neuwon 0.0.0

Neuroscience simulator

Copyright (c) 2020 David McDougall

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Description: # NEUWON

NEUWON is a simulation framework for neuroscience and artificial intelligence specializing in conductance based models. This software is a modern remake of the NEURON simulator. It is accurate, efficient, and easy to use.

## Model Architecture

Models are composed of three types of components: physical structures, reactions, and diffusions.

#### Physical Structures

Neurons are composed of discrete segments which are connected into a tree structure. The shape of each segment is a frustum, also known as a truncated cone. The physical locations of the tips of the frustums in the system serve as tracking points for all cellular processes: intracellular, extracellular, and membrane-related. The extracellular space is partitioned into voronoi cells which are centered on the tracking points. NEUWON provides the following geometric properties for each tracking point:

• Cell Segment Properties

  • Length

  • Diameter

  • Cross-sectional Area

  • Membrane Surface Area

  • Intracellular Volume

  • Tree Structure

    • Parent Segment, unless segment is root of tree

    • Child Segments, list

• Extracellular Space Properties

  • Volume

  • Adjacent Tracking Points

    • Distance between points

    • Surface Area of border

#### Reactions

Chemical reactions are one of the mechanisms which the brain uses to implement differential equations. Complex reactions are capable of performing arbitrary calculations and large proteins can maintain a persistent state. Proteins embedded in the cell membrane can react to the electrical potential across the membrane, and can control the flow of chemicals across the membrane.

#### Diffusions and Electrotonics

Diffusion is the primary means of communication between locations in the brain. Chemicals diffuse through the intracellular and extracellular fluids and across cell membranes. Diffusion is modeled with a linear & time-invariant systems of differential equations, and so it can be simulated using specialized method which are both exact and efficient (Rotter & Diesmann, 1999). Electrically charged ions flow throughout neurons; a phenomenon which is modeled with an equivalent electrical circuit. The equivalent circuit is a linear & time-invariant system of differential equations, and so it is also simulated using the specialized methods.

### Integration Methods

Reactions and diffusions interact at staggered time steps, as explained in chapter 4 of the NEURON book. [Mention that mechanisms & reactions are reported at the unstable timepoint.]

[Talk about exact integration in more detail]

## Usage

#### Installation

Prerequisites: * [Python 3](https://www.python.org/) * numpy & scipy

TODO: Install & Test instructions

#### Model Specification

TODO Document how to use the model builder class.

Platform: UNKNOWN Classifier: License :: OSI Approved :: MIT License Classifier: Development Status :: 1 - Planning Classifier: Programming Language :: Python :: 3 Classifier: Operating System :: OS Independent Classifier: Intended Audience :: Science/Research Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence Requires-Python: >=3.6 Description-Content-Type: text/markdown