Biospaun implementation


Hi everyone! I just started reading HBB and watched some of the videos on youtube where Chris Eliasmith talks about Biospaun. On those videos Chris talks about how they tested some drugs like TTX. My question is if there is an example code of that or how can it be implemented.

Also, I don’t know if I’m posting this in the correct topic.



The TTX drug application was only tested on Spaun, as far as I know, so there isn’t any example code for how this exact experiment can be implemented. In general, to simulate drugs in a nengo model, you will need to either (a) approximate how the drug affects parameters like gain and bias in nengo’s default LIF neurons, or (b) simulate more biologically detailed neuron models where you can simulate the drug’s biophysical effects more directly. The code that was used in the TTX experiment used a simple interface with the NEURON programming language, and can be found in the nengo_detailed_neurons repository. However, this repo is not maintained, and if you are looking for a more general set of tools for this purpose, I’d recommend looking at the bioneuron repo, which contains a set of tools for simulating biologically realistic neurons in nengo.

I am developing the methods in this repo as part of my Master’s thesis, so unfortunately they are not yet sufficiently well-tested or documented for outside users (though you’re welcome to take a stab at it). Hopefully they will become so over the next couple months as I finish writing. Check back in periodically, as I plan to eventually upload a model I’ve built that goes through the process of drug simulation on multiple levels of analysis (an older version can be found here along with the paper here), as well as my thesis, which gives a detailed description of the methods used in the repo.

  • Peter Duggins