- BBClist - maillist.psb.ugent.be

Last few spaces remaining on introductory bioinformatics courses at Edinburgh Genomics
by MEDD Nathan 10 Apr '18

10 Apr '18

Dear All There are still a handful of spaces remaining on this summer's introductory bioinformatics workshops here at Edinburgh Genomics. These excellent courses, taught by Dr Martin Jones (Founder, Python for Biologists, https://pythonforbiologists.com) are the perfect introduction to the world of coding for budding bioinformaticians. MONDAY 14th - FRIDAY 18th MAY - Introduction to Linux and Workflows for Biologists. Most high-throughput bioinformatics work these days takes place on the Linux command line. The programs which do the majority of the computational heavy lifting — genome assemblers, read mappers, and annotation tools — are designed to work best when used with a command-line interface. Because the command line can be an intimidating environment, many biologists learn the bare minimum needed to get their analysis tools working. This means that they miss out on the power of Linux to customise their environment and automate many parts of the bioinformatics workflow. This course will introduce the Linux command line environment from scratch and teach students how to make the most of its tools to achieve a high level of productivity when working with biological data. For more information and to sign up see: https://genomics.ed.ac.uk/services/introduction-linux-and-workflows-biologi… MONDAY 11th - FRIDAY 15th JUNE - Introduction to Python for Biologists "Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackle problems in their own research and (2) continue their Python education in a self-directed way." For more information and to sign up see: https://genomics.ed.ac.uk/about-us/introduction-python-biologists-june-2018 The above courses are both held at the Kings Buildings Campus, University of Edinburgh. Check out the Edinburgh Genomics training page, https://genomics.ed.ac.uk/services/training, for more upcoming courses. Kind Regards Nathan Medd Edinburgh Genomics - Training Assistant -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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PhD position at the Maastricht Centre for Systems Biology
by Adriaens, Michiel (MACSBIO) 09 Apr '18

09 Apr '18

Dear all, The Maastricht Centre for Systems Biology is currently looking for a PhD candidate to strengthen our research activities in mathematical modelling and machine learning approaches to gain a better understanding of blood glucose control and its relation to physical activity and wellbeing. For more information and to apply, please follow the link: https://www.academictransfer.com/employer/UM/vacancy/45921/lang/en/ Kind regards, Michiel Adriaens -- Michiel E. Adriaens, PhD Assistant Professor Maastricht Centre for Systems Biology - MaCSBio Universiteitssingel 60, 6229 ER Maastricht, The Netherlands

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Announcement Elixir-SE RaukR Advanced R Summer school 11-21 June
by Jessica Lindvall, PhD, Training coordinator 08 Apr '18

08 Apr '18

Elixir-SE (NBIS/SciLifeLab, www.nbis.se) is excited to announce a brand new international Summer School in R for Bioinformatics calked "RaukR Summer school: Advanced R for Bioinformatics"! The Summer School is beautifully located in the middle of the UNESCO World Heritage city of Visby, Sweden, and during 2 weeks you will get the opportunity to learn R from internationally renowned R wizzards and senior bioinformatics staff from NBIS/SciLifeLab. We believe that RaukR will take your bioinformatics R analysis and visualization skills to a new level, so don’t miss out on this unique opportunity! RaukR Summer School: Advanced R for Bioinformatics 11-21 June 2018. Visby, Gotland, Sweden Registration deadline: April 15, 2018 Register today at https://nbisweden.github.io/workshop-RaukR-1806/ Please help us spread the word! Best regards,Jessica Lindvall, PhD, Training coordinator Elixir-SE NBIS/SciLifeLab www.nbis.se, www.scilifelab.se Twitter: https://twitter.com/search?q=%23RaukR&src=typd Hashtag: #RaukR Note: A “Rauk” is a characteristically shaped stone formation, common on the Island of Gotland, Sweden. See for example https://sv.wikipedia.org/wiki/Rauk#/media/File:Gotland-F%C3%A5r%C3%B6_Rauka…

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Computational Biology/Bioinformatics PhD-position available at the Erasmus Medical Center.
by Harmen van de Werken 06 Apr '18

06 Apr '18

Could you please add the following text on the bbc mailing list: "Computational Biology/Bioinformatics PhD-position available at the Erasmus Medical Center. The PhD-student will work with a collaborative team from the Department of Medical Oncology and the Cancer Computational Biology Center (CCBC) in the emerging field of Computational Cancer Pharmacogenomics. For more information please visit the website: https://www.werkenbijerasmusmc.nl/en/vacancy/phd-student_120218tddh" Kind regards, Harmen van de Werken -- Harmen van de Werken, Ph.D. Assistant Professor in Computational Biology at the Department of Urology at Erasmus MC & Managing Director Cancer Computational Biology Center (CCBC) at Erasmus MC P.O. Box 2040, Be-355 3000 CA Rotterdam, the Netherlands Visiting address: Josephine Nefkens Building, office Be-330a Wytemaweg 80 3015 CN Rotterdam, the Netherlands Tel: +31-10-7044467 (office) Tel: +31-10-7044488 (department) Fax: +31-10-7044661 https://ccbc.erasmusmc.nl/ Email: h.vandewerken(a)erasmusmc.nl Skype: harmen.vandewerken

