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  • Bulk RNASeq analysis for differential expression

    9 - 20 September 2019

    Leuven, Belgium

    Elixir node event
    Bulk RNASeq analysis for differential expression https://tess.elixir-europe.org/events/bulk-rnaseq-analysis-for-differential-expression During this training you will: execute a complete workflow at command line or in GenePattern to go from raw fastq files to count files execute a complete workflow in R to detect differential expression between two conditions initiate functional annotation and interpretation of the list of differentially expressed genes   2019-09-09 09:00:00 UTC 2019-09-20 00:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • Melbourne R package development workshop

    16 September 2019

    Melbourne, Australia

    Melbourne R package development workshop https://tess.elixir-europe.org/events/melbourne-r-package-development-workshop 2019-09-16 09:00:00 UTC 2019-09-16 17:00:00 UTC COMBINE Walter and Eliza Hall Institute, Melbourne, Australia Walter and Eliza Hall Institute Melbourne Australia Bioinformatics [] [] [] [] [] bioinformatics
  • de.NBI - CeBiTec Nanopore Best Practice Workshop 2019

    25 - 27 September 2019

    Bielefeld, Germany

    de.NBI - CeBiTec Nanopore Best Practice Workshop 2019 https://tess.elixir-europe.org/events/de-nbi-cebitec-nanopore-best-practice-workshop-2019 de.NBI - CeBiTec Nanopore Best Practice Workshop 2019 Bielefeld Educators: Stefan Albaum, Sebastian Jünemann, Nils Kleinbölting, Alexander Sczyrba (BiGi), Daniel Wibberg (CAU), Björn Usadel (GCBN), Christian Rückert, Jörn Kalinowski (CeBiTec) Date: 25 - 27 September 2019 Location: Bielefeld University, Universitätsstraße 25, 33615 Bielefeld Content: Aim of this workshop is to familiarise the participants with the Nanopore sequencing technology, its applications and the "Best Practice" bioinformatics workflow. The Nanopore technology have greatly facilitated the assembly of prokaryotic and eukaryotic genomes. Therefore, the workshop is focused on the establishment of finalized genome sequences. This workshop will be composed of different talks including introductions to the Nanopore sequencing technology and working in the de.NBI cloud as well as different hands-on sessions. During the talks, the advantages and pitfalls of Nanopore sequencing will be discussed. The hands-on sessions will illustrate the typical workflow from the Nanopore sequencing to the final assembled genome. Learning goals: This workshop aims to teach basic skills and best practices to researchers working with Nanopore data. The final goal is to enable them to use the resulting reads for a de novo assembly. Prerequisites: This workshop is intended for PhD students and postdocs with molecular biology background in genomics. Good understanding of command line tools is a plus, but not required. Tool: Canu, Pilon, Albacore, Porechop, Metricor, Poretools Keywords: Nanopore sequencing, genome assembly, genomics 2019-09-25 09:00:00 UTC 2019-09-27 17:00:00 UTC de.NBI / CeBiTec Bielefeld, Bielefeld, Germany Bielefeld Bielefeld Detmold Germany [] [] [] [] [] []
  • Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (Monash University)

    25 - 26 September 2019

    Melbourne, Australia

    Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (Monash University) https://tess.elixir-europe.org/events/implementing-scalable-bioinformatic-workflows-in-snakemake-nextflow-monash-university 2019-09-25 12:00:00 UTC 2019-09-26 16:00:00 UTC EMBL-ABR L1.02, 44 Exhibition Walk Matheson Library Monash University Clayton, VIC, Melbourne, Australia L1.02, 44 Exhibition Walk Matheson Library Monash University Clayton, VIC Melbourne Australia Bioinformatics Monash University [] [] [] [] SnakemakeNextflowbioinformatics
  • Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (Hudson Institute)

