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  • Introduction to MPI

    5 March 2017

    Gent, Belgium

    Elixir node event
    Introduction to MPI https://tess.elixir-europe.org/events/introduction-to-mpi The Message Passing Interface (MPI) is a standardized library specification for message passing between different processes. In layman's terms: MPI provides mechanisms for handling the data communication in a parallel program. It is particularly suited for computational clusters, where the workstations are connected by an interconnection network (e.g. Infiniband, Gigabit Ethernet). In this workshop, the applicability of MPI will be compared to other parallel programming paradigms such as OpenMP, Cuda and MapReduce. Next, the basic principles of MPI will be gradually introduced (Point-to-point communication, collective communication, MPI datatypes, etc). Hands-on exercises allow the participants to immediately turn the newly acquired skills into practice. Finally, some more theoretical considerations regarding scalability of algorithms are presented. About the lecturer: Dr. Jan Fostier. Jan received his MS and PhD degree in physical engineering from Ghent University in 2005 and 2009 respectively. Currently, he is appointed assistant professor in the department of Information Technology (INTEC) at the same university. His main research interests are (parallel) algorithms for biological sciences, high performance computing and computational electromagnetics. 2017-03-05 09:00:00 UTC 2017-03-05 00:00:00 UTC Multimediaroom building S9 Campus De Sterre, Gent, Belgium Multimediaroom building S9 Campus De Sterre Gent Belgium 9000 [] [] [] [] [] []
  • Introduction to Linux

    15 March 2017

    Gent, Belgium

    Elixir node event
    Introduction to Linux https://tess.elixir-europe.org/events/introduction-to-linux A one-day course that gets you started on Linux and the command line interface, with a particular focus on using the HPC infrastructure of Ghent University Detailed time/place info Wednesday 15 March 2017, 10.00am - 5.00pm 2017-03-15 09:00:00 UTC 2017-03-15 00:00:00 UTC Multimediaroom campus de Sterre S9, Gent, Belgium Multimediaroom campus de Sterre S9 Gent Belgium 9000 [] [] [] [] [] []
  • Introduction to multithreading and OpenMP

    18 - 19 April 2017

    Gent, Belgium

    Elixir node event
    Introduction to multithreading and OpenMP https://tess.elixir-europe.org/events/introduction-to-multithreading-and-openmp This workshop gives an introduction to shared-memory parallel programming and optimization on modern multicore systems, focusing on OpenMP. This is the dominant shared-memory programming model in computational science. Parallelism, multicore architecture and the most important shared-memory programming models are discussed. These topics are then applied in the hands-on exercises. About the lecturer: Dr. Reinhold Bader. Reinhold studied physics and mathematics at the Ludwigs-Maximilians University in Munich, completing his studies with a PhD in theoretical solid-state physics in 1998. Since the beginning of 1999, he has worked at Leibniz Supercomputing Centre (LRZ) as a member of the scientific staff, being involved in HPC user support, procurements of new systems, benchmarking of prototypes in the context of the PRACE project, courses for parallel programming, and configuration management for the HPC systems deployed at LRZ. He is currently group leader of the HPC services group at LRZ, which is responsible for operation of all HPC-related systems and system software packages at LRZ. 2017-04-18 09:00:00 UTC 2017-04-19 00:00:00 UTC Oude Infirmerie het Pand, Gent, Belgium Oude Infirmerie het Pand Gent Belgium 9000 [] [] [] [] [] []
  • OpenFOAM user meeting

    13 September 2017

    Gent, Belgium

    Elixir node event
    OpenFOAM user meeting https://tess.elixir-europe.org/events/openfoam-user-meeting The HPC-UGent team is organising an OpenFOAM user meeting, where research groups using the popular open source CFD software on the VSC infrastructure can showcase their work, and collaborate on best practices for using it on HPC clusters. More details are available at http://www.ugent.be/hpc/en/support/openfoamusermeeting 2017-09-13 09:00:00 UTC 2017-09-13 00:00:00 UTC Multimediaroom building S9 Campus De Sterre, Gent, Belgium Multimediaroom building S9 Campus De Sterre Gent Belgium 9000 [] [] [] [] [] []
  • Introduction to gene regulation

