- BBClist - maillist.psb.ugent.be

Last call: BioSB HotTopics: ONT Nanopore sequencing, April 20th, Delft
by Thomas Abeel 12 Apr '17

12 Apr '17

Dear colleagues, April 20, 2017 we organize a BioSB HotTopics workshop on ONT Nanopore sequencing at TU Delft. You are cordially invited. Full program and registration: http://bit.do/biosb_nanopore Nanopore sequencing has been revolutionizing the sequencing arena for the last few years. The last decade, sequencing went from highly-specialized to a commodity product that can be readily purchased from a specialty provider. ONT has taken this again a step further and is now enabling anyone to get into 'do-it-yourself' sequencing. Sequencing now requires no capital investment, very little in lab setup and anybody with a steady hand can start to generate data. While the technology has tremendous potential, there are still a few teething problems and sharing expert knowledge is critical to realize its full potential. The goal of this meeting is to bring the 'local' ONT community together and strengthen information sharing and collaboration within the Netherlands and beyond. The program is aimed at novice and expert users alike. This is the last call for participation and registration. Registration closes April 14, 9am. kind regards, Thomas

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vacancy statistician
by Veronique Storme 12 Apr '17

12 Apr '17

Dear all, The VIB-UGent Center for Plant Systems Biology (PSB) in Ghent, Belgium, is currently looking for a full-time statistician in support of the research activities in the Center. [ http://www.vib.be/en/jobs/Pages/Statistician.aspx | Read more ] kind regards, Veronique Véronique Storme - Biostatistician Applied Bioinformatics And Biostatistics VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 39 50 [ http://www.psb.ugent.be/ | www.psb.ugent.be ]

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Science Manager and Software Engineer positions at ELIXIR-Luxembourg Node
by Venkata Satagopam (TeC) 12 Apr '17

12 Apr '17

Dear all ELIXIR Luxembourg is hiring Software Engineer<http://recruitment.uni.lu/en/details.html?id=QMUFK026203F3VBQB7V7VV4S8&nPos…> to work on web-based knowledge management tools, bioinformatics analysis algorithms and GUI design and implementation. Another opening is for Science Manager<http://recruitment.uni.lu/en/details.html?id=QMUFK026203F3VBQB7V7VV4S8&nPos…> to support the establishment and operation of the Node and manage its strategy development. Best regards Venkata -- Venkata Satagopam Technical Coordinator ELIXIR-Luxembourg Node Bioinformatics Core Luxembourg Centre For Systems Biomedicine (LCSB) University of Luxembourg Campus Belval, House of Biomedicine II 6, avenue du Swing L-4367 Belvaux T +352-466-644-6421 F +352-466-644-6949 venkata.satagopam(a)elixir-luxembourg.org<mailto:venkata.satagopam@elixir-luxembourg.org> https://www.elixir-europe.org/about/elixir-luxembourg ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----

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Workshop GATK Best Practices for Variant Discovery, 17-19 July 2017 - Registration open
by Bert Overduin 12 Apr '17