    25 - 26 September 2019

    Melbourne, Australia

    Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (Hudson Institute) https://tess.elixir-europe.org/events/implementing-scalable-bioinformatic-workflows-in-snakemake-nextflow-c253f254-38a1-4de9-b3cf-8abf216453db 2019-09-25 12:00:00 UTC 2019-09-26 16:00:00 UTC EMBL-ABR Boardroom 1, Level 3 Hudson Institute of Medical Research 27-31 Wright Street Clayton, VIC 3168, Melbourne, Australia Boardroom 1, Level 3 Hudson Institute of Medical Research 27-31 Wright Street Clayton, VIC 3168 Melbourne Australia Bioinformatics [] [] [] [] [] bioinformaticsNextflowSnakemake
  • Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (University of Melbourne)

    25 - 26 September 2019

    Melbourne, Australia

    Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow (University of Melbourne) https://tess.elixir-europe.org/events/implementing-scalable-bioinformatic-workflows-in-snakemake-nextflow-23941db7-c610-4aaf-8789-f55c938edb0d 2019-09-25 12:00:00 UTC 2019-09-26 16:00:00 UTC EMBL-ABR Melbourne Bioinformatics 187 Grattan St University of Melbourne CARLTON, VIC 3053, Melbourne, Australia Melbourne Bioinformatics 187 Grattan St University of Melbourne CARLTON, VIC 3053 Melbourne Australia Bioinformatics University of Melbourne [] [] [] [] bioinformaticsSnakemakeNextflow
  • Linux Introduction

    3 October 2019

    Leuven, Belgium

    Elixir node event
    Linux Introduction https://tess.elixir-europe.org/events/linux-introduction-88e35601-7e20-4a65-8451-ad4baff0ed63 This course will give a short practical summary of the basic things one needs when using mainly the command line in Linux: Overview and distributions How to start working with Linux Short introduction to Graphical User Interface Command line basics: getting help, useful commands Linux File System: navigating, file paths, file manipulation, disk space, archiving Text editing Groups, users, security: access rights Process control This course provides several hands-on sessions 2019-10-03 09:00:00 UTC 2019-10-03 13:00:00 UTC Vlaams Supercomputer Centrum Willem de Croylaan 52, 52, Willem de Croylaan, Leuven, Belgium Willem de Croylaan 52, 52, Willem de Croylaan Leuven Vlaams-Brabant Belgium 3001 [] [] [] workshops_and_courses first_come_first_served Linux basics
  • 4th de.NBI Training Course on Metagenome Analysis

