- BBClist - maillist.psb.ugent.be

FW: Course offering - 2 and 3 July 2015 Disease causing mutation filtering and human connectome
by Alexander Botzki | VIB | 24 Jun '15

24 Jun '15

Dear all, On behalf of Adrian Liston, VIB KU Leuven: We kindly invite you to the seminar of Yuval Itan on July 1 at 11am (KUL, O&N4 auditorium): Finding a needle in a haystack: new approaches to identify disease-causing mutations in patients’ high-throughput sequencing data This seminar provides an insight into a new state-of-the-art gene-level metrics, tackling a crucial question in medicine genomics: how to identify the relevance of a mutated gene to a disease? We identified for the first time the biological distance between all human genes, as well as the accumulated mutational damage and mutation significance cutoff for each human gene. These gene-level approaches were shown to be particularly powerful for the identification of novel disease-causing genes in patients’ high-throughput data. The seminar is followed on July 2nd and 3rd by a practical tutorial on PC. Training 1: Disease causing mutations: filtering out disease-causing mutations Training 2: The human connectome: picking candidate genes for disease from all-exome analysis Trainer: Yuval Itan, Rockefeller University Date : Training 1: 2th July, 9am, ends 1pm Training 2: 3th July, 9am, ends 1pm Place : PC-LOKAAL ANATOMIE 2, ON2, 02.215 (KU Leuven) Host : Adrian.Liston(a)vib.be<mailto:Adrian.Liston@vib.be> Registration is free of charge, but places are limited, so register fast! https://docs.google.com/forms/d/1mYXe5dwh5WMPQn-hj_RRDxc5oEffR6fdfD0Nn1ZY4-… Best regards Alex

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Post-doc and PhD student positions available in the Bonvin lab@Utrecht University
by Alexandre Bonvin 22 Jun '15

22 Jun '15

Dear all I have a number of positions available in my group (bonvinlab.org) for two PhD students (for a four years period starting late 2015 and in 2016) and one post-doc (for a two year period in first instance, with a possibility of extension)(starting date fall 2015). These positions are funded by a number of European and Dutch research projects, related to our information-driven integrative modelling platform HADDOCK and involving various e-Infrastructure components in grid and cloud computing. The ideal candidates should have a good knowledge of structural biology and biomolecular modelling and possess some programming skills. Details of those positions have not yet been published, but some information on the projects can be found at: · http://bonvinlab.org/news/TOP-PUNT-NWO-proposal-granted · http:// bonvinlab.org /news/Two-new-H2020-projects-funded I would be grateful if you could disseminate and share this information with any suitable candidate. Interested candidates can contact me directly. All the best Alexandre --------------------------------------------------------------------------------------------------------------------------- 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 / 2652 | Fax: +31-30-2537623 Email: a.m.j.j.bonvin(a)uu.nl http://www.uu.nl/staff/AMJJBonvin | http://www.bonvinlab.org --------------------------------------------------------------------------------------------------------------------------- EU e-Infrastructure WeNMR project coordinator | http://www.wenmr.eu --------------------------------------------------------------------------------------------------------------------------- Chair GRC on Computational Aspects of Biomolecular NMR - Il Ciocco - June 7-12 2015 http://www.grc.org/programs.aspx?id=14571 ---------------------------------------------------------------------------------------------------------------------------

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position for bioinformatics lecturer/researcher in Groningen
by Noback MA, Michiel 22 Jun '15

22 Jun '15

please follow this link (in Dutch) for details on the position at the Hanze University of Applied Science: http://noorderlink.nl/participanten/hanzehogeschool-groningen/20022-0000001… Only one day left - sorry about that. Dr. M A. Noback | Bioinformatics senior lecturer & researcher | Institute for Life Science and Technology | Hanze University of Applied Sciences | Phone +31 50 5954691 | Postbus 3037 | 9701 DA Groningen | The Netherlands

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[Gtpb] Hands.on Training Course on Advanced Bioistatistics for Biologists
by Pedro Fernandes 19 Jun '15

