From damiand from sic.univ-poitiers.fr Tue Apr 1 10:39:20 2008 From: damiand from sic.univ-poitiers.fr (Guillaume Damiand) Date: Tue Apr 1 11:53:55 2008 Subject: [Computational-biology] CTIC 2008: Second Call for Paper Message-ID: <20080401154000.BCC592FE816@sic.sp2mi.univ-poitiers.fr> ______________________________________________________________________ CTIC'2008 SECOND CALL FOR PAPERS First Workshop on Computational Topology in Image Context June 16-17, 2008 POITIERS - FRANCE http://ctic.sic.sp2mi.univ-poitiers.fr/ ______________________________________________________________________ IMPORTANT DATES: Deadline for abstract submission: May 4, 2008 Notification of acceptance: May 21, 2008 Registration: May 30, 2008 Workshop: June 16-17, 2008 CONTACT: ctic@sic.univ-poitiers.fr ______________________________________________________________________ The aim of CTIC'2008 is to gather researchers dealing with the study of topological invariants from the computational point of view, and/or who want to use topological information in image applications. Indeed, people from different fields related to these studies share a growing interest in collaborating. These fields include: computational geometry, discrete geometry, geometrical modeling, algebraic topology and image processing. The workshop will provide an opportunity for the world's leading scientists and other participants in these fields, including young researchers, to exchange ideas. It will act as a catalyst for creating new collaborations, and starting new transversal projects. To achieve this goal, participants are encouraged to present an up-to-date survey of their research related to one of the topics of the workshop listed below. Research in progress can also be submitted, as well as results that have been published recently. Works related to image applications using topological invariants are particularly welcome. The workshop will offer invited talks by : Isabelle Bloch (ENST, Paris), Francis Sergeraert (UJF, Grenoble), Pedro Real (Sevilla, Spain). ______________________________________________________________________ SCOPE: The range of topics that are within the scope of the Workshop on Computational Topology in Image Context includes (but is not limited to): - Topological invariants and their computation, homology, cohomology, linking number, fundamental groups, ... - Algorithm optimization for image applications, transfer of mathematical tools, parallel computation, hierarchical approaches, ... - Experimental evaluation of algorithms and heuristics, - Numerical issues arising in implementations, - Combinatorial or multi-resolution models, - Discrete or computational topology, - Geometrical modeling guided by topological constraints, - Use of topological information in image applications ______________________________________________________________________ Call for papers: Authors are invited to submit extended abstracts describing either an up-to-date survey of their research related to one of the topics of the workshop listed above. Research in progress can also be submitted, as well as results that have been published recently. Works related to image applications using topological invariants are particularly welcome. Abstracts, written in English, should not exceed 6 single-spaced pages, and should be submitted before 4 May 2008. ______________________________________________________________________ Scientific committee : Dominique Attali (Gipsa-lab, Grenoble, France) Gilles Bertrand (A2SI, Noisy-Le-Grand, France) Luc Brun (GreyC, Caen, France) Eric Colin de Verdière (GéCoaL, ENS, Paris, France) Michel Couprie (A2SI, Noisy-Le-Grand, France) Reinhard Klette (Comp. Sci. Auckland, New Zealand) T. Yung Kong (Queens College, New-York city) Walter G. Kropatsch (Prip, Vienne, Autriche) Jacques-Olivier Lachaud (LAMA, Chambery, France) Francis Lazarus (LIS, Grenoble, France) Bernard Lacolle (LJK, Grenoble, France) Grégoire Malandain (ASCLEPIOS, Sophia, France) Rémy Malgouyres (LAIC, Clermont-Ferrand, France) Cyrille Ospel (MIA, La Rochelle, France) Nicolas Passat (LSIIT, Strasbourg, France) Samuel Peltier (IFP, Paris, France) Pol Vanheacke (LMA, Poitiers, France) Guy Wallet (MIA, La Rochelle, France) ______________________________________________________________________ Full details of the workshop can be found on our website at http://ctic.sic.sp2mi.univ-poitiers.fr/ Please forward this email to all colleagues who may be interested. We look forward to welcoming you in Poitiers for CTIC'2008. ______________________________________________________________________ From Anar.Khan from agresearch.co.nz Tue Apr 1 17:01:02 2008 From: Anar.Khan from agresearch.co.nz (Khan, Anar) Date: Tue Apr 1 21:02:53 2008 Subject: [Computational-biology] Bioinformatician vacancy, AgResearch, New Zealand Message-ID: **Excellence is in our DNA** *Bioinformatician* Many of the world's most amazing scientific discoveries are the result of someone 'taking a closer look'. It's this inquisitive nature and relentless search for answers that fuels scientific advancement. And it's also what we'd like you to apply to us, right now. Mind you, you won't need to look too hard to discover that AgResearch is the best place to break all new ground in your career. At first glance you'll see we are New Zealand's largest research institute -world leaders in pastoral research working at the leading-edge of innovation. Scratch the surface a little more and you'll find all the diversity and intellectual challenge a Bioinformatician could ask for. This is a highly collaborative role where you'll be involved in everything from the analysis of genomic data to the design, development, implementation and testing of bioinformatics tools. Knowledge sharing is a pivotal component of our success, so you can also look forward to acting in consultant capacity (both internally and externally) and the autonomy to contribute to scientific publications. Our people are at the pinnacle in their professions, so with your biological background, higher qualification in bioinformatics or computing and your experience in contributing bioinformatics expertise to research groups, you'll not only fit right in, you'll hit the ground running. An outstanding communicator, time manager and relationship builder, you'll also come to us with a thorough knowledge of Unix, pipeline-development, web based technologies and scripting and programming languages. AgResearch is a unique organisation at the forefront of our field, and as far as your future's concerned, that makes us well worth a closer look. There are many benefits waiting to be discovered here, so isn't it time you experienced them? The job description is available online and applications are invited at www.agresearch.co.nz/recruitment/ Reference AGR661. Applications close 11 April 2008. ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From rres.bab-announce from bbsrc.ac.uk Wed Apr 2 08:07:32 2008 From: rres.bab-announce from bbsrc.ac.uk (rres bab-announce (RRes-Roth)) Date: Wed Apr 2 14:39:17 2008 Subject: [Computational-biology] International Symposium on Integrative Bioinformatics Message-ID: DEADLINE EXTENSION: April 15th, 2008 ***************************************************************** Call for Papers International Symposium on Integrative Bioinformatics 5th annual meeting 20th to 22nd August 2008 Lutherstadt Wittenberg, Germany http://www.imbio.de/conference/ *************************************************************** Papers are invited for oral presentations. Submission must be through the workshop web site. Accepted papers will appear as conference proceedings and also in the Journal of Integrative Bioinformatics http://journal.imbio.de/ *************************************************************** Call for Papers *************************************************************** Biological data are scattered across thousands of biological databases and hundreds of scientific journals. Current high throughput genomics technologies generate large quantities of high dimensional data. Microarray, NMR, mass spectrometry, protein chips, gel electrophoresis data, Yeast-Two-Hybrid, QTL mapping, gene silencing and knockout experiments are all examples of technologies that capture thousands of data points, often in single experiments. The challenge for Integrative Bioinformatics is to capture, model, integrate and analyse these data in a consistent way to provide new and deeper insights into complex biological systems. This, fifth symposium on Integrative Bioinformatics will be of interest to Bioinformaticians, Computer Scientists and others working in, or interested in finding out more about, the developing area of integrative bioinformatics. There will be opportunities to present and discuss methods, theoretical approaches or their practical applications. ************************************************************** Topics of Interest ************************************************************** - Database integration - Combined dry and wetlab studies - Molecular databases / Data warehouses - Errors and inconsistencies in biological databases - Prediction and integration of metabolic and regulatory networks - Genotype-phenotype linkage - Protein-protein interactions - Integrative microarray modeling and analyses - Integrative approaches for drug design - Computational infrastructure for biotechnology - Virtual cell - Tool integration and workflow systems - Laboratory information management systems - Computational systems biology - Quality and consistency of biological ontologies - Integrative modelling and simulation frameworks - Integrative data and text mining approaches - Network analysis - Data visualisation and visual analytics *************************************************************** Important Dates *************************************************************** 5th April 2008 Paper submission deadline (up to 12 pages) 1st June 2008 Notification of acceptance for papers 20th June 2008 Camera ready paper submission deadline 31st July 2008 Poster and software submission deadline 5th August 2008 Notification of acceptance for poster and software demo abstracts 20th - 22nd August 2008 Conference *************************************************************** Keynote Talks *************************************************************** Peter Karp, (SRI International, USA) Dietmar Schomburg, (University of Cologne, Germany) Roland Eils, (DKFZ, Heidelberg, Germany) *************************************************************** Organising Committee *************************************************************** Ralf Hofestaedt University of Bielefeld, Germany Jacob Koehler Eli Lilly, USA Matthias Lange IPK Gatersleben, Germany Uwe Scholz IPK Gatersleben, Germany Falk Schreiber IPK Gatersleben & University of Halle, Germany Paul Verrier Rothamsted Research, UK *************************************************************** Contact *************************************************************** lange AT ipk-gatersleben DOT de From paolo.romano from istge.it Wed Apr 2 08:09:36 2008 From: paolo.romano from istge.it (Paolo Romano) Date: Wed Apr 2 14:39:22 2008 Subject: [Computational-biology] CFP: NETTAB 2008 Message-ID: <200804021320.m32DKXSt056750@ibm43p.biotech.ist.unige.it> Call for Papers for NETTAB 2008 workshop NETTAB 2008 Bioinformatics Methods for Biomedical Complex System Applications 19-21 May 2008, Villa Monastero, Varenna, Lake Como, Italy http://www.nettab.org/2008/ The NETTAB 2008 workshop will focus on all aspects needed to provide the framework for understanding multi-scale, complex biological systems, from the single bio-molecule to the cell, across a wide range of clinical information. A special emphasis will be given to combine theory, experiments, software, and technologies for an integrative systems approach to biological research, which is becoming increasingly