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Fourth Summer school on Advanced Statistics and Data Mining (Madrid, July 6th-17th, 2009)
by Rubén Armañanzas 26 May '09

26 May '09

Dear colleagues, the Technical University of Madrid (UPM) organizes a summer school on "Advanced Statistics and Data Mining" in Madrid between July 6th and July 17th. The summer school comprises 18 courses divided in 2 weeks. Attendees may register in each course independently. Registration will be considered upon strict arrival order. For more information, please, visit http://www.dia.fi.upm.es/index.php?page=presentation&hl=es_ES Best regards. On behalf of the organizers, R. Armañanzas. *List of courses and brief description* Week 1 (July 6th - July 10th, 2009) Course 1: Bayesian networks (15 h). Practical sessions: Hugin, Elvira, Weka, LibB Bayesian networks basics. Inference in Bayesian networks. Learning Bayesian networks from data. Course 2: Multivariate data analysis (15 h). Practical sessions: MATLAB Introduction. Data Examination. Principal component analysis (PCA). Factor Analysis. Multidimensional Scaling (MDS). Correspondence analysis. Multivariate Analysis of Variance (MANOVA). Canonical correlation. Course 3: Dimensionality reduction (15 h). Practical sessions: MATLAB Introduction. Matrix factorization methods. Clustering methods. Projection methods. Applications. Course 4: Supervised pattern recognition (Classification) (15 h). Practical sessions: Weka Introduction. Assessing the Performance of Supervised Classification Algorithms. Classification techniques. Combining Classifiers. Comparing Supervised Classification Algorithms. Course 5: Introduction to MATLAB (15 h) Overview of the Matlab suite. Data structures and files. Programming in Matlab. Visualization tools. Some applications in pattern recognition. Course 6: Datamining: A practical perspective (15h). Practical sessions: MATLAB, R, Weka Introduction to Data Mining and Knowledge Discovery. Prediction in data mining. Classification. Association studies. Data mining in free-form texts: text mining. Course 7: Time series analysis (15 h). Practical sessions: MATLAB Introduction. Probability models to time series. Regression and Fourier analysis. Forecasting and Data mining. Course 8: Neural networks (15 h). Practical sessions: MATLAB Introduction to the biological models. Nomenclature. Perceptron networks. The Hebb rule. Foundations of multivariate optimization. Numerical optimization. Rule of Widrow-Hoff. Backpropagation algorithm. Practical data modelling with neural networks. Course 9: Introduction to SPSS (15 h) Introduction. Describing data. Statistical inference. Time series. Sampling. Classification and regression. Week 2 (July 13th - July 17th, 2009) Course 10: Regression (15 h). Practical sessions: SPSS Introduction. Simple Linear Regression Model. Measures of model adequacy. Multiple Linear Regression. Regression Diagnostics and model violations. Polynomial regression. Variable selection. Indicator variables as regressors. Logistic regression. Nonlinear Regression. Course 11: Practical Statistical Questions (15 h). Practical sessions: study of cases (without computer) I would like to know the intuitive definition and use of …: The basics. How do I collect the data? Experimental design. Now I have data, how do I extract information? Parameter estimation. Can I see any interesting association between two variables, two populations, …? How can I know if what I see is “true”? Hypothesis testing How many samples do I need for my test?: Sample size Can I deduce a model for my data? Other questions? Course 12: Missing data and outliers (15 h). Practical sessions: R Missing Data: Typology of missing data. Simple missing-data methods. Imputation Methods. Diagnostics and Overimputing. Outliers and robust statistics: Typology of outliers. Influence measures. Robust methods. Course 13: Hidden Markov Models (15 h). Practical sessions: HTK Introduction. Discrete Hidden Markov Models. Basic algorithms for Hidden Markov Models. Semicontinuous Hidden Markov Models. Continuous Hidden Markov Models. Unit selection and clustering. Speaker and Environment Adaptation for HMMs. Other applications of HMMs. Course 14: Statistical inference (15 h). Practical sessions: SPSS Introduction. Some basic statistical test. Multiple testing. Introduction to bootstrapping. Course 15: Features Subset Selection (15 h). Practical sessions: MATLAB, R, Weka Filter approaches. Wrapper methods. Embedded methods. Course 16: Introduction to R (15 h) An introductory R session. Data in R. Importing/Exporting data. Programming in R. R Graphics. Statistical Functions in R. Course 17: Unsupervised pattern recognition (clustering) (15 h). Practical sessions: MATLAB Introduction. Prototype-based clustering. Density-based clustering. Graph-based clustering. Cluster evaluation. Miscellanea. Course 18: Evolutionary computation (15 h). Practical sessions: MATLAB Genetic algorithms. Genetic programming. Robust and self-adapting intelligent systems. Introduction to Estimation of Distribution Algorithms. Improvements, extensions and applications of EDAs. Current research in EDAs.