    9 October 2017

    Gent, Belgium

    Elixir node event
    Introduction to gene regulation https://tess.elixir-europe.org/events/introduction-to-gene-regulation 2017-10-09 09:30:00 UTC 2017-10-09 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Gent, Belgium Bio-Accelerator Gent Belgium 9052 [] [] [] [] [] []
  • Introduction to Linux

    13 October 2017

    Gent, Belgium

    Elixir node event
    Introduction to Linux https://tess.elixir-europe.org/events/introduction-to-linux-f2d756c5-0d9b-4e28-a4ea-70c39717a0b8 A one-day course that gets you started on Linux and the command line interface, with a particular focus on using the HPC infrastructure of Ghent University 2017-10-13 09:00:00 UTC 2017-10-13 00:00:00 UTC Multimediaroom campus de Sterre S9, Gent, Belgium Multimediaroom campus de Sterre S9 Gent Belgium 9000 [] [] [] [] [] []
  • Electronic Lab Notebook Introduction Ghent

    25 October 2017

    Gent, Belgium

    Elixir node event
    Electronic Lab Notebook Introduction Ghent https://tess.elixir-europe.org/events/electronic-lab-notebook-introduction-ghent-fcc80d61-9755-4fe2-8067-00f12ea03c2f 2017-10-25 10:00:00 UTC 2017-10-25 12:00:00 UTC VIB Bioinformatics Core PC Room V114 First floor front building VIB Research Building, Gent, Belgium PC Room V114 First floor front building VIB Research Building Gent Belgium 9052 [] [] [] [] [] []
  • Introduction to Machine Learning Algorithms

    23 - 24 November 2017

    Gent, Belgium

    Elixir node event
    Introduction to Machine Learning Algorithms https://tess.elixir-europe.org/events/introduction-to-machine-learning-algorithms This course offers basics of analysing datasets with machine learning algorithms and data mining techniques in order to understand foundations of learning from large quantities of data. It starts with general methods for data analysis in order to understand clustering, classification, and regression. This includes a thorough discussion of test datasets, training datasets, and validation datasets required to learn from data with a high accuracy. Easy application examples will foster the theoretical course elements that also will illustrate problems like overfitting followed by mechanisms such as validation and regularisation that prevent such problems. The course will start from a very simple application example in order to teach foundations like the role of features in data, linear separability, or decision boundaries for machine learning models. In particular this course will point to key challenges in analysing large quantities of data sets (aka ‘big data’) in order to motivate the use of parallel and scalable machine learning algorithms. Hands-on exercises allow the participants to immediately turn the newly acquired skills into practice. After this course participants will have a general understanding how to approach data analysis problems in a systematic way including knowledge where parallel computing provide benefits. About the lecturer: Prof. Dr. – Ing. Morris Riedel received his PhD from the Karlsruhe Institute of Technology (KIT) and he is the head of the ‘high productivity data processing’ research group of the Juelich Supercomputing Centre (JSC) in Germany. As an adjunct associated professor at the School of Natural Sciences and Engineering of the University of Iceland he teaches ‘High Performance Computing’, ‘Cloud Computing and Big Data’, as well as ‘Statistical Data Mining’ and all of these courses are on the intersection of parallel computing and machine learning. He has given tutorials like the course above at numerous occasions like at the Barcelona Supercomputing Centre, Smart Data Innovation Conference, or Prace Spring School in Cyprus. His research interests are parallel and scalable machine learning and data science. (More info at http://www.morrisriedel.de ) 2017-11-23 09:00:00 UTC 2017-11-24 00:00:00 UTC Multimediaroom building S9 Campus De Sterre, Gent, Belgium Multimediaroom building S9 Campus De Sterre Gent Belgium 9000 [] [] [] [] [] []
  • Analysis of public microarray data using Genevestigator

    24 November 2017

    Gent, Belgium

    Elixir node event
    Analysis of public microarray data using Genevestigator https://tess.elixir-europe.org/events/analysis-of-public-microarray-data-using-genevestigator 2017-11-24 09:30:00 UTC 2017-11-24 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Gent, Belgium Bio-Accelerator Gent Belgium 9052 [] [] [] [] [] []
  • Deep Learning using a Convolutional Neural Network

