May 2014 - BBClist - maillist.psb.ugent.be

From NGS to mutation to structural interpretation - Course 3-4 June Nijmegen, the Netherlands
by Celia.vanGelder＠radboudumc.nl 15 May '14

15 May '14

The effects of a mutation on protein structure and function >From NGS to mutation to structural interpretation Date: June 3-4, 2014 Location: CMBI, UMC Radboud, Nijmegen, the Netherlands Course teachers: Gert Vriend (CMBI), Hanka Venselaar (CMBI) Course website & registration: http://swift.cmbi.ru.nl/gv/NGS . More information: Celia.vanGelder(a)radboudumc.nl<mailto:Celia.vanGelder@radboudumc.nl> Course description Much research in NGS human DNA diagnostics labs is aimed at determining mutations causal for disease states. Many journals these days do no longer publish such studies unless accompanied from at least a computational prediction of what the mutation does to the protein in terms of its structure and function. This two day course aims at generating a level of understanding of the relation between protein structures, amino acids, and function. After the course the participants will be able to understand the output of compute servers that predict the structural and functional effects of mutations in proteins with known structure (or for which the structure can be predicted with homology modelling). The users will also be able to perform elementary visual inspections of protein structures with and without mutations using the YASARA software (that is free and runs on all computers). During the course we will work with the YASARA visualizer and the HOPE mutation effect prediction software (http://www.cmbi.ru.nl/hope/ ). The educational material and the seminars will be sufficiently general, though, to be applicable to other computational tools too. Target audience The course is meant for novices in the protein structure field. As prior knowledge we expect that people have some minimal knowledge about amino acids, have an idea about how to operate BLAST, and can use a browser. Course programme The course website, including the full course programme, can be found at : http://swift.cmbi.ru.nl/gv/NGS Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl<http://www.biosb.nl> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Bioinformatician position (Thomson-Reuters)
by Patrice Godard 14 May '14

14 May '14

Hi Thomson-Reuters is looking for a Bioinformatian in Europe. Here is the description of the position: http://jobs.thomsonreuters.com/job/London-Research-Scientist-2C-Bioinformat… Could you forward this job offer please? Many thanks Kind regards Patrice Godard

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[Gtpb] IBSTAT14 Introductory Biostatistics - REMINDER
by Pedro Fernandes 13 May '14

13 May '14

REMINDER GTPB Course Announcement IMPORTANT DATES for this Course Deadline for applications: May 15th 2014 Course date: June 2nd - June 6th 2014 This is one of our "Foundations" type courses, providing a systematic and detailed review of fundamental concepts and techniques in Biostatistics. Participants can expect to go through a set of exercises that are based on biomedical problems. These exercises are preceded by short lectures that are simple to follow. The lectures are designed to provide the conceptual framework that is needed to release the training power of the exercises, not to flood the participants with formality, which will be kept to a minimum. We will make use of a highly interactive methodology, taking advantage of our well equipped Bioinformatics training room. With this approach, we expect to bring the participants to a high degree of usage independence in using the methods that we cover. Main topics: Descriptive Statistics; Probability; Statistical Inference; Design of Experiments. More information, including instructions for applicants Thank you for your interest! Pedro Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt ----- End forwarded message ----- _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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SMLMC14 Structural Modeling for Large Macromolecular Complexes Course June 2014
by Barbara.vanKampen＠radboudumc.nl 13 May '14