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Reminder: Invitation VDI Technology Update
by Axio Systems 26 May '09

26 May '09

Open this mail in your browser: http://tools.emailgarage.com/Pub/jb8zBwAAAAA~/PT2g4LOWekagb5HE1l-ZgQ~~/Text… Technology Update: VDI May 28, 2009, MIRA Volkssterrenwacht http://tools.emailgarage.com/Pub/jb8zBwAAAAA~/D4Zru549AkquUNsVT9AaTw~~/Text…: May 28, 2009 Location: MIRA Volkssterrenwacht Abdijstraat 22, B-1850 Grimbergen Start Time: 13h00 Dear , Axio Systems and Sun Microsystems are pleased to invite you on our next half day Technology Update with focus on virtual desktop infrastructure (VDI). A virtual desktop infrastructure (VDI) provides greater efficiency and performance, centralized management, data protection, and better security. Please join us for an exclusive seminar on how you can make a 'Virtual Desktop Infrastructure' a 'Reality'. Agenda: 13h00: Registration 13h30: Welcome - Mr. Gert Van der Jeugt - Axio Systems 13h35: Sun Technology Update - Mr. Luc Opdebeeck - Sun Microsystems 13h50: The Sun VDI Solution: a technical overview - Mr. Jaap Romers - Sun Microsystems 15h00: Coffee Break 15h15: Desktop Virtualization: maximize the value of your virtualization strategy - Mr. Bert De Loose - VMware 16h15: Customer success story - Mr. Andy Barrett - Yuntaa 16h30: Guest Speaker: An infinate space trip with Frank De Winne - Mr. Philippe Mollet - Mira Volkssterrenwacht 17h00: Visit Mira Volkssterrenwacht 18h00: Drinks and Fingerfood Date: May 28, 2009, 13h00 -18h00 Location: Mira Volkssterrenwacht, Abdijstraat 22, B-1850 Grimbergen Don't miss this unique event and register now http://tools.emailgarage.com/Pub/jb8zBwAAAAA~/wGPmrDSi8E6eZLUu9fgdxA~~/Text… Please feel free to send this invitation to your colleagues as well. We are looking forward to meeting you there. Axio Systems NV • Neerhonderd 15 • B-9230 Wetteren • T. 09 365 45 45 • info(a)axio.be If you do not want to receive any emails on the products and services of Axio Systems, you can unsubscribe here http://tools.emailgarage.com/Pub/jb8zBwAAAAA~/CcqOeFV2qkWDOwcj2JKJvQ~~/Unsu…

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Positions, Bioinformatics for Proteomics, Utrecht University
by Dr. B. van Breukelen 25 May '09

