- BBClist - maillist.psb.ugent.be

Introduction to RNA-seq Data Analysis workshop 29-30 May 2017 now open for applications
by Bert Overduin 27 Mar '17

27 Mar '17

Dear all, Our first upcoming Introduction to RNA-seq Data Analysis workshop is now open for applications: http://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis A few notes: - There will be many more RNA-seq workshop this year. The first one after the 29-30 May one will be on 29-30 June 2017. Application for this one will open once application for the May one has closed. - IMPORTANT: Starting with this workshop a basic working knowledge of Linux (at the level of our "Linux for Genomics" workshop) will be a pre-requirement for the workshop, as our experience is that teaching a short intro into Linux during the workshop was often not really enough for those who had never used the command line before. - If you have applied for this workshop before but haven't been selected, please add this information to your application. 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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[bioinfo] 3rd BeNeLuxFra Student Symposium : First abstracts call
by Alexander Botzki 26 Mar '17

26 Mar '17

On behalf of the Organising committee: The 3rd BeNeLuxFra Student Symposium will be held in Lille on July 6 and 7, directly following the french bioinformatics conference (JOBIM 2017). This symposium is coorganized by RSGs France, Belgium, Netherlands and Luxembourg. The program of this symposium includes contributed talk from early career scientists (Master students, PhD students, Postdoctoral researcher and engineer). We particularly encourage master students and early stage PhD students to submit an abstract. Submissions are now open. Details about the symposium and submissions are available on our website : https://jebif.fr/en/evenements/jebif-workshop/lille-jobim-2017-3eme-symposi… See you in Lille, The organizing committee -- RSG France - JeBiF Association des Jeunes Bioinformaticiens de France contact(a)jebif.fr | https://jebif.fr Twitter @JeBiF Facebook JeBiF.RSG.France

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Postdoc bioinformatics/data science - FAIR data and reproducible science
by Patrick Deelen 25 Mar '17

25 Mar '17

Working environment The postdoc will be part of the Genomics Coordination Centre (GCC), the ‘big data’ research & service hub of the University Medical Centre Groningen (UMCG), and the Franke-Swertz Lab research group ( http://systemsgenetics.nl) situated in the Genetics department of the UMCG. These are exciting times in biotechnology that are producing terabytes of Biobank, DNA, mutation, protein, molecular and phenotype profile data. This wealth of data offers unprecedented possibilities for new ways of predicting both disease and health status, but also presents big challenges in how to share, (re)use and analyse all this new, and sensitive, information. Our 25-member team is working together on diverse local, national and EU projects to produce clever software that expedites medical research and improves healthcare using open source web applications (see http://github.com/molgenis <https://github.com/molgenis>), (HPC) analysis pipelines and large-scale e-infrastructure (cluster, storage, cloud). Through these efforts the GCC contributes to the goal of making scientific research data meet FAIR (Find Able, Accessible, Interoperable, Reusable) principles. Job description We are looking for a postdoc data scientist to develop models, techniques and tools for promoting the re-use and reproducibility of scientific research in accordance with FAIR principles. In recent years, the GCC has been heavily invested in developing smart tools to integrate data using ontologies and semantic search methods (Biobank Connect, SORTA, MOLGENIS/connect) and in developing data models and data structures that promote re-use (Observ-OM, MIABIS, FAIR) and sharing of data (Beacons, CafeVariome). Our work has produced many top-quality MOLGENIS open source software applications, and writing the publications about these tools is part of this postdoc. We expect that this research line will develop further through our (inter)national collaborations with institutes in the BBMRI, CORBEL, ELIXIR, DTL and RD-connect networks, and in cooperation with the six-person MOLGENIS open source team and 20-person Franke-Swertz Lab to produce widely-applicable reusable e-infrastructure, particularly for the life sciences and personalized medicine. What do we need The ideal candidate is a PhD in (Bio)informatics or Data Science who: - Has a passion for data modelling/ontologies/integration/re-use - Communicates easily with colleagues and collaborators, primarily in English - Can write publications about our methods, software and applications - Can implement methods in Java services with Javascript user interfaces - Can test these in practice in the context of large-scale ‘top-level’ biomedical research - Collaborates well in international consortia and with researchers from other disciplines - Is prepared to travel Experience in large-scale biomedical studies involving Biobanks, NGS, molecular experiments and phenotype data and with the resulting bioinformatic data integration and (HPC) analysis pipelines, as well as knowledge of, for example, semantic web/linked data, REST/JSON-LD, linked data fragments, standards in biosharing.org, machine learning and biomedical ontologies is a plus. The UMCG has a preventive Hepatitis B policy. You may be required to build up sufficient protection against Hepatitis B before you can be appointed. Vaccination is provided by the UMCG if necessary. What do we offer An appointment of 0.8-1.0 FTE as a postdoctoral fellow for two years (with a possible extension), embedding in a dynamic department of top genetic researchers (including a Spinoza prize winner), a large group of programmers to publish with, a service desk that assists a wide range of researchers, and the opportunity to work both in Europe and internationally. Your salary will be a maximum of € 4.152,- gross per month (scale 10), depending on your qualifications and relevant experience, based on a full-time appointment. In addition, the UMCG will offer you 8% holiday pay, an 8.3% end-of-year bonus and a development budget. The terms of employment comply with the Collective Labour Agreement for Medical Centers (CAO-UMC). *For more information please contact:* Prof. Morris Swertz, Head of the Genomics Coordination Centre, by telephone +31 (0) 50 361 7100 or email: m.a.swertz(a)rug.nl (please do not use for applications) S. Scholtens, manager, telephone +31 (0)50 361 1087 op email: s.scholtens(a)umcg.nl (please do not use for applications) Applying for a job http://www.umcg.nl/NL/UMCG/Werken_in_het_UMCG/Vacatures/Externe_vacatures/M…