19 Jun '15

Course Announcement / Reminder Applications are OPEN for the hands-on training course ABSTATB15 Advanced Biostatistics for Biologists IMPORTANT DATES for this Course Deadline for applications: July 10th 2015 Course dates: July 13th - July 17th 2015 with Lisete Sousa, Carina Silva and Pedro Fernandes Candidates with adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants. gtpb.igc.gulbenkian.pt/bicourses/ABSTATB15/ Course description: This course is a standalone advanced Biostatistics course that can be taken as a continuation of the Introductory Biostatistics for Bioinformatics (IBSTAT) course, that precedes it in GTPB. It is targeted for Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Participants can expect to attend a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods. Extensive hands-on practice will be the main vehicle for providing the skills and user independence. To keep things in context, the course is exclusively based on biological examples, worked with Bioinformatics tools. Care has been taken not to use any proprietary data or software, so that the hands-on experience can carry on after the course, providing maximum user independence. We will be using custom-built R scripts and packages that are available from the CRAN and Bioconductor repositories. Course duration: 5 days | Attendance fee: Euro 450.00 Thankyou for your interest, P. Fernandes -- Pedro Fernandes GTPB Coordinator 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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PhD POSITION ON BIOINFORMATIC METHODS FOR EPIGENOMICS (ULB, Brussels)
by Matthieu Defrance 17 Jun '15

17 Jun '15

PhD POSITION ON BIOINFORMATIC METHODS FOR EPIGENOMICS (ULB, Brussels) Job description: One PhD position on bioinformatic methods for epigenomics is available in the Laboratory of Cancer Epigenetics (Université Libre de Bruxelles, Belgium). The research goal is to develop new bioinformatic methodologies in order to analyze epigenetic changes (e.g. DNA methylation, histone modifications) that arise in cancers. Both fundamental and clinical aspects of the modifications will be addressed by analyzing high-throughput data generated using cutting edge next-generation sequencing platforms (available in the lab). The position is funded for 2 years, with a 2 years renewal. Screening of applications begins immediately and continues until an outstanding candidate is selected. PhD is expected to start in October 2015. Profile: The candidate should hold a master degree in bioinformatics, bio-engineering, biomedical sciences or eventually in engineering or computer sciences and demonstrate proficiency in statistics, algorithmics, programming (e.g R, python) and in software development. Experience with sequence data, genome-wide data sets (e.g ChIP-Seq, RNA-Seq, ...) or massive datasets analysis will be assets. The applicant should have good organizational skills, a taste for interdisciplinary research, excellent scientific writing and presenting skills and be able to work independently. How to apply? Applications should include a detailed CV (including grades and class ranking), a motivation letter, and names of two referees and should be sent to: Dr. Matthieu Defrance (matthieu.dc.defrance(a)ulb.ac.be) and Pr. François Fuks (ffuks(a)ulb.ac.be) Laboratory of Cancer Epigenetics, Faculty of Medicine, Free University of Brussels, 808 route de Lennik, Brussels, Belgium. Tel.: 32-2-555 62 45. Fax: 32-2-555 62 57. Selected publications: Viré et al. Nature 2006; Villa et al. Cancer Cell 2007; Dedeurwaerder, Defrance et al. EMBO Molecular Medicine. 2011; Dedeurwaerder*, Defrance* et al. Epigenomics 2011; Deplus et al., Cell Reports 2014; Bouhmadi et al., Nature 2014; Dedeurwaerder*, Defrance* et al. Briefings in Bioinformatics 2014.

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[Gtpb] GTPB Bioinformatics Training Course Announcement - Programming in Python
by Pedro Fernandes 15 Jun '15

15 Jun '15

ANNOUNCEMENT / REMINDER Dear Research Applications are open for BPBR15 Bioinformatics using Python for Biomedical Researchers with Allegra Via and Kaja Milanowska IMPORTANT DATES for this Course Deadline for applications: July 7th 2015 Latest notification of acceptance: July 10th 2015 Course date: July 20th - July 24th 2015 Details are available at: http://gtpb.igc.gulbenkian.pt/bicourses/BPBR15/ Course Description Python is an object-oriented programming language that is ideal for biological data analysis. The course will start from zero knowledge, and will introduce the participants to all the basic concepts of Python such as calculating, organizing data, reading and writing files, program logic and writing larger programs. All the examples and practical sessions will focus on solving biological problems. In particular the sessions will cover: working with DNA and protein sequences data retrieval from files and their manipulation running applications, such as BLAST, locally and from a script finding motifs in sequence parsing common file formats (Uniprot, GenBank, PDB, BLAST) with Biopython ways to find and correct program errors The course will be highly interactive and the students will continuously put theory into practice while learning. By the end of the course, the participants will have a good understanding of Python basics and will have acquired the skills to manage any type of bioinformatics database record and to run applications from scripts. Basic Unix/Linux skills will be provided at the beginning of the course. Target Audience End-users of bioinformatics databases and tools that aim at developing hands-on capabilities for biological data analysis, ie writing their own or adapting somebody else's Python scripts in an autonomous way. Course Pre-requisites Basic familiarity with bioinformatics data resources such as Uniprot/Swiss-Prot, Blast, ENSEMBL, PDB, etc. The course is directed to biologists with little or no programming experience and aims at making them capable to use Python to autonomously manage and analyse biological data. Thanks for your interest, Pedro -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Research mailing list Research(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/research ----- End forwarded message ----- _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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[Gtpb] GTPB Bioinformatics Training Course Announcement
by Pedro Fernandes 15 Jun '15

