Optimization of single-cell biophysically detailed models

Installation:

$ python setup.py install

Run:

$ python -m biophys_optimize.scripts.run_preprocessing --help

to get command line options. There are a handful of JSON files for examples in test_input_files.

Follow the Jupyter Notebook at https://github.com/latimerb/GeneralTutorials/blob/master/AllenSDK/cell_types.ipynb to download electrophysiology and SWC data. The specimen ID needs to be added to the test_input_files/test_preprocess_input.json file and you need to update the paths to the data. The sweep IDs are unique for each specimen so you may need to look these up.

$ python -m biophys_optimize.scripts.run_preprocessing --input_json ./test_input_files/test_preprocess_input.json

Change all the paths in the /test_input_files/test_passive_input.json file just as in step 1a. Other parameters should still be the same. Then run:

$ python -m biophys_optimize.scripts.run_passive_fitting --input_json ./test_input_files/test_passive_input_1.json