Show and Tell: Simulator for Conductance Based Models

Hello,

I’d like to show and tell you all about what I’ve been working on for a while now. Here is a short description of the project and its goals:

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.

It is currently in the alpha phase of development, so it is not at all ready to be used. It’s written it in python and freely available under the MIT license. Link: https://github.com/ctrl-z-9000-times/NEUWON

Here are some pictures of action potentials generated by the software:

Merry Christmas

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I’ve now implemented a neuron growth algorithm. The goal of this algorithm is to generate realistic neuronal morphological from a concise description of their basic properties. I use the TREES algorithm combined with the morphological constraints used by the ROOTS algorithm. The algorithm is capable of making both dendrites and axons. Neuronal growth is constrained to an arbitrary area.

This animation shows an action potential propagating through an axonal arbor. The color represents the membrane electric potential: blue = -70mV, red = +55mV. The Soma is the large cylinder in the lower left corner. I constrained the axon into a spiral shape. The width and height of this shape are approximately 200 micrometers and the center of the shape recedes 600 micrometers into the distance. The model populated with Hodgkin-Huxley channels and an AP is initiated at the soma.

TREES:
Cuntz H, Forstner F, Borst A, Hausser M (2010)
One Rule to Grow Them All: A General Theory of Neuronal Branching and Its Practical Application.
PLoS Comput Biol 6(8): e1000877.
doi:10.1371/journal.pcbi.1000877

Bingham CS, Mergenthal A, Bouteiller J-MC, Song D, Lazzi G and Berger TW (2020)
ROOTS: An Algorithm to Generate Biologically Realistic Cortical Axons and an Application to Electroceutical Modeling.
Front. Comput. Neurosci. 14:13.
doi: 10.3389/fncom.2020.00013

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This is quite beautiful work. I haven’t had time to dig in deeply, but very happy to see what you’re sharing. :slight_smile:

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Last month I rewrote the program to run on a graphics card (GPU) using CUDA.

Its still written in 100% python. I use the CuPy and Numba libraries to execute code on the GPU.

This demonstrates that the methods of simulation are embarrassingly parallel.
Furthermore the libraries (Numpy, Scipy, and CUDA) implement all of the difficult mathematics required for the exact integration method (Exact digital simulation of time-invariant linear systems with applications to neuronal modeling).

Sorry no pictures for this update, but it does run a lot faster than before without compromising the accuracy or ease of use.

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In the past month I wrote an interface for NEUWON to use NMODL files. NMODL is a standardized file specification for describing the mechanisms in neuronal simulations. It is custom tailored for neuroscience; it can describe ion channel kinetics and chemical reactions among other things. NMODL files can contain algebraic and differential equations. Most of state-of-the-art simulations of the brain use NMODL, usually along with the NEURON which also supports NMODL.

My implementation of NMODL is still at the prototype stage; it does not support many features and I’m sure there are still bugs in the code. Regardless, I was able to produce an Action Potential using the latest and greatest ion channel models:

For this demonstration I replaced the old Hodgkin-Huxley type channels with newer models of Nav1.1 type sodium channels and Kv1.1 type potassium channels. The first AP was spontaneously generated, and the second AP was caused by a current injection at t=25 ms.

The sources for the kinetic models of the ion channels are: