EModelRunner: a Python package to run online available biological neuron model implementations
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Abstract
The Blue Brain Project hosts several online portals from which users can download single neuron model implementations. These contain the information necessary to simulate the electrical behavior of a neuron. EModelRunner is a Python library that provides a unified interface to the users to run these downloaded models. It gives the users the ability to customize the properties of the neurons, apply various stimuli in order to observe the corresponding behavior, or activate the synapses that are present on the morphology of the neuron. This way neuroscientists can investigate the neurons in a self-contained environment and conduct digital experiments on them.
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Description
The brain is undoubtedly the most complex organ in the human body. Over the decades, scientists have been using theoretical and experimental approaches to understand the brain. With the recent advancement of computer systems and the availability of big data, a new discipline, namely simulation neuroscience, is emerged as a complementary approach alongside experimental, theoretical and clinical neuroscience. As the name suggests, simulation neuroscience attempts to understand the brain by simulating it in a computer. Here we present EModelRunner, a Python package designed to run the simulated neuron model implementations provided by the Blue Brain Project online portals. It is capable of simulating biologically detailed neuron models. A neuron model describes a single cell in the brain and consists of a morphology and equations that simulate its electrical behavior. EModelRunner uses the Neuron simulator under the hood. The Neuron simulator is implemented in C++, but also provides a Python interface to the user. For computing the properties of the membrane channels, Neuron uses compiled mechanisms written using the Neuron Model Description Language (NMODL). EModelRunner abstracts away the Neuron and NMODL implementation layers from the end-users and provides them with a pure Python API. It supplies the users with the ability to customize the properties of the neurons and apply various stimuli to them in order to observe their behavior. Another use-case for the EModelRunner is to provide a standard way of running the neuron models provided by the Blue Brain Project.