August 2012 - BBClist - maillist.psb.ugent.be

Announcement Lorentz Center workshop @Snellius
by Blaisse, R.G. 09 Aug '12

09 Aug '12

Dear Sir/Madam, On behalf of James Glazier, Roeland Merks, Herbert Sauro and Maciej Swat, I would like to ask to send out the attached announcement regarding the workshop Modeling of Multicellular Development and Cancer: European CompuCell3DSBW Hands-on Workshop which will be held from 8-13 October 2012 at the Lorentz Center @Snellius in Leiden. Roeland Merks provided me with your e-mail address. The application deadline for the junior scientists is on 21 August 2012. I hope the provided document is useful for you. Please let me know if you need additional information or when you have any questions. Many thanks in advance! Best regards, Renee (ms) Renee Blaisse MSc Workshop Coordination Niels Bohrweg 2 2333 CA Leiden, Netherlands +31 (0)71 5278523 <mailto:blaisse@lorentzcenter.nl> blaisse(a)lorentzcenter.nl

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Vacancies at the Sequence Analysis Support Core at LUMC (Leiden, the Netherlands)
by Leon Mei 09 Aug '12

09 Aug '12

Dear colleagues, Here are a few vacancies at the new Sequence Analysis Support Core at Leiden University Medical Center. Department : Clinical Genetics Vacancy number : E.12.MB.25 Appointment : 32-36 hours per week Starting date : as soon as possible Educational requirements : HBO Maximum salary : according CLA for University Hospitals Closing date for applications : September 3, 2012 == The position == As a member of the LUMC’s Sequence Analysis Support Core, you will build software that helps medical laboratory specialists and biomedical researchers to analyze different types of next generation sequencing data, including DNA (re)sequencing, RNA sequencing, and ChIP-seq. Your first task will be to develop sequence data analysis pipelines for different genome diagnostic applications based on existing experience from the LUMC research groups. In the future, there is potential for you to grow towards a more service-oriented role where you will work closely with our end-users to deliver end-to-end software solution, including requirement studies, architecture design, implementation and deployment. You will be working closely with people with diverse backgrounds (medicine, biology, chemistry, bioinformatics, statistics, and computer science), who jointly focus on the study of genotype-phenotype relationships in humans. == The department == At the Leiden University Medical Centre (LUMC), we are continually seeking to improve the quality of healthcare. You will work within LUMC’s Department of Clinical Genetics and be a member of the above mentioned LUMC’s SASC facility. At the moment we are in the middle of the exciting transition in which whole exome and genome sequencing is being implemented into diagnostics in order to expand and improve personalized health-care. Our most important research question is how to relate all the DNA sequence variants we find to the health of a patient (phenotype), and to the understanding of disease mechanisms in particular in muscular dystrophies, migraine, metabolic syndrome and cancer. In addition we face stunning technological developments, continuously enhancing the amount of DNA sequence produced per day, but every time using new methods for which new analysis algorithms have to be developed. == Your profile == You hold a BSc or MSc degree in bioinformatics, computer science, or other related field. The candidate must have practical programming experience in some of the programming languages as PERL, R, Java, C/C++ or Python. You have solid experience in working with a Linux system and database systems. You are a dedicated and flexible team player with excellent communicative skills to work in between scientists from different fields. == We offer == You will be employed on the basis of a 32 to 36-hour week. The appointment is initially for one year but can be extended. Your salary will depend on your qualifications, experience and position and is according the Collective Labour Agreement for University Hospitals. The LUMC offers you advantageous working conditions. You are entitled to 8% holiday payments, a Christmas bonus, and a personal pension scheme at ABP. In addition you may join the favourable collective Health Insurance of the UMCs. Furthermore, the LUMC offers you excellent facilities in the field of education, child care and career advice, as well as regulations regarding absence, and other extras. You can read more about our working conditions and facilities on elsewhere on the website. More information You can find the extended vacancy text on www.lumc.nl/vacatures. For more information please contact Dr. Nienke van der Stoep, telephone +31 (0)71 526 9832 e-mail nvdstoep(a)lumc.nl or Dr. Jeroen F. J. Laros, telephone +31 (0) 71 5269504, email j.f.j.laros(a)lumc.nl or Dr. S.M. Kielbasa, telephone +31 (0) 71 5269720, email s.m.kielbasa(a)lumc.nl == Apply == Please go to: http://www.lumc.nl/home/0004/23583/80611011354221/1207300237105721?setlangu… Best regards, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nl Skype: leon_mei Mobile: +31 6 41709231

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TPNC 2012: 2nd call for posters
by GRLMC 04 Aug '12

