February 2013 - BBClist - maillist.psb.ugent.be

Reminder: Metagenomics Satellite Track at the NBIC 2013 conference
by Sacha van Hijum 26 Feb '13

26 Feb '13

The Netherlands Metagenomics Platform cordially invites you to join the Metagenomics Satellite Track at the NBIC 2013 on April 17, 2013 in Lunteren, the Netherlands. Jeroen Raes of the Flemish Bioinformatics Institute and the Free University of Brussels will be present at this satellite meeting and will also give a keynote lecture during the NBIC2013 programme. Abstracts are solicited in any field related to metagenomics or computational analysis of microbial ecosystems. Topics include: - All areas of environmental sequencing (e.g. amplicon sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics) - Prokaryotic, eukaryotic or viral systems - Sequencing strategies and technologies - Quality control, data pre-treatment - Read mapping, taxonomic and functional annotation - Comparative metagenomics - Metagenome assembly - Discovery of novel species, enzymes - Monitoring, public health surveillance - The tree of life, the rare biosphere - Microbial networks and ecosystem modeling - Host-microbe interactions (e.g. human, plants, corals) - Role of microbes in bioremediation, biogeochemical cycles - Visualisation To submit an abstract, please visit the abstract submission page: http://www.aanmelder.nl/nbic2013/wiki/Metagenomics%20satellite Please indicate that you are submitting your abstract for the Metagenomics Satellite track. -- Dr. Sacha van Hijum Group leader CMBI Bacterial Genomics Senior scientist bioinformatics NIZO food research B.V. Bioinformatics platform leader Top Institute Food and Nutrition T: +31(0)318 659 570 F: +31(0)318 650 400 M: +31(0)624782895 E: sacha.vanhijum(a)nizo.nl or svhijum(a)cmbi.ru.nl P.O. Box 20, 6710 BA EDE, The Netherlands Kernhemseweg 2, 6718 ZB EDE, The Netherlands

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Position for a Bioinformatician/Computational biologist in France
by Irene YUJNOVSKY 21 Feb '13

21 Feb '13

Position for a Bioinformatician/Computational biologist A position is open in the Gronemeyer laboratory at IGBMC for a bioinformatician to work in the analysis and integration of genome-wide biological data, develop bioinformatics tools and establish data analysis pipelines for High-Throughput Sequencing data (ChIP Seq, RNA Seq, ChIA-PET, etc). Candidates must be highly motivated to work on biological questions and flexible to interact with the various members of the laboratory. They should have a degree in computational biology, bioinformatics, statistics or equivalent level of knowledge. Candidates must be comfortable working in UNIX/Linux environments and possess excellent programming skills (R, perl, python, etc). Experience in web developing would be considered an advantage. Operating language in the laboratory is English. Applications including a cover letter, curriculum vitae and the names of two referees should be sent by March 15th to: Dr. Irene Yujnovsky at ireneyuj(a)igbmc.fr Information about the institute and the laboratory can be found at: http://www.igbmc.fr/research/department/2/team/21/ Information about the laboratory's bioinformatics expertise: http://archive.igbmc.fr/recherche/Prog_FGC/Eq_HGron/bioinfotools.html

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NBIC2013 – Call for abstracts
by Femke Francissen 21 Feb '13

21 Feb '13

Call for abstracts for the NBIC2013 NBIC2013 – the Netherlands Bioinformatics Conference 2013 Date: 16 & 17 April 2013 Venue: De Werelt, Lunteren, the Netherlands Website: http://www.aanmelder.nl/nbic2013 Call for abstracts You can submit an abstract for an oral presentation, a poster presentation and for a demo during the application showcase for the NBIC2013 programme. Note, there will be a specific session for Data & Technology. Abstracts can also be submitted for the two satellite meetings: the Metagenomics Satellite track and the NSBM Spring Meeting. Submit your abstract via the conference website: http://www.aanmelder.nl/nbic2013 Programme · 5 keynote speakers: Alexander van Oudenaarden, Janet Thornton, Uwe Sauer, Roeland van Ham and Jeroen Raes · Satellite meetings: Spring meeting of the Netherlands Society on Biomolecular Modelling (NSBM) & Metagenomics Satellite Track · Parallel sessions of contributed lectures · Parallel workshops · Poster presentations (NB: evening poster session!) · Industry meeting (BIUP) · RSG Retreat on April 15th Key dates · deadline for abstract submission: Monday March 4, 2013 · notification of selection for oral presentations: Friday March 22, 2013 · registration deadline: April 1, 2013 About The Netherlands Bioinformatics Conference 2013 (NBIC2013) is the 8th edition of the annual conference organized by the Netherlands Bioinformatics Centre (NBIC). NBIC2013 discusses the latest developments in bioinformatics and interrelated disciplines, and their wide-ranging applications in life sciences & health, agriculture, food & nutrition and industrial biotechnology. NBIC2013 offers a cross-disciplinary scientific program of (poster) presentations, application demonstrations and workshops, as well as other opportunities to exchange innovative ideas. More information Contact: Femke Francissen, e-mail: femke.francissen(a)nbic.nl<mailto:femke.francissen@nbic.nl>

