June 2017 - BBClist - maillist.psb.ugent.be

RSG Student Symposium 2017 - Gent_deadline postponed
by Daniele Parisi 06 Jun '17

06 Jun '17

Dear colleagues, the deadline for abstract submission has been postponed to FRIDAY 2ND JUNE. Don't miss the opportunity of meeting the network of Belgian Master, PhD and Postdoc students in Bioinformatics and Computational Biology. TIME: 8TH JUNE, 14:15 PLACE: TECHNOLOGIEPARK-ZWIJNAARDE 927, 9052 GENT, België KEYNOTE: prof YVES VAN DE PEER NETWORK DRINK AND SOCIAL DINNER follows More info, registration and submission here: https://www.facebook.com/events/1813431575641030/?acontext=%7B%22action_his… Short link to the registration and submission form: https://goo.gl/forms/yRDhXSv54EsVTLpE3 I hope to see you all there Kind regards -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Board member of PhD Leuven society Kasteelpark Arenberg 10 - box 2446 3001 Leuven, Belgium Tel: +32488794394

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PhD position in Leuven (computer science / statistics)
by Guy Baele 03 Jun '17

03 Jun '17

The Laboratory of Clinical and Epidemiological Virology (Rega Institute - KU Leuven; https://rega.kuleuven.be/cev/ecv/) is looking for a motivated PhD student to perform research in a multidisciplinary team. This constitutes an exciting opportunity to work on computational and statistical methods in molecular evolution with applications in infectious diseases. Research group The Evolutionary and Computational Virology Laboratory at the Division of Clinical and Epidemiological Virology (Rega Institute, KU Leuven) focuses on the evolutionary processes that shape viral genetic diversity. This encompasses large-scale epidemic processes, such as population growth and spatial dispersal (a popular topic in phylogeographic and phylodynamics research), as well as small-scale transmission histories and within-host evolutionary processes, including adaptation and recombination. It is our objective to gain better insights into these evolutionary and population genetic processes and to clarify how they relate to epidemic and disease dynamics. To this aim we plan to focus on statistical and computational developments to analyze the increasing amount of data brought about by massive sequencing studies, mainly in a framework of Bayesian phylogenetic inference, for which our research group holds a strong track record. We also aim to explore the applicability of novel models and statistical inference tools, developed as part of our research, in different fields of research. Project This project focuses on new developments in a popular Bayesian phylogenetic inference framework (BEAST: https://github.com/beast-dev/beast-mcmc) and its applications to important evolutionary problems, with a particular focus on infectious diseases. The project involves the development of an integrated web system and database that allows users to register, upload and retrieve sequence data to and from the database. Each user will be able to determine the sharing policy for the data he/she has provided. Such a system should be easily distributed so that other research groups can deploy it on their own server(s) and put it to use without technical interventions. Further, this system will interface with the BEAST software package to analyze the sequence data in an efficient manner. The candidate is expected to design and implement such a system and determine an appropriate strategy to properly distribute the developed system as an easily installed/deployed software package. Additionally, multiple parallelization ideas will be implemented in the BEAST software package. BEAST is mostly written in Java, with its high-performance computational library, known as BEAGLE, being implemented in C/C++. The goal is to develop and implement efficient parallelization strategies from both a computational and a statistical perspective. The computational aspect entails the implementation of popular routines typically used in computer architecture, whereas the statistical aspect entails the development and adaptation of novel transition kernels in a Bayesian phylogenetic inference framework. Profile The candidate for this PhD position should have a strong quantitative background, and preferably holds a master's degree in computer science / informatics (or equivalent through experience), with an interest in statistics/mathematics and (bio)informatics. The candidate hence needs to be experienced in an object-oriented programming language such as Java or C/C++. The candidate should be sufficiently proficient in English, motivated to work in a team and publish his/her findings, and willing to travel. Offer The candidate will be able to perform research in a dynamic and multidisciplinary team (computer scientists, data analysts and evolutionary biologists), housed in the brand new facilities of the Rega institute at the University hospital campus, and guided by prolific supervisors. KU Leuven is one of the top universities in Europe and leads the Reuters ranking of Europe’s most innovative universities for the second year in a row. The targeted starting date will be October 1st 2017 and the candidate should obtain his/her master’s degree by that time. All applicants are expected to submit a motivation letter, overview of their study results and two references (with their contact details). Additional information, as well as the application procedure, can be found here: https://icts.kuleuven.be/apps/jobsite/vacatures/54182826 Please use the university’s job portal when applying for this position. For more information, contact Guy Baele (guy.baele(a)kuleuven.be) or Philippe Lemey (philippe.lemey(a)kuleuven.be) -- Guy Baele, PhD. Department of Microbiology and Immunology Evolutionary and Computational Virology Section Rega Institute - KU Leuven Herestraat 49, 3000 Leuven, BELGIUM