25 May '09

The Biomolecular Mass Spectrometry and Proteomics Group (www.chem.uu.nl/bioms) at Utrecht University (www.uu.nl) is a state of the art laboratory at the core of the Netherlands Proteomics Centre (www.netherlandsproteomicscentre.nl) Our group has a focus on technology development, proteome research and quantitative proteomics, all together implementing a large variety of experimental approaches. With the development of high throughput approaches as well as an increase in data production a huge demand for solid bioinformatics has arisen. For our group we are looking for enthusiastic, Scientific programmers and PhD/PostDoc level bioinformaticians, who would like to work in a (small) group of bioinformaticians on building an automated mass spectrometry data analysis and processing pipeline. Within this project we are looking for people who can implement existing and novel algorithms and tools as well as bioinformaticians who would like to develop new approaches in data analysis for mass spectrometry. Our current projects have a focus on ad hoc bioinformatics (small projects to solve specific user/experimental challenges), de novo peptide/protein analysis, data (pre) processing, data annotation and quantitative proteomics approaches. Do you: Have a background in bioinformatics/biotechnology/proteomics Have Good knowledge/experience in programming (Java/Perl) Knowledge or Experience with databases (SQL) Knowledge or Experience with GRID computing Knowledge or Experience with Web services Are you flexible and a team player and do you like to work on several projects at the same time? Then we can offer you a 2 year position at our group (with the possibility of extending your contract for up to 4 years). For more information you can contact: Dr. Bas van Breukelen b.vanbreukelen(a)uu.nl +31(0)30 2539761 ======================= Dr. Ir. B. van Breukelen (PhD) Assist. Prof. (Bioinformatics) Biomolecular Mass Spectrometry and Proteomics Group. Utrecht University Padualaan 8, 3584 CH, Utrecht The Netherland. E: b.vanbreukelen(a)uu.nl T:+31(0)30 2539761 M:+31(0)6 24996046 bioms.science.uu.nl b.vanbreukelen (skype)

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positions in bioinformatics/metagenomics
by jeroen raes 19 May '09

19 May '09

Dear colleagues, friends, I have 3 job openings for enthusiastic PhD students and postdocs in my (new) lab (from sept 1st - see attachment) - would you be so kind to spread this in your group/lab/institute and/or forward it to potentially interested parties? Kind regards, Jeroen Raes ***************************************************************** Jeroen Raes, PhD EMBL - Computational Biology Unit (Bork group) http://www.embl.de/~raes/ *** New address from Sept 1st: *** VIB Dept of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Brussels, Belgium http://www.vib.be/Research/EN/Research+Departments/Department+of+Molecular+… jeroen.raes [at] gmail.com *****************************************************************

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Second Next-Generation Sequencing Users Meeting, July 7th 2009
by NBIC Office 19 May '09

19 May '09

Dear colleague, Last year the first Dutch Next-Generation Sequencing (NGS) users meeting in Utrecht was a great success with more than 80 attendees and a lively discussion on all the ins and outs of this revolutionary new technology that affects many field in biology and medicine. Therefore, we have decided to broaden the initiative and to organize a follow-up to the 2008 meeting, now with the aim to include colleagues from Belgium and Luxemburg. In close collaboration with NBIC we are now organizing the second Benelux (Belgium-Netherlands-Luxemburg) NGS users meeting. The meeting will be held on July 7th 2009, at the Beatrix Theater in Utrecht. At this one-day annual meeting we expect approximately 200 scientists involved/interested in NGS to meet and discuss developments in the field, with a strong focus on practical issues like protocols, bioinformatics issues etc. In addition, a number of plenary presentations will be given by leading scientists in the field of NGS. This users meeting aims to bring together all scientist in the Netherlands that are working with any of the next-generation sequencing platforms, to exchange experiences, identify complementary interests and common problems and to enhance interaction between individuals at all levels. The primary focus of this meeting is on user experiences and networking, rather than scientific breakthroughs. The symposium is free for anyone interested, although registration <http://h094.niob.knaw.nl/symposium/NGS/register.html> is required. You are invited to submit a brief abstract to qualify for selection for oral presentation in one of the dedicated parallel sessions. Please check the website (http://h094.niob.knaw.nl/symposium/NGS) for more details on the program, location, and registration. To express the breadth of the application scope, the meeting will be supported and co-organised by the leading genomics initiatives in the Netherlands, including the Netherlands Cancer Genomics Centre (CGC), The Centre for BioSystems Genomics, the Centre for Medical Systems Biology (CMSB) and the Kluyver Centre for Genomics of Industrial Fermentation, all research centres under the Netherlands Genomics Initiative (NGI: www.genomics.nl) Please forward this email to anyone who might be interested in this meeting. For more information, please contact Edwin Cuppen (e.cuppen(a)niob.knaw.nl) Marc van Driel (marc.van.driel(a)nbic.nl) or Joris Veltman (j.veltman(a)antrg.umcn.nl)  On behalf of the organizers: Dr. Marc van Driel Bioinformatics Coordinator NBIC ************************************** NBIC Office Phone: +31 (0)24 36 19500 E-mail: office(a)nbic.nl Website: www.nbic.nl Netherlands Bioinformatics Centre 260 NBIC P.O. Box 9101 6500 HB Nijmegen Fax: +31 (0)24 36 19395 Visiting address: Geert Grooteplein 28, Route 260 6525 GA Nijmegen

