- BBClist - maillist.psb.ugent.be

FW: Vacancy Bioinformatics position
by I. van der Pluijm 24 Oct '19

24 Oct '19

I received an email that the attachment was too big, therefore I deleted the flyer. Please see my email below. Kind regards, Ingrid van der Pluijm From: I. van der Pluijm Sent: donderdag 24 oktober 2019 10:37 To: 'bbclist(a)psb.ugent.be' <bbclist(a)psb.ugent.be> Cc: N. Taneja <n.taneja(a)erasmusmc.nl> Subject: Vacancy Bioinformatics position Dear sir/madam, We are planning to appoint a Bioinformatician at the Molecular Genetics department (headed by Roland Kanaar) at the Erasmus University Medical Center in Rotterdam. Via this route I would like to ask if you would be willing to send attached vacancy via the BeNeLux bioinformaticians forum. To attract people, we have also made a flyer; please see attached. We would be very grateful if you could forward this vacancy! Kind regards, Ingrid van der Pluijm Nitika Taneja

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VIB: Staff Scientist Integrative Bioinformatics
by Alexander Botzki 23 Oct '19

23 Oct '19

Dear BBC list members, Currently, we have an opening of a Staff Scientist position in Integrative Bioinformatics at the central VIB Bioinformatics Core facility. More information and the application information is available at this web site: https://vibvzw.jobsoid.com/jobs/35bba14f-79b7-4388-b015-a4fb9d97ee41/23329/… Kind regards Alexander Botzki 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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PhD position
by Vanessa Vermeirssen 23 Oct '19

23 Oct '19

Dear colleagues There is a position for a PhD researcher in computational biology in my group. It would be great if you could spread this information to potential candidates. https://www.ugent.be/en/work/vacancies/scientific/phd-student-4ketl Kind regards Vanessa Vermeirssen Vanessa Vermeirssen, PhD ---------------------------------------------------------- Ghent University Department of Biomedical Molecular Biology Department of Biomolecular Medicine Cancer Research Institute Ghent (CRIG) C. Heymanslaan 10, ingang 34 (2MRB1) 9000 Ghent Belgium Email: vanessa.vermeirssen(a)ugent.be Phone: +32 (0) 9 332 3945

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Registration open for ELIXIR-NL Training: Technical Data Stewardship, 2-4 December 2019, Amsterdam, the Netherlands
by Celia van Gelder 22 Oct '19