12 Apr '17

Dear all, I am happy to announce that for the third year in a row we have been able to get three members of the GATK team of the Broad Institute ( https://software.broadinstitute.org/gatk/) over to Edinburgh for a few days to teach a workshop on GATK Best Practices for Variant Discovery. Details of the workshop can be found below. With kind regards, Bert ********** GATK BEST PRACTICES FOR VARIANT DISCOVERY 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) TO REGISTER: http://genomics.ed.ac.uk/services/gatk-best-practices-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. "Excellent opportunity to learn from world-renowned experts!" (April 2016) INSTRUCTORS GATK staff (The Broad Institute, Cambridge, MA, United States) WORKSHOP FORMAT The workshop is composed of one day of lectures (including many opportunities for Q&A) and two optional days of hands-on training, structured as follows: Lectures (day 1): Rationale, theory and application of the GATK Best Practices for Variant Discovery in high-throughput sequencing data. Hands-on 1 (day 2 am): Germline variant discovery (SNPs + Indels) Hands-on 2 (day 2 pm): Germline variant filtering (SNPs + Indels) Hands-on 3 (day 3 am): Somatic variant discovery (SNPs + Indels + CNV) Hands-on 4 (day 3 pm): Pipelining on the cloud with WDL Please note that the lectures part is mandatory. It is not possible to attend any of the hands-on sessions without attending the lectures. In the three optional hands-on sessions focused on analysis, we walk attendees through exercises that teach them how to manipulate the standard data formats involved in variant discovery and how to apply GATK tools appropriately to common use cases and data types. In the course of these exercises, we demonstrate useful tips and tricks for interacting with GATK and Picard tools, dealing with problems, and using third-party tools such as Samtools, IGV, RStudio and RTG Tools. In the optional hands-on session on pipelining, we walk attendees through exercises that teach them to write workflow scripts using WDL, the Broad's new Workflow Description Language, and to execute these workflows locally as well as through publicly available cloud-based services. Please note that this workshop is focused on human data analysis. The majority of the materials presented applies equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points. WHO SHOULD ATTEND The lecture-based component of the workshop is aimed at a mixed audience of people who are new to the topic of variant discovery or to GATK, seeking an introductory course into the tools, or who are already GATK users seeking to improve their understanding of and proficiency with the tools. Attendees should already be familiar with the basic terms and concepts of genetics and genomics. The hands-on component is aimed at novice to intermediate users who are seeking detailed guidance with GATK and related tools. Basic familiarity with the command line environment is required. Please note that for the hands-on sessions attendees will be expected to bring their own laptops with software preinstalled (detailed instructions will be posted two weeks before the workshop). Supported systems are Mac and Unix/Linux systems. MS Windows is not supported. COVERED TOPICS Lectures Introduction to variant discovery analysis and GATK Best Practices Marking Duplicates Indel Realignment Base Recalibration Variant Calling and Joint Genotyping Filtering variants with VQSR Genotype Refinement Workflow Callset Evaluation Somatic variant discovery with MuTect2 Preview of CNV discovery with GATK4 Hands-on 1 Germline variant discovery (SNPs + Indels) Hands-on 2 Germline variant filtering (SNPs + Indels) Hands-on 3 Somatic variant discovery (SNPs + Indels + CNV) Hands-on 4 Pipelining on the cloud with WDL -- 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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Postdoc Computational Biology
by Stein Aerts 11 Apr '17

11 Apr '17

http://www.vib.be/en/jobs/Pages/Postdoc-Computational-Biology.aspx [cid:19996CE1-1D0D-4916-914E-D785735EA06A@home]

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Open PhD and Postdocs positions in Vienna
by Anna.Santaella＠radboudumc.nl 07 Apr '17

07 Apr '17

Hi, A friend working in Vienna inform me about PhD and Postdoc positions in Bioinformatics in his lab. Please, forward these information to whom might be interested. Kind regards, Anna Santaella PhD student Radboud university medical center P.O. Box 9101, 6500 HB Nijmegen, The Netherlands Geert Grooteplein 10 (route 830) Anna.Santaella(a)radboudumc.nl Van: Serebreni,Leonid [mailto:leonid.serebreni@imp.ac.at] Verzonden: vrijdag 7 april 2017 10:19 Aan: Santaella Tortós-Sala, Anna Onderwerp: Fwd: bioinformatician ads Hi Anna, Our lab is looking for new PhD, Postdoc and staff bioinformaticians. Could you please circulate these ads in your institute? Many thanks! Leo > > Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Bioinformatics postdoctoral position in Brussels -IB2
by Tom Lenaerts 07 Apr '17

