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

Data Manipulation and Visualisation with Python 10-14 July 2017 & GATK Best Practices for Variant Discovery 17-19 July 2017 - Few places left
by Bert Overduin 16 Jun '17

16 Jun '17

Dear all, We have very few places left on the following workshops (first come, first served). With kind regards, Bert ************************* DATA MANIPULATION AND VISUALISATION WITH PYTHON One of the strengths of the Python language is the availability of mature, high-quality libraries for working with scientific data. Integration between the most popular libraries has lead to the concept of a "scientific Python stack": a collection of packages which are designed to work well together. In this workshop we will see how to leverage these libraries to efficiently work with and visualise large volumes of data. DATE: Monday 10 – Friday 14 July 2017 VENUE: The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK REGISTRATION DEADLINE: Monday 26 June 2017 noon CANCELLATION DEADLINE: Monday 3 July 2017 noon PLACES: 20 (first come, first served) REGISTRATION FEE: £525 (includes coffee/tea, but no lunch) INFORMATION: Bert Overduin (bert.overduin(a)ed.ac.uk) Martin Jones ( martin(a)pythonforbiologists.com) FOR MORE DETAILS AND TO REGISTER: http://genomics.ed.ac.uk/servi ces/data-manipulation-and-visualisation-python ************************* GATK BEST PRACTICES FOR VARIANT DISCOVERY This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. In the course of this workshop, we highlight key functionalities such as the GVCF workflow for joint variant discovery in cohorts, RNAseq-specific processing, and somatic variant discovery using MuTect2. We also preview capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery, and we demonstrate the use of pipelining tools to assemble and execute GATK workflows. DATE: Monday 17 - Wednesday 19 July 2017 VENUE: The King's Buildings,The University of Edinburgh, Edinburgh, Scotland, UK REGISTRATION DEADLINE: Monday 3 July 2017 CANCELLATION DEADLINE: Monday 10 July 2017 PLACES: 85 (lectures), 30 (hands-on sessions) (first come, first served) REGISTRATION FEE: £70 for the lectures, £35 for each half-day hands-on session (includes coffee/tea, but no lunch) INFORMATION: Bert Overduin (bert.overduin(a)ed.ac.uk) FOR MORE DETAILS AND TO REGISTER: http://genomics.ed.ac.uk/services/gatk-best-practices-variant-discovery ************************ -- 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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Vacancy : Software Developer
by Vandeweyer Geert 15 Jun '17

15 Jun '17

The Centre of Medical Genetics at the University of Antwerp has a vacancy for a Software Developer. For more information, see attachment or https://www.uantwerpen.be/en/jobs/vacancies/ap/2017bapffbdef189/ Best regards, Geert Vandeweyer -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43/6 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)uantwerpen.be https://www.uantwerpen.be/en/rg/cognet/ http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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small molecule bioinformatics software developer position at UAntwerpen
by Laukens Kris 14 Jun '17

14 Jun '17

Dear colleagues, feel free to distribute this vacancy within your network. Thank you. Kind regards, Kris Laukens The Faculty of Sciences of the University of Antwerp is seeking to fill the following full-time vacancy in the Department of Mathematics and Computer Science. Scientific software developer in the field of pharma data analytics. This project will be conducted at the interface of 1) the biodata mining team (under supervision of prof. Kris Laukens), a rapidly growing, multi-disciplinary unit within the ADReM data lab / biomina of the department of Mathematics and Computer Science (University of Antwerp, Belgium); 2) (under supervision of prof. Dirk Valkenborg) the Center for Statistics (University of Hasselt, Belgium); and 3) a major pharmaceutical industry partner. Job description You will develop novel implementations for cutting-edge data mining and machine learning approaches, tailored towards the field of small molecule mass-spectrometry. This chemical field plays a central role in many top-notch pharmaceutical and biotechnological applications. Its enormous data complexity requires novel, robust data processing, management and visualisation techniques. As a scientific programmer, you will fulfill a central role in translating the newest data science approaches to industry-grade applications. While being familiar with the type of data and applications is not a prerequisite, you will work closely with domain experts to understand the data and its particular problems, and you will learn to understand the challenges of their applicability in a real laboratory setting. You will implement your methods in a user-friendly software environment and application-programming interface. You collaborate with academic researchers in different disciplines (from computational sciences to life sciences) within the consortium (biomina- the biomedical informatics network Antwerpen, UAntwerpen, UHasselt) and with the industrial partners of the project. Profile and requirements • You have a master or doctoral degree in computer science (data science, software engineering, ...), bioinformatics or chemoinformatics; • You have a good understanding of data mining, statistics, machine learning and visualisation techniques. • You have excellent (scientific) software and database development skills. • You have a strong interest in translating the newest data science solutions to industry-grade applications. • You have excellent interdisciplinary English communication skills, you are quality-oriented and creative, and eager to emerge in new domains. Proven project management skills and industrial experience are a plus; • Previous experience in data mining for bioinformatics, mass spectrometry or related techniques is an advantage but not a prerequisite; We offer • A software developer or postdoctoral position (depending on your degree) for a period of two years. The default start date of the position is November 1st 2017 (but this is open for negotiation); • A salary commensurate with your experience and qualifications; • A dynamic, stimulating and multinational work environment. Interested? Candidates are invited to send a motivation letter, a detailed CV and contact info of at least two references (including email addresses and phone numbers) to Prof. Kris Laukens (kris.laukens(a)uantwerpen.be<mailto:kris.laukens@uantwerpen.be>) and Prof. Dirk Valkenborg (dirk.valkenborg(a)uhasselt.be<mailto:dirk.valkenborg@uhasselt.be>). Don’t hesitate to contact us in advance for more information. -- Kris Laukens, PhD Associate professor bioinformatics - biodata mining Advanced Database Research and Modelling (ADReM) Biomedical Informatics Network Antwerpen (biomina) Department of Mathematics and Computer Science University of Antwerp Middelheimlaan 1, G.111 B-2020 Antwerpen, Belgium T +32 (0)3 265 33 10 E kris.laukens(a)uantwerpen.be<mailto:kris.laukens@uantwerpen.be> W www.uantwerpen.be/en/staff/kris-laukens/<http://www.uantwerpen.be/en/staff/kris-laukens/>

