Subcellular model building and calibration tool set

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. 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.

Subcellular Model Building And Calibration Toolset

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.

Documentation and source code
Uncertainty quantification and Sensitivity analysis examples
EBRAINS Jupyter Notebook example

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Documentation
Source Code

Other Tools

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Subcellular Simulation Webapp

This tool allows import of SBML model files from the subcellular model building and calibration toolset workflow or other external sources. The tool 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.

siibra-explorer

siibra-explorer is built around an interactive 3D view of the brain displaying a unique selection of detailed templates and parcellation maps for the human, macaque, rat or mouse brain, including BigBrain as a microscopic resolution human brain model at its full resolution of 20 micrometres.

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