07 Apr '17

Postdoctoral Bioinformatics position Interuniversity Institute for Bioinformatics in Brussels (IB2), ULB - VUB, Brussels, Belgium Position description The Brussels Universities (Université Libre de Bruxelles (ULB) and Vrije Universiteit Brussel (VUB)), are seeking candidates for a postdoctoral positions for the project BRIGHTanalysis, which targets the development of predictive methods and online tools for the study of oligogenic diseases. The successful candidates will participate in the Interuniversity Institute of Bioinformatics in Brussels, an institute that brings together the science, engineering and medical faculties of VUB and ULB in a collaborative and open atmosphere. The focus of the (IB)2 is on interdisciplinary research, with expertise in machine learning, big data, rare diseases, oligenic disorders, network analysis, genome analysis, metagenomics and structural bioinformatics. Located in heart of Brussels, both universities are known for quality research through their prestigious affiliate research centers and world-renowned faculty. Brussels, the capital of Belgium and the European Union, is a cosmopolitan city famous for its picturesque squares and buildings, serene parks and gardens and a very vibrant cultural life spiced up by many international languages. *Postdoctoral position in Data Science and Oligogenic diseases: The vacancy available (to be filled asap) offers a position of at least two years. The researcher is expected to carry out fundamental data science and bioinformatics research as well as service development, which is an essential part of the BRIGHTanalysis project that is funding the position. This project’s goal is to develop novel ICT tools for the analysis and identification of variant combinations in diseases related to cephalic, neurodevelopmental or cardiac disorders. Qualifications Applicants for the postdoctoral position should have a recent PhD on a subject related to data science, machine learning or computational statistics. Experience in the analysis of exome data and the prediction/ranking of genes and variants as well as the development of web services will be an asset. Applicants are expected to have strong programming skills, the ability to work independently, strong interpersonal skills, good writing, oral communication and project management skills. Upon offer of a position in IB2, the candidates who are non-EU citizens are required to obtain an appropriate long-term Schengen visa; further information is available from their nearest Belgian embassy. Deadline Applicants are encouraged to apply as soon as possible as the position will remain open until filled by a suitable candidate. Starting date of the contract no later than June 1., 2017. Contact Candidates are invited to send a motivation letter, the contact details for 2 references, CV (Europass format!)+ with the detailed list of publications and a research statement in .pdf format by email to tlenaert(a)ulb.ac.be. The subject field of your email must include IB2-JOB: BRIGHTanalysis position. Equal Opportunity Employer ULB is an equal opportunity employer and is committed to employing more handicapped individuals and especially encourages them to apply. ULB wishes to increase the proportion of women in areas in which they are underrepresented. Women are strongly encouraged to apply.

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Few places left on Introduction to Linux and Workflows for Biologists 24-28 April 2017, Edinburgh
by Bert Overduin 06 Apr '17

06 Apr '17

Dear all, We still have a few places left on our new Introduction to Linux and Workflows for Biologists workshop, which runs from 24-28 April 2017. Cheers, Bert ********** INTRODUCTION TO LINUX AND WORKFLOWS FOR BIOLOGISTS DATE: Monday 24 – Friday 28 April 2017 VENUE: The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK REGISTRATION DEADLINE: Monday 10 April 2017 noon CANCELLATION DEADLINE: Monday 17 April 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) TO REGISTER: http://genomics.ed.ac.uk/services/introduction-linux-and- workflows-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. INSTRUCTORS Dr. Martin Jones (Founder, Python for Biologists) Dr. Bert Overduin (Training and Outreach Bioinformatician, Edinburgh Genomics) WORKSHOP FORMAT The workshop is delivered over nine half-day sessions (see the detailed curriculum below). Each session consists of roughly a one hour lecture followed by two hours of practical exercises, with breaks at the organiser’s discretion. There will also be plenty of time for students to discuss their own problems and data. WHO SHOULD ATTEND This workshop is aimed at researchers and technical workers with a background in biology who want to learn to use the Linux operating system and the command line environment. REQUIREMENTS Students should have enough biological background to appreciate the examples and exercise problems, and have at least some interest in working with DNA sequence data. No previous computer skills are necessary, as we will introduce Linux starting with the very basics. Students need to bring a laptop with a Linux virtual machine installed (we will distribute instructions for downloading and installing the virtual machine before the course starts). SESSION CONTENT 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. 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). 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. 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. 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. 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. 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. 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. 9. Customisation Part of the Linux design is that everything can be customised. 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 last afternoon is reserved for finishing off the next-gen workflow exercise, working on your own datasets, or leaving early for travel. -- 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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Bioinformatician Vacancy & KeyGene N.V.
by Marcel van Verk 06 Apr '17