22 Oct '19

Dear colleague, Please find below the information for our ELIXIR-NL Training on technical aspects of Data Stewardship. Course: Technical Data Stewardship Date: 2-4 December 2019 Location: Amsterdam Science Park Congress Centre, Science Park 123, 1098 XG Amsterdam. Course fee: Registration is free of charge Registration page: <https://www.eventbrite.co.uk/e/elixir-nl-training-technical-data-stewardshi p-registration-77268192243> https://www.eventbrite.co.uk/e/elixir-nl-training-technical-data-stewardship -registration-77268192243 Course description We will explore the ELIXIR Data stewardship wizard and see how one can employ and adopt it towards a community or research project. We will set the first steps on the path to FAIRify metadata by means of linked data. And finally we will see how FAIR data can be used in computational workflows and how to gather provenance data while working with data assets. The training is organised by ELIXIR-NL and will be given by DTL, ELIXIR CZ, SURF and Wageningen University. Target audience The training is targeted at data stewards, data scientists and research software engineers who would like to deepen their knowledge on concepts and practical implementations of data management/stewardship tools. We assume that you are familiar with programming in a language like Python, R or Matlab. Learning outcomes Participants will gain insight into the Data Stewardship Wizard how to employ and adjust the tool towards a special use case. They will learn about the principles of data modeling and making data FAIR by means of linked data. During the course we will apply these technologies to a real world data set. Participants will know afterwards how to approach their own data and can set first steps on the FAIRification process. Finally participants will know how to manage data and metadata in iRODS and how to employ data and metadata stored in iRODS in calculations on a remote compute cluster. Technologies ELIXIR Data stewardship wizard; Linked data; iRODS; python; SURF compute clusters Prerequisites Own laptop; Bash-shell, login to VM by ssh; Elementary knowledge of python Draft programme Monday December 2, 2019 - 12:00-17:00 (onsite & remote training) Trainers: Rob Hooft (ELIXIR-NL, DTL), Robert Pergl (ELIXIR-CZ, CCMI-FIT), Jan Slifka (ELIXIR-CZ, CCMI-FIT) * 12:00 - arrival with lunch * Introduction to Data management plan * Introduction and practical demonstration of the features of DSW: user-view and Data-steward view * Hands-on session Tuesday December 3, 2019 - 09:00 - 17:00 Trainers: Ben Schaap (Agrosystems Research, WUR), Erik van den Berg (WDCC, WUR), Jasper Koehorst (Systems and Synthetic Biology, WUR), Anand Gavai (WFSR, WUR) * Linked data training * Introduction to Linked Open Data * Exercise 1: pencil & paper exercise * Presentation on SPARQL and wikidata * Hands on real data, putting everything into practice Wednesday December 4, 2019 - 09:00 - 17:00 Trainer: Arthur Newton (SURFsara) * iRODS and compute You can find all the information and registration possibilities here: <https://www.eventbrite.co.uk/e/elixir-nl-training-technical-data-stewardshi p-registration-77268192243> https://www.eventbrite.co.uk/e/elixir-nl-training-technical-data-stewardship -registration-77268192243 Please spread this announcement in your organisation as you see fit. Best regards, Celia van Gelder Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl websites: <https://www.dtls.nl/> https://www.dtls.nl/, <https://www.elixir-europe.org/platforms/training> https://www.elixir-europe.org/platforms/training 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 While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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PhD and Researcher / Software Developer positions available
by Anthony Mathelier 21 Oct '19

21 Oct '19

Dear colleagues, We have two open positions in my group. It would be great if you could spread the ads to potential candidates. A funded 3-year PhD candidate position is available to study the binding of TFs to DNA and how aberrant DNA methylation can alter gene regulation in cancers. More info and applications at https://www.jobbnorge.no/en/available-jobs/job/176997/phd-candidate-positio… A funded 2-year Research Scientist / Software Developer position is available to help us develop, maintain, fix, and upgrade our bioinformatics pipelines, tools, and resources. More info and applications at https://www.jobbnorge.no/en/available-jobs/job/177163/researcher-software-d… Thanks for sharing with whoever would be interested. Best AM -- Anthony Mathelier, PhD Group Leader - Computational Biology & Gene Regulation Group Centre for Molecular Medicine Norway (NCMM) Adjunct Researcher - Dept. of Cancer Genetics, Oslo University Hospital http://mathelierlab.com anthony.mathelier(a)ncmm.uio.no (+47) 22840561

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Seminar of Mark Robinson - 3pm October 24 (Thursday) - On the analysis of multi-sample multi-condition replicated single-cell RNA-seq datasets
by Wouter Saelens 21 Oct '19

21 Oct '19

Dear all This week, Mark Robinson (Institute of Molecular Life Sciences, University of Zurich), one of the developers of edgeR, is going to give a talk about his new approach on performing differential expression analysis on single-cell data with multiple samples and multiple conditions: Single-cell RNA-sequencing (scRNA-seq) has become an empowering technology to characterize the transcriptomes of individual cells. Although many early analyses of differential expression (DE) have focused on finding markers for cell sub-populations (experimental units are cells), there is now an emergence of datasets across replicates and multiple conditions where the goal is to make patient-level inferences (experimental units are patients), with 100s to 1000s of cells measured for each patient. This provides an opportunity to go back and make use of the existing robust bulk RNA-seq frameworks, by first aggregating the data into "pseudobulk" counts at the subpopulation level. However, this opens up new questions, which we will address in this talk: how does one track subpopulations across patients? do we lose information by aggregating? normalization? We will present a comprehensive framework for flexible multi-sample multi-condition DE of scRNA-seq experiments. This will take place on October 24 at 3pm in the FSVM seminar room of the VIB-UGent building in Zwijnaarde (Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium). Kind regards

