- BBClist - maillist.psb.ugent.be

+++ 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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Anniversary RSAT / GINsim : Workshop and tutorial
by Morgane Thomas-Chollier 30 Mar '18

30 Mar '18

Workshop Anniversary 20th RSAT/ 15th GINsim ----------------------------------------------------------------- Computational biology softwares tend to be a relatively short life. RSAT (http://rsat.eu/) and GINsim (http://ginsim.org/) are notable exceptions, in large part thanks to active and friendly networks of collaborators. Indeed, 2018 marks the 20th anniversary of the first publication on RSAT, as well as the 15th anniversary of the first publication on GINsim. We propose to celebrate this joint event at IBENS in Paris, on May 16-17, 2018. The first day will be devoted to a series invited talks on the computational modelling and analysis of ci-regulatory regions and cellular networks. The second day will be devoted to tutorials on RSAT and GINsim for biologists. Invited speakers: • Samuel Collombet, Institut Curie, Paris • Claudine Chaouiya, IGC, Lisbon, Portugal • Bruno Contreiras Moreira, Estación Experimental de Aula Dei-CSIC, Zaragoza, Spain • Carl Herrmann, Universität Heidelberg, DKFZ, Heidelberg, Germany • Anthony Mathelier, NCMM, Oslo Norway • Pedro Monteiro, INESC-ID / IST - Universidade de Lisboa, Portugal • Elisabeth Remy, Institut de Mathématiques de Marseille • Hugues Roest Crollius, IBENS, Paris • Jacques van Helden, TAGC Marseille Program and registration (free but compulsory) : https://www.ibens.ens.fr/spip.php?article350 Looking forward to meeting you at this event ! Morgane Thomas-Chollier and Denis Thieffry

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Upcoming Bioinformatics Training Sessions of VIB and ELIXIR Belgium
by Alexander Botzki 29 Mar '18

29 Mar '18

Dear all, We would like to let you know that EBI trainers are coming to Belgium to give workshops on Ensembl Browser and Ensembl REST API in May 2018. Furthermore, ELIXIR Belgium is organising a Data Carpentry workshop in Brussels in June 2018. If you like to have more info and register to any of the courses, please visit https://bit.ly/1PkrdsU Thanks a lot. Best regards, Alexander ________________________________ Ensembl Browser Workshop This workshop offers participants hands-on experience in the use of the Ensembl vertebrate genome browser and provides them with the necessary background information. Ensembl genomes can also be covered if participants are working with bacteria, plants, fungi, protists or (invertebrate) metazoa. Date: 4 May Location: Park Inn, Leuven Trainer: Erin Haskell, EBI ________________________________ Ensembl REST API Workshop This workshop will introduce the basics of working with the Ensembl REST API, including an introduction to the main endpoints, exploring the documentation and writing sample clients. Participants will write their own scripts. Requirements Basic knowledge of a programming language. While any language can be used to access the REST API in practice, the support in this course will be limited to Python and Perl. Date: 14 May Location: BioAccelerator Trainer: Benjamin Moore and Matthew Laird, EBI ________________________________ ELIXIR Data carpentry workshop This is an introductory workshop to data management, databases, and data analysis in R. Researchers can perform simple to complex data management through open source tools and techniques which do not require highly specialist skills. This hands-on workshop will assist you to learn more about basic concepts and tools, including program design, version control, data management, and task automation. Requirements We recommend participants to have a basic understanding of R and its data types. Date: 12 and 13 June Location: Brussels Trainer: Paula Andrea Martinez, Stijn Van Hoey, Tina O'Grady, Christof De B

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Vacancies in Bioinformatics & Data Science @ KeyGene
by Roeland van Ham 28 Mar '18

28 Mar '18

We have vacancies available in Bioinformatics & Data Science at KeyGene, Wageningen, The Netherlands. Check them out at: http://www.keygene.com/scientist-genome-bioinformatics/ http://www.keygene.com/data-scientist-quantitative-genetics/ Interested in a postdoc position in sequence analysis instead? Contact me at rvh(a)keygene.com<mailto:rvh@keygene.com> Prof. Dr. Roeland van Ham Vice President Bioinformatics & Modeling Keygene N.V. | P.O. Box 216 | 6700 AE Wageningen | The Netherlands T (+31) 317 46 68 66 | F (+31) 317 42 49 39 | CoC. 09066631 | http://www.keygene.com<http://www.keygene.com/> [http://www.keygene.com/images/keygenegeneral.jpg]<http://www.keygene.com> Stay up-to-date! Subscribe to our bimonthly newsletter here<http://www.keygene.com/newsletter> [http://www.keygene.com/images/linkedin-grey.png]<https://www.linkedin.com/company/KeyGene> [http://www.keygene.com/images/twitter-grey.png] <https://twitter.com/KeyGeneInfo> [http://www.keygene.com/images/facebook-grey.png] <https://www.facebook.com/KeyGeneNV> The information contained in this message, and attachments if any, may be privileged and/or confidential and is intended to be received only by persons entitled to receive such information. Use of any part of this message and/or its attachments if any, in any other way than as explicitly stated by the sender is strictly prohibited. Should you receive this message unintentionally please notify the sender immediately, and delete it together with all attachments, if any. Thank you. The transmission of messages and/or information via the Internet is not secured and may be intercepted by third parties. KeyGene assumes no liability for any damage caused by any unintentional disclosure and/or use of the content of this message and attachments if any.

