- BBClist - maillist.psb.ugent.be

One year post-doc position available in computational structural biology
by Alexandre M.J.J. Bonvin 08 May '12

08 May '12

Post-doc position in computational structural biology Positions A one year post-doc position is available within the Computational Structural Biolgy group, part of the NMR group at the Bijvoet Center for Biomecular Research, Faculty of Science / Chemistry at Utrecht University. Description of the Research group Research within the computational structural biology group focuses on the development of reliable bioinformatics and computational approaches to predict, model and dissect biomolecular interactions at atomic level. For this, bioinformatics data, structural information and available biochemical or biophysical experimental data are combined to drive the modelling process. This is implemented and further developed in the widely used HADDOCK software for the modelling of biomolecular complexes (http://haddock.science.uu.nl) By following a holistic approach integrating various experimental information sources with computational structural biology methods we aim at obtaining a comprehensive description of the structural and dynamic landscape of complex biomolecular machines, adding the structural dimension to interaction networks and opening the route to systematic and genome-wide studies of biomolecular interactions. Job description You will be part of the team working on predicting, modelling and understanding biomolecular interactions. The successful candidate will be expected to work on the modelling and dissection of interaction pathways in order to add the structural dimension to them. The position is funded for one year, with as latest starting date September 1st, 2012. During that year the candidate is expected to apply for funding to extend his/her position. Qualifications You should have a Ph.D. degree in chemistry, physics, bioinformatics, computational biology or a related field. The successful candidate should (a) possess a strong research background in theory and modelling of biomolecular systems/structures, (b) have experience with Linux and programming skills (python is a plus), and (c) is expected to show initiative and be able to work independently. Salary The gross salary ranges between euros 2861,- and maximum euros 3193,- per month. Conditions of employment The candidate is offered a full-time position for one year. The salary is supplemented with a holiday bonus of 8% and an end-of-year bonus of 8,3% per year. In addition we offer: a pension scheme, a partially paid parental leave, flexible employment conditions. Conditions are based on the Collective Labour Agreement Dutch Universities. Application The deadline for applying is May 31st. Applicants should send their CV together with a motivation letter and contact information of two references to Dr. Alexandre M.J.J. Bonvin (see contact address below). --------------------------------------------------------------------------------------------------------------------------- Dr. Alexandre M.J.J Bonvin | Professor of Computational Structural Biology Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands Phone: +31-30-2533859 | Fax: +31-30-2537623 Email: a.m.j.j.bonvin(a)uu.nl | http://www.nmr.chem.uu.nl/~abonvin --------------------------------------------------------------------------------------------------------------------------- EU e-Infrastructure WeNMR project coordinator | www.wenmr.eu ---------------------------------------------------------------------------------------------------------------------------

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International Chemical Discovery and Design Course, 18-22 June 2012, Nijmegen, the Netherlands
by Celia van Gelder 08 May '12

08 May '12

International Chemical Discovery and Design Course June 18th-22nd 2012, the Computational Drug Discovery (CDD) Group of the Radboud University Nijmegen organizes a course about Chemical Design and Discovery, in cooperation with NBIC and the Netherlands eScience Center. This course covers the recent advances in discovery informatics, with a focus on the application of e-science to real life problems. Different scientific concepts and programs will be introduced and discussed, which are part of the modern drug, food supplement and ingredient discovery pipeline from target discovery & validation to lead discovery & optimization. The morning sessions will introduce key concepts related to the use of computers for chemical discovery in the pharmaceutical industry and other life science pursuits and will be of general interest to anybody in these or other chemistry fields. For the first time we were able to invite keynote speakers from the Netherlands and abroad. As experts in their field of research they will summarize the core message of the course in their presentations. The following speakers have accepted their invitation to give a keynote lecture: ·Dr. John Overington, Computational Chemical Biology, EMBL-EBI, Hinxton, UK ·Prof. Dr. Hugo Kubinyi, Former Head of Drug Design &Combinatorial Chemistry and Molecular Modelling, BASF AG, Ludwigshafen, Germany ·Dr. Ir. Fred van de Velde, NIZO food research BV, The Netherlands ·Prof. Dr. Peter Murray-Rust, Unilever Centre for Molecular Science Informatics, University of Cambridge, UK In the afternoon the hand-ons are targeted at fourth-year university students, PhD students and postdocs, that are interested in the field of computational target and drug discovery. A basic background in bioinformatics or computational chemistry is a prerequisite for attendance. Read more on the course website: http://www.cmbi.ru.nl/ICDD2012. You can also find registration information here. See the course flyer: http://www2.cmbi.ru.nl/site_media/CDD_course2012_flyer2_A4.pdf -- 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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Galaxy Tour de France 2012
by Dave Clements 30 Apr '12

