May 2015 - BBClist - maillist.psb.ugent.be

fwd:Post-doctoral position available in Human Microbiome Research and Women's Health
by Karoline Faust 19 May '15

19 May '15

Forwarded message: >From: jravel(a)som.umaryland.edu >To: (Ravel, Jacques) jravel(a)som.umaryland.edu >Cc: "Brotman, Rebecca" <rbrotman(a)som.umaryland.edu> >Date: Tue, 19 May 2015 16:04:17 +0000 >Subject: Post-doctoral position available in Human Microbiome Research and Women's Health > >Dear Colleagues, > >I am looking to fill two postdoctoral positions to work on collaborative projects with Dr. Rebecca Brotman related to the Human Microbiome and Women?s Health. I would really appreciate it if you could pass along the attached advertisement to any potential candidates. > >Thanks again! > >Best, > >Jacques > >Jacques Ravel, PhD | Professor and Associate Director for Genomics | Institute for Genome Sciences | University of Maryland School of Medicine | 410-706-5674 | www.igs.umaryland.edu<http://www.igs.umaryland.edu> | jravel(a)som.umaryland.edu<mailto:jravel@som.umaryland.edu> > >This electronic message transmission contains information which may be confidential. The information is intended for the use of the individual or entity named above. If you are not the intended recipient, and have received this electronic transmission in error, please notify sender then delete immediately. > > >

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[Gtpb] Bioinformatics Training Course MEVR15 Molecular Epidemiology DEADLINE EXTENSION
by Pedro Fernandes 18 May '15

18 May '15

Dear All, The deadline for applications to the Training Course MEVR15 Molecular Epidemiology of Viruses using R has been extended, due to some tech issues with the e-mail delivery in the last few days. IMPORTANT DATES for this Course Deadline for applications: May 20th 2015 <--- NEW Latest notification of acceptance: May 21st 2015 Course date: May 25th - May 28th 2 with Simon Frost from the University of Cambridge, Cambridge, UK Details at: http://gtpb.igc.gulbenkian.pt/bicourses/MEVR15 PLEASE make sure that you read the description and the detailed program, as reading only the title may convey a different idea about the content. Duration: 4 days Course fee: Euro 360.00 Note: Travelling to Portugal is relatively cheap. Oeiras is 15 km away from Lisboa International Airport (LIS). Subsistence in Oeiras can cost as low as Euro 30 (Lodging and dinner) the rest is covered by the course fee. 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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2015 Galaxy Community Conference, 4-8 July, Norwich UK
by Dave Clements 18 May '15

18 May '15

Hello all, The 2015 Galaxy Community Conference (GCC2015, http://gcc2015.tsl.ac.uk/) is being held at the Sainsbury Lab in Norwich, United Kingdom, 4-8 July. GCC2015 is an opportunity to meet with 200+ others working at the forefront data-intensive biomedical research. The 2015 edition of GCC includes more than ever before (http://gcc2015.tsl.ac.uk/programme/) - Coding and Data Wrangling Hackathons (and a colocated BioJS Hackathon too) - Two days of training offering 18 sessions on 15 topics in up to 5 parallel tracks, covering topics ranging from analysis to administration to tool development. - A two day meeting featuring accepted talks, poster presentations, keynote talks, vendor exhibits, lightning talks, birds-of-a-feather meetups, and plenty of networking. Early registration is now open (but closes Friday, 22 May, *which is this Friday)*. Registering early saves you 40%. Registering now ensures you'll get a spot in the hackathon and training sessions of your choice. Finally, there are also many other events going on before and after GCC2015, and GCC itself ends right before ISMB / ECCB starts in Dublin. See https://wiki.galaxyproject.org/News/NearGCC2015 for a complete list. Hope to see you in Norwich! Dave Clements, on behalf of the GCC2015 Organising Committee -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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FW: BioJS Conference 3-4 July, Norwich, UK - preceding Galaxy Community Conference
by Celia.vanGelder＠radboudumc.nl 16 May '15