06 Apr '17

We have at Keygene N.V. a Bioinformatician vacancy in my team. Below and in the enclosed attachment you can find some more information about this position. Data, information and knowledge are among KeyGene's most important products. As a bioinformatician you will play an important role in our technical research to develop state-of-the-art bioinformatics products for the integration, visualization and extraction of genomic and genetic breeding data. These products serve as a customizable and interactive encyclopedia for our internal research but also for our customers to mine and understand the genomic and genetic background of the crops that they are working on. Besides research and development, you will therefore participate in the delivery of these products to our customers by collecting and adding crop-specific data to the system and by training customers to work with the system. Website: http://www.keygene.com/career/vacancies/ Best, Marcel van Verk p.s. we are also looking for Postdoctoral fellows to apply for a Marie Curie 2017 fellowship jointly with KeyGene. More information check our website! 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/170202.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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Job opening VUmc Amsterdam: Genome biologist / Computational biologist
by Sie, Daud 05 Apr '17

05 Apr '17

Genome and proteome data integration to improve cancer patient treatment =========================================================== Your work environment ================== At the Cancer Center Amsterdam (CCA) of VU University Medical Center (VUmc) we perform internationally recognized research in genomics & proteomics. CCA houses state of the art genome technologies and IT-facilities for medical research. Your challenge =========== We are looking for an enthusiastic, communicative and pro-active bioinformatician / computational biologist. The work involves support of CCA researchers through training, and hands-on analysis of in house and public genomics and proteomics datasets. A focus will be on exploring tools for data mining, -visualization and -integration. One challenge is to adopt and adapt existing bioinformatics implementations to develop an in silico drug prescription strategy. Your profile ========= . University (PhD) education in Life Sciences, ie biology and/or biomedical informatics; . Proven computer programming proficiency and experience with integration of genomics and/ or proteomics data; . Proficient with scripting languages (Python, Perl); . Proficient with a statistical framework (R); . Experience in moving and handling large amounts of (scientific) data reliably and efficiently (UNIX); . Experience with a database framework (Postgress, MySQL); . Experience with programming language (C#/C++/C or Java); . Excellent communication skills and fluency in English (written & spoken); We offer ======= Salary Scale 10: 2618 to 4152 euro gross when employed full-time (depending on qualifications and experience). In addition to a good monthly salary we offer, among others, 8.3% extra allowance at the end of the year and 8% for holidays. For more information on our conditions, please visit www.werkenbijvumc.nl/arbeidsvoorwaarden (with link to English page). We offer a young and dynamic environment in health care, covering an active research group in genomics and data analysis. The project will last 2 years. Employment will initially be for a period of one year, after mutual agreement the contract will be extended till the end of the project. Additional information ================= The anticipated start date will be July 1, 2017. Your position is at the VU University Medical Center, within the Cancer Center Amsterdam. For more information you can visit www.vumc.nl/afdelingen/cca-site/ or the Tumor Genome Analysis Core website via www.tgac.nl. Interested? ========= If you're interested about this position, you can contact Prof. dr. Bauke Ylstra, Dept. Pathology, via telephone number +31(0)20-4442495. If you need more information about the application procedure, contact Faisca Stuiver, corporate recruiter at +31(0)20-4445635. Kind regards, Daoud Sie, PhD Coordinator Genomics Research Facility VU University Medical Center Amsterdam - department of Pathology E: d.sie(a)vumc.nl P: +31204442428 Present: Mon/Tue/Wed/Fri De Boelelaan CCA-1.22, 1081 HV Amsterdam Mailing adress: Postbus 7057, 1007 MB Amsterdam www.vumc.com www.vumc.com/directions --------------------------------------------------- Disclaimer This e-mail is confidential and may contain information that is not intended for you. If you are not the addressee or if this message was sent to you by mistake, you are requested to inform the sender and delete the message. VU University Medical Center accepts no liability for damage of any kind resulting from the risks inherent in the electronic transmission of messages. ---------------------------------------------------

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