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18 events found

Content provider: VIB Bioinformatics Core 

  • Introduction to the analysis of NGS data, autumn session

    15 - 29 September 2020

    Leuven, Belgium

    Elixir node event
    Introduction to the analysis of NGS data, autumn session https://tess.elixir-europe.org/events/introduction-to-the-analysis-of-ngs-data-autumn-session This training is an introduction to a series of trainings on the analysis of Next Generation Sequencing data. This training is intended for newbies to the field and will teach them all background knowledge required to successfully complete the advanced NGS analysis trainings. To this end the training will give an overview of: - The Illumina platform - NGS data formats and file handling - Quality control of NGS data - Mapping of NGS data - Supporting IT: Galaxy and GenePattern platform 2020-09-15 09:00:00 UTC 2020-09-29 00:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []

  • Python for downstream data analysis

    21 - 22 September 2020

    Leuven, Belgium

    Elixir node event
    Python for downstream data analysis https://tess.elixir-europe.org/events/python-for-data-science Use libraries for advanced data manipulation and visualization Working with biological data using Biopython Being able to write scripts and functions from scratch for specific bioinformatics problems 2020-09-21 09:00:00 UTC 2020-09-22 00:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []

  • Deep learning in biology, autumn session

    30 September - 18 December 2020

    Elixir node event
    Deep learning in biology, autumn session https://tess.elixir-europe.org/events/deep-learning-in-biology-autumn-session Large amounts of data and compute resources have enabled the development of high-performance machine learning models. This is particularly due to deep learning techniques. By looking at many data samples, these models can find structure in the data that is useful for predictive and explorative analysis: e.g. classification, clustering, data generation, dimensionality reduction, etc. The most popular applications within biotechnology are concerned with image segmentation, diagnostics, sequence analysis, etc. However, deep learning models are far from straightforward to implement correctly due to the many different hyperparameter settings, optimization procedures, architecture choices, etc. In this course, we will make use of Jupyter Notebok and Keras, which are both based on Python, to apply deep learning techniques on both bio informatics and bio image informatics data. We aim to work towards applications that participants would like to study. 2020-09-30 09:00:00 UTC 2020-12-18 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []

  • Basic statistics in R, online - autumn session

    30 September - 18 December 2020

    Elixir node event
    Basic statistics in R, online - autumn session https://tess.elixir-europe.org/events/basic-statistics-in-r-autumn-session This training gives an introduction to the use of the free statistical software language R. This introduction is aimed at beginners.  The training covers data handling, graphics, and basic statistical techniques (t-tests, one-way ANOVA and non-parametric equivalents). A full overview of statistical analyses in R including regression, two-way ANOVA... will be given in follow-up trainings. By following this training you will: get an idea of what R and Rstudio is use R to handle data: creating, reading, reformatting and writing data use R to create graphics use basic statistical techniques in R : t-tests, wilcoxon tests, one-way ANOVA, Kruskal Wallis tests, chi square tests, correlations, survival analysis... write and use R scripts 2020-09-30 09:00:00 UTC 2020-12-18 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []

  • Challenges in Omics Data Integration

    8 - 9 October 2020

    Elixir node event
    Challenges in Omics Data Integration https://tess.elixir-europe.org/events/challenges-in-omics-data-integration 2020-10-08 09:00:00 UTC 2020-10-09 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []

  • Bulk RNASeq: from counts to differential expression, autumn session

    12 - 19 October 2020

    Elixir node event
    Bulk RNASeq: from counts to differential expression, autumn session https://tess.elixir-europe.org/events/bulk-rnaseq-from-counts-to-differential-expression-autumn-session The course will show: R tools to generate count files like featureCounts, and summarizeOverlaps are demonstrated Count files from HTSeq-Count, FeatureCounts, Salmon or Kallisto are used to identify differentially expressed genes After the live session participants can analyze their own count files. Issues can be handled during the Q&A session. 2020-10-12 09:00:00 UTC 2020-10-19 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []