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PHD Position in bacterial experimental and genomic evolution (University of Bern)
by josephine.daub＠iee.unibe.ch 18 Feb '13

18 Feb '13

=================================================== PhD position in bacterial experimental and genomic evolution =================================================== A PhD position is available for 3 years at the University of Berne to investigate the effect of range expansions on the genomic diversity and fitness of bacteria. Theoretical and simulation results suggest that spatially expanding populations should accumulate non-neutral mutations at a higher rate than stationary populations through the mechanism of gene surfing. The present research project aims at verifying these predictions in bacteria. We are looking for a highly motivated and talented PhD student to perform and analyse the output of a series of experiments with bacteria, measure their fitness at various stages of their expansions, analyse the evolution of their genome by Next Generation Sequencing, and study the effects of the accumulated mutations. These analyses will be done in close collaboration with Prof. Martin Ackermann in ETH Zurich. The candidate is expected to have some background in microbiology and a good grasp of evolutionary concepts. Additional knowledge in population genetics, bioinformatics and statistics (e.g. R) will be a plus. The gross starting salary is about 3,000 CHF per month (plus an additional 13th month) and will follow the Swiss NSF progression scale. The CMPG lab offers an international and very stimulating research environment. It is affiliated to the Swiss Institute of Bioinformatics and to several doctoral schools offering further education for PhD students. Berne is ideally located in the middle of Switzerland and Europe, and provides rich cultural and outdoor activities. Please send before February 28 2013, an application letter stating your motivation for the position, a CV, and contact information of two references to laurent.excoffier(a)iee.unibe.ch<mailto:laurent.excoffier@iee.unibe.ch>. Position starts in March 2013. For more information see our website: www.cmpg.iee.unibe.ch<http://www.cmpg.iee.unibe.ch>.

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[Gtpb] Bioinformatics Training Course Announcement / Reminder
by Pedro Fernandes 16 Feb '13

16 Feb '13

Dear all The GTPB in 2013 begins with its most popular course, that has been run more than 20 times with an evolving set of contents but maintaining its skeleton. The course aims at equipping the participants with basic skills to handle sequence data in order to analyse features and produce various types of inferences. The name Introductory Bioinformatics refers to the low level of pre-requisites, not to the level of difficulty. Indeed, the course is very intensive and becomes rather tough towards the end. Applications are no OPEN for the Bioinformatics Training Course IB13F Introductory Bioinformatics (first Course) IMPORTANT DATES for this Course Deadline for applications: February 20th Latest notification of acceptance: February 21st 2013 Course date: February 25th - March 1st 2013 http://gtpb.igc.gulbenkian.pt/bicourses/IB13F/ As each and every other GTPB course, IB13F provides practical hands-on skills that can be used with a high degree of independence. In this edition, due to a recent agreement, we will be using the Genious software package, on top of a huge amount of public domain software and data resources. This is due to a recent agreement with Biomatters Ltd. that supports us and offers a free 6 months commercial license for each participant to take home. Thank you Pedro Fernandes -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS 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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Bioinformatics Engineer, 36 months contract
by Macha Nikolski 15 Feb '13

