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  • Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2020

    27 - 29 April 2020

    Magdeburg, Germany

    Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2020 https://tess.elixir-europe.org/events/tools-for-systems-biology-modeling-and-data-exchange-copasi-cellnetanalyzer-sabio-rk-fairdomhub-seek-2020 Educators: Axel von Kamp, Steffen Klamt, Sven Thiele (MPI Magdeburg), Frank T. Bergmann, Ursula Kummer (University of Heidelberg), Wolfgang Müller, Maja Rey, Andreas Weidemann, Ulrike Wittig (HITS) (de.NBI-SysBio) Date: 27. - 29 April 2020 Location: MPI Magdeburg Sandtorstrasse 1 39106 Magdeburg Contents: Key concepts of stoichiometric and kinetic modeling of biochemical networks: - stoichiometric matrix and stoichiometric networks - steady state flux distributions - principles of constraint-based modeling - metabolic flux analysis and flux optimization (flux balance analysis) - metabolic pathway analysis with elementary flux modes - metabolic network design via minimal cut sets - simulation of dynamic (kinetic) models - sensitivity analysis - carrying out parameter estimation tasks - model exchange using SBML Data and model management: - manual/programmatic access to reaction kinetics data from SABIO-RK - storage and exchange of data and models using FAIRDOMHub/SEEK - modeling specific functionalities in FAIRDOMHub/SEEK Learning goals: During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day introduces kinetic modeling techniques which will be illustrated and exercised with COPASI. The second day continues with principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOMHub/SEEK is introduced as a data and model management platform fitted to the needs of systems biologists. The hands on exercises throughout the three days will ensure that attendees become familiar with the software tools and with analyzing, creating, editing, importing, simulating and storing biochemical networks. Prerequisites: Some knowledge of mathematical modeling will be advantageous. The participants should bring their own laptop with MATLAB installed (if you do not have MATLAB please let us know during registration). Download and preinstallation of COPASI and CellNetAnalyzer is recommended but not mandatory. Keywords: CellNetAnalyzer (CNA), COPASI, SBML, FAIR, modeling, kinetic data access, database, data and model management Tools: CellNetAnalyzer, COPASI, Matlab, SABIO-RK, FAIRDOMHub/SEEK 2020-04-27 09:00:00 UTC 2020-04-29 17:00:00 UTC de.NBI Magdeburg, Magdeburg, Germany Magdeburg Magdeburg Germany [] [] [] workshops_and_courses [] []
  • Ensembl Browser Workshop, DKFZ, 5 May 2020

    5 May 2020

    Heidelberg, Germany

    Elixir node event
    Ensembl Browser Workshop, DKFZ, 5 May 2020 https://tess.elixir-europe.org/events/ensembl-browser-workshop-dkfz-5-may-2020 Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, and mine these data with BioMart. 2020-05-05 09:00:00 UTC 2020-05-05 09:00:00 UTC Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC), Heidelberg, Germany Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) Heidelberg Germany 69120 [] Astrid Gall [] [] [] [] HDRUK
  • Ensembl REST API Workshop, DKFZ, 6 May 2020

    6 May 2020

    Heidelberg, Germany

    Elixir node event
    Ensembl REST API Workshop, DKFZ, 6 May 2020 https://tess.elixir-europe.org/events/ensembl-rest-api-workshop-dkfz-6-may-2020 Work with Ensembl to master the Ensembl REST API and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments. 2020-05-06 09:00:00 UTC 2020-05-06 09:00:00 UTC Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC), Heidelberg, Germany Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) Heidelberg Germany 69120 [] Astrid Gall [] [] [] [] HDRUK
  • Basic statistics theory, Leuven

    15 May 2020

    Leuven, Belgium

    Elixir node event
    Basic statistics theory, Leuven https://tess.elixir-europe.org/events/basic-statistics-theory-leuven-4d12f147-07ed-4726-a85b-b9d770db84fc After this basic statistics theory session, you should be able to: Understand basic statistical concepts and methods for statistical analysis of life sciences data Choose the correct statistical test for analyzing your data Interpret and critically assess the results of basic statistical analyses 2020-05-15 09:00:00 UTC 2020-05-15 00:00:00 UTC VIB Bioinformatics Core Campus Gasthuisberg, Leuven, Belgium Campus Gasthuisberg Leuven Belgium 3000 [] [] [] [] [] []
  • Introduction to the analysis of NGS data

    25 May 2020

    Leuven, Belgium

    Elixir node event
    Introduction to the analysis of NGS data https://tess.elixir-europe.org/events/introduction-to-the-analysis-of-ngs-data-80436424-f33b-48b6-9b58-59a6044edf90 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 2020-05-25 09:00:00 UTC 2020-05-25 00:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • Gentle hands-on introduction to Python programming

    22 - 26 June 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-b4e7bd30-610a-4157-985f-850853a2c8cf Learning the basics of Python programming: different variables, reading files, writing files, conditional statements Being able to write a basic Python script from scratch 2020-06-22 09:00:00 UTC 2020-06-26 00:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • CABANA: Bioinformatics for Plant Biology

    30 November - 4 December 2020

    San Jose, Costa Rica

    Elixir node event
    CABANA: Bioinformatics for Plant Biology https://tess.elixir-europe.org/events/cabana-bioinformatics-for-plant-biology We are currently developing the course programme for 2020, and as further information about the course becomes available we will update this page. 2020-11-30 09:00:00 UTC 2020-12-04 17:00:00 UTC University of Costa Rica (UCR), San Jose, Costa Rica University of Costa Rica (UCR) San Jose Costa Rica CB10 1SD [] Marina Pujol [] [] [] [] HDRUK

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