  • Using MOFA for integration of omics data, online

    15 - 16 October 2020

    Gent, Belgium

    Elixir node event
    Using MOFA for integration of omics data, online https://tess.elixir-europe.org/events/using-mofa-for-integration-of-omics-data-autumn-session Participants can analyze their own data in 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? 2020-10-15 09:00:00 UTC 2020-10-16 00:00:00 UTC VIB Bioinformatics Core iGent, Gent, Belgium iGent Gent Belgium 9052 [] [] [] [] [] []

  • Image processing for correlated and multimodal imaging techniques

    19 October 2020 - 9 March 2021

    Elixir node event
    Image processing for correlated and multimodal imaging techniques https://tess.elixir-europe.org/events/image-processing-for-correlated-and-multimodal-imaging-techniques The purpose of this event is to dedicate three days of intense training to an audience with little or basic expertise. The program will first cover a full day of online lectures (19 October 2020), followed by two days of hands-on training (8 & 9 March 2021, Ghent). 2020-10-19 09:00:00 UTC 2021-03-09 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []

  • ReproHack - A hackaton on reproducible data analysis

    20 October 2020

    Elixir node event
    ReproHack - A hackaton on reproducible data analysis https://tess.elixir-europe.org/events/reprohack-a-hackaton-on-reproducible-data-analysis During a ReproHack, participants attempt to reproduce published research of their choice from a list of proposed papers with publicly available associated code and data. This approach should provide a low-pressure environment to actually get working with other people's code and data. Besides evaluating the analysis of papers, this hackaton is also about working together, networking and learning from each other!  Disclaimer: It’s imperative to note that this event is by no means an attempt to criticize or discredit work. We see reproduction as beneficial scientific activity in itself, with useful outcomes for authors and valuable learning experiences for the participants and the research community as a whole. Nominate a paper We accept nominations from anyone. Both researchers that have submitted a paper and would like to test whether one of your own papers is reproducible, and researchers that want to dig into the code of another paper! Either way, we encourage proponents to seek consent from the original authors for their nominations. Nominate a paper via this link. The papers will be assembled and showcased before selection via this link.  Register as participant Join us at the hack to dig into exciting science, learn more about reproducibility, working with other people's code and data and more. 2020-10-20 09:00:00 UTC 2020-10-20 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []

  • Containers and Workflow Pipelines for reproducible and automated data analysis

    26 - 27 October 2020

    Elixir node event
    Containers and Workflow Pipelines for reproducible and automated data analysis https://tess.elixir-europe.org/events/containers-and-workflow-pipelines-for-reproducible-and-automated-data-analysis-7a613826-6388-464d-858a-b4dce0da9e43 Containers Learn the concept of and the difference between Docker & Singularity containers  Write a Docker recipe, build and run a Docker image and containers Pull and push Docker container to / from Docker hub Docker files and layers; Docker cashing Working with volumes Pull Docker containers as a Singularity image Pipelines Understand Nextflow's basic concepts: processes, channels, ... Write and run a Nextflow pipeline (using a Singularity containers) 2020-10-26 09:00:00 UTC 2020-10-27 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []

  • Introduction to Protein Structure Analysis, autumn session

    29 October 2020

    Ghent, Belgium

    Elixir node event
    Introduction to Protein Structure Analysis, autumn session https://tess.elixir-europe.org/events/introduction-to-protein-structure-analysis-autumn-session Get to know the data generated from protein structure determination experiments (high-resolution NMR spectroscopy, X-ray crystallography, electron microscopy, ...) and where to get it. Display protein structure data and compare structures, through the use of Yasara. Create high-quality graphical representations of the structures. Calculate the effect of mutations on the stability of your protein. 2020-10-29 09:00:00 UTC 2020-10-29 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []

  • Research Data Management in Life Sciences

    9 - 10 November 2020

    Elixir node event
    Research Data Management in Life Sciences https://tess.elixir-europe.org/events/research-data-management-in-life-sciences Upon completion of this course, participants should have an understanding of what Research Data Management is, and why it is important in academic research.  They should have an understanding of the FAIR data principles, and how they can make data more FAIR. They should be able to successfully manage all types of research data and to document both the research itself, as well as the data in a comprehensive way.  2020-11-09 09:00:00 UTC 2020-11-10 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] publish and share datacreate preservation documentationMigrate data to best mediaMigrate data to best formatcreate user documentationEstablish copyrightcite data sourcesmanage and store datadescribe and document datacapture data with metadataexplore existing data resourcesplan consent for sharingplan data management design research

  • Gentle hands-on introduction to Python programming

    16 - 30 November 2020

    Leuven, Belgium

    Elixir node event
    Gentle hands-on introduction to Python programming https://tess.elixir-europe.org/events/gentle-hands-on-introduction-to-python-programming-tbc-autumn Learning the basics of Python programming: different variables, reading files, writing files, conditional statements Being able to write a basic Python script from scratch 2020-11-16 09:00:00 UTC 2020-11-30 00:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []

  • Research Software Developers Day

    3 December 2020

    Elixir node event
    Research Software Developers Day https://tess.elixir-europe.org/events/research-software-engineers-conference The aim of this conference is to foster a community of research software developers and to collectively improve the standard of software used for scientific research. For this, our first edition, we focus on three main themes: reproducibility, software quality and infrastructure. ​If you have something to say, whether broadly related to the topics mentioned above or not, we kindly request you to submit a talk or workshop proposal via this link. If you miss out, you'll have another opportunity to give a lightning talk on the day.   The schedule is accessible at www.be-rse.org/.  2020-12-03 09:00:00 UTC 2020-12-03 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []

  • Label-free Proteomics data analysis in Galaxy

    3 - 4 December 2020

    Ghent, Belgium

    Elixir node event
    Label-free Proteomics data analysis in Galaxy https://tess.elixir-europe.org/events/label-free-proteomics-data-analysis-in-galaxy In the first part we will introduce you to the Galaxy platform. It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing your work. The proteomics data analysis part comprises label-free data dependent analysis with MaxQuant and label-free data independent acquisition analysis (DIA) with i.a. OpenSwath. A detailed program will be provided shortly.  2020-12-03 09:00:00 UTC 2020-12-04 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []

  • Introduction to Git & GitHub

    10 December 2020

    Ghent, Belgium

    Elixir node event
    Introduction to Git & GitHub https://tess.elixir-europe.org/events/introduction-to-git-github-tbc-autumn Get you started with Git from zero (note that if you already use Git, this workshop will be too basic for you). We'll work with GitHub (Desktop) and have a look into git on a command-line level.  Introduction, set-up & configurations Working locally: Create a repository, clone, edit, staging commits, commit & push Working with your history & logs Working in a project: Forking, branching & pull requests How to version control your code in Rstudio with GitHub 2020-12-10 09:00:00 UTC 2020-12-10 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []

  • Factorial design and analysis

    14 - 15 December 2020

    Elixir node event
    Factorial design and analysis https://tess.elixir-europe.org/events/factorial-design-and-analysis After attending this course, you will be able to reason about you experiment and come up with a design and analysis that fits your situations best, rather than to settle for a suboptimal textbook solution. 2020-12-14 09:00:00 UTC 2020-12-15 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []

  • Liquid-Liquid Phase Separation

    14 - 15 December 2020

    Elixir node event
    Liquid-Liquid Phase Separation https://tess.elixir-europe.org/events/liquid-liquid-phase-separation-09e3b786-957d-4d94-9513-3bcfeb0269b7 The aim of this training day is – after a brief introduction – to provide guidelines for accurate experimental characterization of LLPS processes in vitro and in cells. We will end the day with a discussion on the implications of dysregulation of liquid-liquid phase separation for human disease. We have invited top-notch speakers on this topic to inform you on the latest developments.   2020-12-14 09:00:00 UTC 2020-12-15 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []

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