I am trying to exhaustively download and instance all the conductance based neuron models, and then instantiate them as NEURON simulator models.
I am trying the code below, but I am running into errors
def run_all_cell_bio_configs():
try:
with open('all_allen_cells.p','rb') as f:
cells = pickle.load(f)
except:
ctc = CellTypesCache(manifest_file='cell_types/manifest.json')
cells = ctc.get_cells()
with open('all_allen_cells.p','wb') as f:
pickle.dump(cells,f)
bp = BiophysicalApi()
#bp.cache_stimulus = False # change to False to not download the large stimulus NWB file
#neuronal_model_id = 472451419 # get this from the web site as above
for cell in cells:
#import pdb; pdb.set_trace()
try:
bp.cache_data(cell['id'], working_directory='.')
os.subprocess('nrnivmodl ./modfiles') # compile the model (only needs to be done once)
#import pdb; pdb.set_trace()
print(runner)
except:
pass
return cells
def allen_morph_model(description):
utils = Utils.create_utils(description)
h = utils.h
#The next step is to get the path of the morphology file and pass it to NEURON.
# configure model
manifest = description.manifest
morphology_path = description.manifest.get_path('MORPHOLOGY')
utils.generate_morphology(morphology_path.encode('ascii', 'ignore'))
utils.load_cell_parameters()
I am trying to exhaustively download and instance all the conductance based neuron models, and then instantiate them as NEURON simulator models. I am trying the code below, but I am running into errors