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Real-time Electrophysiology: Using Closed-loop Protocols to Probe Neuronal Dynamics and Beyond
Published on: June 24, 2015
Reaction-diffusion in the NEURON simulator
Robert A McDougal1, Michael L Hines, William W Lytton
1Department of Neurobiology, Yale University New Haven, CT, USA.
Abstract:
In order to support research on the role of cell biological principles (genomics, proteomics, signaling cascades and reaction dynamics) on the dynamics of neuronal response in health and disease, NEURON's Reaction-Diffusion (rxd) module in Python provides specification and simulation for these dynamics, coupled with the electrophysiological dynamics of the cell membrane. Arithmetic operations on species and parameters are overloaded, allowing arbitrary reaction formulas to be specified using Python syntax. These expressions are then transparently compiled into bytecode that uses NumPy for fast vectorized calculations. At each time step, rxd combines NEURON's integrators with SciPy's sparse linear algebra library.
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