- BBClist - maillist.psb.ugent.be

6 september: one-day symposium on machine learning, brain banks and health
by E.Marchiori＠cs.ru.nl 20 Aug '12

20 Aug '12

Dear Colleague, You are cordially invited to participate to the one-day symposium on the integrative analysis of brain diseases: program and abstracts are available at http://macbrain2012.cs.ru.nl/program Registration fee is 50, 25 for master and PhD students. It includes coffee breaks, lunch and drinks. Please register at http://macbrain2012.cs.ru.nl/registration. The registration can be also paid in cash on the same day. Kind regards, Elena Marchiori

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ECCB12: Workshop Bioinformatics Training for Life Scientists: Showcases and Challenges from tutors perspectives
by Celia van Gelder 15 Aug '12

15 Aug '12

Dear colleagues, We invite you to register to the*Workshop Bioinformatics Training for Life Scientists: Showcases and Challenges from tutorsÂ perspectives* taking place on 9 September, 2012, Basel Switzerland (as a Satellite event of the European Conference on Computational Biology ECCB'12). The exciting programme can be found at: http://www.eccb12.org/WS4 *Target Audience* - Experienced and beginner trainers - Researchers involved in training *Advantages in attending* Get inspiration for your own training Be acquainted with training methods that are effectively used by expert trainers Have the opportunity to connect to the network of trainers & organizers (BTN) Be recognized by and become part of the training community This workshop represents a platform where those involved in bioinformatics training to life scientists can meet, confront and share experiences, as well as discuss future directions and collaboration in joint efforts. By the way, send your questions and remarks to celia.van.gelder(a)nbic.nl <mailto:celia.van.gelder@nbic.nl> now, and we will have the pleasure to address them during the Panel discussion of the workshop. Register now at: http://www.eccb12.org/WS4 and forward this information to any one potentially interested. Looking forward to meeting you in Basel on 9 Sept! *The organisers * Patricia Palagi (SIB Swiss Institute of Bioinformatics) Vicky Schneider (European Bioinformatics Institute, EBI) Allegra Via (Dept of Physics, Sapienza University of Rome) Celia van Gelder (Netherlands Bioinformatics Centre, NBIC) -- ECCB'12 - European Conference on Computational Biology 2012 9-12 September 2012, Basel Switzerland http://eccb12.org ---- Stay informed: http://www.eccb12.org/info.html http://twitter.com/eccb12 http://www.facebook.com/eccb12

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NGS workshop Ghent, Belgium
by Michiel Van Bel 13 Aug '12

13 Aug '12

Dear, The Bioinformatics and Systems Biology division of the Department of Plant Systems Biology (VIB -- Ghent University, Belgium) is organizing a scientific event from the 25th of November 2012 until the 5th of December 2012 about *Generation and Analysis of Next Generation Sequence (NGS) data*. This two-week workshop is sponsored by the *European Science Foundation (ESF)*, and will discuss recent advances and future perspectives in next generation sequence analysis, together with the necessary applications on the data of user submitted projects. The workshop is open to participants from across Europe, and is *fully reimbursed* (see http://bioinformatics.psb.ugent.be/ngs_workshop/workshop/registration) through the ESF. Applicants will need to fill in a one page motivation letter which will allow us to identify individuals with suitable bioinformatics experience. The deadline to submit an application is August 15. Please visit http://bioinformatics.psb.ugent.be/ngs_workshop/ for more information. kind regards, The organizing commitee PS: Can this information also be spread to interested European colleagues not subscribed to the BBC-list?NGS workshop -- ================================================================== Michiel Van Bel PhD student 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 mibel(a)psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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(Associate) Scientist Bioinformatics @ DSM
by Roubos, Hans 10 Aug '12