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BioSB Course Quantitative and Predictive Modelling, 26-30 June 2017 in Wageningen, the Netherlands
by Celia van Gelder 11 Jun '17

11 Jun '17

BioSB Course Quantitative and Predictive Modelling Date: 26-30 June, 2017 Location: Wageningen Course Coordinators: Natal van Riel (TUE) & Jaap Molenaar (WUR) Website: http://biosb.nl/education/course-portfolio-2/course-quantitative-and-predic… Registration: http://biosb.nl/education/course-portfolio-2/course-quantitative-and-predic… Please note that this course is free of charge for PhDs who are or become a <http://biosb.nl/about/members/biosb-membership-information/> member of the BioSB research school. Description On June 26-30 2017, BioSB organises the second edition of the course Quantitative and Predictive Modelling (QPM). In this course the participants learn how to describe the dynamic behaviour of biological systems and to integrate experimental data. Concepts of modelling in terms of differential equations are introduced via a great variety of case studies taken from diverse practices. The course offers a math refresher to help those participants who are not (yet) involved in modelling on a daily basis. The emphasis is on providing an introduction into modelling approaches rather than an in-depth treatment of a few techniques and aims as such at a broad audience. The course is a mixture of theory sessions and computer practicals. During the practicals most of the time Matlab will be used. Participants not acquainted with Matlab will get an introduction. The course has to be completed with assignments in the form of practical exercises as homework afterwards. Target audience and learning objectives This course is primarily targeted at academic researchers such as PhD students and Postdocs in Life Sciences, Bioinformatics, Systems Biology or Biomedical Engineering. Participants from the private sector are also welcome. Participants are expected to have some experience in modelling with differential equations. The students will be provided with a theoretical basis, a variety of methods and a computational hands-on experience to handle differential equation modelling, parameter estimation and uncertainty analysis. In the course the students will learn: * How to set-up a dynamic model to represent biological networks using different interaction mechanisms * To implement, simulate and analyse dynamic network models in different software tools * To understand the common ground and the differences for applications in metabolic, regulatory, signalling, population and multi-scale biological processes * To integrate experimental data in modelling, estimate model parameters and assess the accuracy of parameter estimates and model predictions This course is part of the <http://biosb.nl/education/course-portfolio-2/> 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/> . Beste regards, Femke Francissen Femke Francissen Community manager BioSB BioSB Research School Visiting address: Geert Grooteplein 28, route 260, 6525 GA Nijmegen Postal address: P.O. box 9101, route 260, 6500 HB Nijmegen E-mail: <mailto:femke.francissen@biosb.nl> femke.francissen(a)biosb.nl Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl <http://www.biosb.nl/> LinkedIn <http://nl.linkedin.com/in/femkefrancissen> link <http://www.dtls.nl/wp-content/uploads/2014/09/BioSB_logo_full_250x226.jpg>

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Vacancy Bioinformatics and Data Science Trainer ELIXIR-Belgium
by Alexander Botzki 10 Jun '17