multi-disciplinary, multi-dimensional, information driven. Sessions Bioinformatics Methods for Complex Systems Gene networking applications Mathematical Methods for System Biology Oncology Bioinformatics Topics (short list) Computational Systems Biology Model-driven development for biological complex systems Software methodologies for complex adaptive systems Multi-agent systems and cellular automata Database integration and data warehouses Analysis of metabolic and regulatory networks Genetic association studies and linkage analysis Proteomics and protein interactions Microarray modelling and analysis Integrative approaches for drug design Grid based and HPC for bioinformatics applications For the full list of topics please consult the NETTAB web site. Tutorials Systems Biology Tools Systems Biology Standards Important dates 10 April 2008: Paper submission 21 April 2008: Communication of acceptance 22 April 2008: Registration starts 19 May 2008: Tutorials 19-21 May 2008: Workshop Abstracts' submission Submit an extended abstract (max 3 pages) within next 10 April 2008. Guidelines and instructions for submission are available at: http://www.nettab.org/call.html . A MS Word template is available at: http://www.nettab.org/2008/abstract.doc . Registration Registration opens on 22 April 2008. Register for the NETTAB 2008 workshop: http://www.nettab.org/2008/rform.html For all information, please email to nettab2008@itb.cnr.it . Chairs Luciano Milanesi, Institute of Biomedical Technologies, National Research Council, Milan, Italy Paolo Romano, Bioinformatics, National Cancer Research Institute, Genoa, Italy Scientific Committee Lilia Alberghina, University of Milan Bicocca, Italy Alberto Albertini, CNR-ITB, Milano, Italy Claudia Angelini, CNR-IAC, Napoli, Italy Francesco Beltrame, ICT Department, CNR, Rome, Italy Paola Bertolazzi, CNR-IASI, Rome, Italy Flavio Corradini, University of Camerino, Italy Nicola Cannata, University of Camerino, Italy Luca Cardelli, Microsoft Research, Cambridge UK Rita Casadio, University of Bologna, Italy Gastone Castellani, University of Bologna, Italy Gianluigi Condorelli, Medical Department, CNR, Rome, Italy Daniele Cusi, University of Milan, Italy Marie-Dominique Devignes, LORIA, Vandoeuvre les Nancy, France Angelo Facchiano, CNR-ISA, Avellino, Italy Piero Fariselli, University of Bologna, Italy Raffaele Giancarlo, University of Palermo, Italy Radu Grosu, State University of New YorkStony Brook, USA Liliana Ironi, CNR-IMATI, Pavia, Italy Alexander Kel, Biobase, Germany Pietro Li?, University of Cambridge, UK Fabio Macciardi, University of Milan, Italy Roberto Marangoni, University of Pisa, Italy Francesco Masulli, University of Genoa, Italy Giancarlo Mauri, University of Milan Bicocca, Italy Emanuela Merelli, University of Camerino, Italy Andrey Mironov, Moscow University, Russia Marco Muselli, CNR, Genoa, Italy Giovanni Paolella, CEINGE, University of Naples, Itlay Marco Pellegrini, CNR-IIT, Pisa Italy Annibale Puca, Multimedica, Milano, Italy Scott Smolka, State University of New York Stony Brook, USA Roberto Tagliaferri, University of Salento, Italy Giorgio Valentini, University of Milan, Italy We are looking forward to meeting you at NETTAB 2008 in Varenna! Best regards. On behalf of the Organizing Committee Paolo Romano Paolo Romano (paolo.romano@istge.it) Bioinformatics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 Skype: p.romano Web: http://www.nettab.org/promano/ From genomicshakthee2008 from gmail.com Thu Apr 3 02:03:44 2008 From: genomicshakthee2008 from gmail.com (genomicshakthee08) Date: Thu Apr 3 11:36:01 2008 Subject: [Computational-biology] research project Reg.. Message-ID: Dear friends, My Name is Shakthee, I am doing Master Degree in Bioinformatics For my project work . I chose "Analysis of protein-protein Intraction between breast cancer protein, if anybody interest to cowork in my research project. contact me on mail. i will be waiting for veluable reply from my friends. Thanking you Your's friendly Shakthee From cossorzano from gmail.com Mon Apr 7 10:43:01 2008 From: cossorzano from gmail.com (coss) Date: Mon Apr 7 12:32:34 2008 Subject: [Computational-biology] Third CEU Summerschool on Advanced Statistics and Data Mining (June 30th-July 11th, 2008) Message-ID: <48fbc207-37a5-4bcc-9cde-f9db79ff90d8@m1g2000pre.googlegroups.com> Dear colleagues, San Pablo - CEU University in collaboration with other five universities (M?laga, Polit?cnica de Madrid, Pa?s Vasco, Complutense, and Castilla La Mancha), Uni?n 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 nq_flipper from yahoo.com Tue Apr 8 08:12:18 2008 From: nq_flipper from yahoo.com (Chris X. Weichenberger) Date: Tue Apr 8 15:41:58 2008 Subject: [Computational-biology] Errors in protein structures Message-ID: Dear all, We announce the release of NQ-Flipper, a public service for the visualization and correction of unfavorable/incorrect asparagine and glutamine side-chain rotamers. For further information on the NQ-rotamer problem and the NQ-Flipper service see Weichenberger, Byzia & Sippl (2008), Visualization of unfavorable interactions in protein folds. Bioinformatics Advance Access published online on March 29, 2008. http://dx.doi.org/10.1093/bioinformatics/btn108 Weichenberger & Sippl (2007) Recognition and Correction of Erroneous Asparagine and Glutamine Side Chain Rotamers in Protein Structures. Nucleic Acids Res., 35(Web Server issue), W403-406. http://dx.doi.org/10.1093/nar/gkm263 NQ-Flipper is available as a public web service at http://flipper.services.came.sbg.ac.at or may be downloaded as a standalone application for Linux systems. Enjoy! The NQ-Flipper Team CAME - Center of Applied Molecular Engineering University of Salzburg Austria From DCaraviello from dow.com Wed Apr 9 12:13:06 2008 From: DCaraviello from dow.com (Caraviello, Daniel (D)) Date: Wed Apr 9 16:47:04 2008 Subject: [Computational-biology] Computational Biologist position at Dow AgroSciences Message-ID: <7FCEB8C3D787AA4093BE51526102C48EE15F0C@USMDLMDOWX029.dow.com> Dow AgroSciences seeks a Computational Biologist to assist in the analyses of biological datasets. This position is located in Indianapolis, IN, USA. Applicants should have a Ph.D. in computer sciences, bioinformatics, computational biology, statistics or closely related field, with emphasis in machine learning. A solid foundation on statistics is preferred. The successful candidate will join the R&D Operational Excellence function and will work closely with scientists in the company's Plant Genetics & Biotechnology R&D organization. Key job responsibilities will include development and application of machine learning and statistical algorithms and software to mine biological datasets. Extensive development of software to integrate and automate data for mining is also expected. Topics of interest include bioinformatics, Bayesian networks, support vector machines, instance-based algorithms, decision trees, neural networks, and mixed models. Analysis of biological experiments, interpretation and presentation of results are also expected; as well as to act as a guide for the ongoing research process. The candidate will also be expected to identify and implement new quantitative methods that improve the integrity and efficiency of Dow AgroSciences product development cycle. Demonstrated ability to write scientific papers is also desirable. Strong communication skills are essential along with an ability to collaborate effectively with both laboratory and field scientists. Please visit www.dowagro.com/careers to apply online for this position. The deadline for the submission of applications is May 10, 2008. Dow AgroSciences, LLC is a wholly-owned subsidiary of The Dow Chemical Company, one of the top companies for research and development in the US. Dow AgroSciences, LLC is a top tier agricultural company providing innovative crop protection, pest and vegetation management, seed, and agricultural biotechnology solutions to serve the world's growing population. We do this through a people-centric performance culture, through our commitments to sustainable development and environmental stewardship, and through collaborations with world-class institutions. Dow AgroSciences is an equal opportunity employer offering excellent career opportunities, as well as competitive compensation and benefits package. Daniel Caraviello Statistical geneticist R&D Operational Excellence Dow AgroSciences LLC 9330 Zionsville Road Indianapolis, IN 46268 317-337-5958 Office dcaraviello@dow.com From nicosia from dmi.unict.it Thu Apr 10 12:42:17 2008 From: nicosia from dmi.unict.it (Giuseppe Nicosia) Date: Thu Apr 10 19:07:13 2008 Subject: [Computational-biology] International School of Functional Genomics July 5-19, 2008 - Registration Deadline: April 30, 2008 Message-ID: <20080410194217.cmms2bezuo00gg0k@mbox.dmi.unict.it> * Apologize for Multiple Postings * * Please pass this Call for Partecipation to interested Colleagues * INTERNATIONAL SUMMER SCHOOL OF FUNCTIONAL GENOMICS Baia Samuele Conference Centre, Scicli-Sicily, Italy July 5th-19th 2008 http://www.functional-genomics.it/school school@functional-genomics.it Registration *Deadline*: April 30, 2008 LIST OF SPEAKERS Rita Levi-Montalcini, Nobel Laureate, Italy Enrico Alessi, STMicroelectronics, Italy Giorgio Ascoli, Krasnow Institute for Advanced Study, George Mason University, USA Salvatore Baglio, University of Catania, Italy Andrea Ballabio, Telethon Institute of Genetics and Medicine, Italy Lucia Bianchi, Lawyer, Italy Pietro Calissano, European Brain Research Institute, CNR, Italy and Institute of Neurobiology and Molecular Medicine, CNR, Italy Sebastiano Cavallaro, Institute of Neurological Sciences, CNR, Italy Femke de Snoo, Agendia, The Netherlands Pierpaolo Degano, University of Pisa, Italy C. Forbes Dewey, Jr. MIT, USA Filippo Drago, University of Catania, Italy Gerald Fisher, Wyeth, USA Andrew Koo, MIT, USA Carsten Lederer, Telethon Institute for Gene Therapy, Italy Pietro Li?, University of Cambridge, UK Bud Mishra, New York University, USA Ben Oostra, Erasmus University, The Netherlands Corrado Priami, Microsoft Research - University of Trento COSBI, Italy John Quackenbush, Harvard School of Public Health, Harvard University, USA Claudio Schneider, University of Udine, Italy Shiladitya Sengupta, Harvard Medical School, Harvard-MIT Division of Health Sciences and Technology, USA Magdalena Skipper, Nature, UK Elisabetta Tendi, Wyeth, Italy Massimo Tifi, Abel, 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 April 30, 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 April 30, 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* April 30, 2008. Early payment due: before April 30, 2008. Late payment due after April 30, 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, Social Dinner, Two Social Tours. Accepted students may submit a poster and/or a seminar to present their recent research activities. 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 -- Giuseppe Nicosia, Ph.D. Associate Professor Department of Mathematics and Computer Science Phone +39 095 738 30 30 University of Catania Fax +39 095 33 00 94 Viale A. Doria n. 6 Email nicosia@dmi.unict.it 95125 Catania, Italy http://www.dmi.unict.it/nicosia ------------------------------------------------------------------------------ ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From shandar from nibio.go.jp Sun Apr 13 00:20:19 2008 From: shandar from nibio.go.jp (Shandar Ahmad) Date: Sun Apr 13 23:18:22 2008 Subject: [Computational-biology] PRIB 2008: Extension of due date for paper submission Message-ID: <20080413052019.4850C928007@intnewmail.nibio.go.jp> ** Our apologies if you receive multiple copies of this announcement * EXTENSION OF DUE DATE FOR SUBMISSION OF PAPERS, INVITED SESSIONS AND TUTORIALS ************************************************************************ Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2008) October 