AllenInstitute / AllenInstitute/AllenSDK
How to exhaustively download and instance all the conductance based neuron models?
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Description
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()
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
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- Open a pull request that references the issue number.
Research direction
Start with the shown CellTypesCache and BiophysicalApi calls, then trace how the manifest, cached data, and Utils model-loading path are expected to work. Check the NEURON compilation and model-instantiation steps against the documented API behavior. Done means there is a confirmed workflow for downloading and instantiating every conductance-based model, with the reported errors accounted for.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100