15 Feb '13

Job Title : Bioinformatician Employer : SIRIC BRIO Location : Bordeaux, France Reporting to : FX. Mahon, M. Nikolski Job Family : Bioinformatics Engineer Duration of Post : 36 months Salary : dependent on qualification Main Purpose of Role ------------------------------- The Bordeaux SIRIC (Site de Recherche Intégrée sur le Cancer) BRIO is seeking a Bioinformatics Engineer to perform next generation sequence (NGS) data processing and analysis in a dynamic and exciting academic environment at the nexus of cancer biology, computer science, statistics and clinical research. The post holder will concentrate on one major SIRIC project at a time, but part of their activity will be dedicated to helping other groups in the SIRIC to solve short-term problems. The work will be performed in a small group atmosphere at the Bordeaux Bioinformatics Center CBiB (approx. 10 members) and the Bergonié Cancer Institute INSERM labs. Analysis will be performed for the benefit of the SIRIC member labs. Key Duties and Responsibilities -------------------------------------------- The job holder will design, develop and operate computational pipelines for the analysis of next generation sequencing data derived from tumors. Work will include both large-scale projects and small custom jobs, and span a wide variety of analysis problems. - Development of pipelines to process NGS data (for example, for quality control, mapping, SNP and variant calling, and de novo assembly) using public and commercial software or through development of new software tools when appropriate. - Applying statistical and bioinformatics methods to analyse genomic data (for example, NGS data from DNAseq, RNAseq, CHiP-seq, methylation, exome experiments) - Accompany non-bioinformaticians in their data processing and analysis needs - Server administration and next generation data management Qualification ------------------ PhD or Master’s degree in computer science, bioinformatics, mathematics or a related field, and at least 2 years experience in Bioinformatics software development are required. - Strong computational/programming skills; including thorough experience with the following: Unix/Linux environment, Cluster computing (SGE, PBS, or LSF familiarity strongly desired), Next-generation analysis toolkits (e.g, BWA, GATK, samtools, etc.); - Experience in building and using databases (e.g. SQL); - Advanced skills in Perl and Python; - Good knowledge of C++, Java and R is preferred. The candidate should have prior experience of processing NGS data. Experience in constructing web based interfaces, and mathematical and statistical skills would be an advantage. Good communication skills are a must and proven command of English is essential. The post holder should be able to work independently and interact well within a team of geneticists, oncologists and biologists. Interactions with other SIRIC centers in France will be part of the job. How to apply ------------------ Please send a mail to Macha Nikolski (macha(a)labri.fr) and Francois Xavier Mahon (Francois-Xavier.Mahon(a)u-bordeaux2.fr) containing - your CV - a motivation letter - names of at least two scientists who have agreed to recommend you

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job vacancy
by Peters, Sander 14 Feb '13

14 Feb '13

Dear reader, I'd like to point your attention to a vacancy currently available at the Bioinformatics group of Plant Research International in Wageningen. The job description and details for application can be found here http://www.academictransfer.com/employer/WUR/vacancy/17297/lang/en/ Kind regards, Dr. ir. Sander Peters, Applied Bioinformatics, Department of Bioscience, Plant Research International<http://www.pri.wur.nl/UK/>, Wageningen University Research Centre<http://www.wur.nl/UK/>. Address: Building 107, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands. Tel: +31-317-481123 (office) E-mail: sander.peters(a)wur.nl<mailto:sander.peters@wur.nl> [LinkedIn]<http://www.linkedin.com/pub/sander-peters/b/660/837>

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Job opening bioinformatics researcher Groningen (NL)
by Warris S, Sven 13 Feb '13

13 Feb '13

Dear all, The Hanze University of Applied Sciences in Groningen is looking for a bioinformatics researcher: http://www.noorderlink.nl/vacatures/20022-0000000849 Job description: - Carry out and acquire research and consultancy assignments; - Function in project-driven research teams of different composition. Job requirements: - Recent training in the field of Bioinformatics (Bachelor, Master or PhD); - Relevant and visible expertise in a relevant field of bioinformatics; - Interest in eukaryotic genome analysis and affinity with that field; - The ability to participate and collaborate in multidisciplinary teams; - Result-oriented, entrepreneurial, stress resistant and flexible. Organization: The Institute for Life Science & Technology is one of the 18 schools of the Hanze University of Applied Sciences Groningen. It provides training in Medical Biology Laboratory (research and diagnostics), Bioinformatics, Chemistry and Chemical Technology. At present the Institute has about 500 students and 35 employees. The Institute has a growing research group (ALIFE). Teachers, researchers, students and lecturers in ALIFE collaborate closely together in a high quality research environment with well-equipped laboratories and fast computer networks. ALIFE conducts innovative applied research together with various (inter)national partners in the field of energy (Hanze EKC) and healthy ageing (with Hanze CaRES), including in applied bioinformatics (metagenomics, genome analysis). ALIFE participates in various projects, including Flexigas and the Carbohydrate Competence Center (CCC). Cooperation with the University of Groningen (RuG) and regional SME for education and research is of paramount importance. The new researcher will be part of the Bioinformatics team, led by the team leader. Kind regards, Sven Warris Hanze University of Applied Sciences, The Netherlands

