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21	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.
	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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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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	64	+[[image:image-20221213144754-1.png]]
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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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64	64	=== Source Code ===
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66	66	[[https:~~/~~/github.com/bluebrain/bluenaas-subcellular>>url:https://github.com/bluebrain/bluenaas-subcellular]]

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	1	+XWiki.oliviaeriksson

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