I am curious who might be working with the DiffEq packages to do single neuron cell modeling up to small network simulations using Hodgkin Huxley or similar models, either single or multi-compartment, etc. If you’re out there or know someone heavy into Julia + comp neuroscience, I am very curious w…

Anything new on this front? I am interested in a Julia alternative to the Brian simulator.

Nothing that I am aware of and I am from this field. It should not be too difficult to write a Julia replacement though. Same for Neuron. I know a couple people who wrote a grant about writing a Julia analog of Neuron, not sure they got funded. What is it that makes you turn away from Brian?

I love Brian actually. However, we are modling an compartmentalized system with astrocytes with a numerical technique that makes it difficult to work within the Synapse/NeuronGroup framework provided. I had to create an artificial Synaptic group and control the order of execution just so I could imp…

SpikingNeuralNetworks is a really good start on this. The thing I found missing when I briefly played with it was easily composing networks. I have a heap of code that binds LightGraphs to a metadata structure that is more suitable for this sort of thing. It’s littered with notes and untested right …

The thing I am worried about SpikingNeuralNetworks, and it should be a fairly simple addition, is that the time stepper is not that great. It should perhaps give the choice of using OrdinaryDiffEq.jl. For example, the iz neuron blows up in finite time… Hence the precision of the time spikes is not …

Agreed, I think it’d be ideal to convert SNN (SpikingNeuralNetworks.jl) to use OrdinaryDiffEq as the integrator, especially since that would potebtially net us great GPU support. I have somewhat limited time right now, but if someone feels like putting together a PR to convert some or all of the mod…

Would you rate this as a “beginner” friendly task?

I think that it’s a pretty simple task from my standpoint, since the current API for each neuron model’s integrate! call looks reasonably similar to a DiffEq solve call. I can help you debug any issues you run into while doing this, of course.

I am going to give it a try! Hopefully, I can start to work on it tomorrow.

I’m doing exactly this for my final year uni project! It’s largely motivated by a different design principle from Brian. Brian wants the user to express their neuron through a series of differential equations as strings, which makes sense for a mathematician but feels very wrong to a programmer, and…

Neuroscientists using DifferentialEquations.jl ecosystem?

Specific Domains Modelling & Simulations

sbuercklin July 31, 2020, 7:01pm 24

We recently released a SNN sim package as well, WaspNet.jl. Although it doesn’t integrate with DifferentialEquations currently

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Neuroscientists using DifferentialEquations.jl ecosystem?

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