Last modified by oliviaeriksson on 2022/12/13 14:50
From version 20.1
edited by oliviaeriksson
on 2022/12/13 14:50
Change comment: There is no comment for this version
To version 11.1
edited by oliviaeriksson
on 2022/12/08 15:46
Change comment: There is no comment for this version

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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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23 +[[**Golden paragraph **>>https://wiki.ebrains.eu/bin/view/Collabs/technical-coordination/EBRAINS%20components/Molecular%20and%20subcellular%20level%20description/]]
27 27  
28 28  === Source Code ===
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62 62  An online tool for configuring and running compartmental subcellular simulations. This tool allows import of SBML model files from the subcellular model building and calibration toolset workflow or other external sources. The tool ([[https:~~/~~/subcellular.humanbrainproject.eu>>url:https://subcellular.humanbrainproject.eu/]]) allows users to setup and configure BioNetGen and STEPS simulations. Users can populate mesh models of spines and other neural structures, and run stochastic simulations of signalling pathways.
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66 -(% class="small" %)**Subcellular Simulation Webapp **Simulation results can be viewed through the Subcellular App. The simulation tracks calcium entry through NMDA receptors and activation of calcium-mediated pathways in the postsynaptic density (top traces). The geometry (bottom panel) for a dendritic spine (green) and associated parent dendrite (red) are also shown, with molecule positions indicated by points within the structure.
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68 68  === Source Code ===
69 69  
70 70  [[https:~~/~~/github.com/bluebrain/bluenaas-subcellular>>url:https://github.com/bluebrain/bluenaas-subcellular]]
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