October 2019 - BBClist - maillist.psb.ugent.be

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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Extra R2 workshop December 9th 2019
by r2-support 14 Oct '19

14 Oct '19

Dear Researcher, Since the next R2 workshop on Monday October 28th is overbooked, we are organizing another R2 introduction workshop on Monday the 9h of December 2019 (09:30-17:30). R2 is a free, publicly accessible web-based genomics analysis and visualization platform (http://r2.amc.nl<http://r2.amc.nl/>) allowing biomedical researchers, without bioinformatics training, to integrate clinical and genomics data. The workshop will cover the essentials of working with genomics 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<mailto:r2-support@amc.nl> r2.amc.nl<http://r2.amc.nl/> Department of Oncogenomics, M1-132 Amsterdam UMC Location AMC Meibergdreef 9 1105 AZ Amsterdam the Netherlands ________________________________ AMC Disclaimer : https://www.amc.nl/disclaimer ________________________________

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Job offer part time teaching in bioinformatics in Mons / Bergen
by SAND Olivier 11 Oct '19

11 Oct '19

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Helis Academy Course: FAIR Data Stewardship - digital data scholarship for life scientists, 4-6 November 2019, Utrecht, the Netherlands
by Celia van Gelder 08 Oct '19

08 Oct '19

Dear colleague, >From 4-6th November, 2019, we will give another round of the Helis Academy - FAIR Data Stewardship course: FAIR Data Stewardship - digital data scholarship for life scientists The target audience is life scientists - from industry and academia - and graduate students in the Life Sciences who wish to improve their digital scholarship on data handling. Some basic experience with programming and scripting languages like python, perl, R, matlab, etc. are an advantage, but not needed. The course is also relevant for Data Stewards who are supporting the life science researchers. The course will introduce the trainees to important concepts of data stewardship. We start with a general introduction covering the data life cycle, the FAIR principles and a definition of data stewardship and data stewards. The course will introduce the trainees to important concepts of data stewardship <https://www.dtls.nl/fair-data/research-data-management/research-data-manage ment/> . We start with a general introduction covering the data life cycle, the FAIR principles <https://doi.org/10.1038%2Fsdata.2016.18> and a definition of data stewardship and data stewards. We will pass the stages of the data life cycle in more detail in the training modules of this 3 day course. * Day 1: Why use a data management plan and what for? On day one trainees will investigate data management plans, which types are there and how they should be used. * Day 2: Mastering the data chaos during the research phase. On day two the course highlights how to work with data during the research phase, explaining how to create well formatted data which helps in the second module of day two to make data interoperable already during the active research phase. * Day 3: Boost your visibility and get cited for your data! On day three trainees will have an in-depth at persistent identifiers, different use cases and types of identifiers. Finally we are closing the data life cycle by making data fit for sharing, archiving and publishing. The training is organised by <http://www.dtls.nl/> DTL and delivered as a joint effort by DTL partners. You can find all the information, including the full programme and registration possibilities here: https://www.aanmelder.nl/helis-fair-data-stewardship-course This course is part of the Data Analysis and Stewardship theme of Helis Academy <https://www.helisacademy.com/en> and is organised by DTL and DTL collaborators. Info about other courses in the theme of Data Analysis and Stewardship can be found on the Helis Academy website <https://www.helisacademy.com/en/data-analysis-stewardship> and on the Helis Academy page on the DTL website <https://www.dtls.nl/training-and-education/helis-academy/> . 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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postdoc position in Bordeaux on Cancer Bioinformatics
by Nikolski Macha 04 Oct '19

04 Oct '19

Dear all, We are looking for a post-doctoral scientist interested in Cancer Bioinformatics to work in our institute at the University of Bordeaux. The primary focus will be set upon analysis of RNA-seq data by both bulk and single-cell, to elucidate the invasive processes in glioblastoma. -- Head of Bordeaux Bioinformatics Center Research Director IBGC / CNRS CBiB - Université Bordeaux 146, rue Léo Saignat, 33076 Bordeaux www : http://www.labri.fr/perso/macha/ <http://www.labri.fr/perso/macha/> tel : +33 (0)5 57 57 12 47

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Bioinformatics position available at the Erasmus MC Cancer Computational Biology Center
by Harmen van de Werken 04 Oct '19

04 Oct '19

A bioinformatics position is currently available at the Erasmus MC Cancer Computational Biology Center. http://www.erasmusmc.nl/vacature/?num=21578 Please apply, if you are enthusiastic and eager to improve our knowledge on cancer biology. Harmen van de Werken

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