https://github.com/russelljjarvis/nestneuronunit
https://github.com/russelljjarvis/nestneuronunit
Last synced: 4 months ago
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- Host: GitHub
- URL: https://github.com/russelljjarvis/nestneuronunit
- Owner: russelljjarvis
- Created: 2021-10-30T04:44:15.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2021-11-10T00:52:24.000Z (over 3 years ago)
- Last Synced: 2025-01-10T03:18:45.719Z (5 months ago)
- Language: Python
- Size: 85.9 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: changeto_setup_py_requirements.txt
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README
# About
Code to make the NEST ADEXP single cell model optimizable via NeuronUnit and BluePyOpt.
## Install:
### To test interopability
- Install NEST https://nest-simulator.readthedocs.io/en/stable/installation/linux_install.html
- Install sciunit
- Install Neo, quantities
```
pip install git+https://github.com/russelljjarvis/sciunit@dev
```
### Preliminary Run
```python test_interface.py```
```python spike_current_search.py```
# DONE
- [x] Some basic NEST/NU interoperability
- [x] Inject current
- [x] Get spike Count
- [x] set model parameters
- [x] RheobaseTest generate prediction,
- [x] SpikeCurrentSearch Generate Prediction.
## TODO
- [ ] Find sensible NEST, Adexp parameter range.
- [ ] score a NU test against NEST model
- [ ] Run current search algorithm against NEST model
- [ ] Optimize a NEST model
### Future: to Do a BPO data driven optimization on the reduced model via NU model scoring
- Install BPO
- Install sciunit
- Install neuronunit
```
pip install git+https://github.com/russelljjarvis/sciunit@dev
pip install git+https://github.com/russelljjarvis/BluePyOpt@neuronunit_reduced_cells
pip install git+https://github.com/russelljjarvis/neuronunit
```