16 May '15

Van: mc.admin(a)manuelcorpas.com [mailto:mc.admin@manuelcorpas.com] Namens Manuel Corpas Verzonden: vrijdag 15 mei 2015 21:52 Aan: Manuel Corpas Onderwerp: BioJS Conference 3-4 July, Norwich, UK - preceding Galaxy Community Conference BioJS CONFERENCE 3-4 JULY, NORWICH, UK http://conf.biojs.net/ Are you - a researcher interested in interactive visualisation of massive biological datasets on the web? - a developer interested in data visualisation? - interested to understand current industry-based end user needs? Would you like to meet recognised leaders in the field of visualisation in bioinformatics, including representatives from a variety of SMEs, big pharma and for profit organisations? It is our pleasure to invite you to join us for the 1st Annual BioJS Conference (BioJS.conf)<http://conf.biojs.net/> and hackathon on 3-4 July 2015, hosted at The Genome Analysis Centre (TGAC), Norwich, UK. As part of the conference we will have an industry-led session organised by the Repositive.io<http://repositive.io/> SME. The aim of this session is to understand the needs, wants, and limitations of front-end interfaces applied to industry-based end users. Current confirmed speakers include: Suzi Lewis (Berkeley) Henning Hermjakob (EBI) Ian Mulvany (eLife) Michiel Helvensteijn (Leiden) Jessie Kennedy (Napier University, Edinburgh) Registration open NOW!<http://conf.biojs.net/#register> Please help us spread the word! The BioJS.conf Organising Committee<http://conf.biojs.net/#organisers> 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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Vacature praktijkdocent bio-informatica Hogeschool van Arnhem en Nijmegen
by Bruggen Martijn van der 15 May '15

15 May '15

De Hogeschool van Arnhem en Nijmegen heeft een vacature voor een praktijkdocent bio-informatica. Meer informatie is terug te vinden op onze website: http://ssl1.peoplexs.com/Peoplexs22/CandidatesPortalNoLogin/Vacancy.cfm?Vac… Met vriendelijke groet, Martijn. Drs. M.H.H. van der Bruggen Lecturer bioinformatics / Programme director bioinformatics HAN University of Applied Sciences Institute of Applied Sciences (www.han.nl/appliedsciences) Postal address: P.O. Box 6960 | 6503 GL NIJMEGEN | The Netherlands | Martijn.vanderBruggen(a)han.nl<mailto:Martijn.vanderBruggen@han.nl> Visiting Address: Laan van Scheut 2 | Room 0.06 | 6525 EM NIJMEGEN | The Netherlands | +31-6-55206344 Present: Monday - Tuesday - Wednesday - Thursday - Friday [untitled]

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Vacancy for PhD student in bioinformatics
by Christian.Gilissen＠radboudumc.nl 11 May '15

11 May '15

Dear all, We're looking for a PhD student in biofinformatics at the department of Human Genetics and the Centre for Molecular and Biomolecular Informatics, Radboud university medical centre Nijmegen. Job description Project title: A holistic approach to the analysis of genetic variation in patients. Interpretation of the thousands of single nucleotide variants identified in a single individual is one of the most profound challenges in genetics today, both from a research as well as from a diagnostic perspective. This project will combine the strengths of the CMBI on protein structures together with the knowledge on genome-wide variation from the genetics department to develop novel bioinformatic methods that improve the interpretation of genomic variation in patients. The position is that of a shared PhD student between the CMBI and the department of human genetics. See also http://www2.cmbi.ru.nl/ and http://genomicdisorders.nl Key words: Bioinformatics, genomics, genetic variation, intellectual disability Profile We are looking for a bioinformatics scientist with a strong drive to pursue a carrier in science, and the ability to work in a team. A strong background in computer science and programming is required. Some background in genetics is preferred as well as experience with statistical techniques and machine learning techniques. Organization The protein structure bioinformatics group from Prof. Vriend is part of the Centre for Molecular and Biomolecular Informatics and located within the Radboud Institute for Molecular Life Sciences. The department of Human Genetics is one of the largest human genetics departments in Europe performing both high quality research and patient care. The translational genomics group of Prof. Veltman consists of about 20 people with a background in genetics and bioinformatics and applies novel genomic technologies for basic research as well as patient care. We regularly publish in high-ranking journals. Comments and contact information Include your curriculum vitae, description of research experience and names and addresses of 2 references in your application. For more information you can contact Dr. Christian Gilissen, christian.gilissen(a)radboudumc.nl<mailto:christian.gilissen@radboudumc.nl>, +31 24 36 68940, Prof. Gert Vriend, vriend(a)cmbi.ru.nl<mailto:G.Vriend@cmbi.ru.nl> , +31 24 3619521, or Prof. Joris Veltman joris.veltman(a)radboudumc.nl<mailto:joris.veltman@radboudumc.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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Registration open: Advanced de novo assembly and resolving complex genomic regions, 1-3 June 2015, Leiden
by Celia.vanGelder＠radboudumc.nl 09 May '15