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Job opening @ GIGA-University of Liège: Postdoctoral Bioinformatician
by Marilou Ramos Pamplona 08 Feb '13

08 Feb '13

Job opening @ GIGA-University of Liège: Postdoctoral Bioinformatician OPEN POSITION: POSTDOCTORAL BIOINFORMATICIAN LOCATION The Groupe Interdisciplinaire de Génoprotéomique Appliquée* (GIGA) is an interdisciplinary research cluster located within the University of Liège and the University Hospital CHU Sart Tilman campus. The GIGA has eight research themes, which include Cancers, Genetics and Bioinformatics, and nine technological platforms, notably the Genotranscriptomics platform which is equipped with high-throughput sequencing and genotyping facilities. The research environment consists of an international community of scientists, researchers, medical doctors, postdoctoral fellows and PhD students, with English as the main working language. *http://www.giga.ulg.ac.be/jcms/c_5015/en/home JOB DESCRIPTION We are inviting applications for a POSTDOCTORAL BIOINFORMATICIAN who will be responsible for the design and implementation of projects aimed at integrating Next Generation Sequencing (NGS) data in clinical settings. The work will focus on the analysis of high-throughput sequencing data for basic research and clinical applications with emphasis on cancers. The successful applicant will develop bioinformatic tools for genetic and genomic analyses of complex clinical datasets, utilizing own lab data and published datasets. The work will involve regular interactions with a multidisciplinary group including medical doctors, laboratory-based researchers, geneticists and external collaborators. The position will be supervised by principal investigators Profs Michel Georges and Jacques Boniver. The position is available immediately and will be for an initial period of two years with a possibility of extension. RESPONSIBILITIES • Analysis of NGS data including whole genome sequences, exome sequences and RNA-Seq, • Analysis of high-throughput data such as microarrays and SNP genotypes, • Application of bioinformatic tools for genetic and genomic analysis, • Design, construction and maintenance of databases, • Provide bioinformatic assistance to various team members. QUALIFICATIONS • PhD in bioinformatics, biostatistics, statistical genetics, genetics or related fields with a high level of bioinformatic courses, • Strong programming ability including unix/linux system, programming language (eg. Java or Perl) and relational database (eg. mySQL) skills, • Experience in the analysis of NGS data and/or use of bioinformatic tools for genetic and genomic analysis, • Experience in designing/constructing databases, • Background knowledge or strong interest to learn about genetics, cancers, inherited diseases and statistics, • Able to work both independently and as part of a group, • Good interpersonal skills enabling productive interactions with different types of people. APPLICATIONS Applications will be accepted until 15 April 2013. Please send your application documents, which includes a detailed CV with the names of 3 references, to the following email address «marilou.ramospamplona(a)ulg.ac.xn--be-efa and indicate «GIGA-Postdoctoral Bioinformatician» in the subject.

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[Gtpb] Bioinformatics Training Course Announcement / Reminder
by Pedro Fernandes 05 Feb '13

05 Feb '13

Dear all The GTPB in 2013 begins with its most popular course, that has been run more than 20 times with an evolving set of contents but maintaining its skeleton. The course aims at equipping the participants with basic skills to handle sequence data in order to analyse features and produce various types of inferences. The name Introductory Bioinformatics refers to the low level of pre-requisites, not to the level of difficulty. Indeed, the course is very intensive and becomes rather tough towards the end. Applications are no OPEN for the Bioinformatics Training Course IB13F Introductory Bioinformatics (first Course) IMPORTANT DATES for this Course Deadline for applications: February 20th Latest notification of acceptance: February 21st 2013 Course date: February 25th - March 1st 2013 http://gtpb.igc.gulbenkian.pt/bicourses/IB13F/ As each and every other GTPB course, IB13F provides practical hands-on skills that can be used with a high degree of independence. In this edition, due to a recent agreement, we will be using the Genious software package, on top of a huge amount of public domain software and data resources. This is due to a recent agreement with Biomatters Ltd. that supports us and offers a free 6 months commercial license for each participant to take home. Thank you Pedro Fernandes -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS 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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