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The Idea DREAM Challenge is entering its collaborative phase
by Alexander Botzki 24 Mar '17

24 Mar '17

From: Chloe-Agathe Azencott [mailto:chloe-agathe.azencott@mines-paristech.fr] Sent: 24 March 2017 15:39 Subject: The Idea DREAM Challenge is entering its collaborative phase Dear colleagues, The Idea DREAM Challenge has entered its public discussion stage. To date, researchers from the DREAM Community have proposed exciting biological or medical questions, together with appropriate models to serve as strong baselines for new DREAM challenges, and the data they would need to drive their project all the way to an important scientific discovery. We have selected seven most promising of these ideas, and they are now up for discussion! We invite you to help create the next DREAM Challenge by joining us on https://www.synapse.org/#!Synapse:syn5659209/wiki/414654 to learn more about these ideas and debate them on their respective discussion threads. Your input is the key to the success of this innovative process of doing computational research. Please spread the word! The public discussion phase will close on *April 30th, 2017*. Sincerely, Anna Goldenberg and Chloe Azencott, on behalf of the Idea DREAM Challenge Organizers

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PhD position: Amsterdam and Delft, The Netherlands
by Lodewyk Wessels 24 Mar '17

24 Mar '17

PhD position: ‘TRANSFER LEARNING FOR PERSONALISED CANCER TREATMENT’ COLLABORATING INSTITUTES Technical University of Delft (TUDelft), Delft VU University Medical Center, VUMC, Amsterdam and The Netherlands Cancer Institute (NKI), Amsterdam. PROJECT DESCRIPTION How can we find better diagnostic markers for early stages of cancer? How can we better predict which therapy is best for which patient? The aim of the ‘COMPUTE CANCER’ project is to develop a novel methodological and computational framework that improves the selection of diagnostic and predictive biomarkers from cancer genomics data. Our strategy is to adapt known prediction methods (e.g. penalized regression, random forests) to allow for the inclusion of ‘co-data’: auxiliary information on the genomic variables derived from other data sources. Examples include p-values from related external studies or genomic and drug response data from cancer cell lines. INTERDISCIPLINARY COLLABORATION The group of Mark van de Wiel (Biostatistics, VUMC) will focus on developing ‘weighted learners’, where the challenge is to determine weights from co-data in an automatic and objective way. The groups of Marco Loog, Marcel Reinders and Lodewyk Wessels (TUDelft and NKI) will develop transfer learning approaches that exploit large cell line response data sets to predict therapy response in tumors. We will focus on response to chemotherapy in neo-adjuvant breast cancer and metastatic colorectal cancer. The project is embedded within broad oncological collaborations within the VUMC as well as the NKI. The successful candidate will be employed at the TUDelft and will spend at least two days per week at the NKI. Regular meetings between project partners and oncologists will be held to generate sufficient cohesion and momentum. CANDIDATE PROFILE We are seeking a highly motivated PhD candidate with: • A degree in bioinformatics, computer science or a related discipline • Experience in statistics, machine learning and/or pattern recognition • Proficiency in bioinformatics programming languages (e.g. R, Python) • Good cross-disciplinary collaborative and communication skills • Experience in analysing high-throughput molecular data is a plus • Experience in cancer biology and clinical applications is a plus INTERESTED? Please send CV and motivation letter to Magali Michaut (m.michaut(a)nki.nl <mailto:m.michaut@nki.nl>) & Lodewyk Wessels (l.wessels(a)nki.nl <mailto:l.wessels@nki.nl>). Please include the names and contact information of at least two references. DEADLINE 24 April 2017