15 Jun '15

ANNOUNCEMENT / REMINDER Dear Research Applications are open for PGDH15 Population Genetics and Demographic History: model-based approaches with Mark Beaumont, Lounes Chikhi, Willy Rodriguez and Barbara Parreira IMPORTANT DATES for this Course Deadline for applications: June 28th 2015 Latest notification of acceptance: July 1st 2015 Course date: July 6th - July 9th 2015 Details are available at: http://gtpb.igc.gulbenkian.pt/bicourses/PGDH15/ Course description Genetic data are increasingly used by ecologists and evolutionary biologists in general. It has thus become important for many biologists with different levels of experience to produce and analyse genetic (and genomic) data. In this course we will take a practical approach to the analysis of genetic data, but we will also provide some of the theoretical background required to understand the outputs of the software used. This course will be organised so as to mix lectures where important notions are introduced with practicals where freely available software will be used. While this will not be the focus of the course, we will also introduce and discuss genealogical (coalescent-based) simulation methods and those based on forward-in-time simulations. Altogether this will allow to discuss the potentialities and limitations of the tools available to the community. In this four-day course we will introduce the main concepts that underlie many of the models that are frequently used in population genetics. We will focus on the importance of demographic history (e.g. effective sizes and migration patterns) in shaping genetic data. We will go through the basic notions that are central to population genetics, insisting particularly on the statistics used to measure genetic diversity and population differentiation. The course will also cover a short introduction to coalescent theory, Bayesian inference in population genetics and data simulation, as they are connected to what makes landscape genetics today on the basis of multilocus data. We will also introduce two methods that have been recently developed to analyse genomic data. The PSMC of Li and Durbin reconstructs the demographic history of a species or population with the genome of a single individual. The Rehh package is an R implementation of the Extended Haplotype Homozygosity (EHH) test for selective sweeps and looks for signals of selection based on the analysis of genomic regions. Most theory will be put into practice in practical sessions, analyzing real and/or simulated datasets. In these sessions, we will look at measures of genetic diversity and differentiation and use methods to detect population structure as implemented in the program STRUCTURE and discuss related programs such as FastSTRUCTURE. We will learn how to perform coalescent simulations of genetic data (using SPAms and ms). Some exercises will make use of R scripts (R being a freely available statistical program). Basic R knowledge is a pre-requisite but we will provide a short introduction to R. The R statistical package is a very powerful tool to analyse data outputs from many population genetics software, and can also be used to simulate genetic data under simple demographic scenarios. Thanks for your interest, Pedro -- Pedro Fernandes GTPB Coordinator 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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job opening Bayer CropScience
by David De Vleesschauwer 15 Jun '15

15 Jun '15

Dear, We currently have a job opening at Bayer CropScience for a junior researcher skilled in programming (see attachment). Would it be possible to post this job ad on the BBClist website? Thank you very much. Best Regards / Vriendelijke Groeten / Cordialement / Freundliche Grüße David De Vleesschauwer, Phd Postdoctoral fellow - Lysine Nimbus [cid:image001.gif@01D06D24.C63CD4B0] Bayer CropScience NV- INNOVATION CENTER Trait Discovery Tel: +32 9 243 0734 Fax: +32 9 383 6731 E-mail: david.devleesschauwer(a)bayer.com<mailto:david.devleesschauwer@bayer.com> Web: http://www.bayercropscience.com<http://www.bayercropscience.com/> BTW en ondernemingsnummer: BE 0412 639 087 RPR Brussel ________________________________________________________________________ The information contained in this e-mail is for the exclusive use of the intended recipient(s) and may be confidential, proprietary, and/or legally privileged. Inadvertent disclosure of this message does not constitute a waiver of any privilege. If you receive this message in error, please do not directly or indirectly use, print, copy, forward, or disclose any part of this message. Please also delete this e-mail and all copies and notify the sender. Thank you. For alternate languages please go to http://bayerdisclaimer.bayerweb.com ________________________________________________________________________