    30 November - 12 January 2017

    Gent, Belgium

    Elixir node event
    Deep Learning using a Convolutional Neural Network https://tess.elixir-europe.org/events/deep-learning-using-a-convolutional-neural-network This course part focuses on a recent machine learning method known as deep learning that emerged as a promising disruptive approach, allowing knowledge discovery from large datasets in an unprecedented effectiveness and efficiency. It is particularly relevant in research areas, which are not accessible through modelling and simulation often performed in HPC. Traditional learning, which was introduced in the 1950s and became a data-driven paradigm in the 90s, is usually based on an iterative process of feature engineering, learning, and modelling. Although successful on many tasks, the resulting models are often hard to transfer to other datasets and research areas. This course provides an introduction into deep learning and its inherent ability to derive optimal and often quite generic problem representations from the data (aka ‘feature learning’). Concrete architectures such as Convolutional Neural Networks (CNNs) will be applied to real datasets of applications using known deep learning frameworks such as Tensorflow, Keras, or Torch. As the learning process with CNNs is extremely computational-intensive the course will cover aspects of how parallel computing can be leveraged in order to speed-up the learning process using general purpose computing on graphics processing units (GPGPUs). Hands-on exercises allow the participants to immediately turn the newly acquired skills into practice. After this course participants will have a general understanding for which problems CNN learning architectures are useful and how parallel and scalable computing is facilitating the learning process when facing big datasets. About the lecturer: Prof. Dr. – Ing. Morris Riedel received his PhD from the Karlsruhe Institute of Technology (KIT) and he is the head of the ‘high productivity data processing’ research group of the Juelich Supercomputing Centre (JSC) in Germany. As an adjunct associated professor at the School of Natural Sciences and Engineering of the University of Iceland he teaches ‘High Performance Computing’, ‘Cloud Computing and Big Data’, as well as ‘Statistical Data Mining’ and all of these courses are on the intersection of parallel computing and machine learning. He has given tutorials like the course above at numerous occasions like at the Barcelona Supercomputing Centre, Smart Data Innovation Conference, or Prace Spring School in Cyprus. His research interests are parallel and scalable machine learning and data science. (More info at http://www.morrisriedel.de ) 2017-11-30 09:00:00 UTC 2017-01-12 00:00:00 UTC Multimediaroom building S9 Campus De Sterre, Gent, Belgium Multimediaroom building S9 Campus De Sterre Gent Belgium 9000 [] [] [] [] [] []
  • HPC@UGent introduction

    17 January 2018

    Gent, Belgium

    Elixir node event
    HPC@UGent introduction https://tess.elixir-europe.org/events/hpc-ugent-introduction-dd37b1a4-1295-45fd-8447-72f2c2cf9d0d Course to jumpstart new researchers to work on the HPC infrastructure of Ghent University Detailed time/place info 17.01.2018, 10:00-17:00, Multimediaroom, campus de Sterre S9, Krijgslaan 281, 9000 Gent 2018-01-17 09:00:00 UTC 2018-01-17 00:00:00 UTC Multimediaroom campus de Sterre S9, Gent, Belgium Multimediaroom campus de Sterre S9 Gent Belgium 9000 [] [] [] [] [] []
  • Gentle hands-on introduction to Python programming

    22 - 29 January 2018

    Gent, Belgium

    Elixir node event
    Gentle hands-on introduction to Python programming https://tess.elixir-europe.org/events/gentle-hands-on-introduction-to-python-programming 2018-01-22 09:30:00 UTC 2018-01-29 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Gent, Belgium Bio-Accelerator Gent Belgium 9052 [] [] [] [] [] []
  • Introduction to Linux

    21 February 2018

    Gent, Belgium

    Elixir node event
    Introduction to Linux https://tess.elixir-europe.org/events/introduction-to-linux-b2474cbe-966f-480e-98ed-dc32fd1171a0 Get started with Linux and command line interface, with particular focus on using the supercomputing infrastructure of Ghent University Detailed time/place info 21.02.2018, 10:00-17:00, Multimediaroom, campus de Sterre S9, Krijgslaan 281, 9000 Gent 2018-02-21 09:00:00 UTC 2018-02-21 00:00:00 UTC Multimediaroom campus de Sterre S9, Gent, Belgium Multimediaroom campus de Sterre S9 Gent Belgium 9000 [] [] [] [] [] []
  • HPC@UGent introduction

