This code allows reproduction of simulation results from [Mengual2020].
To run, make sure all requirements are installed on your machine. Notably, this code uses [BluePyOpt](https://bluepyopt.readthedocs.io/en/latest/) [VanGeit2016] and [NEAT](https://neatdend.readthedocs.io/en/latest/) [Wybo2020].
Clone this repository and compile the ion channels by running from its source directory:
compilechannels channels/
The optimize the parameters of the ion channels, run the optimizer.optimizeModel() function from a python console.
Optimization results can be plotted with functions in plot_optimization_results.py. The h-current analysis can be ran and plotted with plot_h_analysis.py.
Check out examples.py for specific usage examples of the various optimization or plot functions.
- python >= 3.7.6
- neat >= 0.9.0
- neuron >= 7.7.2
- bluepyopt >= 1.9.3
- numpy >= 1.19.2
- matplotlib >= 3.3.2
- Mengual2020
Ulisses Mengual, Willem Wybo, Lotte Spierenburg, Mirko Santello, Walter Senn, and Thomas Nevian (2020) Efficient low-pass dendro-somatic coupling in the apical dendrite of layer 5 pyramidal neurons in the anterior cingulate cortex, In Press.
- VanGeit2016
Werner Van Geit, Michael Gevaert, Giuseppe Chindemi, Christian Rössert, Jean-Denis Courcol, Eilif Muller, Felix Schürmann, Idan Segev, and Henry Markram (2016) BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience, Front. Neuroinf.
- Wybo2020
Willem Wybo, Jakob Jordan, Benjamin Ellenberger, Ulisses Mengual, Thomas Nevian, and Walter Senn (2020) Data-driven reduction of dendritic morphologies with preserved dendro-somatic responses, bioRxiv preprint