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

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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BioSB course RNA-seq data analysis course (6th edition), 26-28 September 2016
by Celia van Gelder 30 Aug '16

30 Aug '16

BioSB RNA- seq data analysis course (6th edition) Date: 26-28 September, 2016 Location: Leiden, the Netherlands Course coordinators: Peter-Bram 't Hoen (LUMC), Jan Oosting (LUMC), Celia van Gelder (BioSB, <mailto:education@biosb.nl> education(a)biosb.nl ) Course website: <http://biosb.nl/education/course-portfolio/rna-seq/> http://biosb.nl/education/course-portfolio/rna-seq/ . Registration: <http://biosb.nl/education/course-portfolio/rna-seq/enrollment-rnaseq-2016/> http://biosb.nl/education/course-portfolio/rna-seq/enrollment-rnaseq-2016/ More information: <mailto:education@biosb.nl> education(a)biosb.nl Course description BioSB and partner LUMC are organizing a 3-day course on RNA-seq. This is an expert course for people with experience in NGS and a follow-up course on the general NGS data analysis course (coordinator Jeroen Laros, LUMC). The course will consist of seminars and hands-on command line, Galaxy and R practicals and will focus on data preprocessing, quality control, alignment, visualization and statistics for differential transcript expression. Examples will be taken from human and mouse studies. The course does not cover prokaryotic RNA profiling nor plant- and metagenomics aspects. Course topics RNA-seq experimental approaches Alignment and de novo assembly Statistics for differential gene expression eQTL analysis and allele specific expression Variant calling and RNA editing Small RNA profiling Software for RNA-seq data analysis Programme The programme can be found here: <http://biosb.nl/wp-content/uploads/2016/07/RNAseq_program_2016_v4.pdf> http://biosb.nl/wp-content/uploads/2016/07/RNAseq_program_2016_v4.pdf Target audience Participants for the RNA-seq course should preferably have participated in the general NGS course or otherwise have demonstrated hands-on experience with NGS data analysis. The course is aimed at PhD students and post-docs, but scientific programmers and data analysts with a background in biology and bioinformatics may also attend. The practicals are mostly in R. We require that participants have at least basic knowledge of R and experience in running R scripts. Registrations will be handled on a first-come-first-served basis but experience and motivation will be reviewed. Seats have been reserved for participants in the FP7-funded projects <http://rd-connect.eu/> RD-Connect, <http://www.rd-neuromics.eu/> Neuromics, <http://www.eurenomics.eu/> Eurenomics and <https://www.bbmri.nl/> BBMRI-NL. BioSB Course Programme This course is part of the <http://biosb.nl/education/course-portfolio-2/> Course Portfolio 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 <http://www.biosb.nl> www.biosb.nl. More information For more information about the course you can contact Celia van Gelder at <mailto:education@biosb.nl> education(a)biosb.nl. Dr. Celia W.G. van Gelder Programme Manager Learning DTL/ELIXIR-NL Training Education Manager BioSB tel. +31613375327 e-mail: 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 Postal address: DTL PO Box 19245 3501 DE Utrecht

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Job Opening: Data Scientist at Open Analytics (Belgium)
by Tobias Verbeke 31 Jul '16

31 Jul '16

Open Analytics is an international company providing data analysis services and products across geographies and industrial sectors. We are currently looking to expand our data science team with a candidate who fits the following profile: Data Scientist for a MSc / PhD in Computer Science, Engineering or Statistics. Bioinformaticians or computational biologists are likely to have relevant experience as well. A detailed description can be found at http://www.openanalytics.eu/jobs Kind regards, Tobias Verbeke -- Tobias Verbeke Managing Director Open Analytics NV Jupiterstraat 20 2600 Antwerp Belgium E tobias.verbeke(a)openanalytics.eu M +32 499 36 33 15 http://www.openanalytics.eu

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The first EASyM Systems Medicine conference, 26-28 October in Berlin
by Johann Pellet 27 Jul '16

