Salerno (Italy) 3-4 October, 2008 Conference Website: http://cibb08.disi.unige.it/ The main goal of the CIBB meetings is to provide a forum open to researchers from different disciplines to present and discuss problems concerning computational techniques in bioinformatics, systems biology and medical informatics with a particular focus on Neural Networks, Machine Learning, Fuzzy Logic, and Evolutionary Computation methods. CIBB 2008 is jointly organized by: * INNS - International Neural Network Society, SIG Bioinformatics * ISCB International Society for Computational Biology * GNCS Gruppo Nazionale Calcolo Scientifico * SIREN - Italian Neural Networks Society * DISI - Univ. Genova (Italy) * DMI - Univ. Salerno (Italy) Technical areas addressed by CIBB 2008 include, but are not limited to: * Sequence analysis, promoter analysis and identification of transcription factor binding sites * Gene expression data analysis * Methods for the integration of clinical and genetic data * Algorithms for alternative splicing analysis * Methods for the functional classification of genes * Methods for the unsupervised analysis, validation and visualization of structures discovered in bio-molecular data * Prediction of secondary and tertiary protein structures * Mass spectrometry data analysis in proteomics * Methods for comparative genomics * Algorithms for molecular evolution and phylogenetic analysis * Mathematical modelling and simulation of biological systems * Heterogeneous data integration and data fusion for diagnostics * Bio-molecular databases and data mining * Algorithms for pharmacogenetics * Bio-medical text mining and imaging * Methods for diagnosis and prognosis * Software tools for bioinformatics Prof. Giuseppe Russo of Temple Univ, Philadelphia (PA-USA) has confirmed to deliver an invited talk at CIBB 2008. The scientific program will include, besides some plenary talks, contributed papers that will be presented in plenary oral or poster sessions. Accepted papers will be published in the compact disk of conference proceedings. A selection of papers presented at CIBB 2008 will be published as a post conference volume of LECTURE NOTES IN BIOINFORMATICS LNBI/LNCS series of Springer Verlag. Moreover, a selection of more relevant papers will be considered or publication in extended form in a special issue of a scientific journal we are planning. Chairs: Francesco Masulli, Universit? di Genova, Italy and Temple University, PA, USA Roberto Tagliaferri, Universit? di Salerno, Italy Gennady M. Verkhivker, University of Kansas, KS, USA, and University of California San Diego, CA, USA Scientific Program Committee: Klaus-Peter Adlassnig, Medical University of Vienna, Austria Joaquin Dopazo, Centro de Investigaci?n Pr?ncipe Felipe, Valencia, Spain Antonio Giordano, Temple Univ, Philadelphia, PA, USA Emmanuel Ifeachor, University of Plymouth, UK Samuel Kaski, Helsinki University of Technology, Finland Natalio Krasnogor, University of Nottingham, UK Giancarlo Mauri,University of Milano Bicocca, Italy Oleg Okun, University of Oulu, Finland Giulio Pavesi, University of Milan, Italy David Alejandro Pelta, University of Granada, Spain Graziano Pesole, University of Bari, Italy Leif E. Peterson, Baylor College of Medicine Houston, TX, USA Volker Roth, ETH Zurich, Switzerland Giuseppe Russo, Temple Univ, Philadelphia, PA, USA Giorgio Valentini, University of Milan, Italy Giorgio Valle, University of Padua, Italy Jean-Philippe Vert, Ecole des Mines de Paris, France Steering Commitee: Pierre Baldi, University of California, Irvine, CA, USA Alexandru Floares, Oncological Institute Cluj-Napoca, Romania Jon Garibaldi, University of Nottingham, UK Francesco Masulli, University of Genova, Italy and Temple University, PA, USA Roberto Tagliaferri, University of Salerno, Italy Important Dates: Special Session Proposals: 15 May 2008 Paper submission deadline: 30 May 2008 Notification of acceptance: 30 June 2008 Final paper due: 1 September 2008 Conference: 3-4 October 2008 Special sessions: Special sessions proposals including session's title and scope, short cv of sessions chairs, preliminary list of papers (titles and authors) are due by May 15 2008. Proposals of special sessions will be evaluated as soon as they will be submitted. Please, send the proposals to cibb2008chair@disi.unige.it Paper submission: Papers must be prepared following the guidelines illustrated on the CIBB web site and cannot be longer than 10 pages. The submission of papers will be done by uploading their PDF version on the CIBB web site. =================================================== CIBB 2008 FIFTH INTERNATIONAL MEETING ON COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS IIASS - Vietri sul Mare, Salerno (Italy) 3-4 October, 2008 Conference Website: http://cibb08.disi.unige.it/ email: cibb2008chair@disi.unige.it ================================================== -- <--------------------------------------------------------------------> Dr. Francesco Masulli Associate Professor of Computer Science DISI - Dept. Computer and Information Sciences University of Genova - Via Dodecaneso 35, 16146 Genova - ITALY tel. +39 010 353 6604 fax. +39 010 353 6699 and Adjunct Associate Professor Center for Biotechnology - College of Science and Technology Temple University - Philadelphia - PA, USA. email: masulli@disi.unige.it skype id: masulli url: http://www.disi.unige.it/person/MasulliF <--------------------------------------------------------------------> From paola.bertolazzi from iasi.cnr.it Thu May 15 02:34:26 2008 From: paola.bertolazzi from iasi.cnr.it (Paola Bertolazzi) Date: Thu May 15 10:50:24 2008 Subject: [Computational-biology] DEADLINE EXTENSION: Mini EURO Conference on Computational Biology, Bioinformatics and Medicine Message-ID: <482BE782.6030205@iasi.cnr.it> Mini EURO conference on Computational Biology, Bioinformatics and Medicine September 15-17, 2008 CNR,Rome, Italy ABSTRACT SUBMISSION DEADLINE: May 30, 2008 Workshop Website: http://www.iasi.cnr.it/iasi/RomeConference/index.php Areas of interest of Workshop We welcome researchers from different backgrounds addressing challenging problems in computational biology, bioinformatics and medicine including but not limited to: * biomolecular sequence analysis, * comparative genomics, * phylogenetics, * modeling and prediction of gene patterns, * microarray informatics, * protein structure