15-17, 2008 (Melbourne, Australia) Web: www.infotech.monash.edu.au/prib08 Email: prib2008.melb@infotech.monash.edu.au ************************************************************************ Due to many requests, the due date for submission of papers has been extended by one week. The important deadlines are as follows: Paper submission: 22 April 2008 Author notification: 20 May 2008 IMPORTANT: If you have submitted the paper before 15th April and wish to update and resubmit the paper, you can do so. However, you should inform the General Chair about your intentions to resubmit. This will allow the PRIB Chairs to consider your most recent submission for review. ************************************************************************ IAPR STUDENT TRAVEL GRANTS Grants may be possible in a few deserving cases. Students DO NOT apply for these grants. The decision for the award of the grant to deserving cases will be based on the recommendation of the program committee and the reviewers' reports. SPECIAL ISSUES Authors of selected papers presented (both oral and poster) at PRIB 2008 will be invited to extend their work for consideration for publication in following special issues of reputed journals: a) Elsevier's Pattern Recognition Letters (PRL) journal: Special Issue on "Pattern recognition in bioinformatics" b) Elsevier's Neurocomputing journal: Special Issue on "Neurocomputing in bioinformatics and computational biology" SPECIAL SESSIONS Apart from regular sessions, there are now 5 special sessions soliciting paper submissions a) SS1: Special Session on Neuro Computing for microarray data analysis b) SS2: Special Session on Pattern Recognition in bio-molecular interaction networks c) SS3: Special Session on High performance computing in bioinformatics d) SS4: Special Session on Bioinformatics in genetic disorders and computational vaccinology e) SS5: Special Session on Proteins: structure, function and interaction Papers presented in special sessions will undergo the same review process as regular papers and will be included in conference proceedings. ***************************************** CONTACT PRIB 2008 Secretariat Gippsland School of Information Technology Monash University Victoria - 3842, Australia Email: prib2008.melb@infotech.monash.edu.au ***************************************** ----------Unsubsrciption------- To unsubscribe from this mailing list, please send a request to Shandar Ahmad shandar@nibio.go.jp and CC to: prib2008.melb@infotech.monash.edu.au ------------------------------- We apologise if you requested removal and received the mail again, although we have tried to ensure this does not happen. Please send another removal request in that case. From prash from ruc.dk Tue Apr 15 11:54:53 2008 From: prash from ruc.dk (Prash) Date: Tue Apr 15 12:26:45 2008 Subject: [Computational-biology] Travel fellowships: Call for applications! Message-ID: <20080415185453.wrmglwt8g080c0c0@webmail-backend1.ruc.dk> Dear colleagues, We would like to invite you to apply for travel fellowships available for participants in the 4th ISCB Student Council Symposium at ISMB 2008 in Toronto (Canada). We are able to provide 7 travel fellowships worth 1000 USD each. http://symposium.iscbsc.org/content/travel-fellowships The deadline for applications is May 26th. This is also the abstract submission closing date. Keynotes by Mark Gerstein, Timothy Hughes and Burkhard Rost as well as a panel discussion on "Career Paths in Bioinformatics and Computational Biology" with panelists Philip Bourne, Alfonso Valencia, Jong Bhak and Richard Wintle are part of the updated agenda. We are happy to announce that we will again publish a selection of outstanding abstracts as a supplement to BMC Bioinformatics. Please forward this announcement to anyone who might be interested. Thank you very much! Best regards, Nils Gehlenborg Chair, ISCB Student Council Lucia Peixoto Chair, 4th ISCB Student Council Prashanth Suravajhala PhD Fellow http://ruc.dk/~prash/ "We didn't know it at the time, but we found out everything in life is so similar, that the same genes that work in flies are the ones that work in humans" ~~Eric Wieschaus, co-winner of the 1995 Nobel prize in medicine for work on the genetics of Drosophila development From David.Fisher from efs.mq.edu.au Wed Apr 16 00:48:17 2008 From: David.Fisher from efs.mq.edu.au (David Fisher) Date: Wed Apr 16 12:54:36 2008 Subject: [Computational-biology] HP lattice protein folding model Message-ID: <48061FC1.1D9B.0041.0@efs.mq.edu.au> I'm pretty new to computational biology, and I have been looking at Ken Dill's simplified "HP lattice" model of protein folding (which uses polar and hydrophobic monomers only, on a 2D or 3D grid). The energy function he uses gives a value of -1 per hydrophobic monomer that is adjacent in space but not in sequence (described here: http://www3.interscience.wiley.com/cgi-bin/fulltext/36179/PDFSTART). I was wondering why the energy is not based on the amount of exposure of the hydrophobic residues to the surrounding solution instead (eg. the total number of empty points on the lattice adjacent to each "H"). Thanks for any pointers, David F From masulli from disi.unige.it Sat Apr 19 00:16:03 2008 From: masulli from disi.unige.it (Francesco Masulli) Date: Sat Apr 19 13:27:08 2008 Subject: [Computational-biology] CIBB 2008 3-4 October, 2008 Vietri sul Mare, Salerno (Italy) PAPER SUBMISSION OPEN Message-ID: <200804190716.03482.masulli@disi.unige.it> NEWS: The Paper Submission is now open Please, accept our apologies for multiple postings. ========================================================================================= 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 a in post conference volume printed by an international publisher. Moreover, a selection of more relevant papers will be considered for 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 (list to be updated) 