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  • Final OpenRiskNet Workshop

    23 - 24 October 2019

    Amsterdam, Netherlands

    Final OpenRiskNet Workshop https://tess.elixir-europe.org/events/final-openrisknet-workshop The workshop is addressing all OpenRiskNet stakeholders (scientific, industrial and regulatory communities) that are invited to participate in this interactive event. This will ensure that all relevant and target groups that need to be aware of the project achievements have access to this information and are enabled to give feedback, and also be trained on the provided solutions. 2019-10-23 09:00:00 UTC 2019-10-24 17:00:00 UTC OpenRiskNet O|2 Human Life Sciences building, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands, Amsterdam, Netherlands O|2 Human Life Sciences building, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands Amsterdam Netherlands 1081 Vrije Universiteit Amsterdam [] [] workshops_and_courses [] e-infrastructuresrisk assessment
  • Lipidomics MS Data processing, identification & quantification - Lipidomics Forum 2019

    10 November 2019

    Borstel, Germany

    Lipidomics MS Data processing, identification & quantification - Lipidomics Forum 2019 https://tess.elixir-europe.org/events/lipidomics-ms-data-processing-identification-quantification-lipidomics-forum-2019 Educators: Jacobo Miranda Ackermann, Nils Hoffmann (BioInfra.Prot / LIFS) Date: November 10th, 2019 Location: Forschungszentrum Borstel, Borstel, Germany (as part of Lipidomics Forum 2019) Contents: In this course, we will work through a typical use-case for bioinformatics processing lipidomics data following MS acquisition. The first part of the course will start with PeakStrainer and LipidXplorer for filtering, identification and quantification of lipid signals from shotgun lipidomics. The second part of the course will work through an example for targeted LC-MS lipidomics with LipidCreator and Skyline. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to a provided data set. 10:00 - 10:45 Common Introduction 10:45 - 12:30 LipidXplorer Shotgun Lipidomics 12:30 - 13:30 Lunch break 13:30 - 16:30 LipidCreator & Skyline Targeted LC-MS lipidomics Learning goals: Participants will be able to understand and explain the shotgun MS and targeted LC-MS workflows for lipidomics. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline. Prerequisites: Basic knowledge of lipidomics, analytical workflows in lipidomics and basic familiarity with web-based and desktop applications. Participants are required to bring their own laptop in order to work on the hands-on exercises. Keywords: Lipidomics, Shotgun, Targeted, LC-MS Tools: PeakStrainer and LipidXplorer, LipidCreator, Skyline 2019-11-10 09:00:00 UTC 2019-11-10 17:00:00 UTC de.NBI Borstel, Borstel, Germany Borstel Borstel Germany [] [] [] [] [] []
  • Statistical analysis & qualitative and quantitative comparison of lipidomics data - Lipidomics Forum 2019

    10 November 2019

    Borstel, Germany

    Statistical analysis & qualitative and quantitative comparison of lipidomics data - Lipidomics Forum 2019 https://tess.elixir-europe.org/events/statistical-analysis-qualitative-and-quantitative-comparison-of-lipidomics-data-lipidomics-forum-2019 Educators: Fadi al Machot, Nils Hoffmann (BioInfra.Prot / LIFS) Date: November 10th, 2019 Location: Forschungszentrum Borstel, Borstel, Germany (as part of Lipidomics Forum 2019) Contents: In this course, we will work through a typical use-case of downstream data processing of shotgun lipidomics data following MS acquisition with LipidXplorer. We will inspect, check and normalize the data as well as calculate absolute quantities using internal class-specific standards. We will then perform a qualitative comparison of the lipidomes using the LUX Score lipidome homology, before finally comparing and visualizing our quantitative lipidome results with ClovR. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to provided data sets. 10:00 - 10:45 Common Introduction 10:45 - 12:30 R Scripting for LipidXplorer data quantification Quantitative lipidome comparison wiht ClovR 12:30 - 13:30 Lunch break 13:30 - 16:30 Qualitative lipidome with LUX Score Machine learning, clustering and classification for lipidomics data Learning goals: Participants will be able to understand and explain the shotgun lipidomics data analysis workflow. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline. Prerequisites: Basic knowledge of lipidomics, analytical workflows in lipidomics and basic familiarity with web-based applications. Basic knowledge of R and RStudio is a plus to understand the quantitation workflow. Participants are required to bring their own laptop in order to work on the hands-on exercises. Keywords: Lipidomics, Statistical Analysis, Visualization Tools: R, RStudio, LUX Score, ClovR. 2019-11-10 09:00:00 UTC 2019-11-10 17:00:00 UTC de.NBI Borstel, Borstel, Germany Borstel Borstel Germany [] [] [] workshops_and_courses [] []
  • NBIS/SciLifeLab course: Introduction to Bioinformatics using NGS data

    25 - 30 November 2019

    Lund, Sweden

    Elixir node event
    NBIS/SciLifeLab course: Introduction to Bioinformatics using NGS data https://tess.elixir-europe.org/events/nbis-scilifelab-course-introduction-to-bioinformatics-using-ngs-data More information will follow: https://www.scilifelab.se/education/courses%26training questions? mail education@nbis.se 2019-11-25 09:00:00 UTC 2019-11-30 00:00:00 UTC Lund, Sweden Lund Sweden [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • Introduction to Bioinformatics using NGS data, Lund