    28 March 2018

    Gent, Belgium

    Elixir node event
    HPC@UGent introduction https://tess.elixir-europe.org/events/hpc-ugent-introduction-6e0bb756-acaa-4833-8c89-a42fcf2efafa Course to jumpstart new researchers to work on the HPC infrastructure of Ghent University Detailed time/place info 28.03.2018, 10:00-17:00, Multimediaroom, campus de Sterre S9, Krijgslaan 281, 9000 Gent 2018-03-28 09:00:00 UTC 2018-03-28 00:00:00 UTC Multimediaroom campus de Sterre S9, Gent, Belgium Multimediaroom campus de Sterre S9 Gent Belgium 9000 [] [] [] [] [] []
  • A tour of machine learning - Dimensionality reduction and clustering

    23 April 2018

    Gent, Belgium

    Elixir node event
    A tour of machine learning - Dimensionality reduction and clustering https://tess.elixir-europe.org/events/a-tour-of-machine-learning-dimensionality-reduction-and-clustering In this course, you will be introduced to two broad classes of data mining techniques that can be useful when dealing with high-dimensional data: techniques based on dimensionality reduction and techniques based on clustering. This course is intended for people with experience in R. 2018-04-23 09:30:00 UTC 2018-04-23 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Gent, Belgium BioAccelerator Gent Belgium 9052 [] [] [] [] [] []
  • Ensembl REST API Workshop

    14 May 2018

    Gent, Belgium

    Elixir node event
    Ensembl REST API Workshop https://tess.elixir-europe.org/events/ensembl-rest-api-workshop-cacab7f0-969e-47e7-87d0-14b7e0115671 2018-05-14 09:30:00 UTC 2018-05-14 13:00:00 UTC VIB Bioinformatics Core BioAccelerator, Gent, Belgium BioAccelerator Gent Belgium 9052 [] [] [] [] [] []
  • Introducion to multithreading and OpenMP

    22 - 23 May 2018

    Gent, Belgium

    Elixir node event
    Introducion to multithreading and OpenMP https://tess.elixir-europe.org/events/introducion-to-multithreading-and-openmp Introduction to shared-memory parallel programming and optimization on modern multicore systems, focusing on OpenMP Detailed time/place info 22.05.2018, 9:00-18:00, Multimediaroom, campus de Sterre S9, Krijgslaan 281, 9000 Gent 23.05.2018, 9:00-18:00, Multimediaroom, campus de Sterre S9, Krijgslaan 281, 9000 Gent 2018-05-22 09:00:00 UTC 2018-05-23 00:00:00 UTC Multimediaroom campus de Sterre S9, Gent, Belgium Multimediaroom campus de Sterre S9 Gent Belgium 9000 [] [] [] [] [] []
  • Introducion to MPI

    30 May 2018

    Gent, Belgium

    Elixir node event
    Introducion to MPI https://tess.elixir-europe.org/events/introducion-to-mpi Introduction to a standardized library specification for message passing between different processes Detailed time/place info 30.05.2018, 10:00-17:00, Multimediaroom, campus de Sterre S9, Krijgslaan 281, 9000 Gent 2018-05-30 09:00:00 UTC 2018-05-30 00:00:00 UTC Multimediaroom campus de Sterre S9, Gent, Belgium Multimediaroom campus de Sterre S9 Gent Belgium 9000 [] [] [] [] [] []
  • Basic bioinformatics concepts, databases and tools