10 Jun '17

Dear all, At the VIB Bioinformatics Core, we recently opened one position for a bioinformatics and data science trainer: ELIXIR Trainer at VIB Bioinformatics Core http://www.vib.be/en/jobs/Pages/Bioinformatics-and-Data-Science-Trainer-ELI… Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/> [signatureFooter (002)]

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Bioinformatics position at the Princess Maxima Center for Pediatric Oncology
by Patrick Kemmeren 09 Jun '17

09 Jun '17

Dear all, Within the Princess Maxima Center for Pediatric Oncology, we currently have an open vacancy for a Bioinformatician (PhD or Msc)! For more information, please see: http://www.werkenbijprinsesmaximacentrum.nl/vacaturetekst-engels/scientist-… Regards, Patrick -- Patrick Kemmeren, PhD Principal Investigator T +31 (0)88 972 55 05 | M +31 (0)6 53 11 25 53 Princess Maxima Center * * *Princess Máxima Center for Pediatric Oncology* *Location Hubrecht institute*| Uppsalalaan 8 | 3584 CT Utrecht | T +31 (0)88 972 90 00 |***> Website* <http://prinsesmaximacentrum.com/>

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Galaxy Community Conference: Register by 16 June
by Dave Clements 08 Jun '17

08 Jun '17

2017 Galaxy Community Conference (GCC2017) 26-30 June 2017 Montpellier, France https://gcc2017.sciencesconf.org/ https://gcc2017.sched.com/ -- The Galaxy Community Conference (GCC) <https://gcc2017.sciencesconf.org/> brings together researchers working in and supporting data intensive life science research. There is no better place to share your work and learn from others that are addressing diverse questions and facing common challenges in data intensive biology. GCC participants work across the tree of life, around the world, and represent universities, research organizations, industry, medical schools and research hospitals. GCC2017 will be in Montpellier, France, 26-30 June and features two days of presentations, discussions, poster sessions, lightning talks, computer demos, keynotes, and birds-of-a-feather meetups <https://gcc2017.sched.com/overview/type/Conference>, all about data-intensive biology and the tools that support it. GCC2017 also features data and coding hackathons <https://gcc2017.sciencesconf.org/page/hackathon>, and two days of training <https://gcc2017.sched.com/overview/type/Training> covering 16 different topics. GCC2017 will be held at Le Corum Conference Centre <http://www.montpellier-events.com/en/The-Corum/Presentation> in the heart of Montpellier <https://gcc2017.sciencesconf.org/resource/page/id/2>, just 10km from the Mediterranean. Registration closes 16 June <https://gcc2017.sciencesconf.org/page/registration>. Costs start at 75€ per day for postdocs and students. If you work in data intensive life science research then GCC2017 is an ideal opportunity to present your work. Lightning talk <https://gcc2017.sciencesconf.org/page/submit> and birds-of-a-feather <https://docs.google.com/forms/d/e/1FAIpQLSdRCs97OWt47qmMxWZAtSV3TTLJ24IhW0m…> submission are still open, and there is limited space available for late poster and computer demo submissions <https://gcc2017.sciencesconf.org/page/submit>. About Galaxy Galaxy <https://galaxyproject.org/> is an open, web-based platform for data-intensive biomedical analysis used by tens of thousands of researchers around the world. It supports ad hoc exploration and analysis through scalable and repeatable data analysis pipelines for large research studies. Galaxy is available in over 90 free and publicly accessible web servers, on public and national cloud infrastructures, and is locally installed at hundreds, if not thousands, of research organisations around the world. We hope to see you in Montpellier! Au revoir, The GCC2017 Organising Committee -- https://galaxyproject.org/ https://getgalaxy.org/ https://usegalaxy.org/ https://gcc2017.sciencesconf.org/

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Call for position: PhD STUDENT ON BIOINFORMATICS FOR EPIGENOMICS
by mbizet 08 Jun '17