09 May '15

BioSB Course Advanced de novo assembly and resolving complex genomic regions Date: 1-3 June, 2015 Location: Leiden Course Coordinators: Yahya Anvar (LUMC), Johan den Dunnen (LUMC) Website: http://biosb.nl/education/course-portfolio-2/course-advanced-de-novo-assemb… Registration: http://biosb.nl/education/course-portfolio-2/enrollment-advanced-de-novo-as… This course is targeted at PhD students and Postdocs in Life Sciences or Bioinformatics with basic knowledge of next-generation sequencing (NGS) technology and data analysis. This course covers topics on what every biologist should know about de novo assembly and study design, overview of available technologies and sampling strategies, methodologies and framework for de novo assembly (haploid and polyploid genomes), gap closure, quality assessment and functional annotation. In addition, we will showcase recent achievements, novel discoveries and current limitations in resolving complex genomes. The practical sessions are designed in such a way to promote lively discussions on how to design your study, the best practices, dos and don'ts, and provide you with an outlook on how to move from sequencing data to high-quality assembly and meaningful biological interpretation. After following this course, participants will gain insights on how to design a genome assembly study and will have an overview of challenges and various techniques to choose the most fitting strategy in order to produce a high-quality genome assembly. This course is primarily targeted at academic researchers such as PhD students and Postdocs in Life Sciences or Bioinformatics with experience in genomics or NGS data analysis. However, participants from private sector are also welcome. Participants are expected to have experience in NGS data analysis or to have followed the NGS data analysis course. This course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl<http://www.biosb.nl>. Best regards Celia van Gelder Dr. Celia W.G. van Gelder Education Manager NBIC/BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl, www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.dtls.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre 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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Registration now open for ICBO 2015. Apply now for early career travel grants!
by Francisco Couto 08 May '15

08 May '15

Registration is now open for the International Conference on Biomedical Ontology taking place July 27-30, 2015. Save costs: don’t miss the early registration deadline of May 30th, 2015: http://icbo2015.fc.ul.pt/registration.html. A limited number of travel grants for students or early career researchers (within 5 years of completion of PhD) are available. To apply, please send a one to two page application with the following information: - a brief CV - reason for attending ICBO (e.g. accepted poster or presentation, workshop etc.) - paragraph on why the grant is needed (e.g. your institute doesn’t have funding for your travel) - an estimate of how much your travel will cost By email to Janna Hastings (hastings(a)ebi.ac.uk) by May 25th. Note that travel grant recipients will be required to join the IAOA (iaoa.org) Don’t forget to submit your poster or software demonstration abstract by May 18th: http://icbo2015.fc.ul.pt/callposters.html

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PhD position at TU Eindhoven: Thermal therapy for MR-HIFU pain palliation in bone metastases
by Bosnacki, D. 07 May '15