prediction, * protein interactions, * genetic networks, * analysis of genetic variations, * systems biology, * gene classification (e.g., for protection of gene pools), * docking and drug design, * modeling and analysis of metabolic networks. -- ************************ Paola Bertolazzi IASI/CNR Viale Manzoni 30, 00185 Roma tel +39 06 7716444 fax +39 06 7716461 e.m. bertola@iasi.cnr.it http://www.iasi.cnr.it From hra from pixel.cviog.uga.edu Sat May 17 12:00:39 2008 From: hra from pixel.cviog.uga.edu (Hamid R. Arabnia) Date: Sat May 17 13:35:13 2008 Subject: [Computational-biology] Call For Papers: Extended deadline: June 1, 2008 - WORLDCOMP'08 Congress (CS and CE Conferences - July 2008, USA) Message-ID: <20080517170039.92CAC22455A0@pixel.cviog.uga.edu> Call For Papers - Deadline: June 1, 2008 WORLDCOMP'08 The 2008 World Congress in Computer Science, Computer Engineering, and Applied Computing Date and Location: July 14-17, 2008, Las Vegas, USA http://www.world-academy-of-science.org/ You are invited to submit a paper (see instructions below.) WORLDCOMP'08 is composed of a number of tracks (joint-conferences, tutorials, and workshops); all will be held simultaneously, same location and dates: July 14-17, 2008. See http://www.world-academy-of-science.org/ for the complete list of joint-conferences. This is a Call For Papers for publication in the Final Edition of the conference proceedings. All papers submitted in response to this announcement will be evaluated for publication in the Final Edition of the proceedings which will go to press soon after the conference (publication date: late August 2008). This announcement is ONLY for those who missed the opportunity to submit their papers in response to earlier announcements (authors who have already been notified that their papers have been accepted/not-accepted should ignore this announcement.) IMPORTANT DATES: June 1, 2008: Submission of full papers (less than 8 pages) June 14, 2008: Notification of acceptance June 27, 2008: Registration July 14-17, 2008: WORLDCOMP'08 Congress (all joint-conferences) July 20, 2008: Camera-Ready Papers Due for publication in the Final Edition of the proceedings. SUBMISSION OF PAPERS: Prospective authors are invited to submit their papers to hra@cs.uga.edu (no more than 7 pages, single spaced and font size of 10 to 12 - all reasonable typesetting formats are acceptable). Authors should write the following in the subject header of their email: "Submission for Consideration in Final Edition of Proceedings" + name of conference that the paper is being submitted to. Papers should be attached to emails and must be either in Word Doc or PDF formats. Papers must not have been previously published or currently submitted for publication elsewhere. The first page of the paper should include: title of the paper, name, affiliation, postal address, and email address for each author. The first page should also include the name of the conference the paper is being submitted to (the list of conferences appears below.) Accepted papers will be published in the final edition of the respective proceedings/books. All submissions will be evaluated for originality, significance, clarity, and soundness. Each paper will be refereed by two researchers in the topical area. The authors of accepted papers will later be asked to follow a particular typing instructions to prepare their final paper for publication. LIST OF CONFERENCES: PDPTA: Parallel and Distributed Processing Techniques and Applications GCA: Grid Computing and Applications CDES: The 2008 International Conference on Computer Design CSC: Scientific Computing ICAI: Artificial Intelligence GEM: Genetic and Evolutionary Methods MLMTA: Machine Learning; Models, Technologies and Applications BIOCOMP: Bioinformatics and Computational Biology SERP: Software Engineering Research and Practice ICWN: Wireless Networks IPCV: Image Processing, Computer Vision, and Pattern Recognition MSV: Modeling, Simulation and Visualization Methods CGVR: Computer Graphics and Virtual Reality ICOMP: Internet Computing SWWS: Semantic Web and Web Services SAM: Security and Management DMIN: Data Mining IKE: Information and Knowledge Engineering EEE: e-Learning, e-Business, Enterprise Information Systems, and e-Government ESA: Embedded Systems and Applications FECS: Frontiers in Education: Computer Science and Computer Engineering FCS: Foundations of Computer Science CIC: Communications in Computing PLANNED TUTORIALS: See the following web site for a partial list: http://www.world-academy-of-science.org/worldcomp08/ws/tutorials KEYNOTE LECTURES: See the following web site for a partial list: http://www.world-academy-of-science.org/worldcomp08/ws/keynotes LOCATION OF CONFERENCE: WORLDCOMP will be held in the Monte Carlo hotel, Las Vegas, Nevada, USA (with any overflows at other near-by hotels). This is a mega hotel with excellent conference facilities and over 3,000 rooms. It is minutes from the airport with 24-hour shuttle service to and from the airport. This hotel has many recreational attractions, including: spa, pools, sunning decks, Easy River, wave pool, lighted tennis courts, nightly shows, a number of restaurants, ... The negotiated room rate for conference attendees is very reasonable. The hotel is within walking distance from most other attractions. SPONSORS: Academic/Technical Co-Sponsors: (a partial list) --> Computational Biology and Functional Genomics Laboratory, Harvard University, Cambridge, Massachusetts, USA --> International Society of Intelligent Biological Medicine --> Horvath Lab., University of California, Los Angeles (UCLA), USA --> Minnesota Supercomputing Institute, University of Minnesota, USA --> Functional Genomics Laboratory, University of Illinois at Urbana-Champaign, USA --> BioMedical Informatics & Bio-Imaging Laboratory, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA --> Intelligent Data Exploration and Analysis Laboratory, University of Texas at Austin, Austin, Texas, USA --> Biomedical Cybernetics Laboratory, HST of Harvard University and MIT, USA --> Center for the Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, Georgia, USA --> Harvard Statistical Genomics and Computational Laboratory, Harvard University, Cambridge, Massachusetts, USA --> Bioinformatics & Computational Biology Program George Mason University, Virginia, USA --> Hawkeye Radiology