    4 - 18 June 2018

    Gent, Belgium

    Elixir node event
    Basic bioinformatics concepts, databases and tools https://tess.elixir-europe.org/events/basic-bioinformatics-concepts-databases-and-tools b'\r\n\nUnderstand the capabilities and pitfalls of bioinformatics.\r\nFunctioning of the most used bioinformatics algorithms and terms for reliable interpretation of the results.\r\nNavigate with confidence to numerous online data repositories. Know where to search for them.\r\nBasic analyses of single genes as well as groups of genes (gene lists)\n\r\n\r\n\n During this 3-day introduction to bioinformatics, we will take you along a guided tour that covers all basic aspects of biological sequence analysis. This workshop is an ideal opportunity to get familiar with bioinformatics and its many faces! At the end, you should be able to start tackling any basic bioinformatics problem: how to obtain relevant information about your gene, you know where to get the required sequence data, manipulate the sequences, and how basic software and algorithms function so you can fine-tune them in order the get the most out of your analysis.\r\n\n \n\nGenBank, SwissProt, RefSeq, Gene\r\nGQuery\r\nEnsembl\r\nUgene\n\r\nBLAST, OrthoMCL, EMBOSS Needle, EMBOSS Water, Muscle, WebLogo, iceLogo\r\nHMMER, PSIBLAST, PROSITE, SMART, InterPro\r\nmiRWalk, Pscan, Motiflab\r\nPrimer3 PLUS, Primer BLAST, OligoAnalyzer, Ambion siRNA finder\r\nEMBOSS, Mobyle, Expasy\r\nPDB, Yasara\r\nGO, AmiGO, QuickGO, KEGG, STRING, DAVID, ToppGene, EnrichR, WebGestalt, Cytoscape\r\nGEO, GEO2R, GEO DataSet Browser\r\nOMIM, Variant reporter, Genomic variation server\n\r\nBiomart\n\r\n​​​​​​​​\r\n\n' 2018-06-04 09:30:00 UTC 2018-06-18 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Gent, Belgium BioAccelerator Gent Belgium 9052 [] [] [] [] [] []
  • Data Carpentry June 2018

    12 - 13 June 2018

    Brussels, Belgium

    Elixir node event
    Data Carpentry June 2018 https://tess.elixir-europe.org/events/data-carpentry-june-2018 2018-06-12 09:30:00 UTC 2018-06-13 17:00:00 UTC ELIXIR Belgium Brussels, Belgium Brussels Belgium 1050 [] [] [] [] [] []
  • HPC@UGent introduction

    13 June 2018

    Gent, Belgium

    Elixir node event
    HPC@UGent introduction https://tess.elixir-europe.org/events/hpc-ugent-introduction-0d847260-50ae-4d65-89f5-bc0dbc546bef Course to jumpstart new researchers to work on the HPC infrastructure of Ghent University Detailed time/place info 13.06.2018, 10:00-17:00, Multimediaroom, campus de Sterre S9, Krijgslaan 281, 9000 Gent 2018-06-13 09:00:00 UTC 2018-06-13 00:00:00 UTC Multimediaroom campus de Sterre S9, Gent, Belgium Multimediaroom campus de Sterre S9 Gent Belgium 9000 [] [] [] [] [] []
  • Basic statistics in R, part II

    25 - 1 June 2018

    Gent, Belgium

    Elixir node event
    Basic statistics in R, part II https://tess.elixir-europe.org/events/basic-statistics-in-r-part-ii 2018-06-25 09:30:00 UTC 2018-06-01 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Gent, Belgium BioAccelerator Gent Belgium 9052 [] [] [] [] [] []
  • Git for humans

    25 June 2018

    Gent, Belgium

    Elixir node event
    Git for humans https://tess.elixir-europe.org/events/git-for-humans 2018-06-25 09:30:00 UTC 2018-06-25 12:30:00 UTC ELIXIR Belgium Campus: Boekentoren/Book Tower Room: Didacticum, Gent, Belgium Campus: Boekentoren/Book Tower Room: Didacticum Gent Belgium 9000 [] [] [] [] [] []
  • VIB Community Meeting - Bioinformatics and Computational Biology

    6 September 2018

    Brussels, Belgium

    Elixir node event
    VIB Community Meeting - Bioinformatics and Computational Biology https://tess.elixir-europe.org/events/vib-community-meeting-bioinformatics-and-computational-biology b'\r\n\r\n\n \r\n\r\n\n \r\n\n' 2018-09-06 09:30:00 UTC 2018-09-06 16:00:00 UTC VIB Bioinformatics Core U-Residence, Brussels, Belgium U-Residence Brussels Belgium 1050 [] [] [] [] [] []
  • Comparative genomics in eukaryotes

