Questions about the article"A Biologically Plausible Spiking Neural Model of Eyeblink Conditioning in the Cerebellum"

General Discussion
22

I looked into this some more and there are multiple potential issues:

  • You have to use pip install -e . if you want changes made to the source repository to be visible. In other words, you cannot use pip install nengo-bio and then make changes to the source repository (e.g., check out an older revision).
  • The code for running the model in Plot - Results - Basic.ipynb was just for debugging; as I wrote above [1] you have to use Run Model.ipynb and then load the results in the appropriate places in Plot - Results - Basic.ipynb. You’re likely using the debug data to plot your results (at least your plots are very similar to what I get when I plot the debug data).
  • The Plot - Results - Basic.ipynb in the repository was not exactly the version we used for the paper; that’s why the overall layout was not what’s in the paper. I’ve restored a version from Feb 3 from our backups and replaced the file on GitHub.

To make things easier for you, I’ve prepared a Docker container that sets everything up. See the Dockerfile [2] in the repository for the exact sequence of commands required in a fresh Debian 10.8 installation. See the updated README [3] for how to use the Docker container. Note that my knowledge of Docker boils down to ten minutes of using Google; so I cannot help you if you run into any issues with Docker.

Sorry for making this entire process so complicated; but (unfortunately) this is how things typically are with research code.

[1] Questions about the article"A Biologically Plausible Spiking Neural Model of Eyeblink Conditioning in the Cerebellum" - #12 by astoecke

[2] cogsci2020-cerebellum/Dockerfile at master · ctn-waterloo/cogsci2020-cerebellum · GitHub

[3] cogsci2020-cerebellum/README.md at master · ctn-waterloo/cogsci2020-cerebellum · GitHub