27 Jul '16

Dear colleague(s), We cordially invite you to present your research at the 1st conference of the European Association of Systems Medicine which will take place at the Kaiserin-Friedrich Haus (near Charité) in Berlin, Germany, on the 26th-28th October 2016. This international event will bring together researchers from all over Europe, including biologists, physicians, health professionals and specialists in mathematical and computational programming. At the conference, cases of successful usage of Systems Medicine will be presented, as well as talks and tutorials about big data, omics, bioinformatics, doctor and patient involvement, and compliance with privacy regulations. Key note speakers include Leroy Hood, MD, PhD, Co-founder and President of the Institute for Systems Biology, Seattle, USA, Paul-Peter Tak, MD, PhD, Senior Vice-President and Head of Immuno-Inflammation R&D at GlaxoSmithKline, Dame Janet Thornton, PhD, former director of EMBL-EBI and a high-level representative of the European Commission (to be defined). The conference is aimed at basic and clinical researchers in academia and industry who want to apply Systems Medicine approaches to address unmet clinical needs. For further details and registration, please visit our website www.easym.eu <http://www.easym.eu/> The abstract submission deadline has been extended until the 5th August, and early bird registration until the 12th August. Multiple slots for oral presentations are still opened for each session. NEW: the coordinators and leaders of European research projects and consortia will be given the opportunity of a 5-minute presentation and dedicated table at the Wednesday 26th October networking evening reception. Please email info.easym(a)gmail.com <mailto:info.easym@gmail.com> with the same deadline as for the abstract submission if you are interested to introduce your initiative. Important information for MDs and doctoral students: in addition to the main meeting, the « 2nd SysBioMed Tutorial: Modelling and bioinformatics for personalised medicine » that will take place on Wednesday 26th October is in the process of being accredited by CME and ECTS. Another workshop entitled « Get to know SysmedIBD - Systems Medicine of chronic inflammatory bowel disease » will take place on the same day. We are very much looking forward to welcoming you in Berlin, Yours sincerely, Dr. Charles Auffray, Chair of the Executive Board European Association of Systems Medicine and Professor Tim Radstake, Vice-Chair of the Executive Board European Association of Systems Medicine Chair of the Scientific Committee ABOUT EASyM The European Association of System Medicine (EASyM) is the implementation of Systems Medicine in European clinical research and healthcare. EASyM has been initiated by the European FP7-funded Coordinating Action Systems Medicine (CASyM, www.casym.eu <http://www.casym.eu/>). EASyM is a charitable association open to everyone with an interest in personalised medicine and systems medicine. The association strives to integrate all relevant stakeholders, including clinicians, researchers, medical and patient organisations, industry, funders and policy makers. EASyM organises annual conferences, offers training in Systems Medicine, and provides regular updates about Systems Medicine development and findings. EASyM was founded on 30th September 2015 in Brussels by 27 medical doctors, researchers and health care stakeholders from 12 different countries.

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Registration deadline ESCS 2016!
by ISCBSC announcement 26 Jul '16

26 Jul '16

Dear colleague, *We would like to remind you that the early-bird registration deadline for ESCS 2016 will close this Friday on 29 July! Please visit http://escs2016.iscbsc.org/escs2016-registration <http://escs2016.iscbsc.org/escs2016-registration> for more information.* The ESCS is a biennial interdisciplinary symposium that brings together students and young researchers from computational biology, bioinformatics, systems biology, and related fields. This symposium offers you a great opportunity to present your research to an international audience, get insights into hot topics and newly developed methods and build a network within the computational biology community of Europe. The symposium includes ice-breaking, oral presentations, keynote talks, poster presentations and an evening social event that offer you the opportunity to get to know fellow young scientists from all over Europe in a casual setting. We welcome students and young researchers from all areas of computational biology to join our community. Please help us spread the word by using the hashtag #ESCS16 on social media. Please visit our website http://escs2016.iscbsc.org/ regularly as more information will be announced soon. We look forward to welcome you in The Hague! Annika Jacobsen and Kevin Schwahn, chair and co-chair, ESCS 2016

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Genome Science, Liverpool, 30th August - 1st September 2016
by Bert Overduin 26 Jul '16