Informatics, Department of Radiology, College of Medicine, University of Iowa, Iowa, USA --> Medical Image HPC & Informatics Lab (MiHi Lab), University of Iowa, Iowa, USA --> The University of North Dakota, Grand Forks, North Dakota, USA --> PSU - Prince Sultan University --> Institute for Informatics Problems of the Russian Academy of Sciences, Moscow, Russia. --> NEMO/European Union at Institute of Discrete Mathematics and Geometry, TU Vienna Corporate Co-Sponsors: (a partial list) --> Google, Inc. --> Salford Systems --> Synplicity --> NIIT Technologies Other Co-Sponsors: (a partial list) --> High Performance Computing for Nanotechnology (HPCNano) --> International Technology Institute (ITI) --> GridToday - enewsletter focused on Grid, SOA, Virtualization, Storage, Networking and Service-Oriented IT --> HPCwire - The Leading Source for Global News and Information Covering the Ecosystem of High Productivity Computing --> Hodges' Health (H2CM), UK From David.Martens from econ.kuleuven.be Sun May 18 13:20:45 2008 From: David.Martens from econ.kuleuven.be (Martens, David) Date: Sun May 18 15:36:59 2008 Subject: [Computational-biology] CFP Machine Learning Message-ID: <4BE25954E0547B48B1780B61CFC2D34F1D6D81D457@ECONSRVEX6.econ.kuleuven.ac.be> ============================================================= | 2nd Call for Papers | | Swarm Intelligence for Knowledge Discovery in Data | | Special Issue for the International Journal | | Machine Learning | ============================================================= CFP can be found online at: http://www.econ.kuleuven.be/public/ndbaf65/CFP.pdf Guest editors ------------- David Martens (K.U.Leuven) Tom Fawcett (Stanford University) Bart Baesens (K.U.Leuven/University of Southampton) Scope ----- Swarm Intelligence is a relatively new subfield of artificial intelligence which studies the emergent collective intelligence of groups of simple agents. It is based on the social insects' metaphor where a number of insects with limited capabilities are able to come to intelligent solutions for complex problems. In recent decades the Swarm Intelligence paradigm has received widespread attention in research, mainly as Ant Colony Optimization (ACO) and Particle Swarm Optimization (PSO). Successful applications of swarm intelligence include the modelling of agent behaviour, such as the large numbers of fighting individuals in the battle scenes of the Lord of the Rings movies, and various optimization problems, such as the routing of packages through networks, the travelling salesman problem, scheduling, etc. This special issue focuses on the intersection of the swarm intelligence paradigm with Machine Learning and Knowledge Discovery in Data. We solicit high-quality, previously unpublished papers where both domains are properly addressed. Possible topics for papers include: The application of * Particle Swarm Optimization * Ant Colony Optimization * Stochastic Diffusion Search * Any algorithmic approach based on biological swarm intelligence, such as bird flocking, fish schooling, bee behaviours, bacterial growth, animal herding, etc. For * Clustering * Classification * Regression * Association Rule Mining * Time Series Analysis * Feature Selection Other topics of interest are: * Computational models of self-organizing systems * Use of fine-grained parallel models, such as cellular automata, in machine learning and knowledge discovery * Emergent behavior and its relationship to pattern recognition and learning Important Dates --------------- Submission deadline: June 20, 2008 First notification: September 26, 2008 Revised manuscripts due: December 30, 2008 Final acceptance notification: February, 2009 Intended publication date: 2009 Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From nicso2008 from gmail.com Mon May 19 08:29:25 2008 From: nicso2008 from gmail.com (NICSO 2008) Date: Mon May 19 10:56:11 2008 Subject: [Computational-biology] NICSO 2008. 2nd call for papers In-Reply-To: <5802ceed0805190509s47673a17r10e8ec9df2e79f3f@mail.gmail.com> References: <5802ceed0805190509s47673a17r10e8ec9df2e79f3f@mail.gmail.com> Message-ID: <5802ceed0805190629q34dc109do7db3a3e44ed7dc90@mail.gmail.com> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D (Apologies for multiple postings) S E C O N D CALL FOR PAPERS NICSO 2008 International Workshop on Nature Inspired Cooperative Strategies for Optimization Puerto Palace Hotel Puerto de La Cruz, Tenerife 12-14 November 2008 http://www.gci.org.es/nicso2008 (pre-registration available) nicso2008@gci.org.es NICSO 2008 is the third edition of the International Workshop on Nature Inspired Cooperative Strategies for Optimization. Its aims are (1) to foster a deeper understanding of "cooperativity" in computational optimisation systems, and (2) to encourage a vigorous exchange of ideas about emerging research areas in cooperative problem solving strategies. The accepted papers will be published in the Springer book series on Studies in Computational Intelligence. The authors of the best accepted papers will be invited to revise and expand their contributions for publication in a special issue in the Memetic Computing Journal (Springer) shortly after the event. IMPORTANT DATES: =95 Deadline for Submission: September, 1 =95 Notification of Acceptance: September, 30 =95 Deadline for Camera-ready: October, 20 All submissions (only pdf file) must be sent at nicso2008@gci.org.es. The length of each contribution will not exceed 12 pages. Produce a camera ready copy using NICSO2008 latex style found at http://www.gci.org.es/nicso2008. Each contribution must providing original results, insights and experimental innovations. All submitted papers will be blind reviewed and acceptance will be based on originality, significance, technical soundness and clarity. WORKSHOP-CHAIR: =95 Jos=E9 Andr=E9s Moreno P=E9rez, University of La Laguna STEERING COMMITTEE: =95 David A. Pelta, University of Granada =95 Natalio Krasnogor, University of Nottingham ORGANIZING COMMITTEE MEMBERS =95 J. Marcos Moreno, University of La Laguna =95 Bel=E9n Mel=ED=E1n, University of La Laguna =95 Julio Brito, University of La Laguna =95 Clara Campos, University of La Laguna =95 F. Javier Mart=EDnez, University of La Laguna =95 David Beltr=E1n, University of La Laguna =95 Jos=E9 Luis Gonz=E1lez, University of La Laguna TOPICS OF INTEREST (but not limited to them): =95 Adaptive