Package: neuwon
Copyright (c) 2020 David McDougallPermission is hereby granted, free of charge, to any person obtaining a copy
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SOFTWARE.Description: # NEUWONNEUWON 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 ArchitectureModels are composed of three types of components: physical structures,
reactions, and diffusions.#### Physical StructuresNeurons 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 PropertiesLengthDiameterCross-sectional AreaMembrane Surface AreaIntracellular VolumeTree StructureParent Segment, unless segment is root of treeChild Segments, listExtracellular Space PropertiesVolumeAdjacent Tracking PointsDistance between pointsSurface Area of border#### ReactionsChemical 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 ElectrotonicsDiffusion 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 MethodsReactions 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#### InstallationPrerequisites:
* [Python 3](https://www.python.org/)
* numpy & scipyTODO: Install & Test instructions#### Model SpecificationTODO 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