30 Apr '12

Galaxy Tour de France 2012 Galaxy is going on tour in France during the last week of May. We will be holding workshops in Perpignan, Lyon, and Paris. Details are below. Galaxy is an open-source web-based framework for data integration and analysis in the life sciences (http://galaxyproject.org/) Galaxy is available as a free public web site, or as software that can be installed and run locally, or on the cloud. Workshop registration is free, but space is limited and registration for each workshop will be closed as each fills up. http://wiki.g2.bx.psu.edu/**Events/GalaxyTourDeFrance2012<http://wiki.g2.bx.psu.edu/Events/GalaxyTourDeFrance2012> 28 mai : Perpignan 30 Mai : Lyon 1 juin : Institut Curie Amphithéatre Constant Burg, 12 rue Lhomond, 75005 Paris, France Galaxy for Biologists 9:00-12:00 Basic concepts: interface, histories, workflows Analysis of NGS data: polymorphism discovery, ChIP-seq. RNA-seq Using your own instance on the Cloud Publishing supplemental results with Galaxy Pages Galaxy for Developers 14:00-17:00 Galaxy architecture Wrapping tools for Galaxy system, Galaxy Toolshed API Running Production Galaxy sites: Infrastructure, Job Scheduling, Data and User management -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Call for Registration: BeneLearn 2012
by Michael Rademaker 27 Apr '12

27 Apr '12

(Apologies for multiple postings) ------------------------------------------------------------------------ CALL FOR PARTICIPATION BENELEARN 2012 The 21st annual machine learning conference of Belgium and The Netherlands in combination with the PMLS (Predictive Modelling for the Life Sciences) workshop. http://www.benelearn2012.ugent.be May 24 and 25, 2012 Universiteit Gent, Belgium ------------------------------------------------------------------------ Scope BeneLearn is the annual machine learning conference of Belgium and The Netherlands. It serves as a forum for researchers to exchange ideas, present recent work, and foster collaboration in the broad field of Machine Learning and its applications. BeneLearn 2012 is organised by the KERMIT research unit at the Department of Mathematical Modelling, Statistics and Bioinformatics of Universiteit Gent (Ghent University). The conference and its satellite workshop will take place on May 24 and 25, 2012 in Ghent, Belgium. Program The two day program will include invited talks by Ricardo Silva (Department of Statistical Science/CSML, UCL (UK)), Peter Challenor (National Oceanography Centre (UK)) and Tijl De Bie (University of Bristol (UK)) and a satellite workshop on applications of predictive modelling in the life sciences. Next to the invited speakers, we have scheduled about 20 talks on recent machine learning research and applications, as well as a poster session presenting another 15 or so theoretical or practical achievements. Important dates Early bird registration deadline: May 8th Electronic registration deadline: May 21st Conference: May 24th - 25th, 2012 Information about registration costs, the venue, specific program details etc. can be found at: http://www.benelearn2012.ugent.be <http://www.benelearn2012.ugent.be/> Organising Committee Bernard De Baets, KERMIT UGent Bernard Manderick, VUB Willem Waegeman, KERMIT UGent Michael Rademaker, KERMIT UGent Contact: benelearn2012(a)ugent.be

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Postdoctoral position Australian National University
by Conrad Burden 26 Apr '12

26 Apr '12

Postdoctoral Fellow/ Research Fellow in Statistical and Mathematical Analyses of Biological Sequence Data. Australian National University, Canberra The Centre for Mathematics and its Applications at ANU is seeking to appoint a Postdoctoral Fellow (Level A) or Research Fellow (Level B). The successful applicant will have strong research interests and activities in Statistical and Mathematical Analyses of Sequence Data. The appointment will be located in the Bioinformation Science program of the Mathematical Sciences Institute and is solely a research position. The Australian Research Council under a grant awarded to Dr Conrad Burden will fund the position. This position is a fixed term appointment at either Academic Level A or Academic Level B. Appointment at Academic Level A will be for two (2) years and three (3) months. Appointment at Academic Level B will be for one (1) year and ten (10) months. Applicants should address the selection criteria found within the position description, in their online application. Details at http://jobs.anu.edu.au/PositionDetail.aspx?p=2676 For enquiries regarding this position please email conrad.burden(a)anu.edu.au or telephone 61-2-6125 0730. Note that the closing date for applications is 14 May 2012.

