NEURONpyxl: fast, flexible, Python-integrated simulation of biophysical neural networks with complex plastic synapses

NEURON has been widely used as an empirically-based simulation tool, especially for multi-compartment conductance-based neuronal modeling. The network mediating feeding in Aplysia californica has been extensively studied as a model central pattern generator. Understanding the relationship between network parameter values and their effect on animal behavior is of key importance in systems such as the Aplysia feeding apparatus, where detailed biophysical models can be constructed.

This study aims to develop a new Python tool called NEURONpyxl that reads parameters from a spreadsheet to construct full neural networks to make it easier to create complex models in the NEURON simulation environment, incorporating short-term forms of plasticity such as depression or facilitation.

Test simulations from well-understood networks were created in NEURONpyxl, and compared to simulation results of the same network in another neural simulator, the Simulator for Neural Networks and Action Potentials (SNNAP), which has previously been used to model conductance-based networks that include complex synaptic connections and multiple forms of synaptic plasticity. NEURONpyxl was then used to conduct a parameter grid search to optimize conductances in a previously developed network model of Aplysia feeding behavior.

Simulations of the test networks in NEURONpyxl and SNNAP produced numerically equivalent results, with differences remaining within the expected margin of error arising from numerical integration and implementation details. We then located parameter values that generated simulated motor patterns with durations of protraction and retraction that matched biological feeding behavior under different mechanical loads.

NEURONpyxl simplifies building and simulating complex neural networks with different forms of synaptic plasticity, and locating physiologically relevant parameter values. With NEURONpyxl, future work may include the creation of ensembles of network models and the integration of biomechanics with complex conductance-based networks.