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[BBC} Postdoctoral / junior researcher position at Maastricht University
by Coort, Susan (BIGCAT) 17 Oct '19

17 Oct '19

Dear all, Interested in joining the European Food, Nutrition and Security (FNS)-Cloud project (Horizon2020) on FNS data infrastructure and analysis? Check out our postdoctoral / junior researcher position at Academic Transfer. https://www.academictransfer.com/nl/286663/fhml-nutrim-junior-researcher-or… With kind regards, Susan [cid:image001.jpg@01D584BD.E033E380] Susan Steinbusch-Coort, PhD Bioinformatics-BiGCaT, NUTRIM School of Nutrition and Translational Research in Metabolism susan.coort(a)maastrichtuniversity.nl <mailto:susan.coort@maastrichtuniversity.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl> Universiteitssingel 50, 6229 ER, Maastricht, the Netherlands P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 3882913 Disclaimer<http://www.maastrichtuniversity.nl/web/show/id=6568779/langid=42> [cid:image002.jpg@01D584BD.E033E380]Please consider your environmental responsibility before printing this e-mail.

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Fwd: [rsg-belgium] RSG Belgium Hackathon #2 | 06/12/2019 in Brussels
by Daniele Parisi 16 Oct '19

16 Oct '19

-------- Original Message -------- SUBJECT: [rsg-belgium] RSG Belgium Hackathon #2 | 06/12/2019 in Brussels DATE: 2019-10-10 12:15 FROM: Sofia Papadimitriou <sofiapapad.bio(a)gmail.com> TO: <rsg-belgium(a)supersympa.ua.ac.be> Dear all, The RSG Belgium team is excited to announce that registrations for the RSG BELGIUM HACHATHON #2 are now open! WHEN: 06/12/2019, starting at 09.00 am WHERE: Université Libre de Bruxelles, La Plaine Campus, Building NO, 9th floor, room: 2NO906 ("Salle des professeurs"), Brussels, Belgium This full-day event is a great opportunity for students and young researchers from different scientific fields (bioinformatics, computer science, biology, biotechnology, mathematics, etc.) to meet and improve their problem solving, teamwork and coding skills, by working in a multidisciplinary team and trying to solve a particular problem. The event is free for all participants, but REGISTRATION IS REQUIRED using the following form: https://forms.gle/mcVQXsDNRxPD91Tf9. We have chosen a number of different projects that could be tackled during the event and in the registration form we ask you to already indicate your preference, so that we can make preparations for the most popular topics. Please note that the REGISTRATION DEADLINE IS UNTIL 10TH NOVEMBER. You can find all required information and further updates on our website: http://www.rsg-belgium.iscbsc.org/news/event/hackathon/second-hackathon/. We look forward to seeing you in the Hackathon! Best regards, The RSG Belgium board team -- DANIELE PARISI PhD student at ESAT-STADIUS, KULeuven, Yves Moreau's group Board member of RSG Belgium Kasteelpark Arenberg 10 - box 01.34 3001 Leuven, Belgium Tel: +32488794394

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Save the date: ELIXIR-NL Training on technical aspects of Data Stewardship, 2-4 December 2019, Amsterdam
by Celia van Gelder 15 Oct '19

