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[BBPBGLIB-762] The ability to update single cell features mid simulation #204

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WeinaJi opened this issue Oct 22, 2024 · 1 comment
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enhancement New feature or request

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@WeinaJi
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WeinaJi commented Oct 22, 2024

This is a duplicate of the JIRA ticket BBPBGLIB-762.

In the case of thalamus simulations, it is very interesting to see the transition from a wake-like to a sleep-like state, which in part amounts to increasing potassium leak conductance (e.g. from 0.5gk_leak to 1.5gk_leak) during a simulation.

Current solution working for both NEURON and CORENEURON:
We will implement a new parameter "delay" in the "modifications" section under "conditions". An example to update the "gk_leak" of a certain mechanism(TC_??) will be like:

"conditions": {
    "v_init": -65,
    "randomize_gaba_rise_time": true,
    "modifications": [
       {
            "name": "gk_leak_t15",
             "node_set": "small",
            "type": "ConfigureAllSections",
            "section_configure": "%s.gk_leak_TC_?? *= 0.5"
        },
        {
            "name": "gk_max_t20",
            "node_set": "small",
            "type": "ConfigureAllSections",
            "section_configure": "%s.gk_leak_TC_?? *= 2",
            "delay" : 20
        }
     ]
}
@WeinaJi WeinaJi added the enhancement New feature or request label Oct 22, 2024
@WeinaJi WeinaJi linked a pull request Oct 22, 2024 that will close this issue
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@WeinaJi
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WeinaJi commented Nov 13, 2024

Required changes:

  1. neurodamus branch: https://github.com/BlueBrain/neurodamus/tree/weji/polina_copy
  2. libsonata branch for adding "delay" key in the simulation config https://github.com/BlueBrain/libsonata/tree/weji/simconf_modifications
  3. neuron branch for update coreneuron report in the middle of simulation https://github.com/neuronsimulator/nrn/tree/weji/update_reports_v2

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