neuwon 0.0.0
Neuroscience simulator
License: MIT License

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