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  • Computing Skills for Reproducible Research: Software Carpentry Course 2020

    19 - 23 October 2020

    Computing Skills for Reproducible Research: Software Carpentry Course 2020 https://tess.elixir-europe.org/events/computing-skills-for-reproducible-research-software-carpentry-course-2020 Educators: Renato Alves (HD-HuB) Date: 19-10-2020 - 23-10-2020 09:00-18:00 Location: Online Contents: Computation is an integral part of today's research as data has grown too large or too complex to be analysed by hand. An ever-growing fraction of science is performed computationally and many wet-lab biologists spend part of their time on the computer. Many scientists struggle with this aspect of research as they have not been properly trained in the necessary set of skills. The result is that too much time is spent using inefficient tools when progress could be faster. This course provides training in several key tools, with a focus on good development practices that encourage efficient and reproducible research computing. Topics covered include: Introduction to Python scripting Introduction to the Unix shell and usage of cluster resources Version control with Git and Github Analysis pipeline management Scientific Python & working with biological data Literate programming with Jupyter notebooks Learning goals: This course aims to teach software writing skills and best practices to researchers in biology who wish to analyse data, and to introduce a toolset that can help them in their work. The goal is to enable them to be more productive and to make their science better and more reproducible. Prerequisites: This is a course for researchers in the life sciences who are using computers for their analyses, even if not full time. The target student will be familiar with some command line/programmatic computer usage, will want to become more confident using these tools efficiently and reproducibly. A target student will have written a for loop in some language before, but will not know what git is (or at least not be very comfortable using git). Keywords: Programming; Command Line; Version Control; Bioinformatics; Data Analysis; Cluster Computing Tools: Python; Bash; Unix/Linux; Git; GitHub; SnakeMake; Biopython; Pandas; Numpy; SciPy; Matplotlib 2020-10-19 09:00:00 UTC 2020-10-23 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • ELIXIR CZ Artificial Intelligence in Life Sciences I

    26 - 27 October 2020

    Prague, Czechia

    Elixir node event
    ELIXIR CZ Artificial Intelligence in Life Sciences I https://tess.elixir-europe.org/events/elixir-cz-artificial-intelligence-in-life-sciences-i This workshop will provide a basic introduction to machine learning and its application in Life Sciences, with a special focus on molecular and cell biology. Data-driven approaches penetrate various scientific disciplines, including the fields of biology, biochemistry and biotechnology. Novel technologies of high-throughput data collection and advanced data analysis, such as deep neural networks, offer exceptional opportunities for the development of very complex and accurate mathematical models. The theoretical lectures will cover main methods, algorithms and technologies, illustrate their use in biology and biochemistry research using real-life examples. Hands-on practicals will provide participants with essential skills for the application of machine learning methods and software tools for solving problems in Life Sciences. We plan to continue in our effort to organize follow-ups of this meeting and focus on challenging issues in life science disciplines approachable by AI technology. 2020-10-26 11:00:00 UTC 2020-10-27 14:00:00 UTC ELIXIR CZ, IOCB, FNUSA – ICRC, University of West Bohemia Flemingovo nám. 542, 542, Flemingovo náměstí, Prague, Czechia Flemingovo nám. 542, 542, Flemingovo náměstí Prague Hlavní město Praha Czechia 166 10 [] https://www.elixir-czech.cz/events/elixir-cz-artificial-intelligence-in-life-sciences-oct-2020 [] [] 75 workshops_and_courses first_come_first_served Artificial Intelligencemachine learningDrug design
  • 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 [] [] [] [] [] []
  • Introduction to Protein Structure Analysis, winter session

    30 November 2020 - 19 March 2021

    Ghent, Belgium

    Elixir node event
    Introduction to Protein Structure Analysis, winter session https://tess.elixir-europe.org/events/introduction-to-protein-structure-analysis-winter-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. 2020-11-30 09:00:00 UTC 2021-03-19 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []
  • DDA and DIA proteomic analysis in Galaxy

    3 - 4 December 2020

    Ghent, Belgium

    Elixir node event
    DDA and DIA proteomic analysis in Galaxy https://tess.elixir-europe.org/events/label-free-proteomics-data-analysis-in-galaxy At the beginning of the course we will introduce you to the Galaxy platform and teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing your work.  Then, we will dive into proteomic analyses which are split up into two parts. First, we will use MaxQuant to analyze classical proteomic shotgun (label-free data dependent acquisition = DDA) data. MaxQuant is a standalone tool that enables peptide and protein identification as well as quantification.  In the second part we will perform a complete analysis workflow for data independent acquisition (DIA) data using a variety of open-source tools (including diapysef, OpenSwath, Pyprophet, MSstats). This includes generating a peptide library, refining the library and utilizing the library to identify and quantify peptides in DIA data.  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 [] [] [] [] [] []

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