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Data Visualization for Biology: a practical workshop on design, techniques and tools 23-27 November 2015
by Alexander Botzki | VIB | 12 Jun '15

12 Jun '15

Web Version<http://trainingvib.cmail2.com/t/r-e-atdelt-dlhhdihde-r/> | Update preferences<http://trainingvib.updatemyprofile.com/r-atdelt-67B0562B-dlhhdihde-y> | Unsubscribe<http://trainingvib.cmail2.com/t/r-u-atdelt-dlhhdihde-j/> [Forward icon]<http://trainingvib.forwardtomyfriend.com/r-dlhhdihde-67B0562B-atdelt-l-t> Forward<http://trainingvib.forwardtomyfriend.com/r-dlhhdihde-67B0562B-atdelt-l-i> Data Visualization for Biology: a practical workshop on design, techniques and tools We would like to invite you to 'Data Visualization for Biology: a practical workshop on design, techniques and tools' - a workshop jointly organized by KU Leuven ESAT/STADIUS, EMBL-EBI and VIB, taking place in Leuven from 23 to 27 November 2015. As biological datasets increase in size and complexity, we are moving more and more from an hypothesis-driven research paradigm to a data-driven one. As a result, exploration of that data has become even more crucial than in the past. In this 5-day workshop, we will dive into the topic of biological data visualization and how it can be used to gain insight in and get a "feel" for a dataset, so that targeted analyses can be defined. We will start by covering theoretical questions like: What is data visualization? How do we perceive images? How can we visualise data in the best possible way? As the workshop continues, it will become more and more hands-on and interactive; a large part will be committed to creating visualisations using the D3 javascript library, including 2-day projects creating interactive visualisations based on data brought by the students themselves. Confirmed speakers and instructors: · Jan Aerts (KU Leuven ESAT/STADIUS, Belgium) · Eamonn Maguire (University of Oxford, UK) · Francis Rowland (EMBL-EBI, UK) · Marc Streit (Johannes Kepler University Linz, Austria) · Herwig Van Marck (VIB BioInformatics Training and Service facility, Belgium) Have a look at the training website<http://trainingvib.cmail2.com/t/r-l-atdelt-dlhhdihde-x/> and sign up to join us from 23 to 27 November 2015 in Leuven (KU Leuven ESAT/STADIUS). Please get in touch, if you need further information. Best regards, Alexander VIB BITS, on behalf of the organizers

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bioinformatics openings @ IMGT
by Sofia KOSSIDA 05 Jun '15

05 Jun '15

Bioinformatics / Immunnoinformatics positions @ IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org, in Montpellier, France IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org, is the global reference in immunogenetics and immunoinformatics, created in 1989 by Marie-Paule Lefranc (Université de Montpellier<http://www.umontpellier.fr/> and CNRS<http://www.cnrs.fr>). IMGT® is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MH superfamily (MhSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates. IMGT® provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT® works in close collaboration with EBI<http://www.ebi.ac.uk/> (Europe), DDBJ<http://arsa.ddbj.nig.ac.jp/top-e.html> (Japan) and NCBI<http://www.ncbi.nlm.nih.gov/gene> (USA). IMGT® consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools. IMGT® is located within IGH, http://www.igh.cnrs.fr , in Montpellier, France and close to the University of Montpellier. The successful applicants will join a multidisciplinary team, working with biologists, chemists, engineers and bioinformatics scientists, independently and as team players. We are looking to recruit: 1. A computer scientist with proven programming capability. Good knowledge of Java is required. Knowledge of R is a plus. 2. A biocurator with knowledge of molecular biology and usage of bioinformatics tools. Knowledge of immunology is a plus. 3. A bioinformatician with programming capability and usage of bioinformatics tools. Good team player and oral communication skills are required for all the positions. A Master's degree is a plus but not required. An initial contract of 2 years with possible extension of 1 plus 1 year, 4 years in total maximum is offered for all the positions. The positions remain open up until they are filled. For more information please contact: sofia.kossida(a)igh.cnrs.fr<mailto:sofia.kossida@igh.cnrs.fr> or marie-paule.lefranc(a)igh.cnrs.fr<mailto:marie-paule.lefranc@igh.cnrs.fr>

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