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Job opening for a Single-Cell Bioinformatics Specialist
by Stein Aerts 06 Apr '18

06 Apr '18

Dear all, We have a job opening for a Single-Cell Bioinformatics Specialist in the VIB Center for Brain and Disease Research: https://www.nature.com/naturejobs/science/jobs/638647-single-cell-bioinform… Best regards, Stein Aerts

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+++ Bioinformatics and Computational Biology European Student Council Symspoiusm 2018 - registration and submission open +++
by Daniele Parisi 06 Apr '18

06 Apr '18

Dear students and researchers in BIOINFORMATICS and COMPUTATIONAL BIOLOGY, The EUROPEAN STUDENT COUNCIL SYMPOSIUM organizing committee is happy to announce the opening of the registration and submission call for ESCS2018 (see flyer attached) . Would you like to join the main event of the European students in Bioinformatics and computational biology? REGISTER now through the ECCB Registration page http://eccb18.org/registration/ REGISTRATION WILL BE OPEN TILL 08.08.2018 Would you like to share your results with the community of young researchers and receive feedbacks on your work? SUBMIT your work for a talk or poster through the ESCS2018 submission page http://escs.iscbsc.org/escs-submission [1] SUBMISSION WILL BE OPEN TILL 23.07.2018 More information about the program, the key dates, keynotes and more on the website http://escs.iscbsc.org/ We are looking forward to meet you there, Best regards -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Chair of ESCS 2018 Kasteelpark Arenberg 10 - box 01.34 3001 Leuven, Belgium Tel: +32488794394 Links: ------ [1] http://escs.iscbsc.org/escs-submission

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Extra Workshop: R2 - Genomics analysis and visualization platform
by r2-support 06 Apr '18

06 Apr '18

Dear Researcher, Since the next R2 workshop on April 23rd is overbooked, we are organizing another R2 introduction workshop on Monday the 25th of June 2018 (09:30-17:00). R2 is a free, publicly accessible web-based genomics analysis and visualization platform (http://r2.amc.nl<http://r2.amc.nl/>) allowing biomedical researchers, without bioinformatics training, to integrate clinical and genomics data. The workshop will cover the essentials of working with genomics data in R2 and will be an excellent opportunity to learn how to use this versatile tool. If you are: Studying a specific pathway in disease Trying to find biomarkers in specific tissue Investigating the function of a specific protein Involved in any kind of molecular biology Then this workshop may be of interest to you. Every participant will receive a printed tutorial book. Coffee / tea and a simple lunch will be provided during the workshop. If you are interested in participating in the workshop then please visit the R2 website for more information and registration (http://hgserver1.amc.nl/cgi-bin/r2/main.cgi?option=about_intro_workshop ). The workshop is provided free of charge, however, we will have to charge 25 euro (for administration, lunch, printing costs) in case of a no show on the workshop. Best regards, R2-support r2-support(a)amc.nl r2.amc.nl Department of Oncogenomics, M1-132 Academic Medical Center University of Amsterdam Meibergdreef 9 1105 AZ Amsterdam the Netherlands ________________________________ AMC Disclaimer : https://www.amc.nl/disclaimer ________________________________

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PhD position cancer genetics and bioinformatics | Human Molecular Genetics | Center for Medical Genetics | Belgium
by mheydt 04 Apr '18

04 Apr '18

The Human Molecular Genetics research group of the Center for Medical Genetics of the University of Antwerp (UA) and the division of Thorax oncology of the University Hospital Antwerp have an ongoing collaborative research project aiming at the unraveling of the genetics of Malignant Pleural Mesothelioma. Within this collaboration, we are currently hiring: *A PhD student* *Job Profile* You will perform research through the generation, analysis and integration of different genetic datasets, with a focus on next generation sequencing data, with the final goal of understanding the complex biology of mesothelioma. You will join an enthusiastic team, within an established and extensive international research network. In your daily work, you willwork in close collaboration with both laboratory-oriented researchers and bioinformaticians, as well as with clinically-oriented researchers working on mesothelioma. You will perform both laboratory work and data-analysis. In case of applicants with a strong bio-informatics background, the emphasis of the project can be shifted more towards the data-analysis. *Requirements* You are (or will be by July 2018) a master in one of the life sciences (Biomedical sciences, Biochemistry, Bio-engineering, Bio-informatics…). You have a very strong interest in genetic research and data analysis as well as in cancer biology. You have a thorough understanding of human genetics, in particular cancer genetics. You have detailed knowledge of molecular genetic techniques used for research, and you have basic laboratory skills using one or more of these techniques. You have strong ICT as well as statistical skills or you have a strong commitment to achieve these. Experience with Linux and one or more programming languages is a strong advantage. You are willing to work on a PhD project, starting the academy year 2018-2019. You have good communication skills, you are highly motivated to do research, and you like to work in an interactive internationally oriented research team. Proficiency in English is required. You are willing to apply for a personal fellowship as a PhD student with funding agencies such as the Flemish FWO. *What we offer* We offer a salary as a PhD student according to the scales of the University of Antwerp, for a period of one year. Extension of this period is possible up to a total of 4 years, after positive evaluation. *Interested?* For additional information please contact the Medical Genetics research manager Dr. Arvid Suls (arvid.suls(a)uantwerpen.be <mailto:arvid.suls@uantwerpen.be>). To apply, send a copy of your CV and motivation statement by e-mail to Arvid Suls before May 7, 2018.

