September 2016 - BBClist - maillist.psb.ugent.be

Bioinformatics scientist vacancy in HZPC
by Sanchez Perez, Gabino 30 Sep '16

30 Sep '16

Dear all, There is a job opening for bioinformatics at the breeding company HZPC. See attached file for more detailed information. Please, forward to any interested colleagues, Kind regards, Gabino

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GIGA Imaging Platform - Bioinformatician position available
by rh.giga＠ulg.ac.be 27 Sep '16

27 Sep '16

Dear all, The GIGA Imaging Platform is recruiting a bioinformatician. Please find attached the job description. Regards, Sandra Lopez and Sandrina Evrard GIGA Université de Liège Quartier Hôpital Avenue de l'Hôpital 11 - B34 B-4000 LIEGE Tél + 32 4 366 98 03 Fax + 32 4 366 41 98 www.giga.ulg.ac.be

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Internship – Bayesian methods for disease subtype discovery
by Johann Pellet 23 Sep '16

23 Sep '16

6-month Programming Internship: France (Lyon) Employer: CNRS Location: CNRS-EISBM, Lyon, France Qualifications: Undergraduate – Bachelor’s degree Salary: Depending on qualifications and experience, based on CNRS salary grid Duration: 6 months Starting date: Available immediately, expected to start by January/February 2017 Key words: Programming, GP-GPU, Python, R, C, Java, Bioconductor, disease sub-types, Systems Biology An internship position is available as a part of the European Translational Research Information and Knowledge Management Services project (eTRIKS), funded by the Innovative Medicines Initiative (IMI) of the European Commission 7th Framework Programme and the European Federation of Pharmaceutical Industries and Associations (EFPIA). The selected candidate will be based in Lyon-Gerland within the CNRS-EISBM team led by Charles Auffray, hosted by Claude Bernard University on the Charles Mérieux campus. He will work closely with the team led by Prof Yi-Ke Guo at the Data Science Institute of Imperial College in London, UK. The aim of the internship is to evaluate the performance of recent algorithms for identification of disease sub-types using Bayesian methods; specifically, this will involve implementing existing programs, where possible exploiting GP-GPU and Apache spark architectures to address the computationally intensive aspect of the problem. It is anticipated that some of the approaches evaluated will be used for analysis of multi omics datasets from new systems medicine projects. This position allows an intern to participate in a state-of-the-art EU systems biomedicine project. Required skills: Good programming skills (eg. python, java, C, R); good communication skills in English. Enthusiastic and motivated candidates are encouraged to contact Prof. Charles Auffray jobs(a)eisbm.org with a CV and a brief description of their programming skills.

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Internship – Programmer / Software Developer
by Johann Pellet 23 Sep '16

23 Sep '16

Employer: CNRS Location: CNRS-EISBM, Lyon, France Expires: 15th December 2016 Qualifications: BSc, MSc Salary: Depending on qualifications and experience, based on CNRS salary grid Duration: 6 months Starting date: Available immediately, expected to start by February/March 2017 Key words: web development, open-source, data visualisation, layout algorithms, computational systems biology, systems medicine, graphical standard A software developer intenship position is available as a part of the European Translational Research Information and Knowledge Management Services project (eTRIKS), funded by the Innovative Medicines Initiative (IMI) of the European Commission 7th Framework Programme and the European Federation of Pharmaceutical Industries and Associations (EFPIA). The successful applicant will work on developing an application that enables automatic assembly and layout of biological networks. The goal of this project is to develop a plugin for an open-source web-based graph editor which functionality is based on Cytoscape.js. The work will be done in close interaction with a team of experiences software architects, software developers, experts in layout algorithms, systems biologists and bioinformaticians. The selected candidate will be based in Lyon-Gerland within the CNRS-EISBM team led by Dr. Charles Auffray, hosted by Claude Bernard University on the Charles Mérieux campus. Required qualification and skills: Candidates should have a BSc or MSc in Computer Science, in Bioinformatics or equivalent. Strong programming skills are required. Experience in Web programming (HTML, or/and JavaScript, or/and CSS) and in graph visualisation tools / libraries is an advantage. Background in pathway informatics / system biology / data visualization is a plus. The position requires good communication skills in English and involves working in collaboration with eTRIKS partners on translational medicine projects across Europe. Application: Please send your CV and motivation letter to Dr. Charles Auffray: jobs(a)eisbm.org.