Behaviour =95 Ants Colonies =95 Amorphous Computing =95 Artificial Li fe =95 Artificial Immune Systems =95 Coevolution =95 Distributed Computing =95 Evolutionary Robotics =95 Evolvable Systems =95 Genetic Algorithms =95 Genetic Programming =95 Membrane Computing =95 Quantum Computing =95 Software Self Assembly =95 Swarm Intelligence Cooperative Strategies for: =95 Numerical Optimization =95 Combinatorial Optimization =95 Non Linear Optimization =95 Dynamic Optimization =95 Noisy Optimization =95 Bioinformatics and Systems Biology =95 Game Theory =95 Complex Systems =95 Optimal Adaptable Control SECOND CALL FOR PAPERS in pdf format at: http://www.gci.org.es/NICSO2008/documentos/NICSO2008_2ndCFP.pdf --=20 Jos=E9 Andr=E9s Moreno P=E9rez Catedr=E1tico de Ciencias de la Computaci=F3n e I.A. Universidad de La Laguna. SPAIN. Tel.: +34-922318186. http://webpages.ull.es/users/jamoreno/ Group of Intelligent Computing http://www.gci.org.es/ "NICSO 2008" http://www.gci.org.es/nicso2008/ TRANSNOVA 2008 http://www.transnova.es From karin.hummel from univie.ac.at Tue May 20 11:26:31 2008 From: karin.hummel from univie.ac.at (karin anna hummel) Date: Tue May 20 17:20:22 2008 Subject: [Computational-biology] 2nd CfP: IWSOS 2008 - 3rd Int. Workshop on Self-Organizing Systems Message-ID: <4832FBB7.1030005@univie.ac.at> Please accept our apologies if you receive multiple copies of the cfp. ************************ 2nd CALL FOR PAPERS ************************ IWSOS 2008 3rd International Workshop on Self-Organizing Systems - Self-Organizing Networks and Networked Systems - December 10-12, 2008 Vienna, Austria http://iwsos.ani.univie.ac.at/ Submission deadline (full papers): June 22, 2008 ********************************************************************* Workshop Scope -------------- IWSOS 2008 is the third workshop in a series of annual workshops dedicated to self-organization in networks and networked systems. The necessity for and expected benefit of self-organization is caused by the growing scale, complexity, and heterogeneity of future networked systems, like the future Internet. For example, these networks will consist of interconnected infrastructure-based, mobile ad-hoc, and sensor networks that could be spontaneously deployed in hostile environments, have a dynamic population and a potentially short life time. In spite of this, there will be stringent user requirements, such as resilience and real-time guarantees. Although self-organization is desirable for these kinds of networks, it is not yet clear to what extent self-organization can be exploited. Research into networked systems has recently started to systematically investigate self-organization, which has lead to a multitude of open research issues. The applicability of well-known self-organizing techniques to specific networks and networked systems has to be investigated, as well as adaptations and novel approaches inspired by, e.g., cooperation in nature and evolutionary dynamics, sociology, and game theory. Additionally, models originating from areas like feedback control and complex system's research, are required for these networked systems in order to analyze their controllability and emergent behavior. Aspects of engineering self-organizing networked systems should be studied that discuss paradigms like programmable networks, and tools and frameworks for deploying, testing, and monitoring self-organizing networks. The role of self-organization in the future Internet and the impact on its architecture is an important topic, as well as the application of self-organization in future intelligent transportation systems and vehicular ad-hoc networks. Building on the success of its predecessors, this workshop aims at bringing together leading international researchers to create a visionary forum for investigating the potential of self-organization for networked systems by including the following key topics (not a restricted list): * Self-organization and self-management * Self-configuration and self-optimization * Self-protection, -diagnosis, and -healing * Autonomic networking principles and practice * Control theory based models and approaches of self-organization * Feedback control in networked systems * Group-forming networks and techniques * Programmable and cognitive networks for self-organization * Visualization of network system state * Inspiring models of self-organization in nature and society (e.g., bio-inspired or based on game theory) * Risks in self-organization and risk management techniques * The (un-)controllability of self-organizing emergent systems * Quality of Service / service level agreements and self-organization * Resilience, robustness, and fault tolerance for networked systems * Security in self-organizing networked systems * Self-* sensor and ad-hoc networks * Self-* techniques in peer-to-peer networks * Self-organization of over- and underlays and in cross-layering * Self-* networks and networked systems for ubiquitous computing * Self-organization in heterogeneous network convergence * Evolutionary principles of the (future, emerging) Internet * Self-configuring place-and-play mobile networks * Self-organizing vehicular ad-hoc networks * Self-organizing multi-service networks and multi-network services * Methods for configuration and management of large, complex networks * Applications, e.g. the self-organizing home network * The human in the loop of self-organizing networked systems Important Dates --------------- * Paper submission deadline (full papers): June 22, 2008 * Notification of acceptance (full papers): September 1, 2008 Initial Submission (full papers) -------------------------------- IWSOS invites submission of manuscripts that present original research results, and that have not been previously published or are currently under review by another conference or journal. Any previous or simultaneous publication of related material should be explicitly noted in the submission. Submissions should be full-length papers up to 10 pages using the LNCS style, including all figures and references, and must include an abstract of 100 - 150 words. All papers must be submitted in PDF format. Submissions will be peer reviewed by at least three members of the international TPC and judged on originality, significance, interest, clarity, relevance, and correctness. Accepted Full Papers -------------------- The