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Invitation: Ready made IT concepts for Life Sciences
by Axio Systems 19 May '09

19 May '09

Open this mail in your browser: http://tools.emailgarage.com/Pub/CGgZBwAAAAA~/Xzc2OV8cjkaG7kotlTslog~~/Text… Ready made IT Concepts for Life Sciences Axio Systems and partners Sun Microsystems, Oracle and VMware will present their latest trends for Life Sciences on a half day seminar. The 'Life Sciences' sector is facing some serious challenges such as decreased budgets, focus on the core business (R&D), increased time to delivery and suchlike. To meet all these business challenges, Axio Systems helps to further integrate science and technology with a powerful combination of specific solutions that saves time and lowers costs. Date: Thursday 4 June, 2009 Location: Archipel Business Center, Tramstraat 61, B-9052 Gent (Zwijnaarde) Time: 13h30 - 16h30 AGENDA: 13h30 Registration 14h00 Ready-made concepts for Life Sciences Mr. Gert Van der Jeugt - Axio Systems 14h15 Plug & Play Storage Mr. Jan Steurbaut - Sun Microsystems 14h45 Increase your business continuity: vCloud and VMotion Mr. Luc Gallet - VMware 15h15 Coffee Break 15h30 Oracle Database Options + One flew over Oracle Business Intelligence Mr. Yves Van Looy - Oracle 16h00 Work @Anywhere Mr. Philippe De Meyer - Axio Systems 16h15 Q & A 16h30 Closing drink More info and registration on http://tools.emailgarage.com/Pub/CGgZBwAAAAA~/NhCWfHc_Vkyqg44judfp4Q~~/Text…

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CWI Lectures in Mathematics and Computer Science: computational and mathematical biology
by Roeland Merks 19 May '09

19 May '09

CWI Lectures in Mathematics and Computer Science: computational and mathematical biology CWI, the Dutch national research center for mathematics and computer sciences, and the Netherlands Institute for Systems Biology (NISB) cordially invite you to the 2009 edition of the annual CWI Lectures in Mathematics and Computer Science. To celebrate the start of CWI's new research group "Life Sciences", this year's theme will be Computational and Mathematical Biology. The lectures feature Turing Award winner Richard Karp from the University of California at Berkely, and tumor modeling specialist Luigi Preziosi from the Politecnico di Torino. For registration and more information about the lectures and Life Sciences research at CWI, please visit: http://www.cwi.nl/CWILectures2009. For more information please contact Gunnar Klau (gunnar.klau(a)cwi.nl; 020-5924012) or Roeland Merks (roeland.merks(a)cwi.nl; 020-5924117). Date: June 4th, 2009 Location: Centrum Wiskunde & Informatica, Science Park 123, 1098 XG Amsterdam. Note: old address (same location): Kruislaan 403, 1098SJ The Science Park has a frequent bus connection from railway stations Amsterdam Amstel and Amsterdam Muiderpoort: line 40 or 240. It can also be reached on foot (15-20 mins) from Amsterdam Muiderpoort. Program: 09.30 Welcome with coffee 10.00 - 10.05 Introduction Jan Karel Lenstra (general director of CWI) 10.05 - 11.00 Richard Karp (UC Berkeley, USA): Combinatorial Methods in Computational Molecular Biology 11.00 - 11.30 Coffee break 11.30 - 12.15 Gunnar Klau (CWI, Amsterdam) : What does city heating have to do with lymph cancer? 12.15 - 14.00 Lunch 14.00 - 15.00 Luigi Preziosi (Politecnico di Torino, Italy): Modelling Cell Motion, Aggregation and Scattering 15.00 - 15.30 Coffee break 15.30 - 16.15 Roeland Merks (CWI Amsterdam): Culturing embryonic tissues in the computer 16.15 - 17.30 Closing drinks