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REMINDER: BeMGI 2016-Brussels Meeting, Wednesday-13 April
by Marilou Ramos Pamplona 23 Sep '16

23 Sep '16

Dear BBC colleagues, We would like to remind you of the 2016 Annual Meeting of the Belgian Medical Genomics Initiative (BeMGI) entitled "From predisposing germline and somatic variants to disease-driving mechanisms.," which will feature the two keynote lectures: Genetic basis and mechanisms of Parkinson’s disease. Alexis Brice, MD Brain and Spine Institute Hôpital Pitié Salpêtrière Paris, France Search for predisposing factors in myeloid malignancies. Christine Bellanné-Chantelot, PhD Centre de Génétique Moléculaire et Chromosomique Groupe Hospitalier Pitié-Salpétrière Paris, France This meeting will take place on Wednesday (13 April 2016) from 12h00-17h30 at the Auditoire central 51E of UCLouvain Brussels campus (Avenue Mounier 51, 1200 Bruxelles, www.uclouvain.be/286287.html) The complete meeting info document with directions to the meeting venue, is available via: https://edc.ulg.ac.be/merci/BeMGI2016-Brussels_Meetin_d1f1ea81615957fe5c13_… The online meeting registration (http://bit.do/BeMGI2016register) is available until tomorrow noon (Tuesday, 12-Apr, 12h00). We kindly request all interested meeting participants to either register online by tomorrow noon or to register on site upon arrival at the meeting venue. See you soon in Brussels! Regards, The BeMGI network

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Edinburgh Genomics bioinformatics workshops - MinION, ChIP-seq, RAD-seq, Python, Linux
by Bert Overduin 22 Sep '16

22 Sep '16

Dear all, Application / registration is currently open for a wide variety of bioinformatics workshops at Edinburgh Genomics: *1-day Oxford Nanopore MinION Sequencing - Data Handling, Analysis and Applications* Date: Tue 1 November 2016 Application deadline: Tue 4 October 2016 Places: 12 (selection of applicants) Instructors: Dr. Rob Stewart (The Roslin Institute); Dr. Judith Risse (Wageningen University, The Netherlands) Fee: £175 More info: http://genomics.ed.ac.uk/services/oxford-nanopore-mini on-sequencing-data-handling-analysis-and-applications *2-day Introduction to ChIP-seq Data Analysis and Visualisation using Ensembl* Date: Tue 22 - Wed 23 November 2016 Application deadline: Tue 25 Octoberr 2016 Places: 12 (selection of applicants) Instructors: Dr. Myrto Kostadima (European Bioinformatics Institute); Dr. Ben Moore (European Bioinformatics Institute) Fee: £310 More info: https://genomics.ed.ac.uk/services/introduction-chip-s eq-data-analysis-and-visualisation-using-ensembl *2-day Introduction to RAD-seq Data Analysis* Date: Tue 29 - Wed 30 November 2016 Application deadline: Tue 1 November 2016 Places: 12 (selection of applicants) Instructors: Dr. Judith Risse (Wageningen University, The Netherlands); Dr. John Davey (York University) Fee: £375 More info: http://genomics.ed.ac.uk/services/introduction-rad-seq -data-analysis *5-day Introduction to Python for Biologists* Date: Mon 12 - Fri 16 December 2016 Registration deadline: Mon 28 November 2016 Places: 20 (first come, first served) Fee: £500 Instructors: Dr. Martin Jones (Python for Biologists); Dr. Bert Overduin (Edinburgh Genomics) More info: http://genomics.ed.ac.uk/services/introduction-python-biologists *5-day Introduction to Linux and Workflows for Biologists* Date: Mon 24 - Fri 28 April 2017 Registration deadline: Mon 10 April 2017 Places: 20 (first come, first served) Fee: £525 Instructors: Dr. Martin Jones (Python for Biologists); Dr. Bert Overduin (Edinburgh Genomics) More info: http://genomics.ed.ac.uk/services/introduction-linux-and-wor kflows-biologists *5-day Data Manipulation and Visualisation with Python* Date: Mon 10 - Fri 14 July 2017 Registration deadline: Mon 26 June 2017 Places: 15 (first come, first served) Fee: £525 Instructors: Dr. Martin Jones (Python for Biologists); Dr. Bert Overduin (Edinburgh Genomics) More info: http://genomics.ed.ac.uk/services/data-manipulation-an d-visualisation-python *5-day Advanced Python for Biologists* Date: Mon 24 - Fri 28 July 2017 Registration deadline: Mon 10 July 2017 Places: 15 (first come, first served) Fee: £525 Instructors: Dr. Martin Jones (Python for Biologists); Dr. Bert Overduin (Edinburgh Genomics) More info: https://genomics.ed.ac.uk/services/advanced-python-biologists -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk orcid.org/0000-0002-5281-8838 EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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PhD Opportunity in Genomic Privacy at the University of Lisbon
by Francisco Couto 21 Sep '16