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Probabilistic Graphical Models (PGM2012) Third Call for Papers and deadline extension
by Manuel Gómez Olmedo 24 Apr '12

24 Apr '12

Probabilistic Graphical Models (PGM2012) Workshop Granada, Spain, 19-21 September 2012 (http://leo.ugr.es/pgm2012) The submission deadline has been extended to June 4th (abstract) and June 8th (full paper) (see list of important dates below) *Call for papers:* The aim of the workshop is to bring together people interested in probabilistic graphical models and provide a forum for discussion of the latest research developments in this field. The workshop is organized so as to facilitate discussions and collaboration among the participants also outside the workshop sessions. To facilitate the spreading of research results and promote interactions among the participants, parallel sessions will be avoided and the workshop will be organized around a single thread of plenary and posters sessions. We welcome theoretical and applied contributions related to the following topics: - Principles of Bayesian (belief) networks, chain graphs, decision networks, influence diagrams, and other probabilistic graphical models (PGMs). - Information processing in PGMs (exact and approximate inference). - Learning and data mining in the context of PGMs: machine learning approaches, statistical testing and search methods, MCMC simulation. - Exploitation of results from related disciplines for the construction of PGMs, e.g., statistics, information theory, optimization, decision making under uncertainty, multivariate statistical analysis. - Software systems based on PGMs. - Application of PGMs to real-world problems. We invite submissions that concern oneCHANGED or more of the above topics, or any other aspects related to probabilistic graphical models. Papers submitted for review should report on original, previously unpublished work. Each submitted paper will be reviewed by at least two reviewers. Submission procedure PGM 2012 requires electronic submission of papers according to the instructions found on the web page http://leo.ugr.es/pgm2012/author-instructions.php. The authors must prepare their papers according to the PGM proceedings format, and submit the full version of the papers by the deadline found below. The page limit is 8 pages, including figures and bibliography. The page for author instructions contains format information and provides access to style files and templates. Paper presentation Papers will be accepted for plenary or poster presentation. All accepted papers will be included in the proceedings (with ISBN), which will be made available at the workshop reception. At least one author of accepted papers is expected to attend the workshop. After the workshop, authors of selected papers will be invited to submit an extended version of their paper to appear in a special issue of a high quality journal. All of the submitted papers will undergo a full reviewing process. Important Dates Call for papers opened November 2011 *CHANGED*: Deadline for abstract submissions June 4, 23:59 GMT, 2012 *CHANGED*: Paper submissions June 8, 23:59 GMT, 2012 *CHANGED*: Notification of acceptance July 20, 2012 *CHANGED*: Final versions due August 24, 23:59 GMT, 2012 Welcoming reception September 18, 2012 Workshop dates September 19-21, 2012 -- Manuel Gomez Olmedo e-mail:mgomez@decsai.ugr.es Dpto. de Ciencias de la Computacion e Inteligencia Artificial E.T.S. Ingenierias Informatica y de Telecomunicacion Universidad de Granada Tel.: +34 958 246143 18071 - GRANADA (Spain) Fax: +34 958 243317

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Job openings for a bioinformatician and data manager at the University of Antwerp
by Anthony Liekens 24 Apr '12

24 Apr '12

Dear colleagues, We have two openings for support functions, a bioinformatician and a data manager, at the VIB Department of Molecular Genetics at the University of Antwerp. Please find the vacancies at the following URLs: http://www.vib.be/en/jobs/Pages/Bioinformaticus.aspx http://www.vib.be/en/jobs/Pages/Data-Manager.aspx Please be warned that applications close 30 April 2012! Sincerely, Anthony Liekens,- -- The contents of this email may be confidential and may be privileged. They are intended for the named addressee(s) only. If you are not the addressee, nor a person authorised to receive for the addressee, please do not copy, use or disclose the contents of this message. Kindly notify me immediately of this erroneous reception, and destroy the message.

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Postdoctoral Position in Computational Protein Design (Brussels/Belgium)
by Yves Dehouck 23 Apr '12

23 Apr '12

Postdoctoral Position in Computational Protein Design (Brussels/Belgium) A two-year Postdoctoral Position is available in the Genomic and Structural BioInformatics Unit of the Université Libre de Bruxelles (Brussels, Belgium), to work on the development of computational tools for the rational design of proteins with modified (thermal) stability, solubility, or activity. The position is open immediately. The starting date should be no later than October 2012. Competitive salary commensurate with experience is offered. The candidate should hold a PhD degree in bioinformatics, computational biology or in a related field, have an extensive experience in programming (preferably in C), a strong publication record, and a high motivation to carry out research in this area. The candidate should not have been domiciled in Belgium during the last two years. Candidates with a background in physics, mathematics, statistics, computer science or engineering, and with a strong desire to develop and apply rational and computational tools to problems of biological or medical interest are also encouraged to apply. Interested individuals should send an e-mail to Marianne Rooman (mrooman(a)ulb.ac.be) containing their CV, a cover letter, and contact information to two references. Review of the applications will start immediately, and continue until the position is filled.

