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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 [] []
  • Phylogenetic reconstruction course 2020

    20 May 2020

    Kiel, Germany

    Phylogenetic reconstruction course 2020 https://tess.elixir-europe.org/events/phylogenetic-reconstruction-course-2020 Educators: Tal Dagan (CAU) Date: 20.05.2019, 08:15 - 16:00 Location: Kiel Contents/Learning goals: The evolutionary history of genes or species is best studied and described by phylogenetic trees. The accumulating sequence data enable the reconstruction of phylogenetic trees for many diverse gene and species. A robust phylogeny is helpful in identifying phyletic groups as well as ancestral relations in the data and lateral gene transfer. Notwithstanding phylogenetic reconstruction is sensitive to various biases in the analysis that originate in alignment and phylogenetic reconstruction artifacts. Students in the workshop will learn to reconstruct multiple sequence alignment and phylogenetic trees of focal sequences. This includes a quantification of possible biases in the phylogenetic reconstruction and ways to counteract their influence on the results. In addition, the students will learn how to identify the root of phylogenetic trees and extract ancestral-descendent relations. The workshop is intended to address scientists from undergraduate to postdoc level and does not expect previous experience in phylogenetics. Basic knowledge on how to work with Linux will be advantageous. Prerequisites: None Keywords: Tree phylogeny, gene homology, rooting, robustness Tools: MAFFT, Guidance, PhyML, IQTree, MAD rooting, FigTree. 2020-05-20 09:00:00 UTC 2020-05-20 17:00:00 UTC de.NBI Kiel, Kiel, Germany Kiel Kiel Germany [] [] [] workshops_and_courses [] []

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