13 May '14

SMLMC14 Structural Modeling for Large Macromolecular Complexes with Joanna Kasprzak and Grzegorz Chojnowski IMPORTANT DATES for this Course Deadline for applications: May 20th 2014 < New deadline Latest notification of acceptance: May 21st 2014 Course date: June 11th - June 13th 2014 This course is a quick and efficient way to acquire *skills* and *user-independence* in modeling of structures of proteins, RNA and their complexes. In particular we will train participants using PyRy3D, a modeling toolset for macromolecular complexes that can be used in a wide range of situations, using experimental data from X-ray diffraction, NMR, FRET, Cryo-EM, chemical cross-linking, etc. More details about the course at: http://gtpb.igc.gulbenkian.pt/bicourses/SMLMC14/ Please visit the PyRy3D website: http://genesilico.pl/pyry3d/ Here are some opinions issued by PyRy3D users: http://bit.ly/1hCoplC Thank you for your interest! Pedro Fernandes, SMLMC14 organiser GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt You receive this email as participant in the NSBM mailing list --- Barbara van Kampen Operational manager [Radboudumckleine.png] CMBI 260 Radboud university medical center / RIMLS CMBI Office / Room 0.02 PO Box 9101 Geert-Grooteplein 26-28 6500 HB Nijmegen 6525 GA Nijmegen Phone: +31(0)24 36 19390 Fax: +31 (0)24 36 19395 www.cmbi.ru.nl<http://www.cmbi.ru.nl/> Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Extended deadline META'2014
by El-ghazali Talbi 10 May '14

10 May '14

********************************************************************** META'2014 International Conference on Metaheuristics and Nature Inspired Computing 27-31 Oct 2014 Marrakech, Morocco http://meta2014.sciencesconf.org/ Extended deadline: 23 May 2014. ********************************************************************** The 5th International Conference on Metaheuristics and Nature Inspired Computing META'14 will held in Marrakech, Morocco from 27 to 31 Oct 2014. The Conference will be an exchange space thanks to the sessions, tutorials, workshops and a vocational training of metaheuristics and nature inspired computing. The scope of the META'2014 conference includes, but is not limited to: * Local search, tabu search, simulated annealing, VNS, ILS, ... * Evolutionary algorithms, swarm optimization, scatter search, ... * Emergent nature inspired algorithms: quantum computing, artificial immune systems, bee colony, DNA computing, ... * Parallel algorithms * Hybrid methods with machine learning, game theory, mathematical programming, constraint programming, co-evolutionary, ... * Application to: logistics and transportation, networks, scheduling, data mining, engineering design, energy, bio-medical, cloud, ... * Theory of metaheuristics, landscape analysis, convergence, problem difficulty, very large neighbourhoods, ... * Multi-objective optimization, bi-level optimization * Dynamic optimization, problems with uncertainty, ... * Parameter tuning (static, dynamic, adaptive, self-adaptive) * Software frameworks for metaheuristics and nature inspired computing Submission papers: _________________ - Submission of papers should be in shape of an abstract of two pages sent before the 23th May 2014 via the website. - Proceedings of the conference will be provided. Selected papers will be published in international journals (ISI journals). - Predefined styles are available on the website http://meta2014.sciencesconf.org/ - Proposals for invited sessions, workshops and tutorials: Deadline 26th April 2014. contact talbi(a)lifl.fr 4 tutorials and 35 special sessions are already organized. E-G. Talbi (Conference Chair) -- Prof. E-G. Talbi Univ. Lille, CNRS, INRIA META'2014 27-31 Oct 2014, Marrakech, Morocco http://meta2014.sciencesconf.org/

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[Gtpb] Structural Modeling for Large Macromolecular Complexes - SMLMC14 in Oeiras, Portugal
by Pedro Fernandes 09 May '14

09 May '14

Applications are open for another Bioinformatics Training course: SMLMC14 Structural Modeling for Large Macromolecular Complexes with Joanna Kasprzak and Grzegorz Chojnowski IMPORTANT DATES for this Course Deadline for applications: May 20th 2014 < New deadline Latest notification of acceptance: May 17th 2014 Course date: June 11th - June 13th 2014 This course is a quick and efficient way to acquire *skills* and *user-independence* in modeling of structures of proteins, RNA and their complexes. In particular we will train participants using PyRy3D, a modeling toolset for macromolecular complexes that can be used in a wide range of situations, using experimental data from X-ray diffraction, NMR, FRET, Cryo-EM, chemical cross-linking, etc. More details about the course at: http://gtpb.igc.gulbenkian.pt/bicourses/SMLMC14/ Please visit the PyRy3D wesite: http://genesilico.pl/pyry3d/ Here are some opinions issued by PyRy3D users: http://bit.ly/1hCoplC Thank you for your interest! Pedro Fernandes, SMLMC14 organiser GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Postdoc position at University of Liège
by Thomas Van Parys 09 May '14

