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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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Call for papers: Machine Learning in Systems Biology, Slovenia, 5-6 September
by Pierre Geurts 24 Apr '09

24 Apr '09

[apologies for multiple postings] ************************** Call for Papers ********************************* MLSB 09 Third International Workshop on Machine Learning in Systems Biology 5-6 September 2009, Ljubljana, Slovenia ****************************************************************************** http://mlsb09.ijs.si/ MOTIVATION Molecular biology and all the biomedical sciences are undergoing a true revolution as a result of the emergence and growing impact of a series of new disciplines/tools sharing the "-omics" suffix in their name. These include in particular genomics, transcriptomics, proteomics and metabolomics, devoted respectively to the examination of the entire systems of genes, transcripts, proteins and metabolites present in a given cell or tissue type. The availability of these new, highly effective tools for biological exploration is dramatically changing the way one performs research in at least two respects. First, the amount of available experimental data is not a limiting factor any more; on the contrary, there is a plethora of it. Given the research question, the challenge has shifted towards identifying the relevant pieces of information and making sense out of it (a "data mining" issue). Second, rather than focus on components in isolation, we can now try to understand how biological systems behave as a result of the integration and interaction between the individual components that one can now monitor simultaneously (so called "systems biology"). Taking advantage of this wealth of "genomic" information has become a conditio sine qua non for whoever ambitions to remain competitive in molecular biology and in the biomedical sciences in general. Machine learning naturally appears as one of the main drivers of progress in this context, where most of the targets of interest deal with complex structured objects: sequences, 2D and 3D structures or interaction networks. At the same time bioinformatics and systems biology have already induced significant new developments of general interest in machine learning, for example in the context of learning with structured data, graph inference, semi-supervised learning, system identification, and novel combinations of optimization and learning algorithms. OBJECTIVE The aim of this workshop is to contribute to the cross-fertilization between the research in machine learning methods and their applications to systems biology (i.e., complex biological and medical questions) by bringing together method developers and experimentalists. We encourage submissions bringing forward methods for discovering complex structures (e.g. interaction networks, molecule structures) and methods supporting genome-wide data analysis. LOCATION AND CO-LOCATION The workshop will take place 5-6 September 2009 at the Jozef Stefan Institute, Ljubljana, Slovenia. It will immediately precede ECML PKDD 2009, taking place 7-11 September 2009 in Bled, Slovenia (Bled is 30 miles from Ljubljana, transport will be organized). SUBMISSIONS INSTRUCTIONS For an oral presentation, please submit an extended abstract of maximum eight pages. Formatting instructions are available on the website of the workshop. Extended abstracts should be submitted online by 1 June 2009 via the Easychair submission system at http://www.easychair.org/conferences/?conf=mlsb09. The accepted submissions will be collected in the proceedings of the workshop. KEY DATES 01 June: deadline for submission of extended abstracts for oral presentation 03 July: notification for oral presentations 03 August: deadline for submission of abstracts for poster presentations 10 August: notification for posters & camera ready versions due 5-6 September: workshop TOPICS A non-exhaustive list of topics suitable for this workshop is given below: Methods Machine learning algorithms Bayesian methods Data integration/fusion Feature/subspace selection Clustering Biclustering/association rules Kernel methods Probabilistic inference Structured output prediction Systems identification Graph inference, completion, smoothing Semi-supervised learning Applications Sequence annotation Gene expression and post-transcriptional regulation Inference of gene regulation networks Gene prediction and whole genome association studies Metabolic pathway modeling Signaling networks Systems biology approaches to biomarker identification Rational drug design methods Metabolic reconstruction Protein function and structure prediction Protein-protein interaction networks Synthetic biology CONFIRMED INVITED SPEAKERS Ross D. King, Aberystwyth University, UK William Stafford Noble, University of Washington, USA MLSB09 PROGRAM CHAIRS Sašo Džeroski, Jozef Stefan Institute, Ljubljana, Slovenia Pierre Geurts, Department of EE and CS & GIGA-Research, University of Liège, Belgium Juho Rousu, Department of Computer Science, University of Helsinki, Finland SCIENTIFIC PROGRAM COMMITTEE Florence d'Alché-Buc, University of Evry, France Saso Dzeroski, Jozef Stefan Institute, Slovenia Paolo Frasconi, Università degli Studi di Firenze, Italy Cesare Furlanello, Fondazione Bruno Kessler, Trento, Italy Pierre Geurts, University of Liège, Belgium Mark Girolami, University of Glasgow, UK Dirk Husmeier, Biomathematics & Statistics Scotland, UK Samuel Kaski, Helsinki University of Technology, Finland Ross D. King, Aberystwyth University, UK Neil Lawrence, University of Manchester, UK Elena Marchiori, Vrije Universiteit Amsterdam, The Netherlands Yves Moreau, Katholieke Universiteit Leuven, Belgium William Stafford Noble, University of Washington, USA Gunnar Rätsch, FML, Max Planck Society, Tübingen Juho Rousu, University of Helsinki, Finland Céline Rouveirol, University of Paris XIII, France Yvan Saeys, University of Gent, Belgium Guido Sanguinetti, University of Sheffield, UK Ljupco Todorovski, University of Ljubljana, Slovenia Koji Tsuda, Max Planck Institute, Tuebingen Jean-Philippe Vert, Ecole des Mines, France Louis Wehenkel, University of Liège, Belgium Jean-Daniel Zucker, University of Paris XIII, France Blaz Zupan, University of Ljubljana, Slovenia LOCAL ORGANIZATION Ivica Slavkov, Dragi Kocev, Tina Anžič, Jozef Stefan Institute, Ljubljana, Slovenia