26 Jul '16

Forwarding on behalf of Mick Watson: Dear All I’m delighted to invite you to a conference I help organise every year, Genome Science, with speakers who use the latest genomic technologies to tackle problems from across the life sciences: Genome Science 2016 http://genomescience.org.uk/, Liverpool, 30th August - 1st September 2016 We have sessions on: Bioinformatics and Computational genomics Clinical and translational genomics Environmental genomics Developmental biology Genome engineering and synthetic biology (NEW this year) Microbial genomics New Technologies, incl. highlight single cell genomics Plant and animal genomics Vendor sessions Science Communication Career development/opportunities Speakers include: Ed Yong, Science Communicator and author recent book “I contain multitudes” (http://tinyurl.com/zk6qaw3) Dr Kosuke Yusa, Sanger, Genome Engineering Dr Jack Gilbert, Argonne National Laboratory, Microbiome Dr Jose Clemente, Mount Sinai Dr David Aanensen, Sanger, Pathogen Surveillanece Prof Allan Downie, John Innes, Ash Dieback Our very own Jeffrey Schoenebeck! Michael Baym, Harvard, Systems Biology And many many more! I look forward to seeing you there! Cheers Mick The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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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2 places left on Bioinformatics using LINUX course
by Oliver Hooker 26 Jul '16

26 Jul '16

Introduction to Bioinformatics using LINUX 2 places left!! http://prstatistics.com/course/introduction-to-linux-workflows-for-biologis… Instructor: Dr. Martin Jones This course will run from 15th – 19th August 2016 at SCENE (the Scottish Centre for Ecology and the Natural Environment), Loch Lomond National Park, Glasgow. Course overview: 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 customize 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. Availability: 15 places total. Course programme Monday 15th – Classes from 09:00 to 17:00 (approximately) ● Session 1 - The design of Linux In the first session we briefly cover the design of Linux: how is it different from Windows/OSX and how is it best used? We'll then jump straight onto the command line and learn about the layout of the Linux filesystem and how to navigate it. We'll describe Linux's file permission system (which often trips up beginners), how paths work, and how we actually run programs on the command line. We'll learn a few tricks for using the command line more efficiently, and how to deal with programs that are misbehaving. We'll finish this session by looking at the built in help system and how to read and interpret manual pages. ● Session 2 - System management We'll first look at a few command line tools for monitoring the status of the system and keeping track of what's happening to processor power, memory, and disk space. We'll go over the process of installing new software from the built in repositories (which is easy) and from source code downloads (which is trickier). We'll also introduce some tools for benchmarking software (measuring the time/memory requirements of processing large datasets). Tuesday 16th - Classes from 09:00 to 17:00 (approximately) ● Session 3 - Manipulating tabular data Many data types we want to work with in bioinformatics are stored as tabular plain text files, and here we learn all about manipulating tabular data on the command line. We'll start with simple things like extracting columns, filtering and sorting, searching for text before moving on to more complex tasks like searching for duplicated values, summarizing large files, and combining simple tools into long commands. ● Session 4 - Constructing pipelines In this session we will look at the various tools Linux has for constructing pipelines out of individual commands. Aliases, shell redirection, pipes, and shell scripting will all be introduced here. We'll also look at a couple of specific tools to help with running tools on multiple processors, and for monitoring the progress of long running tasks. Wednesday 17th - Classes from 09:00 to 17:00 (approximately) ● Session 5 – EMBOSS EMBOSS is a suite of bioinformatics command-line tools explicitly designed to work in the Linux paradigm. We'll get an overview of the different sequence data formats that we might expect to work with, and put what we learned about shell scripting to biological use by building a pipeline to compare codon usage across two collections of DNA sequences. ● Session 6 – Using a Linux server Often in bioinformatics we'll be working on a Linux server rather than our own computer— typically because we need access to more computing power, or to specialized tools and datasets. In this session we'll learn how to connect to a Linux server and how to manage sessions. We'll also consider the various ways of moving data to and from a server from your own computer, and finish with a discussion of the considerations we have to make when working on a shared computer. Thursday 18th - Classes from 09:00 to 17:00 (approximately) ● Session 7 – Combining methods In the next two sessions — i.e. one full day — we'll put everything we have learned together and implement a workflow for next-gen sequence analysis. In this first session we'll carry out quality control on some paired-end Illumina data and map these reads to a reference genome. We'll then look at various approaches to automating this pipeline, allowing us to quickly do the same for a second dataset. ● Session 8 – Combining methods The second part of the next-gen workflow is to call variants to identify SNPs between our two samples and the reference genome. We'll look at the VCF file format and figure out how to filter SNPs for read coverage and quality. By counting the number of SNPs between each sample and the reference we will try to figure out something about the biology of the two samples. We'll attempt to automate this analysis in various ways so that we could easily repeat the pipeline for additional samples. Friday 19th - Classes from 09:00 to 16:00 (approximately) ● Session 9 – Customization Part of the Linux design is that everything can be customized. This can be intimidating at first but, given that bioinformatics work is often fairly repetitive, can be used to good effect. Here we'll learn about environment variables, custom prompts, soft links, and ssh configuration — a collection of tools with modest capabilities, but which together can make life on the command line much more pleasant. In this last session there will also be time to continue working on the next-gen sequencing pipeline. The afternoon of Friday 19th is reserved for finishing off the next-gen workflow exercise, working on your own datasets, or leaving early for travel. The cost is £530 (+VAT) including lunches and course materials. An all-inclusive option is also available at £660 (+VAT); this includes breakfast, lunch, dinner, refreshments, accommodation and course materials. Participants will need a laptop with a recent version of Python installed. Please send inquiries to oliverhooker(a)prstatistics.com or visit the website www.prstatistics.com Please feel free to distribute this information anywhere you think suitable Upcoming courses - email for details oliverhooker(a)prstatistics.com INTRODUCTION TO PYTHON FOR BIOLOGISTS (May) ADVANCES IN SPATIAL ANALYSIS OF MULTIVARIATE ECOLOGICAL DATA: THEORY AND PRACTICE (July) GENETIC DATA ANALYSIS USING R (August) INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING (August) MODEL BASED MULTIVARIATE ANALYSIS OF ECOLOGICAL DATA USING R (October) LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R (October) APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS (October) PHYLOGENETIC DATA ANALYSIS USING R (October/November) SPATIAL ANALYSIS OF ECOLOGIC AL DATA USING R (November ADVANCING IN STATISTICAL MODELLING USING R (December) Dates still to be confirmed - email for details oliverhooker(a)prstatistics.com STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR USING R INTRODUCTION TO R AND STATISTICS FOR BIOLOGISTS BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS Oliver Hooker PR~Statistics -- Oliver Hooker PR statistics 3/1 128 Brunswick Street Glasgow G1 1TF +44 (0) 7966500340 www.prstatistics.com www.prstatistics.com/organiser/oliver-hooker/