proceedings will be published by Springer-Verlag in their Lecture Notes for Computer Science (LNCS) series. At least one of the authors of each accepted paper must attend IWSOS 2008 to present the paper. Steering Committee ------------------ * Hermann de Meer, University of Passau, Germany * David Hutchison, Lancaster University, UK * Bernhard Plattner, ETH Zurich, Switzerland * James Sterbenz, University of Kansas, USA * Randy Katz, UC Berkeley, USA General Chair ------------- * Helmut Hlavacs, University of Vienna, Austria Technical Program Co-Chairs --------------------------- * Karin Anna Hummel, University of Vienna, Austria * James Sterbenz, University of Kansas, USA Technical Program Committee --------------------------- * Marin Bertier, IRISA/INSA-Rennes, France * Christian Bettstetter, University of Klagenfurt, Austria * Ernst Biersack, Institute Eurecom, France * Georg Carle, University of Tuebingen, Germany * Tarik Cicic, University of Oslo, Norway * Alexander Clemm, Cisco Systems, USA * Costas Courcoubetis, AUEB, Greece * Simon Dobson, University College Dublin, Ireland * Stefan Fischer, University of Luebeck, Germany * Frank Fitzek, Univ. of Aalborg, Denmark * Michael Fry, University of Sydney, Australia * David Garlan, Carnegie Mellon University, USA * Indranil Gupta, University of Illinois at Urbana Champaign, USA * Hannes Hartenstein, University of Karlsruhe, Germany * Manfred Hauswirth, National University of Ireland, Ireland * Joseph L. Hellerstein, Microsoft Developer Division, USA * Matthias Hollick, Technical University of Darmstadt, Germany * Amine Houyou, University of Passau, Germany * Alexander Keller, IBM T.J. Watson Research Center, USA * Wolfgang Kellerer, DoCoMo Lab Europe, Germany * Alexander V. Konstantinou, IBM T.J. Watson Research Center, USA * Rajesh Krishnan, BBN Technologies, USA * Guy Leduc, University of Liege, Belgium * Baochun Li, University of Toronto, Canada * Marco Mamei, University di Modena e Reggio Emilia, Italy * Andreas Mauthe, Lancaster University, UK * Paul Mueller, Kaiserslautern University, Germany * Masayuki Murata, Osaka University, Japan * Ben Paechter, Napier University, UK * Manish Parashar, Rutgers University, USA * Christian Prehofer, Nokia Research, Finland * Lukas Ruf, Consecom AG, Switzerland * Mikhail Smirnov, Fraunhofer Fokus, Germany * Paul Smith, Lancaster University, UK * Marcus Schoeller, NEC Laboratories Europe, Germany * Thrasyvoulos Spyropoulos, ETH Zurich, Switzerland * Burkhard Stiller, University of Zurich and ETH Zurich, Switzerland * John Strassner, Motorola Labs, USA * Zhili Sun, University of Surrey, UK * Kurt Tutschku, Wuerzburg University, Germany * Patrick Wuechner, University of Passau, Germany * Albert Zomaya, University of Sydney, Australia Local Organizing Committee --------------------------- * Shelley Buchinger, University of Vienna, Austria * Alexander Adrowitzer, University of Vienna, Austria * Harald Meyer, University of Vienna, Austria From masulli from disi.unige.it Thu May 22 12:56:36 2008 From: masulli from disi.unige.it (Francesco Masulli) Date: Thu May 22 17:01:46 2008 Subject: [Computational-biology] LAST CPF: CIBB 2008 3-4 October, 2008 Vietri sul Mare, Salerno (Italy) - Paper submission deadline: 30 May 2008 Message-ID: <200805221956.37231.masulli@disi.unige.it> Please, accept our apologies for multiple postings. Last Call for Papers ========================================================================================= CIBB 2008 FIFTH INTERNATIONAL MEETING ON COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS IIASS - Vietri sul Mare, Salerno (Italy) 3-4 October, 2008 Conference Website: http://cibb08.disi.unige.it/ The main goal of the CIBB meetings is to provide a forum open to researchers from different disciplines to present and discuss problems concerning computational techniques in bioinformatics, systems biology and medical informatics with a particular focus on Neural Networks, Machine Learning, Fuzzy Logic, and Evolutionary Computation methods. CIBB 2008 is jointly organized by: * INNS - International Neural Network Society, SIG Bioinformatics * ISCB International Society for Computational Biology * GNCS Gruppo Nazionale Calcolo Scientifico * SIREN - Italian Neural Networks Society * DISI - Univ. Genova (Italy) * DMI - Univ. Salerno (Italy) Technical areas addressed by CIBB 2008 include, but are not limited to: * Sequence analysis, promoter analysis and identification of transcription factor binding sites * Gene expression data analysis * Methods for the integration of clinical and genetic data * Algorithms for alternative splicing analysis * Methods for the functional classification of genes * Methods for the unsupervised analysis, validation and visualization of structures discovered in bio-molecular data * Prediction of secondary and tertiary protein structures * Mass spectrometry data analysis in proteomics * Methods for comparative genomics * Algorithms for molecular evolution and phylogenetic analysis * Mathematical modelling and simulation of biological systems * Heterogeneous data integration and data fusion for diagnostics * Bio-molecular databases and data mining * Algorithms for pharmacogenetics * Bio-medical text mining and imaging * Methods for diagnosis and prognosis * Software tools for bioinformatics Prof. Giuseppe Russo of Temple Univ, Philadelphia (PA-USA) has confirmed to deliver an invited talk at CIBB 2008. The scientific program will include, besides some plenary talks, contributed papers that will be presented in plenary oral or poster sessions. Accepted papers will be published in the compact disk of conference proceedings. A selection of papers presented at CIBB 2008 will be published as a post conference volume of LECTURE NOTES IN BIOINFORMATICS LNBI/LNCS series of Springer Verlag. Moreover, a selection of more relevant papers will be considered or publication in extended form in a special issue of a scientific journal we are planning. Chairs: Francesco Masulli, Universit? di Genova, Italy and Temple University, PA, USA Roberto Tagliaferri, Universit? di Salerno, Italy Gennady M. Verkhivker, University of Kansas, KS, USA, and University of California San Diego, CA, USA Scientific Program Committee: Klaus-Peter Adlassnig, Medical University of Vienna, Austria Joaquin Dopazo, Centro de Investigaci?n Pr?ncipe Felipe, Valencia, Spain Antonio Giordano, Temple