21 Sep '16

The BioSys PhD Program is offering a PhD scholarship for the project: "What are the determinants of human genetic individuality?" The graduate will have the opportunity to work with world-leading researchers from BioISI (BioSystems and Integrative Sciences Institute) and LaSIGE at the University of Lisbon under the supervision of Prof. Francisco Couto (LASIGE) and Prof. Margarida Gama-Carvalho (BioISI) Applications until *October 21st (12PM, CET)* How to apply: http://biosys.campus.ciencias.ulisboa.pt/node/6 Objectives: With the conclusion of the human genome project and the advent of next-generation sequencing, research on the human genome advanced towards a deeper understanding of human population diversity, focusing primarily on the identification of common genetic variants. With this project we want to evolve from studying the diversity within a population to the individual. We aim at establishing a measure for genomic similarity (involving both the sequence and structural levels) between an individual genome and a single or group of genomes. Genomics information can spell much more about an individual than thought in the last decades, but the complexity of human behaviour is enormous and the determinants of human genetic individuality may be hard to predict from single genomic properties. This project will follow a systems biology approach to reach for a deeper understanding of the complexity of the human genome by analysing what defines us as individuals. The main goal is to understand how well we can predict if one specific person belongs to a group (for example, defined by a phenotype) by only using genomics data. The results generated by this project will be based on the intensive analysis of human sequencing datasets. By identifying the determinants of human genetic individuality, we will also be able to address some of the current concerns regarding the preservation of individual privacy when addressing the prominent necessity for data sharing [1]. [1] Cogo, V. V., Bessani, A., Couto, F. M., & Verissimo, P. (2015, October). A high-throughput method to detect privacy-sensitive human genomic data. In *Proceedings of the 14th ACM Workshop on Privacy in the Electronic Society*(pp. 101-110). ACM.

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[Course] Biological Data Visualization, January/February 2017
by Jan Aerts 20 Sep '16

20 Sep '16

Hi all, Registration is now open for our "Data Visualization for Biology" course, which will take place from January 30th to February 3rd 2017 at the European Bioinformatics Institute near Cambridge, UK. In this course, we will go into why we need interactive visualization of complex biological data, and teach students how to design and implement novel representations. More information at http://www.ebi.ac.uk/training/events/2017/data-visualisation-biology-practi… Please distribute this widely. Thank you, jan. ================================================ Prof Jan Aerts * Visual Data Analysis Lab (vda-lab.be) * Data Visualization Lab (datavislab.org) * Bioinformatics - ESAT/STADIUS, Faculty of Engineering ( www.kuleuven.be/bioinformatics) * iMinds Medical IT Department (www.iminds.be) KU Leuven - University of Leuven Kasteelpark Arenberg 10 bus 2446 3001 Leuven-Heverlee ORCID: http://orcid.org/0000-0002-6416-2717 Tel: +32 16 321053 Fax: +32 16 321970 VAT BE 0419 052173

