Last modified by oliviaeriksson on 2022/12/13 14:50
From version 9.1
edited by oliviaeriksson
on 2022/12/08 15:29
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To version 16.1
edited by oliviaeriksson
on 2022/12/13 14:33
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12 12  (((
13 13  == Introduction ==
14 14  
15 -The subcellular modeling and simulation services consist of tools for building and simulating subcellular level models. Such models often describe molecular signaling pathways within the cell. The service contains two different projects. //The subcellular model building and calibration tool set// (1) is focused on model calibration (parameter estimation) using simpler, one compartmental, models. //The subcellular simulation webapp (2),// allows the user to construct more detailed compartmental models using the STEPs or BioNetGen simulators. The tools are interoperable so that e.g. models can be constructed and calibrated using (1) and then simulated with more details in (2). The calibration toolset also allows uncertainty quantification and sensitivity analysis.
15 +The subcellular modeling and simulation services consist of tools for building and simulating subcellular level models. Such models often describe molecular signaling pathways within the cell. The service contains two different projects. //The subcellular model building and calibration tool set// (1) is focused on model calibration (parameter estimation) using simpler, one compartmental, models. //The subcellular simulation webapp (2),// allows the user to construct more detailed compartmental models using the [[STEPS>>https://steps.sourceforge.net/STEPS/default.php]] or [[BioNetGen>>https://bionetgen.org]] simulators. The tools are interoperable so that e.g. models can be constructed and calibrated using (1) and then simulated with more details in (2). The calibration toolset also allows uncertainty quantification and sensitivity analysis.
16 16  
17 17  == (% class="row" %)1. Subcellular model building and calibration tool set(%%) ==
18 18  
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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21 +[[image:image-20221213143123-1.png]]
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23 +**The Subcellular Model building and Calibration toolset. **//Model and data box~:// The model together with the experimental data used for calibration are contained within the SBtab format. Here are also information on model parameters, like prior knowledge/assumptions on possible ranges for parameters before parameter estimation/calibration takes place. //Calibration or Analysis box~:// the toolset includes different methods for calibration (estimation) of parameters as well as methods for model analysis, like different kinds of sensitivity analysis methods. The information retrieved within this box are fed back to the SBtab files of the //Model and data box//. //Communication and Other simulations boxes: //For interoperability, the toolset also consists of functionalities for transferring the SBtab files to other model formats like SBML. By this the model can for example be run in the Subcellular Simulation Webapp (see below). It is also possible to perform //model reduction //before the calibration takes place.
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21 21  [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.
22 22  
23 -[[**Golden paragraph **>>https://wiki.ebrains.eu/bin/view/Collabs/technical-coordination/EBRAINS%20components/Molecular%20and%20subcellular%20level%20description/]]
24 24  
25 25  === Source Code ===
26 26  
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