    9 - 11 October 2019

    Bielefeld, Germany

    4th de.NBI Training Course on Metagenome Analysis https://tess.elixir-europe.org/events/4th-de-nbi-training-course-on-metagenome-analysis Educators: Sebastian Jünemann (Bielefeld University), Dr. Alex Sczyrba (Bielefeld University), Sebastian Jaenicke (Giessen University), Nils Kleinboelting (Bielefeld University) Location: Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Room V6-113 Date: October the 9th to 11th, 2019 Content: The aim of this 3-day workshop will be to give students a brief overview of the tools and bioinformatics techniques available for the analysis of next generation sequence (NGS) data from microbial communities. The format will comprise a mixture of lectures and hands-on tutorials where students will process example data sets in real-time in the de.NBI cloud environment. After covering general aspects of sequence based analysis (e.g. pre-processing, quality measurements, error handling, and so on) the course is divided into two parts: targeted (16S rRNA gene amplicons) and untargeted (whole-genome shotgun; WGS) metagenome analysis. On demand, a compact introduction into the Linux operating system and the usage of the command line interface will be given upstream to the introducing part to guarantee a consistent baseline for the following lectures. The main aspects of the 16S part are the common pipeline steps beginning with pre-processing and filtering followed by OTU clustering, taxonomic classification, and different statistical measurements. Then, the new ASV/zOTU approach will be introduced followed by similar statistics and both approaches discussed with the attendants in conclusion. In the third part, advantages and disadvantages of whole metagenome sequencing will be illustrated. As WGS metagenomics has the potential to address the full spectra of genome-based issues, the focus here will be on taxonomic and functional analysis with the aid of different bioinformatic tools. Two different techniques to analyze WGS metagenome data are part of this section: (1) in the read-based approach the software solution MGX, an integrated platform for metagenome analysis and data visualization, will be demonstrated. (2) the assembly-based approach to potentially recover near-complete genome by assembling reads into contigs which are subject to binning methods to group individual contigs into genome bins. Prerequisites: - basic knowledge in microbiology and NGS-based analysis - practical experience in a Linux/Unix derivatives, the command line interface and file system required Prerequisites for the workshop plus the optional Linux introduction: - basic knowledge in microbiology and NGS-based analysis Please not that participation to this course does not depend on the actual Linux experience of the applicant. Both, experienced as well as inexperienced Linux users are encouraged to submit an application. However, the Linux introducing session in the morning of the first day is optional only for applicants fulfilling the Linux prerequisite. Application: Please send your application to denbi-courses@cebitec.uni-bielefeld.de (subject MG­course2019) including a short motivation, a few words about your background, your level of experience on the command line (Linux/Unix), and your experience within the field of metagenomic analysis and related bioinformatic tools. There will be no participation fee, yet travel and accommodation expenses need to be paid by the participants. 2019-10-09 09:00:00 UTC 2019-10-11 17:00:00 UTC de.NBI Bielefeld, Bielefeld, Germany Bielefeld Bielefeld Detmold Germany [] [] [] workshops_and_courses [] metagenomics
  • The Brain Mosaic: Cellular heterogeneity in the CNS (2nd edition)

    10 - 11 October 2019

    Leuven, Belgium

    The Brain Mosaic: Cellular heterogeneity in the CNS (2nd edition) https://tess.elixir-europe.org/events/the-brain-mosaic-cellular-heterogeneity-in-the-cns-2nd-edition Recent advances in technology now allow us to explore multiple aspects of heterogeneity at the single cell level. Nowhere is this more important than in the Central Nervous System (CNS), where cellular heterogeneity has profound effects on all aspects of normal brain function and behavior and explains important aspects of disease pathology. With the second edition of the Brain Mosaic conference we aim to bring together leaders in this emerging discipline to discuss how it is advancing our knowledge of CNS function and disease. Speakers at this neuroscience meeting on ‘single cell’ will emphasize the multi-disciplinary nature of the field in several sessions: • Single cell sequencing and cell diversity • Spatial transcriptomics • New developments in technology and bioinformatics • CNS sequencing and relevance to disease research • Connections an activity Poster information: Format: A0 (841 x 1189 mm / 33.1 x 46.8 in), portrait orientation Deadlines: • Early Bird: 8 September 2019 • Late Registration: 26 September 2019 • Abstract deadline: 29 August 2019 2019-10-10 08:00:00 UTC 2019-10-11 18:00:00 UTC VIB Conferences KU Leuven - Promotion & Jubileumzaal, Naamsestraat 22, 22, Naamsestraat, Leuven, Belgium KU Leuven - Promotion & Jubileumzaal, Naamsestraat 22, 22, Naamsestraat Leuven Vlaams-Brabant Belgium 3000 Bioinformatics Transcriptomics Sequencing [] Evy Vierstraete +32 9 244 66 11 conferences@vib.be [] [] meetings_and_conferences [] Single cell sequencing Sequencingcell diversitySpatial transcriptomicsTranscriptomicstranscriptomicsAlzheimers Clinical Trials And StudiesAlzheimers DiseaseAmnesiaAnimal Models In DementiaAnxiety Autoimmune Disorders & Multiple SclerosisBehavioral IssuesBiopsychiatry Blood-Brain BarrierBrain DiagnosisBrain Disease & FailureBrain InjuryBrain TumourCentral Nervous SystemCerebrovascular DiseaseChild NeurologyClinical NeurophysiologyCNS TumorsCognitive DisordersDementiaDementia CareDemyelinationDiagnosis And TherapyEpilepsyGenetics Genetics And Epigenetics Geriatric NeurologyGut- Brain AxisHeadacheIntervention NeuroradiologyMeningitisMental HealthMental Health NursingMetastatisMovement DisordersMultiple SclerosisMultiple Sclerosis DiagnosisNervous SystemNeural EngineeringNeural EnhancementNeuro-Oncology NeuroanaatomyNeuroanatomyNeurocritical CareNeurodegenerationNeurodegenerative DisorderNeurodegenerative DisordersNeurogeneticsNeuroimagingNeuroimmunologyNeurological DisordersNeurological Disorders And StrokeNeurological InfectionsNeurological SurgeryNeurologistNeurologyNeuromedicinesNeuromuscular MedicineNeuronal AutoantibodiesNeuropathyNeuropeptidesNeuropharmacologyNeuroscienceNeurosurgeryNeurotoxicologyNeurotoxinsNeurotransmissionNeurotransmittersParkinsonParkinsons DiseasePediatric NeurologyPharmacology Psychiatry Psychology PsychoneuroimmunologyRecent Research And Case StudiesRehabilitation TherapyStem Cell Treatment For Neurological DisordersStrokesTraumatic Brain InjuryCNS sequencing disease researchbioinformatics• New developments in technology
  • Genome Engineering