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Python for Life Scientists, , Fall edition, November 10-11, Amsterdam
by Alvise Trevisan 16 Sep '16

16 Sep '16

Dear all, I am writing to announce the Fall edition of the course "Python for Life Scientists". Tailored to life scientists with little or no prior programming experience, the course is driven by real-life use cases. Participants will learn by doing, completing snippets of code that they will be able to reuse in their everyday tasks. Extensive use of IPython Notebooks (Jupyter) will encourage participants to annotate and document the code, building the basis for a sound and reproducible methodology for data analysis . The course will run on November 10-11, 2016 in Amsterdam. More information and the registration form are available at the web site: http://www.enpicom.com/training/python Feel free to spread this information to people that might be interested. Kind Regards, Alvise Trevisan -- Alvise Trevisan ENPICOM | Science Park 402 | 1098 XH Amsterdam | The Netherlands www.enpicom.com<http://www.enpicom.com/> +31 20 895 0964 +31 61 496 4730

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Vacancy PhD student in Genetics at UMC Utrecht
by Renkema, K.Y. 13 Sep '16

13 Sep '16

PhD student - Molecular mechanisms of kidney malformations We offer a job at the forefront of medical (nephro-)genetics, at the Department of Genetics. As a PhD student, you will set foot on unexplored territory, by participating in an exciting new research project. The project aims to elucidate the molecular mechanisms involved in the etiology of congenital kidney malformations, using an integrative biology approach including whole genome sequencing, RNA sequencing, and big data analysis. The project is funded by the Dutch Kidney Foundation. Department The candidate will be appointed at the research section of the Department of Genetics that is part of the UMC Utrecht Center for Molecular Medicine (http://cmm.umcutrecht.nl) of which the key expertise include next-generation sequencing and bioinformatics. The research section provides a stimulating, international, and dynamic learning environment where people aim at high quality research. You will work in a multidisciplinary team of PhD students, postdocs, research technicians, and clinical investigators. The Department of Genetics is responsible for the diagnosis of genetic changes that cause disease. In addition, the department plays an important role in the teaching and training of medical doctors, molecular geneticists, PhD students and undergraduate students. The nephrogenetics group in particular, is focusing on the identification and functional characterization of novel kidney disease genes. Profile We are looking for a motivated and skilled PhD student with a background in biomedical research and experience in bioinformatics. You have a master’s degree in bioinformatics, biomedical sciences or a related discipline and a strong motivation to conduct scientific research. The ideal candidate has affinity with the analysis of next generation sequencing data. You are motivated by the challenge of novel scientific concepts and have the ambition to become an independent scientist. Because of the multidisciplinary nature of the research, communication and social skills directed at working in a team as well as proficiency in English are a prerequisite. The maximum salary for this position (100%) is € 2.874,00 gross per month based on full-time employment (work week 36 hours). This job is based on a temporary position for 4 years. Details This job is based on a temporary, full-time position for a period of four years. The starting date is December 1st, 2016. The monthly salary is according to the standard conditions for PhD students in the Netherlands. Please send applications including your CV with a letter of motivation, a list of the courses/internships you followed with grades, and contact details of at least two references. More information If you have any questions about this vacancy, please contact Dr. K.Y. Renkema, Senior Postdoc, phone 0031 88 75 67925. Email AMG-stafsecretariaat(a)umcutrecht.nl<mailto:AMG-stafsecretariaat@umcutrecht.nl>. ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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