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New book on Metaheuristics
by talbi 07 May '09

07 May '09

------------------New book -------------------- Title : "Metaheuristics: from design to implementation" Author: Prof. El-Ghazali Talbi (University of Lille, CNRS, INRIA) Wiley 2009 (624pp), http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470278587.html ISBN: 978-0-470-27858-1 ----------------------------------------------- Enclosed the table of contents ================================ A unified view of metaheuristics ================================ Abstract: This book provides a complete background on metaheuristics and shows readers how to design and implement powerful search algorithms to solve complex optimization problems across a diverse range of optimization problems in science and industry. It presents the main design questions for all families of metaheuristics (e.g. representations, neighborhoods, parameter tuning, constraint handling, performance evaluation). The key search components of metaheuristics are considered as a toolbox for: • Designing efficient single-solution based metaheuristics (e.g. local search, tabu search simulated annealing, GRASP, variable neighborhood search, iterative local search, guided local search). • Designing efficient population based metaheuristics (e.g. evolutionary algorithms, scatter search, particle swarm, ant colonies, bee colonies, artificial immune systems, EDA, differential evolution). • Designing efficient metaheuristics for multi-objective optimization. • Designing hybrid, parallel and distributed metaheuristics. • Implementing metaheuristics on sequential and parallel machines. It clearly illustrates how to implement algorithms to reuse both the design and code. With more than 200 illustrative examples using various case studies and treating design and implementation independently, this book gives readers the skills necessary to solve large-scale problems quickly and efficiently. It is a valuable reference for practicing engineers from diverse areas dealing with optimization; researchers and developers designing metaheuristics; and graduate or undergraduate students in business, management, computer science, operations research, engineering, and applied mathematics. More than 200 exercises are also provided. -- Prof. El-Ghazali TALBI University of Lille - INRIA - CNRS http: www.lifl.fr/~talbi ------------------New book -------------------- "Metaheuristics: from design to implementation" E-G. Talbi Wiley 2009 (600pp) ISBN: 978-0-470-27858-1 -----------------------------------------------

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Vacancy Hogeschool van Arnhem en Nijmegen
by Paffen I 07 May '09