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Open position: Bio-Informatician PhD in Laboratory for Molecular Diagnostics at AZ Sint-Jan Hospital Brugge
by Friedel Nollet 03 Apr '18

03 Apr '18

Dear, I am looking for a new colleague, Bio-Informatician (PhD). We have introduced NGS 4 years ago for the following testing : HLA-tissue typing, B/T cell clonality analysis, Clarigo NIPT and targeted mutation analysis (hemato-oncology). We want to expand our test portfolio in the nearby future towards whole genome NIPT, liquid biopsy, comprehensive cancer gene panel testing, ... Job application is until 16/4/2018! See : https://jobs.azsintjan.be/Jobs/VacatureDetail/1099870000001338 Kind regards, Friedel -- Friedel Nollet, Ph.D. Molecular Biologist Department of Laboratory Medicine AZ Sint-Jan Brugge-Oostende AV Ruddershove 10 B8000 BRUGGE BELGIUM Tel. + 32 50 452766 / Fax. +32 50 452619 friedel.nollet(a)azsintjan.be<mailto:friedel.nollet@azsintjan.be>

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[Gtpb] PGDH18 Course announcement / Reminder
by GTPB Administration 02 Apr '18

02 Apr '18

Course Announcement / Reminder PGDH18 Population Genetics and Demographic History: model-based approaches with Mark Beaumont, Lounès Chikhi, Willy Rodriguez and Vitor Sousa Key terms: Model-based Population Genetics IMPORTANT DATES for this Course Deadline for applications: May 4th 2018 Course date: May 14th - May 18th 2018 The GTPB is proud to announce that the above referenced hands-on training course is open for applications Admission: Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course description: Genetic and genomic data are increasingly used by ecologists and evolutionary biologists in general. It has thus become important for many biologists with different levels of experience to produce and analyse genetic (and genomic) data. In this course we will take a practical approach to the analysis of genetic and genomic data, but we will also provide some of the theoretical background required to understand the outputs of the software used. This course will be organised so as to mix lectures where important notions are introduced with practicals where freely available software will be used. While this will not be the focus of the course, we will also introduce and discuss genealogical (coalescent-based) simulation methods and those based on forward-in-time simulations. Altogether this will allow to discuss the potentialities and limitations of the tools available to the community. In this five-day course we will introduce the main concepts that underlie many of the models that are frequently used in population genetics. We will focus on the importance of demographic history (e.g. effective sizes and migration patterns) in shaping genetic data. We will go through the basic notions that are central to population genetics, insisting particularly on the statistics used to measure genetic diversity and population differentiation. The course will also cover a short introduction to coalescent theory, Bayesian inference in population genetics and data simulation. We will also introduce methods that have been recently developed to analyse genomic data such as the PSMC method of Li and Durbin that reconstructs the demographic history of a species or population with the genome of a single individual. Most theory will be put into practice in practical sessions, analyzing real and/or simulated datasets. In these sessions, we will look at measures of genetic diversity and differentiation and use methods to infer demographic history. We will learn how to perform coalescent simulations of genetic/genomic data (using mainly Richard Hudson's ms program). We will also show how to simulate data for PSMC analyses. This will allow users to compare the PSMC obtained with real data to those obtained for the models they used. We will also look at how habitat fragmentation can be simulated using an in-house program. Some exercises will make use of R scripts (R being a freely available statistical program). Basic R knowledge is a pre-requisite but we will provide a short introduction to R. The R statistical package is a very powerful tool to analyse data outputs from many population genetics software, and can also be used to simulate genetic data under simple demographic scenarios. More information at the GTPB website, http://gtpb.igc.gulbenkian.pt/bicourses/2018/PGDH18/ Hoping that this course meets your interests, Pedro Fernandes -- Pedro L Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt -- The Gulbenkian Training Programme in Bioinformatics General Office Rua da Quinta Grande, 6 2780-156 OEIRAS Portugal _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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