15 Oct '19

Dear all, I would like to announce an upcoming ELIXIR-NL training on the technical aspects of data stewardship in Amsterdam. Registration will open soon but if you are interested please save the date! Topic: Technical aspects of Data Stewardship Date: 2-4 December 2019 Location : Conference Centre, Amsterdam Science Park, Amsterdam We will explore the ELIXIR Data stewardship wizard and see how one can employ and adopt it towards a community or research project. We will set the first steps on the path to FAIRify metadata by the means of linked data. And finally we will see how FAIR data can be used in computational workflows and how to gather provenance data while working with data assets. Technologies: * ELIXIR Data stewardship wizard * Linked data * iRODS * Python * SURF compute clusters Target audience The training is targeted at data stewards, data scientists and research software engineers who would like to deepen their knowledge on concepts and practical implementations of data management/stewardship tools. We assume that you are familiar with programming in a language like python, R or Matlab. Trainers The training is organised by ELIXIR-NL and will be given by DTL, ELIXIR CZ, SURF and Wageningen University. Please note this date in your calendar if you are interested. If you need more information you can contact Christine Staiger (christine.staiger(a)dtls.nl <mailto:christine.staiger@dtls.nl> ) who is coordinating the course. Best Celia Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl websites: <https://www.dtls.nl/> https://www.dtls.nl/, <https://www.elixir-europe.org/platforms/training> https://www.elixir-europe.org/platforms/training 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 While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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EuBIC 2020 Developer’s Meeting – Save the date & call for project proposals
by eubic 2020 14 Oct '19

14 Oct '19

Dear colleagues, We are pleased to announce that the upcoming EuBIC 2020 developer's meeting will be held in Nyborg, Denmark, on JANUARY 13TH TO 17TH 2020. The EuBIC 2020 developer's meeting will bring together scientists active in the field of bioinformatics and computational proteomics. It provides a highly interactive platform to develop projects that are relevant to the proteomics community. _Date_: January 13-17, 2020 _Venue_: Sinatur Hotel Storebælt, Østerøvej 121, 5800 Nyborg, Denmark _Website_: https://www.proteomics-academy.org/eubic-dev-meeting-2020 KEY DATES _September 18_, 2019: Project proposal submission deadline _October 1_, 2019: Announcement of selected projects _October 1_, 2019: Conference registration opens _January 13-17_, 2020: EuBIC 2020 developer's meeting in Nyborg CALL FOR PROJECT PROPOSALS _Do you want other researchers working on your project and set up future collaborations? _ The call for topics for the hackathon sessions during the EuBIC 2020 developer's meeting is now open! During the EuBIC 2020 developer's meeting the participants will engage in hackathon sessions where they will develop bioinformatics tools and resources. The participants will break up into small groups to work together on these topics in an open, constructive, and productive atmosphere. You can now submit project proposals for inclusion into the EuBIC 2020 developer's meeting program. Submit your project proposal before 18 September through the following website: https://github.com/eubic/EuBIC2020 5-8 hackathon projects will be selected by a community vote arranged by the EuBIC program committee and announced on the conference webpage. TOPICS Hackathon projects can cover all topics in computational mass spectrometry and proteomics bioinformatics, including, but not limited to: - Tools - Extension of existing bioinformatics tools under the guidance of their original authors - Development of novel bioinformatics tools to solve open problems - Benchmarking - Compilation of gold-truth datasets - Collection of reference algorithmic implementations - Specification of benchmarking criteria - Workflows - Definition of formal protocols - Development of tutorials for bioinformatics software usage - Data analysis - (Re)analysis of publicly available proteomics datasets - Functional data analysis and integration MORE INFORMATION - Website: https://github.com/eubic/EuBIC2020 - Social media hashtag: #EuBIC20 - Conference email: eubic2020(a)rub.de SPONSORSHIP inquiries are welcome at eubic2020(a)rub.de We are grateful to the European Proteomics Association (EuPA) for supporting EuBIC and to the Novo Nordisk Foundation for their generous support of the conference! We look forward to welcoming you in Nyborg! The organizing committee. Veit Schwämmle Marie Locard-Paulet Wout Bittremieux David Bouyssié Viktoria Dorfer Dominik Kopczynski Alessio Soggiu Julian Uszkoreit Bart Van Puyvelde Sander Willems

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