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SCS2017 Prague announcement
by Julien Fumey 23 Mar '17

23 Mar '17

The ISCB Student Council is excited to announce the 13th Student Council Symposium (SCS) which will be hosted, preceding ISMB/ECCB 2017, at the Prague Convention Centre in Czech Republic on July 21, 2017. The SCS is an annual student-organised event, with a goal to highlight latest research from a wide variety of subfields of bioinformatics and computational biology. This year, SCS 2017 will bring an exciting program that includes keynote talks, contributed talks, poster session, and a social event in the evening. The symposium is a great opportunity to present your research to an international audience, learn about latest advances, and build a worldwide scientific network. We are pleased to announce our first keynote speaker, Professor Christine Orengo from University College London (UCL). Prof. Orengo is an expert in bioinformatics and research group, at UCL, focuses on understanding how protein domains are conserved over evolutionary time and developing methods to predict protein function. Please visit our website http://scs2017.iscbsc.org/scs2017-keynotes to read more. Abstract submission for SCS 2017 is currently open! We encourage you to visit symposium.iscbsc.org to submit your research today! All abstracts will be subjected to peer-review. Travel fellowship call will open soon for all presenting authors (oral and poster). Important Dates: Abstract submission deadline: April 17, 2017 Abstract notification of acceptance: May 22, 2017 Late Poster Submission Deadline: April 30, 2017 You can help us spread the word by using the hashtag #SCS17 on social media. We look forward to welcome you in Prague this summer! Julien Fumey (Chair) and Mehedi Hassan (Co-chair)

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ELIXIR/GOBLET/GTN hackathon for Galaxy training material re-use
by Frederik Coppens 21 Mar '17

21 Mar '17

Dear all we are organizing an ELIXIR/GOBLET/GTN hackathon for Galaxy training material re-use, aiming to extend and improve the content of the Galaxy Training material repo (https://github.com/galaxy-project/training-material <https://github.com/bgruening/training-material>). You can find more details here <https://docs.google.com/document/d/1dLCL5-2pkWTvmGTz7GyQkb5LEIZ3FBkPvCBoqUP…>. This workshop will take place in Cambridge, UK from 22nd to 24th of May in the framework of ELIXIR-EXCELERATE. If you have experience and interest in improving, streamlining, sharing of training performed using Galaxy, consider to join ! To ensure the hackathon is relevant for all participants, there is a selection procedure. Details how to apply are here <https://docs.google.com/document/d/1dLCL5-2pkWTvmGTz7GyQkb5LEIZ3FBkPvCBoqUP…>, please do so before March 31st ! We will get back to you asap. cheers the organizing committee Frederik Coppens - Project leader & IT manager Applied Bioinformatics And Biostatistics I.T. Support VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 12 www.psb.ugent.be <http://www.psb.ugent.be/>

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Workshop: R2 - Genomics analysis and visualization platform
by r2-support 20 Mar '17

20 Mar '17

Dear Researcher, R2 is a free, publicly accessible web-based genomics analysis and visualization platform (http://r2.amc.nl) allowing biomedical researchers, without bioinformatics training, to integrate clinical and genomics data. To help researchers get started, the department of Oncogenomics is organizing a 1 day introduction workshop with hands-on training on Tuesday May 2nd 2017 (09:30-17:00). The workshop will cover the essentials of working with mRNA 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 administation, lunch, printing costs) in case of a no show on the workshop. Best regards, R2-support r2-support(a)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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GenotypTissue Expression (GTEx) Project Community Meeting. Barcelona April 20-21st. Registration OPEN!
by Alexander Botzki 20 Mar '17

20 Mar '17

Dear all, For your information the GTEx community meeting at CRG, Barcelona: http://www.bdebate.org/ca/debat/genotype-tissue-expression-gtex-project-com… Cheers, Alex

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Vacancy ELIXIR Belgium
by Kim DE RUYCK 20 Mar '17

20 Mar '17

Dear all, Within ELIXIR Belgium, we are looking for a Software Developer . The position is in Gent, all information can be found on the provided link. Kind regards, Kim De Ruyck Kim De Ruyck PhD Coordinator ELIXIR Belgium VIB, Technologiepark 927, 9052 GENT | +32 (0)9 33 13 694 www.elixir-belgium.org @ELIXIRnodeBE Subscribe to our mailing list

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