08 Jun '17

Hello, A Ph.D. student position on bioinformatics is opening in the "Laboratory of Cancer Epigenetics", ULB, Brussels, Belgium. Job description: ---------------- A position is available for a highly motivated Master student that wishes to realise a Ph.D thesis at the Laboratory of Cancer Epigenetics headed by Prof. François Fuks (ULB-Cancer Research Center, Brussels). The research goal will be the analysis of transcriptomic and epigenomic changes (e.g. DNA methylation, histone modifications) that arise in cancers. Particularly the analysis of next generation sequencing data concerning a novel epigenetic modification, which our lab recently investigated, will also be one of the tasks of the candidate (Delatte et al., Science 2016). The integrative analysis of these different biological levels of information will be one of the main challenging tasks of the candidate, together with the extraction of predictive signatures that may help to improve patient therapy. Working environment: -------------------- The host lab is running a Next Generation Sequencing platform: EPICS (http://epics.ulb.be/) and is part of the ULB-Cancer Research Center (U-CRC), providing a high profile scientific environment. The candidate will join other experienced bioinformaticians working on transcriptomics and epigenomics, and in addition he/she will have to opportunity to interact with other bioinformaticians from the “Interuniversity Institute of Bioinformatics in Brussels” (http://ibsquare.be) Profile/Starting date: ---------------------- The candidate should hold a master in bioinformatics, bio-engineering, biomedical sciences or eventually in engineering or computer sciences and demonstrate proficiency in statistics and programming (e.g. R, python). Knowledge of sequencing data, genome-wide data sets (e.g. ChIP-Seq, RNA-Seq ...) or massive datasets analysis will be assets. The applicant should have good organizational skills and a taste for interdisciplinary research. The interaction with the biologists in the lab will be key for the success of this project and genuine interest for biology and clinical researches is required. A good biological background will be valuable. The position is associated to a Belgian grant funded for 4 years. Screening of applications begins immediately and continues until an outstanding candidate is selected (flexible starting date). How to apply? ------------- Informal enquiries, a motivation letter, a CV (including grades and ranking) and names of two referees should be sent to: Martin Bizet (mbizet(a)ulb.ac.be) Lab website: http://www.ulb.ac.be/medecine/fukslab Lab NGS platform: http://epics.ulb.be/ Selected publications: ---------------------- - Van Grembergen et al Sci Adv 2016 - Delatte et al. Science 2016 - Boumahdi et al. Nature 2014 - Deplus et al. Cell Rep. 2014 - Dedeurwaerder et al. Briefings in Bioinformatics 2014 - Delatte et al. EMBO J. 2014 - Deplus et al. EMBO J. 2013 - Volkmar et al. EMBO J. 2012 - Dedeurwaerder et al. EMBO Mol Med.2011 - Dedeurwaerder et al. Epigenomics 2011 - Fuks F. Nature 2010 - Villa et al. Cancer Cell 2007 - Viré et al. Nature 2006

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PhD position in Bioinformatics/Computerscience
by Kathleen Marchal 08 Jun '17

08 Jun '17

Dear all, The research group DBN (dataintegration & Biological networks) has an open PhD position in the domain of method development for precision oncology. The goal of the PhD research is to develop and apply systems genetics approaches to identify driver pathways and prognostic biomarkers underlying clinical phenotypes relevant to cancer. Hereto innovative methods need to be developed that integrate genomic information derived from cohorts of tumor samples with clinical information (e.g., therapy outcome). The focus will be on studying the importance of network rewiring during cancer development and on assessing the added value of whole genome sequencing for optimal patient stratification. The research will be performed in close collaboration with clinicians, experts in molecular diagnosis and software engineers to facilitate the transfer of the developed methods to a clinical setting. •You hold a Master degree in Engineering, in Sciences; in Bioinformatics, in Applied Biological Sciences; in Health Sciences or an equivalent degree. Last year students can also apply. •A strong interest in interdisciplinary research •A strong interest in fundamental and/or applied research •Minimal background in biology or molecular biology •Strong background in computer hard- and software systems •Proficiency in programming languages such as Java, Perl or Python, as well as Linux systems. •Fluency in spoken and written English is a strong requirement For more information on how to apply see attachment. Please contact us if you are interested and have more questions. Regards, Kathleen Marchal -- Prof. Kathleen Marchal Dept. of Plant Biotechnology and Bioinformatics, Ghent University Dept. of Information Technology, IDLab, imec, Dept. of Genetics, University of Pretoria, South Africa http://bioinformatics.psb.ugent.be/DBN iGent Toren, Technologiepark 15, 9052 Gent, Belgium

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Introduction to RNA-seq Data Analysis - 21/22 September 2017 workshop open for applications and one place left on 29/30 June 2017workshop
by Bert Overduin 07 Jun '17

07 Jun '17

Dear all, Applications are now accepted for the Introduction to RNA-seq Data Analysis workshop on Thu 21& Fri 22 September 2017. Details and a link to the application form can be found here: http://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis We also have one place left on the workshop on Thu 29 & Fri 30 June 2017. If you're interested in this spot, please fill in the application form you can find at: https://www.surveymonkey.co.uk/r/W63XZDL Other workshops that are currently open for registration / application can be found on the Edinburgh Genomics training page: http://genomics.ed.ac.uk/services/training With kind regards, Bert -- 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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