04 Aug '12

The 1st International Conference on the Theory and Practice of Natural Computing (TPNC 2012) invites authors to submit poster presentations. TPNC 2012 will be held in Tarragona (Spain) on 2-4 October, 2012. See http://grammars.grlmc.com/tpnc2012/ Poster presentations are intended to enhance informal interactions with the conference participants, at the same time permitting in-depth discussion. TOPICS We encourage authors to submit presentations that discuss novel work in progress on: - nature-inspired models of computation, - synthesis of nature by means of computation, - nature-inspired materials, - information processing in nature, - applications of natural computing. Posters do not need to present final research results. Work that is being developed and may lead to new interesting ideas is welcome. KEY DATES Submission deadline: August 26, 2012 Notification of poster acceptance or rejection: September 2, 2012 SUBMISSION Please submit an abstract through: https://www.easychair.org/conferences/?conf=tpnc2012 The abstract should contain the title, author(s) and detailed affiliation, and should not exceed 500 words. PRESENTATION Posters will be allocated 10 minutes each in the programme for oral presentation. Moreover, they will remain hanging during the whole conference for discussion. PUBLICATION Posters will not be published in the LNCS proceedings volume of TPNC 2012. However, there will be a specific section in the LNCS proceedings volume of TPNC 2013 reserved for those accepted papers that derive from 2012 posters. REGISTRATION Authors of accepted posters have to register to the conference. Their registration fare, however, will be very reduced: 135 Euro (one third of the early fare for PhD students).

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WANTED: postdoc visual analytics in next-generation sequencing
by Jan Aerts 01 Aug '12

01 Aug '12

*Postdoctoral scientist - Genomic variation discovery through visual analytics* SymBioSys is a consortium of computational scientists and molecular biologists at the University of Leuven, Belgium focusing on how individual genomic variation leads to disease through cascading effects across biological networks (in specific types of constitutional disorders and cancers). We develop innovative computational strategies for next-generation sequencing and biological network analysis, with demonstrated impact on actual biological breakthroughs. The candidate will be a key player in the SymBioSys workpackage that focuses on genomic variation detection based on *next-generation sequencing data* (454, Illumina, PacBio) using a *visual analytics* approach (i.e. combining machine learning with interactive data visualization). This includes applying and improving existing algorithms and tools for the detection of *structural genomic variation* (insertions, deletions, inversions and translocations), as well as developing interactive data visualizations in order to investigate *parameter space* of these algorithms. These methods will be applied to specific genetic disorders in day-to-day collaboration with the human geneticists within the consortium. We offer a competitive package and a fun, dynamic environment with a top-notch consortium of young leading scientists in bioinformatics, human genetics and cancer. Our consortium offers a rare level of interdisciplinarity, from machine learning algorithms and data visualization to fundamental advances in molecular biology, to direct access to the clinic. The University of Leuven is one of Europe’s leading research universities, with English as the working language for research. Leuven lies just east of Brussels, at the heart of Europe. *Profile* The ideal candidate holds a PhD degree in bioinformatics/genomics and has good analytical, algorithmic and mathematical skills. Programming and data analysis experience is essential. Prior experience working with sequencing data, i.c. alignment of next-generation data, as well as genome-wide detection of genetic variation would be a distinct advantage. Experience in data visualization - e.g. using tools like D3 (http://d3js.org) or Processing (http://processing.org) - would also be considered a big plus. Good communication skills are important for this role. The candidate will collaborate closely with researchers across the consortium and contribute to the reporting of the project. Qualified candidates will be offered the opportunity to work semi-independently under the supervision of a senior investigator, mentor PhD students, and contribute to the acquisition of new funding. A three-year commitment is expected from the candidate. Preferred start date is November/December 2012. *Relevant publications* - Conrad D, Pinto D, Redon R, Feuk L, Gokumen O, Zhang Y, Aerts J, Andrews D, Barnes C, Campbell P et al. Origins and functional impact of copy number variation in the human genome. Nature 464:704-712 (2010) - Medvedev P, Stanciu M & Brudno M. Computational methods for discovering structural variation with next-generation sequencing. Nat Methods 6(11):S13-S20 (2009) - Nielsen CB, Cantor M, Dubchak I, Gordon D & Ting W. Visualizing genomes: techniques and challenges. Nat Methods 7:S5-S15 (2010) *Application* Please send in PDF: (1) a CV including education (with Grade Point Average, class rank, honors, etc.), research experience, and bibliography, (2) a one-page research statement, and (3) two references (with phone and email) to Dr Jan Aerts (jan.aerts(a)esat.kuleuven.be) cc Dr Yves Moreau ( yves.moreau(a)esat.kuleuven.be) and Ms Ida Tassens ( ida.tassens(a)esat.kuleuven.be) URL: http://www.kuleuven.be/bioinformatics/ ================================ Dr Jan Aerts Assistant Professor Faculty of Engineering - ESAT/SCD University of Leuven Kasteelpark Arenberg 10 bus 2446 3001 Leuven-Heverlee Tel: +32 16 321053 Fax: +32 16 321970

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