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 prash from ruc.dk Tue Apr 22 04:14:02 2008 From: prash from ruc.dk (Prash) Date: Tue Apr 22 08:43:17 2008 Subject: [Computational-biology] Call for Applications: ISCB Student Council DREAM Team Message-ID: <20080422111402.a8e0i9ibk0s4cg48@webmail-backend2.ruc.dk> Dear colleagues, the ISCB Student Council is looking for highly motivated Bioinformatics students to join our team for the DREAM 2008 network reconstruction competition. The team will be mentored and advised by a senior researcher and expert in the field of network reverse engineering, Dr Alberto de la Fuente. It's not necessary to be a member of the ISCB to apply - we will sponsor a one year ISCB membership for the successful applicants! For details please see http://www.iscbsc.org/dreamteam. This is a unique opportunity for students from all over the world to participate in an international, high-profile research competition. The students will collaborate and network with peers from other parts of the world and work under the guidance of an expert in Computational Biology. Please forward this announcement to anyone who might be interested. Thank you very much! Best regards, Nils Gehlenborg Chair, ISCB Student Council From bioinformaticsww from gmail.com Tue Apr 22 12:43:30 2008 From: bioinformaticsww from gmail.com (BWW) Date: Tue Apr 22 15:39:58 2008 Subject: [Computational-biology] New Bioinformatics World Wide Community - Invitation to diffuse Message-ID: <7463ec88-e0e9-4bec-bb71-35c101bd83c8@c58g2000hsc.googlegroups.com> Dear Scientist, This is an invitation to join (and invite people) Bioinformatics World Wide (http://www.bioinformaticsworldwide.com), a community maintained web site dedicated to the fields of Bioinformatics and Computational Biology. This is an open community to people working in or with Bioinformatics related field. On this site you shall find: * News postings about the goings on in the field and possibility to post your own events * Job and studentship adverts that our users have found and submitted to the site * A calendar/event list detailing upcoming events relevant to the fields * Active forums for people to come and ask for help or for a chat * Each member can create groups, invite friends and find online help through our chat rooms around topics such as Genomes, Nucleotide Sequences, Protein sequences, Databases, Gene Expression, Molecular Interactions, Reactions and Pathways, Ontologies, Sequence analysis & comparison, Patterns & Motifs, 3D Structures, Text and Data mining and more. * Each member can personnalize his homepage and create his own bioinformatics Blog since at BWW we want to consider our members more than email adresses. We hope that you find the site a useful resource and encourage you to join us and to ask your friends do the same. This site is made for you and will be enriched by you. Looking forward to see you in BWW. From ivanoe.defalco from na.icar.cnr.it Wed Apr 23 04:42:17 2008 From: ivanoe.defalco from na.icar.cnr.it (Ivanoe De Falco) Date: Wed Apr 23 11:50:51 2008 Subject: [Computational-biology] EvoStar 2009 - first Call for Papers Message-ID: <480F0479.8000507@na.icar.cnr.it> * Our apologies if you receive multiple copies of this announcement * --------------------------------------------------------------- F I R S T C A L L F O R P A P E R S --------------------------------------------------------------- EVO* 2009 including EuroGP, EvoCOP, EvoBIO and EvoWorkshops 15-17 April, 2009, T?bingen, Germany http://www.evostar.org --------------------------------------------------------------- The EuroGP, EvoCOP and EvoBIO conferences and the workshops collectively entitled EvoWorkshops compose EVO*: Europe's premier co-located events in the field of Evolutionary Computing. Featuring the latest in theoretical and applied research, EVO* topics include recent genetic programming challenges, evolutionary and other meta-heuristic approaches for combinatorial optimisation, evolutionary algorithms, machine learning and data mining techniques in the biosciences, in numerical optimisation, in music and art domains, in image analysis and signal processing, in hardware optimisation and in a wide range of applications to scientific, industrial, financial and other real-world problems. EuroGP: Twelfth European Conference on Genetic Programming: high quality papers are sought on topics strongly related to the evolution of computer programs, ranging from theoretical work to innovative applications. EvoCOP: Ninth European Conference on Evolutionary Computation in Combinatorial Optimisation: practical and theoretical contributions are invited, related to evolutionary computation techniques and other meta-heuristics for solving combinatorial optimisation problems. EvoBIO: Seventh European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics: the emphasis is on evolutionary computation and other advanced techniques addressing important problems in molecular biology, proteomics, genomics and genetics, that have been implemented and tested in simulations and on real-life datasets. EvoWorkshops: The twelve workshops which make up this event are focused on the use of Evolutionary Computation in different application areas: EvoCOMNET: Telecommunication networks and other connected systems EvoENVIRONMENT: Environmental issues EvoFIN: Finance and economics EvoGAMES: Games EvoHOT: Design automation EvoIASP: Image analysis and signal processing EvoINTERACTION: Interactive evolution and humanized computational intelligence EvoMUSART: Music, sound, art and design EvoNUM: Continuous parameter optimisation EvoPHD: Graduate student workshop on evolutionary computation EvoSTOC: Stochastic and dynamic environments EvoTRANSLOG: Transportation and logistics In 2009, the event will take place in T?bingen, a traditional university town in Baden-W?rttemberg, Germany, situated on a ridge between the Neckar and Ammer rivers in the southwest of the country, about 30 kms