Where can I find synaptic calcium concentration values in this simulation?

[Sangyoon-Bae]

Hi,
Thank you for sharing the code! It is very interesting works.
Based on what I've read from your papers, it seems like this GitHub repository is a simulation of how pre-synaptic spikes influence synaptic calcium concentration, and how this calcium concentration affects synaptic efficacy, ultimately leading to variations in the magnitude of EPSP.
However, no matter how hard I look, I can't find the part related to calcium concentration.

The calcium-related code I found only involves setting the depression and potentiation thresholds with C_pre and C_post.
(https://github.com/BlueBrain/EModelRunner/blob/main/emodelrunner/synapses/glusynapse.py)

Could you kindly tell me that which code is related to mapping of pre-synaptic spikes to synaptic calcium concentration?

Thank you so much!

Sincerely, Stella.

[AurelienJaquier]

Hi @Sangyoon-Bae sorry for late response.
The calcium concentration code can be found in the mechanisms folder of the cell data (can be found on zenodo, under cell_packages.zip). You can also find one example for one cell on this packages, here. I think the mechanism responsible for calcium concentration talked in the paper is GluSynapse.mod. CaDynamics_DC0.mod also has an influence on the calcium concentration.

If you want to look at the code used to produce the images of the paper (e.g. mapping between pre-synaptic spikes and EPSP ratio), it can also be found on zenodo, under analysis.zip.

Cheers,
Aurélien