    25 - 29 November 2019

    Lund, Sweden

    Elixir node event
    Introduction to Bioinformatics using NGS data, Lund https://tess.elixir-europe.org/events/introduction-to-bioinformatics-using-ngs-data-lund #training #url: https://www.scilifelab.se/events/introduction-to-bioinformatics-using-ngs-data-lund/ More information will follow: https://www.scilifelab.se/education/courses%26training questions? mail education@nbis.se 2019-11-25 09:00:00 UTC 2019-11-29 00:00:00 UTC Lund, Sweden Lund Sweden [] jessica.lindvall@scilifelab.se [] [] workshops_and_courses [] #trainingtraining
  • NBIS course: RNAseq

    26 - 29 November 2019

    Lund, Sweden

    Elixir node event
    NBIS course: RNAseq https://tess.elixir-europe.org/events/nbis-course-rnaseq More information will follow: https://www.scilifelab.se/education/courses%26training questions? mail education@nbis.se 2019-11-26 09:00:00 UTC 2019-11-29 00:00:00 UTC Lund, Sweden Lund Sweden [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • RNA-Seq

    26 - 28 November 2019

    Lund, Sweden

    Elixir node event
    RNA-Seq https://tess.elixir-europe.org/events/rna-seq-eeffa88f-ba9a-4512-a44d-e29b6be6394f #training #url: https://www.scilifelab.se/events/rna-seq-3/ More information will follow: https://www.scilifelab.se/education/courses%26training questions? mail education@nbis.se 2019-11-26 09:00:00 UTC 2019-11-28 00:00:00 UTC Lund, Sweden Lund Sweden [] jessica.lindvall@scilifelab.se [] [] workshops_and_courses [] #trainingtraining
  • 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
  • A tour of machine learning: classification

    13 - 14 January 2020

    Gent, Belgium

    Elixir node event
    A tour of machine learning: classification https://tess.elixir-europe.org/events/a-tour-of-machine-learning-classification-b217275f-0a31-4994-b5c6-be3d999cc9f7 Machine learning has become ubiquitous in biotechnology (as in many other fields), fueled largely by the increasing availability and amount of data. Learning algorithms can figure out how to perform important tasks by generalizing examples. Typical applications are diagnoses/prognoses, gene/protein annotation, drug design, image recognition, text mining and many others. However, building successful machine learning models requires a substantial amount of “black art” that is hard to find in textbooks. This course is an interactive Jupyter Notebook (Python) that will teach you how to build successful machine learning models. No background in machine learning is assumed, just a keen interest. 2020-01-13 09:00:00 UTC 2020-01-14 00:00:00 UTC VIB Bioinformatics Core iGent, Gent, Belgium iGent Gent Belgium 9052 [] [] [] [] [] []
  • Hands-On introduction to NGS variant analysis

    20 - 21 January 2020

    Gent, Belgium

    Elixir node event
    Hands-On introduction to NGS variant analysis https://tess.elixir-europe.org/events/hands-on-introduction-to-ngs-variant-analysis-9abd671c-4d42-4124-b084-9f2453cc9799 Using a full publicly available chromosome read-set from one of the 1000 genome samples: ​Perform a complete analysis workflow including QC, read mapping, read coverage analysis, and variant calling against the human reference genome. Use GenePattern and open source software to evaluate each step of a classical NGS variant workflow and feel the complexity of the task. Quickly compare the obtained results with gold standard public data The skills acquired during this session should allow participants understand what variant calling implies. Participants with experience in command line can do the workflow using command line tools. 2020-01-20 09:00:00 UTC 2020-01-21 00:00:00 UTC VIB Bioinformatics Core iGent, Gent, Belgium iGent Gent Belgium 9052 [] [] [] [] [] []
  • Mass spectrometry data processing

    2 - 3 June 2020

    Gent, Belgium

    Elixir node event
    Mass spectrometry data processing https://tess.elixir-europe.org/events/mass-spectrometry-data-processing-f80a1c34-fcd4-40bf-83df-1ba4b05dd38e 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 2020-06-02 09:00:00 UTC 2020-06-03 00:00:00 UTC VIB Bioinformatics Core iGent, Gent, Belgium iGent Gent Belgium 9052 [] [] [] [] [] []
  • Using MOFA for integration of omics data

    15 June 2020

    Gent, Belgium

    Elixir node event
    Using MOFA for integration of omics data https://tess.elixir-europe.org/events/using-mofa-for-integration-of-omics-data-f849603e-3ab6-453b-b6d4-6d22f3666d6e Participants can bring their own data to the course. What kind of preprocessing of the data is required for MOFA? How to train MOFA on a multi-omic data set? How to interpret the MOFA factors by their loadings, using gene set enrichment or sample ordination? How to use MOFA for downstream analyses including regression, classification or clustering? How to impute missing values with MOFA? How to select the number of factors and compare different MOFA fits? 2020-06-15 09:00:00 UTC 2020-06-15 00:00:00 UTC VIB Bioinformatics Core iGent, Gent, Belgium iGent Gent Belgium 9052 [] [] [] [] [] []
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