southwest of Stuttgart. The Eberhard Karls University of T?bingen was founded in 1477 and is one of the oldest universities in Germany. Important Dates for all events are: *** Submission deadline: 5 November 2008 *** Conference: 15-17 April 2009 Evo* 2009 proceedings will be published by Springer Verlag in the Lecture Notes in Computer Science series. The website http://www.evostar.org offers information relevant to all events, including calls for papers, deadlines, organising committees, submission requirements, local information and a thorough view on the previous editions. From stevet from bio.fsu.edu Wed Apr 23 12:41:04 2008 From: stevet from bio.fsu.edu (Steve Thompson) Date: Wed Apr 23 14:39:08 2008 Subject: [Computational-biology] Other: Accelrys petition followup Message-ID: <20080423114117.X29516@epsilon.bio.fsu.edu> Hi all - re. http://www.petitiononline.com/gcg/ A huge THANKS to all of you that signed my petition! Within the first week online I got almost 150 signatures, and John Devereux himself most recently signed it. I sent Rob Brown of Accelrys an 'official' copy of the petition and the signatures at the end of last month. However, but not surprisingly, I have yet to receive one word back from Accelrys. I realize that we can't force them to do anything, but I at least thought that they would have the courtesy to respond to it somehow. The petition did result in a news story though. GenomeWeb News' bioinformatics newsletter, BioInform, published the story on April 4th. See my copy at: http://bio.fsu.edu/~stevet/BioInformGCG.pdf Some may feel that the BioInform story suggests the petition was merely a means of influencing commercial negotiations with Accelrys regarding code release, and have nothing to do with public domain availability, but this was never my objective. It is and remains a plea not to kill the package, and in particular SeqLab, by whatever means possible, but preferably within some type of open source arrangement. Furthermore, Accelrys argues in the article that many more people have signed the petition than subscribe to the package, and that this somehow invalidates the petition. This is completely irrelevant as the GCG license has always been to an institution, allowing as many people in that institution access as wanted, not to individual investigators. Here at FSU I have supported over 100 GCG users with one GCG license over the years. June should be interesting for us all. We'll have to see if Accelrys honors their commitment to those of us with "perpetual" licenses to provide non-node-locked, non- expiring versions of the license after June 30, 2008. Time will tell. Cheers - Steve Steven M. Thompson A C T G stevet@bio.fsu.edu \-/ http://bio.fsu.edu/~stevet/cv.html /\ /--| FSU SCS / BioInfo 4U /---/ |--/ Florida State University School of \-/ Computational Science /\ /--\ 1st floor DIRAC 150G |---\ Tallahassee, Florida \---\ 32306-4120 \--| 850-644-4490 \-/ /\ 2538 Winnwood Circle /--\ Valdosta, Georgia /---| 31601-7953 |--/ 229-249-9751 From stevet from bio.fsu.edu Fri Apr 25 08:16:28 2008 From: stevet from bio.fsu.edu (Steve Thompson) Date: Fri Apr 25 10:31:44 2008 Subject: [Computational-biology] Other: followup to Accelrys petition followup Message-ID: <20080425085739.N36764@epsilon.bio.fsu.edu> Hello all - A brief note to let you know what's happened since my posting this last Wednesday: Rob Brown of Accelrys did contact me, finally. He says, and I quote: "The petition and the subsequent BioInform article produced a significant response and generated inquiries from a number of third party companies who now wish to discuss various possibilities relating to GCG with us. We are now in the process of following up on all of those which is taking some time." So, it looks like some good has come out of the process, although this doesn't look like the open source type of arrangement that many of us hoped for. Regardless, it may mean that the package will not be dying. And, Accelrys sent me my new non-node-locked, non-expiring license key! Cheers - Steve Steven M. Thompson A C T G stevet@bio.fsu.edu \-/ http://bio.fsu.edu/~stevet/cv.html /\ /--| FSU SCS / BioInfo 4U /---/ |--/ Florida State University School of \-/ Computational Science /\ /--\ 1st floor DIRAC 150G |---\ Tallahassee, Florida \---\ 32306-4120 \--| 850-644-4490 \-/ /\ 2538 Winnwood Circle /--\ Valdosta, Georgia /---| 31601-7953 |--/ 229-249-9751 From mpavone from dmi.unict.it Sat Apr 26 17:04:02 2008 From: mpavone from dmi.unict.it (Mario Pavone) Date: Sat Apr 26 19:21:16 2008 Subject: [Computational-biology] International Summer School of Functional Genomics, July 5-19, 2008 - Registration Deadline: April 30th Message-ID: <20080427000402.h3y4npbpesw44ssk@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 Registration *Deadline*: April 30th, 2008 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 week: "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 April 30, 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 April 30, 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* April 30, 2008. Early payment due: before April 30, 2008. Late payment due after April 30, 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. 