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Call for participation: Workshop on Feature Selection in Bioinformatics
by Pierre Geurts 22 Apr '09

22 Apr '09

[apologies for multiple postings] ************** Call for Participation ******************** FSBIO 09 Feature Selection in Bioinformatics Workshop May 25th, 2009 Ghent, Belgium http://www.psb.ugent.be/~yvsae/fsbio09/ ********************************************************* MOTIVATION Feature or variable selection is an important topic in Bioinformatics, Systems Biology, and related fields. Important advantages of feature selection in these fields include the ability to create better and more compact models, as well as gaining a better insight into the processes described by the data. This workshop focuses on recent challenges for feature selection in Bioinformatics, such as the design of feature selection algorithms that scale well to high-dimensional spaces, can deal with small sample sizes, design robust feature sets and are able to support interactions or dependencies between variables. PROGRAM 09.50h Welcome 10.00h Badih Ghattas, Institut de Mathématiques de Luminy, Marseille, France Comparing different strategies for variable selection in large dimensions 11.00h Carolin Strobl, Institut für Statistik, Ludwig-Maximilians- Universität München, Germany Unbiased measures of variable importance for random forests 12.00h Alexandros Kalousis, Department of Computer Science, University of Geneva, Switzerland Stability of Feature Selection Algorithms LOCATION Department of Plant Systems Biology Ghent University Technologiepark 927 B-9052 Gent (Zwijnaarde) Belgium REGISTRATION Registration to the workshop is free of charge. In order to register, send a mail with your name and contact details to yvan.saeys(a)psb.ugent.be ORGANIZATION Yvan Saeys, Bioinformatics and Evolutionary Genomics group, Ghent University, Belgium Pierre Geurts, Department of EE and CS & GIGA-Research, University of Liège, Belgium

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NBIC PhD-Course: Managing life science information
by Celia van Gelder 17 Apr '09

17 Apr '09

*NBIC PhD-Course: Managing life science information* Date: 25-29 May 2009 Location: Science Park, Amsterdam, the Netherlands Course Coordinator: Marco Roos, UvA. This course introduces modern techniques for the management of life science data and knowledge for bioinformatics applications. Students will gain insight into Semantic Web languages and tools, XML and XQuery, data integration, data warehouses, federated databases, (Taverna) workflows, and Web2.0. More information about the course can be found on the NBIC-website: http://www.nbic.nl/biowise/school/EduProg/InfoMan09/ . Please note: the course is free for PhD students working in a BioRange project. Others can participate as well when paying a course fee (see course information on website). This course is part of the Education Programme of the NBIC PhD School. The PhD School is an initiative of NBIC together with a number of universities to organize high level education and training for PhD-students in bioinformatics. More information about the latest developments of the NBIC PhD School can also be found on the NBIC website: http://www.nbic.nl/biowise/school/ . Best regards, Celia van Gelder Projectleader Education NBIC ------------ 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, celia.van.gelder(a)nbic.nl websites: www.cmbi.ru.nl, www.nbic.nl NBIC Office Phone: +31 (0)24 36 19500 E-mail: office(a)nbic.nl Netherlands Bioinformatics Centre 260 NBIC P.O. Box 9101 6500 HB Nijmegen Fax: +31 (0)24 36 19395