Univ, Philadelphia, PA, USA Emmanuel Ifeachor, University of Plymouth, UK Samuel Kaski, Helsinki University of Technology, Finland Natalio Krasnogor, University of Nottingham, UK Giancarlo Mauri,University of Milano Bicocca, Italy Oleg Okun, University of Oulu, Finland Giulio Pavesi, University of Milan, Italy David Alejandro Pelta, University of Granada, Spain Graziano Pesole, University of Bari, Italy Leif E. Peterson, Baylor College of Medicine Houston, TX, USA Volker Roth, ETH Zurich, Switzerland Giuseppe Russo, Temple Univ, Philadelphia, PA, USA Giorgio Valentini, University of Milan, Italy Giorgio Valle, University of Padua, Italy Jean-Philippe Vert, Ecole des Mines de Paris, France Steering Commitee: Pierre Baldi, University of California, Irvine, CA, USA Alexandru Floares, Oncological Institute Cluj-Napoca, Romania Jon Garibaldi, University of Nottingham, UK Francesco Masulli, University of Genova, Italy and Temple University, PA, USA Roberto Tagliaferri, University of Salerno, Italy Important Dates: Special Session Proposals: 15 May 2008 Paper submission deadline: 30 May 2008 Notification of acceptance: 30 June 2008 Final paper due: 1 September 2008 Conference: 3-4 October 2008 Special sessions: Special sessions proposals including session's title and scope, short cv of sessions chairs, preliminary list of papers (titles and authors) are due by May 15 2008. Proposals of special sessions will be evaluated as soon as they will be submitted. Please, send the proposals to cibb2008chair@disi.unige.it Paper submission: Papers must be prepared following the guidelines illustrated on the CIBB web site and cannot be longer than 10 pages. The submission of papers will be done by uploading their PDF version on the CIBB web site. =================================================== CIBB 2008 FIFTH INTERNATIONAL MEETING ON COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS IIASS - Vietri sul Mare, Salerno (Italy) 3-4 October, 2008 Conference Website: http://cibb08.disi.unige.it/ email: cibb2008chair@disi.unige.it ================================================== -- From masulli from disi.unige.it Thu May 29 08:57:54 2008 From: masulli from disi.unige.it (Francesco Masulli) Date: Thu May 29 10:00:26 2008 Subject: [Computational-biology] CIBB 2008: Paper deadline extension 15 June 2008 Message-ID: <200805291557.54404.masulli@disi.unige.it> Please, accept our apologies for multiple postings. After several requests, the paper submission deadline for CIBB 2008 has been extended to 10 June 2008. ========================================================================================= CIBB 2008 FIFTH INTERNATIONAL MEETING ON COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS IIASS - Vietri sul Mare, Salerno (Italy) 3-4 October, 2008 Conference Website: http://cibb08.disi.unige.it/ The main goal of the CIBB meetings is to provide a forum open to researchers from different disciplines to present and discuss problems concerning computational techniques in bioinformatics, systems biology and medical informatics with a particular focus on Neural Networks, Machine Learning, Fuzzy Logic, and Evolutionary Computation methods. CIBB 2008 is jointly organized by: * INNS - International Neural Network Society, SIG Bioinformatics * ISCB International Society for Computational Biology * GNCS Gruppo Nazionale Calcolo Scientifico * SIREN - Italian Neural Networks Society * DISI - Univ. Genova (Italy) * DMI - Univ. Salerno (Italy) Technical areas addressed by CIBB 2008 include, but are not limited to: * Sequence analysis, promoter analysis and identification of transcription factor binding sites * Gene expression data analysis * Methods for the integration of clinical and genetic data * Algorithms for alternative splicing analysis * Methods for the functional classification of genes * Methods for the unsupervised analysis, validation and visualization of structures discovered in bio-molecular data * Prediction of secondary and tertiary protein structures * Mass spectrometry data analysis in proteomics * Methods for comparative genomics * Algorithms for molecular evolution and phylogenetic analysis * Mathematical modelling and simulation of biological systems * Heterogeneous data integration and data fusion for diagnostics * Bio-molecular databases and data mining * Algorithms for pharmacogenetics * Bio-medical text mining and imaging * Methods for diagnosis and prognosis * Software tools for bioinformatics Prof. Giuseppe Russo of Temple Univ, Philadelphia (PA-USA) has confirmed to deliver an invited talk at CIBB 2008. The scientific program will include, besides some plenary talks, contributed papers that will be presented in plenary oral or poster sessions. Accepted papers will be published in the compact disk of conference proceedings. A selection of papers presented at CIBB 2008 will be published as a post conference volume of LECTURE NOTES IN BIOINFORMATICS LNBI/LNCS series of Springer Verlag. Moreover, a selection of more relevant papers will be considered or publication in extended form in a special issue of a scientific journal we are planning. Chairs: Francesco Masulli, Universit? di Genova, Italy and Temple University, PA, USA Roberto Tagliaferri, Universit? di Salerno, Italy Gennady M. Verkhivker, University of Kansas, KS, USA, and University of California San Diego, CA, USA Scientific Program Committee: Klaus-Peter Adlassnig, Medical University of Vienna, Austria Joaquin Dopazo, Centro de Investigaci?n Pr?ncipe Felipe, Valencia, Spain Antonio Giordano, University of Siena, Italy & Temple Univ, Phil, PA, USA Emmanuel Ifeachor, University of Plymouth, UK Samuel Kaski, Helsinki University of Technology, Finland Natalio Krasnogor, University of Nottingham, UK Giancarlo Mauri, University of Milano Bicocca, Italy Oleg Okun, University of Oulu, Finland Giulio Pavesi, University of Milan, Italy David Alejandro Pelta, University of Granada, Spain Graziano Pesole, University of Bari, Italy Leif E. Peterson, Baylor College of Medicine Houston, TX, USA Volker Roth, ETH Zurich, Switzerland Giuseppe Russo, Temple Univ, Philadelphia, PA, USA Giorgio Valentini, University of Milan, Italy Giorgio Valle, University of Padua, Italy Jean-Philippe Vert, Ecole des Mines de Paris, France Steering Commitee: Pierre Baldi, University of California, Irvine, CA, USA Alexandru Floares, Oncological Institute Cluj-Napoca, Romania