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 -- Dr. Mario Pavone (PhD) Assistant Professor Department of Mathematics and Computer Science University of Catania V.le A. Doria 6 - 95125 Catania, Italy tel: 0039 095 7383038 fax: 0039 095 330094 Email: mpavone@dmi.unict.it http://www.dmi.unict.it/mpavone ------------------------------------------------ ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From stevet from bio.fsu.edu Sun Apr 27 19:08:49 2008 From: stevet from bio.fsu.edu (Steve Thompson) Date: Sun Apr 27 19:51:38 2008 Subject: [Computational-biology] Other: another followup (apology) Message-ID: <20080427200719.B51990@epsilon.bio.fsu.edu> Hi all - I would like to offer my apology to Accelrys and its employees for suggesting that the company would not follow through on their commitment to supply non-node-locked, non-expiring license keys to all current GCG custyomers with "perpetual" licenses. As I mentioned in my last posting Accelrys is now involved in that process and I have received my new key. It was never my intent to discredit Accelrys, nor its employess. I merely had not been informed that the process was underway. I am sorry that I miswrote and hope that any hard feelings can be overcome. Thank you. Cheers - Steve Steven M. Thompson A C T G stevet@bio.fsu.edu \-/ http://bio.fsu.edu/~stevet/cv.html /\ /--| FSU SCS / BioInfo 4U /---/ |--/ Florida State University School of \-/ Computational Science /\ /--\ 1st floor DIRAC 150G |---\ Tallahassee, Florida \---\ 32306-4120 \--| 850-644-4490 \-/ /\ 2538 Winnwood Circle /--\ Valdosta, Georgia /---| 31601-7953 |--/ 229-249-9751 From lvannesc from disco.unimib.it Mon Apr 28 02:39:55 2008 From: lvannesc from disco.unimib.it (Vanneschi Leonardo) Date: Tue Apr 29 11:42:19 2008 Subject: [Computational-biology] =?iso-8859-1?q?ANNOUNCEMENT=3A_European_?= =?iso-8859-1?q?Conference_on_Genetic_Programming=2C_EUROGP_2009=2C?= =?iso-8859-1?q?_T=FCbingen=2C_Germany=2C_April_15-17=2C_2009?= Message-ID: <301E01E95DB8684CAFA9EC28E1032FF215E85C@disco-exchange.disco.local> -------------------------------------------------------------------------------------------------------- EuroGP 2009 12th European Conference on Genetic Programming T?bingen, Germany, April 15-17 2009 -------------------------------------------------------------------------------------------------------- EuroGP 2009 will take place in conjunction with EvoCOP 2009 (9th European Conference on Evolutionary Computation in Combinatorial Optimization), EvoBIO 2009 (7th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics), and EvoWorkshops 2009 (the specialist workshops on a range of evolutionary computation topics and applications), forming a joint event collectively intituled EvoStar. EuroGP 2009 important dates are: ********* Submission deadline: November 5, 2008 *********************** Conference: April 15-17, 2009 All information about these events can be found at the page: http://www.evostar.org Topics include but are not limited to: * Theoretical developments * Empirical studies of GP performance and behavior * Algorithms, representations and operators * Applications of GP to real-life problems * Hybrid architectures including GP components * Unconventional evolvable computation * Evolutionary design * Evolutionary robotics * Grammar-based GP * Evolvable hardware * Linear GP * Self-reproducing programs * Evolution of tree or graph structures * Evolution of various classes of automata or machines (e.g. cellular automata, finite state machines, pushdown automata, Turing machines) * Object-oriented genetic programming EuroGP 2009 Program Chairs Leonardo Vanneschi, University of Milano-Bicocca, Italy vanneschi(at)disco(dot)unimib(dot)it Steven Gustafson, General Electric Global Research Center, Niskayuna, New York, USA steven(dot)gustafson(at)research(dot)ge(dot)com From ian.n.davidson from gmail.com Mon Apr 28 18:58:27 2008 From: ian.n.davidson from gmail.com (Ian Davidson) Date: Tue Apr 29 11:42:26 2008 Subject: [Computational-biology] CFP - Data Mining with Constraints Workshop - Colocated at KDD 2008 In-Reply-To: <9d1dd1270804280846nf2cf5cax255bbe5c80f1041a@mail.gmail.com> References: <9d1dd1270804280846nf2cf5cax255bbe5c80f1041a@mail.gmail.com> Message-ID: <9d1dd1270804281658o1a0bec62p7239b1815607069d@mail.gmail.com> Call For Papers --------------- Data Mining with Constraints 1/2 a day Workshop co-located with KDD 2008, Las Vegas Nevada www.constrained-clustering.org/KDDWS.html The purpose of data mining is to find novel and actionable patterns in data. However, in many domains there already exists considerable domain knowledge and the chance of finding patterns consistent with and novel with respect to this knowledge is small unless the algorithm is informed of it. The area of data mining with constraints codifies domain expertise and knowledge in the form of constraints and modifies the aim of data mining to find patterns that satisfy these constraints. This idea has actively been explored in the context of association rules, clustering and classification, with many papers being published in machine learning and data mining conferences. Tutorials been given on the topic at ECML/PKDD 2002, IEEE ICDM 2005 and KDD 2006, and several workshops have been held on the topic of constraint-based mining and inductive databases (cMILE 2007, KDID 2002-2006) next to the ECML/PKDD conference. This workshop has two aims: 1) Bring together people in different areas of data mining that make use of constraints, including people from the constrained clustering and inductive databases/queries communities 2) Actively explore the foundations and future of the area. A dinner or lunch will be organized to continue the discussion after the workshop. We invite papers describing novel research dealing with the use of constraints in data mining and related areas of interest, including but not limited to . Association rule mining with constraints . Clustering with constraints . Inductive databases and queries . Learning distance metrics from constraints . Learning predictive models with constraints In particular, we encourage the submission of well written position papers, and thought-provoking papers that would stimulate a discussion on the future of the field. Submissions should be made in the KDD 2008 paper format to both PC-chairs. If you are considering submitting to the workshop and need further information, please do not hesitate to contact the PC chairs. Key Dates: Submission: 05/27/08 Acceptance: 06/16/08 Camera Ready Copies: 06/20/08 Workshop Date: 08/24/08 PC Chairs - Ian Davidson (davidson@cs.ucdavis.edu ) and Saso Dzeroski (Saso.Dzeroski@ijs.si ) Please go to www.constrained-clustering.org/KDDWS.html for details.