09 May '14

Postdoc position: "Gene expression networks in the microalga Chlamydomonas" See attachment. -- ================================================================== Thomas Van Parys Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM thomas.vanparys(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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EISBM symposium 2014 - Lyon, 25
by Johann Pellet 08 May '14

08 May '14

============================================================= EISBM Symposium on Systems Medicine: Pioneers of Health and Wellness ============================================================= Dates: 25 June 2014 Location: Lyon, France Website: http://symposium.eisbm.org/ ----------------------------------------------------------------------------------- REGISTRATION Register online via http://symposium.eisbm.org/register.html The registration is free but mandatory. PROGRAM Session 1 - The Road from Systems Biology to Systems Medicine with the following speakers: Charles AUFFRAY, Ines THIELE, Vincent LOTTEAU Session 2 – Revolutionizing Healthcare and Wellness through P4 Medicine with the following speakers: Leroy HOOD, Jesper TEGNER Session 3 – Systems Medicine of Respiratory Diseases with the following speakers: Fan CHUNG, Antoine MAGNAN, Ab OSTERHAUS Theme 4 – Systems Medicine for Personalized Healthcare and Healthy Aging with the following speakers: Martine LAVILLE, Olaf DAMMANN, Manlio VINCIGUERRA ----------------------------------------------------------------------------------- ABOUT Come to Lyon to listen to the Pioneers of Health and Wellness and how they are triggering the advent of Participatory, Personalized, Predictive and Preventive (P4) Medicine. The 2014 EISBM Symposium will be a unique opportunity to discuss the formation of an International Network of Systems Medicine Centres and of an International Society of Systems Biomedicine. This is the third annual EISBM Symposium, following those organized in June 2012 on Knowledge Management for Translational Research and in June 2013 on the Philosophical and Engineering Foundations of Systems Biology. They gathered leading international experts and representatives of EU-FP7-funded consortia to review the state-of-the-art and the road map to foster the revolutionary transition from systems biology to systems medicine. This year the EISBM Symposium will highlight initial implementations of systems approaches in respiratory medicine and personalized healthcare and discuss the prospects for implementation of systems medicine in Horizon 2020. The initial results of the plans presented last year to perform extensive individual monitoring of lifestyle and environment exposures, biological and clinical features integrated with deep genomics assessments will be reported.

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ECCB 2014 Tutorial : Analysis of Cis-Regulatory Motifs from High-Throughput Sequence Sets
by Jacques van Helden 08 May '14