    16 October 2018

    Gent, Belgium

    Elixir node event
    Comparative genomics in eukaryotes https://tess.elixir-europe.org/events/comparative-genomics-in-eukaryotes-9b93222d-3432-4065-a24e-3b9be0337a6d b'\r\n\r\n\n \r\n\r\n\n \r\n\r\n\n \r\n\r\n\n   9h30-11h00  Introduction + Gene family analysis\r\n\n' 2018-10-16 09:30:00 UTC 2018-10-16 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Gent, Belgium Bio-Accelerator Gent Belgium 9052 [] [] [] [] [] []
  • Mass spectrometry data processing

    22 - 23 October 2018

    Gent, Belgium

    Elixir node event
    Mass spectrometry data processing https://tess.elixir-europe.org/events/mass-spectrometry-data-processing 2018-10-22 09:30:00 UTC 2018-10-23 17:00:00 UTC VIB Bioinformatics Core BioAccelerator, Gent, Belgium BioAccelerator Gent Belgium 9052 [] [] [] [] [] []
  • OpenRiskNet/NanoCommons ontology meeting

    13 - 14 December 2018

    Brussels, Belgium

    OpenRiskNet/NanoCommons ontology meeting https://tess.elixir-europe.org/events/openrisknet-nanocommons-ontology-meeting The goal of this meeting is to get a picture of the ongoing ontology activities in the toxicology area, harmonize these efforts and the developed ontologies therein, and extend the existing toxicology ontology to support OpenRiskNet and NanoCommons tasks. Part of this will be the ontological annotation of OpenRiskNet Application Programming Interfaces (APIs) as used on their cloud. Other goals include extension of the ontology with missing terms (if any), potentially write up guidance documents, and annotation of data sets (possible via OpenRiskNet data APIs). 2018-12-13 13:00:00 UTC 2018-12-14 14:00:00 UTC University of Birmingham office in Brussels, Brussels, Belgium University of Birmingham office in Brussels Brussels Belgium Ontology and terminology Toxicology [] NanoCommonsOpenRiskNetH2020 [] workshops_and_courses [] risk assessmentnanosafetydata annotationservice descriptions
  • VIB Interest Group Meeting - containers and workflows

    25 January 2019

    Gent, Belgium

    Elixir node event
    VIB Interest Group Meeting - containers and workflows https://tess.elixir-europe.org/events/vib-interest-group-meeting-containers-and-workflows 2019-01-25 09:30:00 UTC 2019-01-25 16:30:00 UTC VIB Bioinformatics Core Clemenspoort - zaal Seelos, Gent, Belgium Clemenspoort - zaal Seelos Gent Belgium 9000 [] [] [] [] [] []
  • Mass spectrometry data processing

    3 - 4 June 2019

    Gent, Belgium

    Elixir node event
    Mass spectrometry data processing https://tess.elixir-europe.org/events/mass-spectrometry-data-processing-510f0379-0d6e-4f42-bf52-ee6ea58066be Obtain a good understanding of the origins and properties of mass spec data Obtain an understanding of the processing of mass spec data, aimed at identifying and quantifying peptides and proteins Gain sufficient understanding of the software tools and database used, and of the issues and caveats involved, to critically analyse and assess results from mass spectrometry based proteomics experiments 2019-06-03 09:00:00 UTC 2019-06-04 00:00:00 UTC VIB Bioinformatics Core iGent, Gent, Belgium iGent Gent Belgium 9052 [] [] [] [] [] []
  • Analysis of single cell RNA-Seq data from 10x Genomics

    29 - 30 August 2019

    Gent, Belgium

    Elixir node event
    Analysis of single cell RNA-Seq data from 10x Genomics https://tess.elixir-europe.org/events/analysis-of-single-cell-rna-seq-data-from-10x-genomics-5360606b-8116-48e6-929f-5e3b1bd1de5b In this course we will discuss some of the advantages and pitfalls of scRNA-Seq and go through the whole scRNA-seq analysis pipeline. We will teach you how to do proper quality control and filtering on gene level and cell level, how to do create tSNE plots, how to get potential markers for a subset of cells ...  2019-08-29 09:00:00 UTC 2019-08-30 00:00:00 UTC VIB Bioinformatics Core iGent, Gent, Belgium iGent Gent Belgium 9052 [] [] [] [] [] []

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