    19 November 2019

    Leuven, Belgium

    Elixir node event
    Genome Engineering https://tess.elixir-europe.org/events/genome-engineering 2019-11-19 09:00:00 UTC 2019-11-19 00:00:00 UTC VIB Bioinformatics Core Provinciehuis Vlaams-Brabant, Leuven, Belgium Provinciehuis Vlaams-Brabant Leuven Belgium 3010 [] [] [] [] [] []
  • Analysis of 16S rRNA metagenomic experiments

    25 November 2019

    Leuven, Belgium

    Elixir node event
    Analysis of 16S rRNA metagenomic experiments https://tess.elixir-europe.org/events/analysis-of-16s-rrna-metagenomic-experiments Processing and statistical analysis of 16S rRNA metagenomic experiments using R & Lotus pipeline. The following analytical steps from raw data to communicable results will be on the programme: - Preparation of sequencing data, read filtering, data cleaning - Data normalization - Numerical ecology: Clustering, Ordination, Diversity, Modelling - Univariate & Multivariate Statistics - Biological interpretation 2019-11-25 09:00:00 UTC 2019-11-25 00:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • CABANA Workshop: Analysis of Crop Genomics Data

    2 - 6 December 2019

    Bogota, Colombia

    Elixir node event
    CABANA Workshop: Analysis of Crop Genomics Data https://tess.elixir-europe.org/events/cabana-workshop-analysis-of-crop-genomics-data This course will introduce crop biologists to methods and approaches for analysing crop genomics data. 2019-12-02 08:30:00 UTC 2019-12-06 12:45:00 UTC Universidad de los Andes - UniAndes, Bogota, Colombia Universidad de los Andes - UniAndes Bogota Colombia 111711 [] Marco Cristancho [] [] [] [] HDRUK
  • Hands on introduction to ChIP-seq and ATAC-seq analysis

    17 February 2020

    Leuven, Belgium

    Elixir node event
    Hands on introduction to ChIP-seq and ATAC-seq analysis https://tess.elixir-europe.org/events/hands-on-introduction-to-chip-seq-and-atac-seq-analysis The aim is to: have an understanding of the nature of ChIP-seq and ATAC-seq data perform a complete analysis workflow including QC, read mapping, visualization in a genome browser and peak-calling using command line and open source software for each each step  have an overview of possible downstream analyses perform a motif analysis with online web programs This training does not cover all methods available today. It does not aim at bringing users to a professional NGS analyst level but provides enough information to allow biologists understand what DNA sequencing practically is and to communicate with NGS experts for more in-depth needs. 2020-02-17 09:00:00 UTC 2020-02-17 00:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
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