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2 events found

Country: Japan 

  • COMBINE & de.NBI Tutorial: Modelling and Simulation Tools in Systems Biology – ICSB 2019

    31 October 2019

    Japan

    COMBINE & de.NBI Tutorial: Modelling and Simulation Tools in Systems Biology – ICSB 2019 https://tess.elixir-europe.org/events/combine-de-nbi-tutorial-modelling-and-simulation-tools-in-systems-biology-icsb-2019 Educators: Andreas Weidemann, Martin Golebiewski (HITS gGmbH, Heidelberg, Germany), Frank Bergmann, Jürgen Pahle, Sven Sahle (University of Heidelberg, Germany) (de.NBI-SysBio) in collaboration with educators from UK, New Zealand, Japan, Germany, USA Date: Thursday, October 31st, 2019 Links: http://co.mbine.org/events/tutorial2019 Location: Okinawa Insitute of Science and Technology Graduate University Okinawa, Japan Contents: This tutorial workshop is a satellite of the 20th International Conference on Systems Biology (ICSB). Participants will learn how to set up computer models of biological systems (e.g. metabolic or signalling networks) using experimental kinetic data and how to simulate them in different systems biology platforms. Hands-on sessions, lectures and software demonstrations will be included, providing attendees with the necessary skills to access experimental kinetics data from available resources, to assemble computer models with these data, and finally to simulate the generated models using simulation tools. Also handling and exchange of biological models based on existing community standards will be demonstrated along with the basic principles of the underlying standard formats and how they support reproducible and FAIR computational modelling. The topics covered will include: - Reproducibility and FAIR (Findable, Accessible, Interoperable and Re-usable) data - Curation services - Model setup using different software tools and systems biology platforms - Using experimental data for setting up quantitative models - Parameter estimation, optimization and model fitting - Simulation, analysis and visualization of biochemical models, and multicellular modelling - Constraint-based and logical modeling of metabolic and signaling networks - Database supported modelling: integrated data management and model databases - Community standards and formats for systems and synthetic biology models - Machine learning for model reduction and image analysis Prerequisites: Laptop Keywords: systems biology, software tools, quantitative models, parameter estimation, model simulation, logical modeling, metabolic networks, model databases, community standards Tools: BioModels, CellDesigner, COPASI, Morpheus, Physiome Model Repository / OpenCOR, SABIO-RK, SEEK/FAIRDOMhub, tellurium, Virtual Cell 2019-10-31 09:00:00 UTC 2019-10-31 17:00:00 UTC de.NBI Präfektur Okinawa, Japan Präfektur Okinawa Japan [] [] [] workshops_and_courses [] []
  • Advanced modeling with COPASI - ICSB 2019

    31 October 2019

    Japan

    Advanced modeling with COPASI - ICSB 2019 https://tess.elixir-europe.org/events/advanced-modeling-with-copasi-icsb-2019 Educators: Sven Sahle (Heidelberg University), Frank Bergmann (Heidelberg University), Stefan Hoops (University of Virginia), Ursula Kummer (Heidelberg University), Pedro Mendes (University of Connecticut), Jürgen Pahle (Heidelberg University), Egils Stalidzans (University of Latvia) (de.NBI-SysBio / de.NBI-ModSim) Date: Thursday, October 31st, 2019 Links: http://denbi-modsim.de/icsb_copasi_2019/ Registration: https://forms.gle/NepBmMjrXmTzuCpy9 Location: Room 3, Okinawa Institute of Science and Technology Graduate University Okinawa, Japan Contents: COPASI is a widely used software tool for creating, simulating and analysing models of biochemical reaction networks. It is open source free software and available for all major operating systems. Its features include deterministic and stochastic simulation, steady state analysis, stoichiometric analysis, optimisation and parameter estimation, time scale analysis, sensitivities and metabolic control analysis, Lyapunov exponents, linear noise approximation, etc. In the workshop we will demonstrate the use of advanced features of COPASI, focusing on parameter estimation and parameter identifiability analysis, and the use of COPASI from scripting languages. For experienced users of the software, we will present an overview of new features added in the latest releases, such as stochastic differential equation models. A special session will demonstrate an optimisation workflow, highlighting how COPASI can be integrated in third party software projects. The developers of COPASI will also be available for the discussion of individual questions from the participants. Prerequisites: Laptop Keywords: systems biology, software tools, quantitative models, parameter estimation, model simulation, metabolic networks, model databases, community standards Tools: COPASI, 2019-10-31 09:00:00 UTC 2019-10-31 17:00:00 UTC de.NBI Präfektur Okinawa, Japan Präfektur Okinawa Japan [] [] [] meetings_and_conferences [] []
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