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18 PhD Student Positions in Cancer Research in Luxembourg
by Francisco Azuaje 22 Jul '16

22 Jul '16

Dear BeNeLux bioinformatics colleagues, CANBIO, a new PhD training program in cancer research, is seeking candidates in different areas, including Bioinformatics and Systems Biology. For further information and submitting applications, please visit: https://www.lih.lu/jobs/detail/18-phd-student-positions-in-cancer-research-… Sincerely, Francisco. _________________________________ Francisco Azuaje, PhD Principal Investigator NORLUX Neuro-Oncology Laboratory 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 http://www.norlux.lu 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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Call for Poster abstracts: 10th International Workshop Machine Learning in Systems Biology (MLSB-2016)
by Dijk, Aalt-Jan van 19 Jul '16

19 Jul '16

Hi all, Organized as an ECCB pre-conference workshop (September 3-4, 2016, The Hague), MLSB is a scientific forum for the exchange between researchers from Systems Biology and Machine Learning, to promote the exchange of ideas, interactions and collaborations between these communities. There is still the opportunity to submit a poster abstract. Deadline is August 19; see http://www.eccb2016.org/wp-content/uploads/2016/07/MLSB_postercall.pdf for more information. General information about MLSB can be found here: http://www.eccb2016.org/programme/workshops/w1/ best, Aalt-Jan van Dijk Wageningen University and Research Centre

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job offer in Jeroen Raes's Lab
by Stephane Rombauts 19 Jul '16

19 Jul '16

Job Offer in Jeroen Raes-lab (KU-Leuven) see attachment -- Stephane Rombauts Senior staff scientist Tel:+32 (0)9 331 38 21 Department of Plant Systems Biology VIB, Ghent University Technologiepark 927 9052 Ghent, Belgium http://www.psb.ugent.be

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