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call for abstracts 'Regulatory Genomics Special Interest Group – RegGenSIG'
by Michiel Van Bel 23 Apr '12

23 Apr '12

Dear All, Note that the deadline for abstract submission of the 'Regulatory Genomics Special Interest Group – RegGenSIG' satellite meeting of ISMB is fastly approaching (April 27 for oral presentations and May 18 for poster presentations). RegGenSIG 2012 will include presentations and posters that cover the broad spectrum of topics important to regulatory genomics research, and a joint panel discussion with the Alternative Splicing SIG. RegGenSIG will bring together experts in experimental methods and computational methods to consider sequence-based reconstruction of regulatory networks and prediction of gene expression. Topics to be addressed in the SIG include the following ·inference of gene regulatory networks, ·utilization of information pertaining to epigenetics, chromatin structure, and histone modifications, ·determination of the roles of regulatory RNAs, ·prediction of transcriptional regulation from RNA-seq data and ChIP-seq data, ·pattern discovery in sequences, and ·sequence based modeling of gene expression. If you would still consider submitting an abstract please consult http://www.iscb.org/ismb2012-program/ismb2012-satellitemeetings#regulatory Looking forward seeing you at ISMB 2012 Best Regards, Finn Drabløs, Norwegian Univ. of Science and Technology, Norway Kathleen Marchal, Univ Ghent/K.U. Leuven, Belgium Isidore Rigoutsos, Thomas Jefferson University, USA Saurabh Sinha, University of Illinois, USA Lonnie R. Welch, Ohio University, USA

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Seventh Summer School on Advanced Statistics and Data Mining (Madrid, June 25th - July 6th, 2012)
by Rubén Armañanzas 12 Apr '12

12 Apr '12

Dear colleagues, The Technical University of Madrid (UPM) will once more organize the summer school on 'Advanced Statistics and Data Mining' in Madrid between June 25th and July 6th. This year's programme comprises 12 courses divided into 2 weeks. Attendees may register in each course independently. Early registration is now *OPEN*. Extended information on course programmes, price, venue, accommodation and transport is available at the school's website: http://www.dia.fi.upm.es/ASDM Best regards, -- The coordinators of the school. *List of courses and brief description* Week 1 (June 25th - June 29th, 2012) Course 1: Bayesian networks (15 h) Basics of Bayesian networks. Inference in Bayesian networks. Learning Bayesian networks from data. Course 2: Statistical inference (15 h) Introduction. Some basic statistical test. Multiple testing. Introduction to bootstrap methods. Introduction to Robust Statistics. Course 3: Supervised pattern recognition (15 h) Introduction. Assessing the performance of supervised classification algorithms. Preprocessing. Classification techniques. Combining multiple classifiers. Comparing supervised classification algorithms. Course 4: Multivariate data analysis (15 h) Introduction. Data Examination. Principal component analysis (PCA). Factor Analysis. Multidimensional Scaling (MDS). Correspondence analysis. Multivariate Analysis of Variance (MANOVA). Canonical correlation. Course 5: Neural networks (15 h) Introduction. Perceptrons. Training algorithms. Accelerating convergence. Useful tricks for MLPs. Deep networks. Course 6: Feature Subset Selection (15 h) Introduction. Filter approaches. Wrapper methods. Embedded methods. Drawbacks and future strands. Practical session. Week 2 (July 2nd - July 6th, 2012) Course 7: Time series analysis (15 h) Introduction. Probability models to time series. Regression and Fourier analysis. Forecasting and Data mining. Course 8: Hidden Markov Models (15 h) 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 9: Hot topics in intelligent data analysis (15 h) Multi-label and multi-dimensional classification. Advanced Bayesian classifiers. Advanced Clustering. Partially supervised classification with uncertain class labels. Directional statistics. Spatial point processes. Course 10: Unsupervised pattern recognition (15 h) Introduction. Prototype-based clustering. Density-based clustering. Graph-based clustering. Cluster evaluation. Miscellanea. Course 11: Support vector machines and kernel methods (15 h) Introduction. SVM models. SVM learning algorithms. Other kernel methods: Kernel PCA, Kernel FDA, Kernel K-means. Practical work. Course 12: Regression (15 h) 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.

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