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Tenure track Computational Biology vacancy at CCA (Amsterdam)
by Ylstra, B 27 Mar '18

27 Mar '18

Anyone interested in a Tenure track Computational Biologist / PI-position? Please apply within the coming 2 weeks via https://www.werkenbijvumc.nl/vacatures/assistant-professor-computational-on…

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Registration open: Workshop Applying bioinformatics and data science competency frameworks to ELIXIR Training, 5-6 April 2018, Amsterdam
by Celia van Gelder 27 Mar '18

27 Mar '18

Workshop Applying bioinformatics and data science competency frameworks to ELIXIR Training, 5-6 April 2018, Amsterdam Date: 5-6 April 2018 (preceded by an optional seminar on April 4) Venue: Amsterdam Science Park Congress Centre, Science Park 123, 1098 XG Amsterdam Website & registration: <https://www.eventbrite.co.uk/e/applying-bioinformatics-and-data-science-com petency-frameworks-to-elixir-training-registration-43087835877> Eventbrite page. Registration is free of charge and you can register for each day separately. Full Programme: <https://www.dtls.nl/wp-content/uploads/2018/03/Full-Programme-120318.pdf> https://www.dtls.nl/wp-content/uploads/2018/03/Full-Programme-120318.pdf Organizers: Celia van Gelder (DTL/ELIXIR-Netherlands), Gabriella Rustici (University of Cambridge, ELIXIR-UK), Vera Matser (BioExcel), Allegra Via (ELIXIR-Italy) Target audience: Individuals working in training and education who are interested in learning the state of the art about bioinformatics and data science competency frameworks and their application to date. Description Much work is currently being done in developing and applying competency frameworks, both in bioinformatics and in data science. In the context of ELIXIR Training, we aim to build on the existing expertise in this area and, together with the training stakeholders, to derive a proper implementation strategy. This international workshop will bring together individuals from organisations and projects who have expertise in defining and in applying competency bioinformatics and data science frameworks in their own organisations. In a series of interactive sessions, we will build on the existing knowledge and work towards the following workshop goals: * Identify competency frameworks that are relevant to the ELIXIR user community and learn about successful implementation examples of these frameworks * Further define the relevant "personas" we are targeting with (ELIXIR) training * Extract from the existing work a set of core competencies and sets of KSAs (knowledge, skills and abilities) that can subsequently be used: * to map courses in TeSS, the ELIXIR Training Portal * to build a curriculum for a one-week Advanced Bioinformatics Workshop (which will be part of the CODATA RDA Research Data Science Summer school series) * to set the first steps towards defining routes through a specific set of courses (learning paths) Workshop Speakers: Implementing a competency-based training strategy for biomolecular researchers with high computational needs - Vera Matser (BioExcel) ISCB competencies and their implementation in H3ABioNet - Nicola Mulder (Computational Biology Division, University of Cape Town, H3ABioNet PI) Mapping bioinformatics competencies to University of Cambridge trainings - Gabriella Rustici (University of Cambridge) Application of EDISON Data Science Framework (EDSF) for customisable Data Science curricula development - Yuri Demchenko (University of Amsterdam, EDISON project) The curriculum of the CODATA-RDA Research Data Science Summer School - Hugh Shananan (Royal Holloway University of London) A critical look at competencies (Allegra Via, CNR-IBPM, ELIXIR-Italy) Learning Paths in the ERUDITE portal - John van Horn (University of Southern California, BD2K Training Coordination Center) Workflows in TeS - Niall Beard (ELIXIR-UK, University of Manchester) Seminar April 4, 14.40-16.30 Designing effective instruction and interpretable assessment by Allegra Via (CNR-IBPM, ELIXIR-Italy). See https://www.dtls.nl/wp-content/uploads/2018/03/April-4-pdf-2.pdf for more info. More information? Please contact Celia van Gelder ( <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl) if you need more information. Dr. Celia W.G. van Gelder Programme Manager Learning DTL/ELIXIR-NL Training Education Manager BioSB ELIXIR Training Platform Leader tel. +31613375327 e-mail: <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl websites: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.nl/> www.biosb.nl skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht

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