Multiscale Modeling with MOOSE MOOSE provides the capability to simulate coupled electrical-chemical compartmental models, which are particularly relevant for neuronal plasticity. In these studies, the cell geometry is spatially subdivided for electrical and chemical calculations, and distinct kinds of chemical network occupy different zones of the neuron. The electrical events, through neurotransmitter release and calcium influx, affect the chemical signaling, and the chemical events, through ion channel phosphorylation and receptor cycling, influence the electrical properties of the cell.
Biophysical model of rat olfactory bulbOur detailed model having mitral, granule and peri-glomerular cells, shows how decorrelation and linearity of odour responses, as seen experimentally by other lab-members, might emerge from network connectivity. Olfactory Bulb Model Olfactory Bulb Model: Two Glomeruli
MOOSE Graphical User InterfaceIncluded is Kinetikit: a toolkit for viewing and editing Biochemical models. Also part of the GUI is Neurokit: a graphical toolkit for managing neuronal simulations, and plotting their results. Simulation of Purkinje Cell Model Kinetikit 12: Viewing and Editing a Biochemical Model Plotting
Interoperability and StandardsThere are multiple standards for model specification at various levels and MOOSE supports three of them: the GENESIS scripting language, SBML and NeuroML. Moreover, it aims to support the Network Interchange format for NEuroscience (NineML) as the specification matures. In the absence of a common framework to combine model components specified in different formats, the user has to put significant effort in developing composite models and such models remain non-standard. However, as simulating composite models out of existing ones becomes easier, it will be important for the community to find a way to integrate the existing standards for maximum productivity. MOOSE is one of the first simulators with this cross-scale capability, and provides a key test-bed for implementations of multiscale model definition standards.
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