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Business Personality of the Year 2009 !
by benjdami＠bioxpr.be 09 Apr '09

09 Apr '09

Good day, Here is an unusual request on this mailing-list. My name in Benjamin Damien, manager of BioXpr (bioinformatics service company in Belgium) and one of the 10 finalists of the "business personality of the year" contest. This final step is the results of several rounds of selection and trials. For the last trial, I need to gather as much votes as possible on the website : http://www.bpy2009.be This kind of prize is usually given to more "casual" businesses (marketing, sales, fashion,...) and it would be great to see biotech (and bioinformatics) win that kind of contest for once. Moreover, the "winner" will be able to communicate in the media regularly in the next 12 months (tv and newspapers), and I plan to use this platform to promote entrepreneurship and the scientific/technical careers (biotech first of all, of course). So I need your help to win this trial (I'm in second position, and the votes are closing on sunday 12/04), and to vote on http://www.bpy2009.be Thanks for your help in advance, and best regards, Benjamin

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[Biomath-ned] Positions in biological modeling and simulation
by Roeland Merks 08 Apr '09

08 Apr '09

Positions in biological modeling and simulation in Amsterdam, The Netherlands Within the Netherlands Consortium for Systems Biology (NCSB), biologists, computer scientists, physicists and mathematicians of Dutch universities and research institutes have joint forces to develop innovative systems biology approaches for tackling challenging, multi-factorial biological problems related to human health, plant sciences, and white biotechnology. Computer modeling and simulation are central to this highly multidisciplinary effort. NCSB’s core modeling group Biomodeling and Biosystems Analysis at CWI, the Dutch national research institute for mathematics and computer science, develops innovative simulation approaches and coordinates modeling projects at the participating institutes. The Biomodeling and Biosystems Analysis group invites applications for the following positions: Postdoctoral researcher Modeling dynamics and evolution of hierarchically regulated, eukaryotic gene networks See: http://www.cwi.nl/en/node/1044 PhD student Cell-based modeling of blood vessel formation See http://www.cwi.nl/en/node/1045 Scientific programmer / PhD student Bringing modeling and simulation to the biologist’s lab bench See http://www.cwi.nl/en/node/1043 Requirements for all positions: - A scientific background in simulation and modeling: a degree in theoretical biology or computational physics, computational science, or equivalent experience - Able to communicate with scientists in biology and mathematics - Good programming skills in C++ or equivalent - Minimum academic degree: for postdoc, PhD; for PhD, M.Sc.; for programmer, B.Sc. Information For full description of these positions, see http://www.cwi.nl/en/ jobs. For more information about CWI, NISB, NCSB and the Biomodeling and Biosystems Analysis group, visit http://www.cwi.nl, http://www.sysbio.nl , and http://www.cwi.nl/~merks. Contact: Roeland Merks, CWI, Roeland.Merks(a)sysbio.nl, Tel. +31-20-5624117 Application deadline is May 1st, 2009. ----- Roeland M. H. Merks Netherlands Institute for Systems Biology (NISB) and Centrum Wiskunde & Informatica (CWI) Science Park 123, 1098 XG Amsterdam, The Netherlands Mailing address: P.O. Box 94079, 1090 GB Amsterdam CWI Office Room M136 Roeland.Merks(a)sysbio.nl / Roeland.Merks(a)cwi.nl http://www.cwi.nl/~merks Phone +31 20 592 4117 Fax +31 20 592 4199 _______________________________________________ Biomath-ned mailing list Biomath-ned(a)few.vu.nl http://mailman.few.vu.nl/mailman/listinfo/biomath-ned

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