07 May '09

Dear Madam/Dear Sir, Would you please be so kind to inform all your list members about this vacancy (see text below) at the HAN University (Hogeschool van Arnhem en Nijmegen, HAN). Kind regards, Hans Wanningen Recruiment Officer Hogeschool van Arnhem en Nijmegen (HAN) E: Personeelsadvertenties(a)han.nl<mailto:Personeelsadvertenties@han.nl> T: (024) 353 04 85 P: Postbus 30011, 6503 HN Nijmegen F: (024) 344 97 94 B: Heyendaalseweg 141 (kamer N 01.150) 6525 AJ Nijmegen; werkdagen: ma., di., wo., do.ochtend Vacancy: De Hogeschool van Arnhem en Nijmegen (HAN) zoekt ten behoeve van de Faculteit Techniek (FT) voor de campus in Nijmegen zo spoedig mogelijk een Docent Bio-informatica 0,8-1,0 fte Wat zijn uw werkzaamheden? U verzorgt onderwijs in de Nederlandse en Engelse taal voor alle studiejaren. U ontwikkelt nieuw competentiegericht onderwijs en past bestaand onderwijs aan. Ook begeleidt u leerprocessen (onder andere in de rol van tutor en expert) en stages en afstudeeropdrachten, zowel nationaal als internationaal. U voert scholings- en onderzoeksactiviteiten uit voor externe relaties. Wat zijn uw kwaliteiten? U hebt: - een academisch denk- en werkniveau op het gebied van bio-informatica - kennis van en ervaring met moleculaire biologie - bij voorkeur deskundigheid in programmeren en/of chemie - affiniteit met onderwijs U bent: - communicatief en sociaal vaardig - enthousiast en flexibel - resultaatgericht - collegiaal Wat bieden wij u? Een interessante en afwisselende functie in een dynamische, informele werkomgeving. Aanstelling vindt plaats voor de duur van een jaar met uitzicht op een vast dienstverband. Afhankelijk van uw ervaring bedraagt het bruto maandsalaris maximaal € 4.203,83 (cao-hbo schaal 11) bij een fulltime aanstelling. Het salaris is exclusief 8% vakantietoeslag en 8,3% eindejaarsuitkering. Daarnaast biedt de HAN goede voorzieningen op het vlak van pensioen, ziektekosten, scholingsfaciliteiten, mobiliteit en betaald ouderschapsverlof. Wilt u meer informatie? Meer over de HAN vindt u op www.han.nl<http://www.han.nl/>. Voor meer informatie over deze functie kunt u contact opnemen met de heer C.W. van Verseveld, Directeur, T (024) 353 19 05. Hebt u belangstelling? Herkent u zich in bovenstaand profiel en voldoet u aan de eisen? Reageert u dan voor 20 mei 2009 door uw sollicitatiebrief met CV te sturen naar: Hogeschool van Arnhem en Nijmegen, Service Unit P&O, t.a.v. mevrouw E. Straalman, Postbus 5375, 6802 EJ Arnhem. U kunt ook solliciteren via e-mail: Edith.Straalman(a)han.nl<mailto:Edith.Straalman@han.nl> Wilt u daarbij vacaturenummer 09-068 vermelden? De sollicitatiegesprekken zullen plaatsvinden op 27 en 29 mei 2009. Waar gaat u werken? De Faculteit Techniek verzorgt de technische opleidingen van de HAN. Studenten volgen competentiegericht onderwijs in moderne werkvormen en in diverse trajecten, zoals in voltijd, deeltijd en duaal. Ze worden opgeleid tot gekwalificeerde bachelors/ingenieurs in het specifieke beroepenveld. Medewerkers van de Faculteit Techniek (FT) kunnen naast het leveren van een bijdrage aan het reguliere onderwijs, ook activiteiten verrichten voor post-hbo-, internationale en masteropleidingen, voor toegepaste onderzoeksopdrachten van én voor bedrijven en instellingen. Acquisitie naar aanleiding van deze advertentie wordt niet op prijs gesteld.

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International Computational Drug Discovery Course 2009
by Celia van Gelder 25 Apr '09

25 Apr '09

*International Computational Drug Discovery Course 2009 * June 29 – July 10, 2009 Nijmegen, the Netherlands From June 29 - July 10 2009, the Computational Drug Discovery (CDD) Group from the Centre of Molecular and Biomolecular Informatics (CMBI) will present the seventh annual Computational Drug Discovery Course. This course was developed by the CDD group together with the pharmaceutical company Schering-Plough (former Organon) and is supported by NBIC. The two-week course discusses recent advances in drug discovery informatics, with a focus on the application of e-science to real life problems. The course is targeted at MSc students, PhD students, and postdocs, who are interested in the field of computational target and drug discovery. For more information see the course website (http://www.cmbi.ru.nl/ICDD2009) -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)cmbi.ru.nl websites: www.cmbi.ru.nl, www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

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