08 May '14

================================================================ ECCB 2014 Tutorial Analysis of Cis-Regulatory Motifs from High-Throughput Sequence Sets http://www.eccb14.org/program/tutorials/cis-r ================================================================ Date: Saturday Sept 6, 2014 Place: Forum building of the Faculty of Medicine of Strasbourg. Contact e-mail: mthomas(a)biologie.ens.fr ---------- Short description ---------- This tutorial aims at introducing the theoretical principles and giving practical skills to use specialized software tools to extract motifs from full-scaled NGS datasets (typically covering tens of Mb). --------- Teachers ---------- - Jacques van Helden, Aix-Marseille Université (France) - Morgane Thomas-Chollier, Ecole Normale Supérieure (France) - Carl Herrmann, University Heidelberg (Germany). - Alejandra Medina-Rivera, SickKids Research Institute, Toronto (Canada) ---------- Description ---------- Next Generation Sequencing led to the development of novel methods (ChIP-seq, FAIRE-seq, clip-seq, ) to acquire massive data about diverse signals involved in genome regulation and function (cis-regulation, chromatin conformation, RNA maturation, recombination, replication, …). Extracting relevant information from the raw data requires not only specialized software tools, but also a good understanding of their principles and parameters. In this tutorial we will demonstrate how to analyze ChIP-seq data using the Regulatory Sequence Analysis Tools (RSAT, http://www.rsat.eu/) via their different ways of access: web-interface, command-line, and web-services. This tutorial aims at introducing the theoretical principles and giving practical skills to use specialized software tools to extract motifs from full-scaled NGS datasets (typically covering tens of Mb). ---------- Contents ---------- The tutorial will be organized in 2 half days: 1) Analysis of cis-regulatory elements with the Regulatory Sequence Analysis Tools (RSAT): methods and website utilization (http://www.rsat.eu/) 2) Using RSAT in command-line and via web services (SOAP/WSDL). Topics: • Motif discovery in NGS peak sets. • Impact of the background models. • Comparison between motifs. • Motif enrichment in peak sequences. • Evaluating the quality of motifs extracted from NGS peaks. • Building control sets to estimate the rates of false positives. ---------- Topics not covered ---------- Other steps for the analysis of ChIP-seq data (e.g. read mapping, peak calling, functional enrichment of peaks, other tools for pattern discovery and matching). ---------- Target audience ---------- The course is addressed to bioinformaticians and biologists. The afternoon will require being familiar with the Unix shell (Linux) and basic programming skills (Perl or Python) to implement clients for web services. ---------- In practice ---------- * Participants will need to bring their own laptop * All command-line programs will be run on the IDB's cloud platform (https://idee-b.ibcp.fr/cloud.html) managed by Christophe Blanchet (IBCP, Lyon, France). Each participant will be given a (free) account to access this cloud and thereby a fully functional virtual machine with RSAT. * Wireless internet will be available at the conference venue. In the worse case, where the network would become unavailable during the day, we would still be able to give a demo on the teacher laptops. * An indicative reading list will be available a few weeks before the tutorial. * The hands-on will be organized in a cookbook mode: we will distribute protocols explaining the steps to solve selected test cases. * For the practicals, we ensure that there is no need to transfer data from the conference room to the servers. ================================================================ Jacques van Helden Jacques.van.Helden(a)ulb.ac.be http://www.bigre.ulb.ac.be/Users/jvanheld/ Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) Université Libre de Bruxelles, CP263 Boulevard du Triomphe, Accès 2, Campus Plaine. B-1050 Bruxelles, Belgium

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Structural Modeling for Large Macromolecular Complexes - SMLMC14 in Oeiras, Portugal
by Pedro Fernandes 08 May '14

08 May '14

Applications are open for another Bioinformatics Training course: SMLMC14 Structural Modeling for Large Macromolecular Complexes with Joanna Kasprzak and Grzegorz Chojnowski IMPORTANT DATES for this Course Deadline for applications: May 20th 2014 < New deadline Latest notification of acceptance: May 17th 2014 Course date: June 11th - June 13th 2014 For a reference about the use of the methodology: http://dx.doi.org/10.1016/j.ymeth.2013.09.014 *Computational modeling of proteinRNA complex structures* Irina Tuszynska, Dorota Matelska, Marcin Magnus, Grzegorz Chojnowski, Joanna M. Kasprzak, Lukasz P. Kozlowski, Stanislaw Dunin-Horkawicz, Janusz M. Bujnicki Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, PL-61-614 Poznan, Poland *********************************************************************** Course description One of the major challenges in structural biology is to determine the structures of macromolecular complexes and to understand their function and mechanism of action. However, structural characterisation of macromolecular assemblies is very difficult. To begin addressing this problem, we have developed PyRy3D. In a nutshell, PyRy3D employs a hybrid computational approach that incorporates spatial information from a variety of experimental methods into the modelling procedure to build low-resolution models of large macromolecular complexes. The PyRy3D model building procedure uses a Monte Carlo approach to sample the solutions-space. It uses spatial restraints to define components interacting with each other, and a simple scoring function is applied to pack them tightly into contours of the entire complex (e.g. cryoEM density maps). More details at http://gtpb.igc.gulbenkian.pt/bicourses/SMLMC14/ Thank you for your interest! Pedro Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt

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