10 Aug '12

Vacancy: (Associate) Scientist Bioinformatics @ DSM The Challenge As a member of the DBC Genetics Bioinformatics group, you will take part in multi-disciplinary project teams working on rational strain engineering, bioprocess development and novel bio-based products for food, feed, pharma and industrial biotechnology. Another important responsibility will be your participation in the organization, design and development of in-house data repositories and custom software. Specific duties may include database design, setting up analytical workflows, developing requirements for user interfaces, and participation in software testing. This will require effective communication and collaboration with end users, other bioinformatics experts and protein engineers. Depending on your experience, processing NGS, transcriptomics, proteomics and metabolomics data, or metabolic engineering and strain design, will be part of your activities. The Ideal We are looking for candidates with a minimum of 3 years bioinformatics experience, including thesis work, post-doctoral and/or professional experience. Expertise in NGS data analysis, integration of data from different "omics" assay types, and/or systems biology is preferred. The successful applicant will have a combined expertise on bioinformatics, computers and biology. Preferably, you are familiar with micro-organisms, HT screening and/or biotech processes. Hands-on experience with the organization and/or programming of software pipelines will be an advantage. You are a multidisciplinary team player, who takes initiative. Personal skills like problem analysis, judgment, creativity, leadership and adaptability characterize your identity. You are a good communicator. Further details: http://www.dsm.com/taleo-portal-component/en_US/cworld/index.do;jsessionid=… Hans Roubos, PhD Senior Scientist Bioinformatics DSM Biotechnology Center | Alexander Fleminglaan 1 | 2613 AX Delft | The Netherlands | T +31 15 2792147 | F +31 15 2793771 | hans.roubos(a)dsm.com | www.dsm.com | Trade Registration number 27235314 ________________________________ DISCLAIMER : This e-mail is for the intended recipient only If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

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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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[Gtpb] ARANGS12 - Bioinformatics Training Course anouncement
by Pedro Fernandes 31 Jul '12

31 Jul '12

ANNOUNCEMENT Here is a useful NGS analysis course suitable for a wide variety of researchers. The requirements are minimal. Participants will understand usage of NGS data analysis tools and will know how to chain them into very handy analytical pipelines. Plenty of worked examples and exercises in 4 days. NOTE: The application deadline is quite short, our excuses. We are using an unforeseen window of availabilities. It does matter to apply quickly, as the course dates are in early September. BIOINFORMARICS HANDS-ON TRAINING COURSE ARANGS12 - Automated and reproducible analysis of NGS data with Rutger Vos (Naturalis, Leiden, NL) and Darin London (Duke University, USA) IMPORTANT DATES for ARANGS12 Deadline for applications: August 27th 2012 Notification of acceptance dates: EARLY: August 15th 2012 (on special request, see Application) NORMAL: September 3rd 2012 Course date: September 11th - September 14th 2012 Course Description Next generation sequencing (NGS) technologies for DNA have resulted in a yet a bigger deluge of data. Researchers are learning that analysing such data sets is becoming the bottleneck in their work. In many cases, several steps in these analyses are fairly generic (e.g. quality control filtering, alignment to reference sequences, typing) so that off-the-shelf pipelines can be applied. In other cases, novel research approaches require development of new analysis pipelines. Either way, all analysis steps should be repeatable and any changes made to the data (e.g. renaming, annotation, alignment) should be recorded so that the provenance of the results is clear and inferences are reproducible. In this brief workshop we will establish several best practices of reproducibility and provenance recording in the (comparative) analysis of data obtained by NGS. In doing so we will encounter the commonly used technologies that enable these best practices by working through use cases that illustrate the underlying principles. Target audience This course is aimed at researchers who've recently embarked on NGS projects and now, faced with large amounts of data, would like to learn how to automate generic analysis steps and develop new ones in a reproducible (and shareable) way. The course will be illustrated with examples from specific single-celled and multicellular taxa but the concepts are applicable to any species not explicitly referred to in the course. The ideal attendee is a scientist who is not afraid to get his/her hands dirty to acquire the computer-literacy skills for dealing with the informatics side of data analysis. Futher details, including application instructions available at http://gtpb.igc.gulbenkian.pt/bicourses/ARANGS12 thank you for your interest Pedro Fernandes -- Pedro Fernandes GTPB Coordinator 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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PhD Position: Engineering Executable Models of Biological Networks
by Anton Feenstra 31 Jul '12

31 Jul '12

Dear colleagues, Please find attached a vacancy for a a PhD position in our group on /Engineering Executable Models of Biological Networks/. Deadline for application: September 1st. Sincerely, Anton Feenstra _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam | |( | )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 | | | Feenstra(a)few.vu.nl - www.few.vu.nl/~feenstra/ | |_____________|_______________________________________________________|

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