Jon Garibaldi, University of Nottingham, UK Francesco Masulli, University of Genova, Italy and Temple University, PA, USA Roberto Tagliaferri, University of Salerno, Italy Important Dates: Paper submission deadline: 15 June 2008 Notification of acceptance: 10 July 2008 Final paper due: 1 September 2008 Conference: 3-4 October 2008 Special sessions: Special sessions proposals including session's title and scope, short cv of sessions chairs, preliminary list of papers (titles and authors) are due by May 15 2008. Proposals of special sessions will be evaluated as soon as they will be submitted. Please, send the proposals to cibb2008chair@disi.unige.it Paper submission: Papers must be prepared following the guidelines illustrated on the CIBB web site and cannot be longer than 10 pages. The submission of papers will be done by uploading their PDF version on the CIBB web site. =================================================== CIBB 2008 FIFTH INTERNATIONAL MEETING ON COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS IIASS - Vietri sul Mare, Salerno (Italy) 3-4 October, 2008 Conference Website: http://cibb08.disi.unige.it/ email: cibb2008chair@disi.unige.it ================================================== From nicosia from dmi.unict.it Fri May 30 01:29:22 2008 From: nicosia from dmi.unict.it (Giuseppe Nicosia) Date: Fri May 30 13:27:31 2008 Subject: [Computational-biology] International School of Natural Computation - Registration Deadline June 16th, 2008 Message-ID: <20080530082922.znd81riwfkscg8sw@mbox.dmi.unict.it> * Our apologies if you receive multiple copies of this announcement * * Please pass this Call for Partecipation to interested Colleagues * Bertinoro International Summer School of Natural Computation - BNC 2008 University Residential Center - Bertinoro (Forl?-Cesena), Italy September 20-27, 2008 http://www.dmi.unict.it/~bnc/index.html The registration deadline is: June 16th, 2008 The International Summer School of Natural Computing is devoted to disseminate the various branches of Natural Computing. The school will gather leading specialists from several horizons lecturing and discussing on the achievements and perspectives both fundamental and applied, non excluding junior scientists and PhD students. List of topics: Self-Organizing Systems; DNA, BioMolecular and Chemistry Computing; Artificial Immune Systems; Metabolic Systems and Artificial Biochemistry; Bio-Inspired Robotics; Rule-Based Modeling of Biochemical Systems; Synthetic Biology for Natural Computing vs. Synthetic Biology for Bioengineering. The school is interdisciplinary in nature, and can be seen both as a School for advanced students, and as a Workshop for researchers. Leading world-renowned researchers in various research areas of Natural Computing will hold tutorials on their subject area, while new ideas will be presented in poster sessions, discussions and short seminars. The school is structured in lectures in the morning and poster/seminar sessions and informal discussion in the afternoon. Students in different area of computer science, natural sciences and mathematics are particularly encouraged to apply. Accepted students may submit a poster and/or a seminar to present their recent research activities. The main goal of this International school is to develop the mutual interaction between specialists from natural computing scientists and biologists. For the students, the prime objective is to learn state-of-art methodologies, algorithms and problems in Natural Computing. The School is supported by BiCi with its Leonardo Melandri Program, University of Cambridge and University of Catania. List of Speakers Bruno Apolloni, University of Milan, Italy Paolo Arena, University of Catania, Italy Andrea Brand, University of Cambridge, UK Luca Cardelli, Microsoft Research, Cambridge, UK Vincenzo Cutello, University of Catania, Italy Troels Damgaard, University of Copenhagen, Denmark Vincent Danos, CNRS, Universite Denis Diderot, France Pierpaolo Degano, University of Pisa, Italy Walter Fontana, Harvard University, USA Jim Haseloff, University of Cambridge, UK Jean Krivine, Ecole Polytechnique, Palaiseau Cedex, France Pietro Li?, University of Cambridge, UK Lakshminarayanan Mahadevan, Harvard University, USA Vincenzo Manca, University of Verona, Italy Vittorio Maniezzo, University of Bologna, Italy Giancarlo Mauri, University of Milan - Bicocca, Italy Giuseppe Nicosia, University of Catania, Italy Corrado Priami, Microsoft Research - University of Trento CoSBi, Italy Grzegorz Rozenberg, Leiden University, The Netherlands Ehud Shapiro, Weizmann Institute of Science, Israel Jon Timmis, York University, UK Luca Zammataro, Cnr, Italy Seminars There will be several seminars complementing the topics treated in the course. Paolo Bellavista, University of Bologna, Italy Tammy Cheng, University of Cambridge, UK Eric Yu-En Lu, University of Cambridge, UK Marco Mamei, University of Modena, Italy Emanuela Merelli, University of Camerino, Italy Registrations Close: June 16th, 2008 The registration fee for the School is 990 Euro (resp. 1190 Euro) and includes all local expenses from the evening of Saturday September 20th to morning on Saturday September 27th including * all meals (breakfast, lunch, dinner), * on-site lodging in double-occupancy (resp. single) rooms, * all Courses, * Lecture Notes, * Coffee Breaks, * Computer rooms and Internet Connection. Attendance is limited to 60 students (M.Sc students, Ph.D. students, Post-Doc) and will be allocated on a first-come-first-served basis. All applicants must complete a Registration Form by June 16th 2008. After this is complete, they should pay, following the instructions, as soon as possible, and before June 30th, 2008 (Applications are considered complete only after the payment has been received). The form is available here. Follow instructions from the form, in order to complete the registration. You will receive a confirmation email. The registration deadline is: June 16th, 2008 Past this deadline, the Bertinoro Center will accept registrations on a space availability basis. For any questions regarding registration, accomodations, accompanying persons, etc. please contact Eleonora Campori at ecampori@ceub.it. For any question please send email to bnc@dmi.unict.it or Pietro Li?: pl219@cam.ac.uk Giuseppe Nicosia: nicosia@dmi.unict.it http://www.dmi.unict.it/~bnc/index.html -- Giuseppe Nicosia, Ph.D. Associate Professor Department of Mathematics & Computer Science Ph +39 095 7383030 University of Catania F +39 095 330094 Viale A. Doria, 6 E nicosia@dmi.unict.it 95125 Catania, Italy W www.dmi.unict.it/nicosia ------------------------------------------------------------------------ ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From nicosia from dmi.unict.it Fri May 30 01:30:46 2008 From: nicosia from dmi.unict.it (Giuseppe Nicosia) Date: Fri May 30 13:27:44 2008 Subject: [Computational-biology] International Summer School of Functional Genomics, July 5-19, 2008 - Accomodation Deadline: May 31 Message-ID: <20080530083046.1l9s5ilz4wokgo4k@mbox.dmi.unict.it> * Apologize for Multiple Postings * * Please pass this Call for Partecipation to interested Colleagues & students * INTERNATIONAL SUMMER SCHOOL OF FUNCTIONAL GENOMICS Baia Samuele Conference Centre, Scicli, Sicily, Italy July 5th-19th 2008 http://www.functional-genomics.it/school Due to numerous requests we decided to extend the Accomodation deadline. Accomodation *Deadline*: May 31, 2008 The International School of Functional Genomics consists of two modules. Each module is one week long. Participants may register for one or both modules. First week: "Cutting edge genomic technologies" (July 5-12, 2008) "Lectio Magistralis" Rita Levi-Montalcini, Nobel Laureate, Italy "In-CheckTM platform: a highly integrated solution for rapid and accurate Nucleic Acid testing" Enrico Alessi, STMicroelectronics, Italy "Magnetic strategies for biosensors" Salvatore Baglio, University of Catania, Italy "System neurobiology: from a reductionistic to an olistic approach" Pietro Calissano, European Brain Research Institute, Italy and Institute of Neurobiology and Molecular Medicine, CNR, Italy "New technologies and products for healthcare" Salvo Coffa, STMicroelectronics, Italy "Executable models for synaptic plasticity and VICE: a virtual cell" Pierpaolo Degano, University of Pisa, Italy "Practical course on pathway analysis and gene expression" Mark Hughes, MetaCore, UK "Practical Course on gene ontologies and pathway analysis" Carsten Lederer, Telethon Institute for Gene Therapy, Italy "Linkage and association studies using markers and SNP arrays" Ben Oostra, Erasmus University, The Netherlands "Microarray data analysis" John Quackenbush, Harvard School of Public Health, Harvard University, USA "Integrating glycomics and genomics" Shiladitya Sengupta, Harvard Medical School, Harvard-MIT Division of Health Sciences and Technology, USA "Practical course on DNA microarray analysis" Massimo Tifi, Abel, Italy Second module: ?Application of genomic technologies to the biomedical field? (July 12-19, 2008) "Introduction to neuroinformatics and computational neuroanatomy" Giorgio Ascoli, Krasnow Institute for Advanced Study, George Mason University, USA "Forensic DNA" Lucia Bianchi, Lawyer, Italy "Genomics: at the intersection of neuronal life and death" Sebastiano Cavallaro, ISN CNR, Italy "Applying genomic profiling to enable personalized medicine" Femke de Snoo, Agendia, The Netherlands "Pharmacogenetics, pharmacogenomics and individualized therapies" Filippo Drago, University of Catania, Italy "A web-based architecture for parallel computation of molecular pathway models" C. Forbes Dewey, Jr. MIT, USA "Functional genomics: new frontiers in drug discovery" Gerald Fisher, Wyeth, USA "Practical course on biological pathways analysis simulation" Andrew Koo, MIT, USA "Methods and models in computational genomics" Pietro Li?, Computer Laboratory, University of Cambridge, UK "Computational systems biology: a programming language approach" Corrado Priami, Microsoft Research - University of Trento COSBI, Italy "Tumor classification by genomic analysis" John Quackenbush, Harvard School of Public Health, Harvard University, USA "Gene expression profiling of advanced ovarian cancer" Claudio Schneider, University of Udine, Italy "Careers in science publishing" Magdalena Skipper, Nature Publishing Group, UK "Toxicogenomics" Elisabetta Tendi, Wyeth, Italy SCHOOL VENUE The School will be hosted by Hotel Village Baia Samuele, Scicli, (RG), Sicily: http://www.baiasamuele.it/ Scicli is one the Late Baroque Towns of the Val di Noto in the South-Eastern Sicily. The Val di Noto area is included in the UNESCO World Heritage List http://whc.unesco.org/en/list/1024/documents/ The eight towns in south-eastern Sicily: Caltagirone, Militello Val di Catania, Catania, Modica, Noto, Palazzolo, Ragusa and Scicli, were all rebuilt after 1693 on or beside towns existing at the time of the earthquake which took place in that year. They represent a considerable collective undertaking, successfully carried out at a high level of architectural and artistic achievement. Keeping within the late Baroque style of the day, they also depict distinctive innovations in town planning and urban building. SCHOOL FEES & DEADLINES * Early Registration before May 20, 2008: o One Week Student Registration (M.Sc. and Ph.D. Students): 350 Euro. o One Week Registration: 600 Euro. o Both Weeks Student Registration: 650 Euro. o Both Weeks Registration: 1100 Euro. * Late Registration after May 20, 2008: o One Week Late Student Registration (M.Sc. and Ph.D. Students): 450 Euro. o One Week Late Registration: 800 Euro. o Both Weeks Late Student Registration: 750 Euro. o Both Weeks Late Registration: 1500 Euro. The application should be done *before* May 20, 2008. Early payment due: before May 20, 2008. Late payment due after May 20, 2008 The fee will include, all Courses, Lecture Notes, Coffee Breaks, Bus service from Catania Airport to School Venue and vice-versa, WiFi Internet Connection, Two Social Tours. Accepted students may submit a poster and/or a seminar to present their recent research activities. Participants are responsible for arranging their own hotel accommodation Download, complile and send by FAX the accomodation bill form - Deadline May 20th http://www.functional-genomics.it/school/BaiaSamuele.pdf School Director: Sebastiano Cavallaro, CNR, Italy Scientific Committee: Sebastiano Cavallaro, CNR, Italy. Pietro Li?, University of Cambridge, UK. Giuseppe Nicosia, University of Catania, Italy. Enrico Rizzarelli, University of Catania, Italy For more information, please send an email to: school@functional-genomics.it ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.