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Lecture Series in "Translational Bioinformatics and Systems Biomedicine".
by Francisco Azuaje 02 Jun '17

02 Jun '17

Dear Colleagues, This year in Luxembourg ?we begin hosting a Lecture Series in "Translational Bioinformatics and Systems Biomedicine" . Full provisional program is now available at:?? https://files.lih.lu/events/2017/Overview%20translational%20bioinformatics_… Our first lecture (on 19 June) will be given by Prof. Luonan Chen (Director of the Key Laboratory of Systems Biology @ Shanghai Institutes for Biological Sciences): http://tinyurl.com/y95k3bgv? Sincerely, Francisco. _________________________________ Francisco Azuaje, PhD Principal Investigator Proteome and Genome Research Unit Department of Oncology Luxembourg Institute of Health 1A-B, rue Thomas Edison, L-1445 Strassen Luxembourg Tel: +352 26970-875 Fax: +352 26970-719 Email: francisco.azuaje(a)lih.lu<mailto:francisco.azuaje@lih.lu> Website: https://www.lih.lu/ [http://files.lih.lu/outlookSignature/lih.jpg] Join us on Facebook and follow our activities on Twitter: https://www.facebook.com/Luxembourg.Institute.of.Health http://twitter.com/LIH_Luxembourg This message (including any attachments) is intended for the addressee only and may contain confidential and/or privileged information and/or information protected by intellectual property rights. If you have received this message by mistake, please notify the sender by return e-mail and delete this message from your system. You should not use, alter, copy or distribute this message or disclose its contents to anyone. E-mail transmission can not be guaranteed to be secure or error free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. Luxembourg Institute of Health shall not be responsible nor liable for the proper and complete transmission of the information contained in this communication nor for any delay in its receipt or damage to your system.

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[Gtpb] Reproducible and Open Data Science - a hands-on course
by Pedro L. Fernandes 01 Jun '17

01 Jun '17

ANNOUNCEMENT/REMINDER RODS17 Reproducible and Open Data Science with Rutger Vos and Pedro Fernandes (Instructors) The above referenced hands-on training course is open for applications IMPORTANT DATES for this Course Deadline for applications: June 16th, 2017 <=== Course date: June 21st - 23rd 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Description: In an age of increasingly complex and data-intensive, collaborative scientific practices, scandals of irreproducibility, and a growing societal ethos of transparency and accountability, a new paradigm has arisen: Open Science. In this three day course, we will introduce to you the three organizing principles and practices that under-gird this paradigm: Open Access scholarly publishing Open Source software development Open Data integration and sharing For this, we will be introducing a set of technologies and ways of using them. The reasonable expectation is that the participants will feel empowered and start using them for the above purposes in a highly productive way. The use-cases that we will be working on are going to be based on bioinformatics, but the principles are very broadly applicable to other fields. You do not need to have any particular programming or otherwise computational experience beyond what is normally required from a scientist in graduate school and beyond, i.e., you should not be afraid of interacting with a computer and editing simple text files. http://gtpb.igc.gulbenkian.pt/bicourses/RODS17/ Hoping that this course meets your interests, Pedro Fernandes -- Pedro Fernandes Bioinformatics Training 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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