Last modified by oliviaeriksson on 2022/12/13 14:50
From version 17.1
edited by oliviaeriksson
on 2022/12/13 14:45
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To version 14.1
edited by oliviaeriksson
on 2022/12/13 14:31
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19 19  Toolset for data-driven building of subcellular biochemical signaling pathway models. The toolset includes interoperable modules for: model building, calibration (parameter estimation) and model analysis. All information needed to perform these tasks are stored in a structured, human- and machine-readable file format based on SBtab (Lubitz et al. 2016). This information includes: models, experimental calibration data and prior assumptions on parameter distributions. The toolset enables simulations of the same model in simulators with different characteristics, e.g. STEPS, NEURON, MATLAB’s Simbiology and R via automatic code generation. The parameter estimation is done by optimization or Bayesian approaches. Model analysis includes global sensitivity analysis and functionality for analyzing thermodynamic constraints and conserved moieties.
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23 -(% class="small" %)**The Subcellular Model building and Calibration tool set. **The model together with the experimental data and other information used for calibration are contained within a unified format based on SBtab [1] (//Model and data box//).  This is the input to the calibration (parameter estimation) and analysis tools (//Calibration or Analysis box). //The model can also be transferred to different other// formats //like SBML or MOD// (Communication and Other simulations boxes). //Before calibration is performed the model can be reduced in size// (model reduction).//
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25 25  [1] Lubitz, T., Hahn, J., Bergmann, F.T., Noor, E.,. Klipp, E, Liebermeister, W. (2016). SBtab: A flexible table format for data exchange in systems biology. Bioinformatics, 15;32(16), 2559-61.
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