07 May '15

The Eindhoven University of Technology (TU/e) has the following vacancy PhD student "Thermal therapy for MR-HIFU pain palliation in bone metastases” (V50.2257) at Computational Biology, Department of Biomedical Engineering & Philips Research To apply and for more information please visit: http://jobs.tue.nl/en/vacancy/phdstudent-thermal-therapy-for-mrhifu-pain-pa… Project description Bone pain palliation achieved through the use of Magnetic Resonance guided High Intensity Focused Ultrasound (MR-HIFU) has greatly improved patients’ quality of lives. This technique provides an alternative treatment to radiation therapy, which is the standard palliative treatment but only benefitted 50-70% of patients. With an increasing interest in clinical application of MR-HIFU on metastatic bone pain, understanding the interaction of focused ultrasound with soft tissue and bone is pivotal to ensure treatment efficacy. For this aim a project to estimate the temperature increase in bone during MR-HIFU treatment has started. First results based on a ray tracing approach, which is a first approximation of these physical effects, are encouraging and can already be used in treatment planning simulations. Within the key research objectives it will be your challenge to make the next step towards more exact and validated simulation methods. This should lead to a (prototype) tool, which can also be used in treatment pre-procedure planning and adaptive feedback during therapy. To this end initially you should be able to understand the current methods and simulation software and later define and implement strategies towards a better treatment plan. For example, this includes combining a wave equation based approach with the currently used ray tracer. The goal is to create a full clinical flow which starts with Magnetic Resonance Imaging and ultimately computes the temperature distribution in muscle and bone. The developed methods will be validated with pre-clinical/clinical data in cooperation with medical specialists. For this purpose the current software platform should be extended to enable usage in a clinical environment. As PhD Student, you will: * perform scientific research; * collaborate with other researchers in this project; * assist in teaching undergraduate/graduate courses; * work on the implementation of (prototype) tools; * present results at international conferences; * publish results in conference proceedings and scientific journals; * write a Ph.D. thesis; * participate in activities of the group and of the department. Your work environment will be at TU/e and Philips Research Eindhoven. Other possible partners are radiologists and clinical Physicist in University Hospitals, possibly in the Netherlands as well as in Germany and England. Requirements We are looking for a candidate who: * has (or soon will have) an MSc degree in Biomedical Engineering, Computer Science/Engineering, Mathematics, Physics, Electrical Engineering (or an equivalent qualification); * has interest and experience in (bio)physical modeling and programming; * has interest in data visualization; * is a fast learner, creative, autonomous, and shows dedication; * is able to work in a multi-disciplinary team; * has good communication- and writing skills in English. Appointment and Salary We offer: * An exciting job in a dynamic environment * A full time appointment for four years by Eindhoven University of Technology (www.tue.nl/en<http://www.tue.nl/en>) * A gross monthly salary from €2125 (first year) to €2717 (fourth year) in line with the Collective Agreement for Dutch Universities. * An attractive package of fringe benefits, including end-of-year allowance, excellent sports facilities and a personal development program for PhD students (PROOF program, w3.tue.nl/en/services/dpo/career_and_development/proof_program) Biomedical Engineering (BME) The Department of Biomedical Engineering offers Bachelor’s and Master’s programs in Biomedical Engineering, Medical Sciences and Technology, and Medical Engineering. In addition, the department participates in leading national and international research programs. Research areas range from Molecular Bioengineering and Molecular Imaging, Biomechanics and Tissue Engineering to Biomedical Imaging and Modeling. The department has more than 750 students and 200 staff members. Computational Biology Group The group investigates and applies molecular modeling methods, machine learning, systems biology, and parameter estimation techniques to construct computational models. With these models we improve our qualitative and quantitative knowledge of biomedical processes and structures such as biomembranes, protein interactions, complex biochemical networks and diseases like metabolic syndrome and diabetes mellitus. Visualization Group at the Department of Mathematics & Computer Science The group develops new methods and techniques for interactive visualization in order to analyze and understand large datasets. The main fields of interest are information visualization and visual analytics, both aiming at insight in abstract data (such as tree structures, networks, and multivariate data) and spatial data (such as volumetric biomedical data and moving objects). Our aims are to develop new visual representations and interaction methods, as well as new evaluation methods to obtain a better understanding of the visualization process itself. Philips Research Philips Research is a global organization that helps Philips to introduce meaningful innovations that improve people’s lives. We provide technology options for innovations in the area of health and well-being, targeted at both developed and emerging markets. Positioned at the front-end of the innovation process, we work on everything from spotting trends and ideation to proof of concept and – where needed – first-of-a-kind product development. Information More information can be obtained from: * Dr. Huub ten Eikelder (mail: H.M.M.t.Eikelder(a)tue.nl<mailto:H.M.M.t.Eikelder@tue.nl> , phone: +31(0)40 247 5153) * Dr. Dragan Bosnacki (mail: D.Bosnacki(a)tue.nl<mailto:D.Bosnacki@tue.nl> , phone: +31(0)40 247 5159) * Dr. Michel Westenberg (mail: M.A.Westenberg(a)tue.nl<mailto:M.A.Westenberg@tue.nl> phone: +31(0)40 247 4893) * Aaldert Elevelt, MSc. (mail: Aaldert.Elevelt(a)philips.com<mailto:Aaldert.elevelt@philips.com> phone: +31(0) 6 10364128) Application If you are interested this position, please send us your application by using the 'apply now’ button on the TU/e website: http://jobs.tue.nl/en/vacancy/phdstudent-thermal-therapy-for-mrhifu-pain-pa… Your application should be addressed to Dr. Huub ten Eikelder. Application must include a personal motivation letter (about 1 page) accompanied by a Curriculum Vitae, academic credentials (mark sheets and degree statements), a digital copy of your MSc thesis and names and contact details of at least two references (previous academic supervisors).Submissions will be not considered eligible without these documents. Screening of applications will start as soon as applications are received and will continue until the position has been filled.

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New URL BIG N2N website: http://www.bign2n.ugent.be/
by Katrijn Vannerum 07 May '15

07 May '15

Dear all, Together with the new name BIG N2N (Bioinformatics Institute Ghent From Nucleotides to Networks) and the new logo (see below) comes the new URL for our website: http://www.bign2n.ugent.be/ The website where you find bioinformatics events, bioinformatics tools and databases to use freely, job vacancies, information about the new master program, news about BIG N2N, latest publications, ... ! (The old URL www.nucleotides2networks.be<http://www.nucleotides2networks.be> will stay functional for a while.) Enjoy! Katrijn Vannerum PhD Project manager BIG N2N (Bioinformatics Institute Ghent From Nucleotides to Networks) Ghent University http://www.bign2n.ugent.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [cid:image002.jpg@01D088D4.024A4350]

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