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Merge pull request cnr-ibf-pa#28 from cnr-ibf-pa/hhnb2.1
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HHNB 2.1
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@rcsm17
rcsm17 authored Dec 20, 2022
2 parents a9ed25c + 3b9e8e0 commit f267f40
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Showing 62 changed files with 3,074 additions and 1,243 deletions.
3 changes: 0 additions & 3 deletions efelg/tools/resources.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,9 @@
import sys
import json
import collections
import neo
import pprint
from datetime import datetime
import requests
import logging
import bluepyefe.formats.axon as fa

# set logging up
logging.basicConfig(stream=sys.stdout)
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6 changes: 3 additions & 3 deletions efelg/views.py
100755 → 100644
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Expand Up @@ -188,7 +188,7 @@ def get_data(request, cellname=""):

trace_info['coefficient'] = coefficient
trace_info['disp_sampling_rate'] = disp_sampling_rate
trace_info['md5'] = content['md5']
trace_info['md5'] = content.get('md5')
trace_info['sampling_rate'] = content['sampling_rate']
trace_info['etype'] = content['etype']

Expand Down Expand Up @@ -618,7 +618,7 @@ def file_formats_docs(request):
"""
Render Guidebook file formats page
"""
logger.info(LOG_ACTION.format(request.session['username'], 'access FILE_FORMATS page'))
logger.info(LOG_ACTION.format(request.session.get('username', 'anonymous'), 'access FILE_FORMATS page'))

return render(request, 'efelg/docs/file_formats.html')

Expand All @@ -638,7 +638,7 @@ def dataset(request):
"""
Return Guidebook dataset page
"""
logger.info(LOG_ACTION.format(request.session['username'], 'access DATASET page'))
logger.info(LOG_ACTION.format(request.session.get('username', 'anonymous'), 'access DATASET page'))

return render(request, 'efelg/docs/dataset.html')

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4 changes: 2 additions & 2 deletions hh_neuron_builder/config/dev_conf.py.example
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Expand Up @@ -36,6 +36,6 @@ DATABASES = {
}
}

MEDIA_ROOT = os.path.join('/apps', 'media')
MEDIA_ROOT = os.path.join(BASE_DIR, '../app', 'media')

LOG_ROOT_PATH = './'
LOG_ROOT_PATH = os.path.join(BASE_DIR, '../log/')
60 changes: 0 additions & 60 deletions hh_neuron_builder/config/hhf_template/parameters.json
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This file was deleted.

276 changes: 276 additions & 0 deletions hh_neuron_builder/config/hhf_template/parameters/interneuron/parameters.json
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@@ -0,0 +1,276 @@
{
"W_20221102163317": {
"mechanisms": {
"all": [
"pas",
"kdrb",
"na3"
],
"somatic": [
"kdb",
"kmb",
"kap",
"hd",
"can",
"cal",
"cat",
"cagk",
"kca",
"cacum"
],
"axonal": [
"kmb",
"kap"
],
"alldend": [
"hd",
"can",
"cal",
"cat",
"cagk",
"kca",
"cacum",
"kad"
]
},
"distributions": {
"exp_na_dend": "math.exp((-{distance})/50)*{value}"
},
"fixed": {
"global": [
[
"v_init",
-80
],
[
"celsius",
34
]
],
"all": [
[
"cm",
1,
"secvar"
],
[
"ena",
50,
"secvar"
],
[
"ek",
-90,
"secvar"
]
]
},
"optimized": {
"all": [],
"axonal": [
[
"gbar_na3",
0.025,
0.15,
"uniform"
],
[
"gkdrbar_kdrb",
0.01,
0.08,
"uniform"
],
[
"gkabar_kap",
0.001,
0.04,
"uniform"
],
[
"gbar_kmb",
0.004,
0.05,
"uniform"
],
[
"Ra",
50,
300,
"secvar"
],
[
"g_pas",
1e-06,
8e-05,
"uniform"
],
[
"e_pas",
-95,
-75,
"uniform"
]
],
"somatic": [
[
"gbar_na3",
0.02,
0.06,
"uniform"
],
[
"gkdrbar_kdrb",
0.001,
0.08,
"uniform"
],
[
"gkabar_kap",
0.005,
0.04,
"uniform"
],
[
"gkdbar_kdb",
1e-05,
0.0001,
"uniform"
],
[
"gbar_kmb",
0.001,
0.02,
"uniform"
],
[
"ghdbar_hd",
1e-06,
0.0005,
"uniform"
],
[
"gcalbar_cal",
1e-06,
3e-05,
"uniform"
],
[
"gcanbar_can",
1e-06,
3e-05,
"uniform"
],
[
"gcatbar_cat",
1e-06,
3e-05,
"uniform"
],
[
"gbar_kca",
1e-06,
1e-05,
"uniform"
],
[
"gbar_cagk",
5e-06,
0.0003,
"uniform"
],
[
"Ra",
50,
400,
"secvar"
],
[
"g_pas",
1e-06,
0.0002,
"uniform"
],
[
"e_pas",
-120,
-75,
"uniform"
]
],
"alldend": [
[
"gbar_na3",
0.02,
0.06,
"exp_na_dend"
],
[
"gkdrbar_kdrb",
0.001,
0.8,
"uniform"
],
[
"gkabar_kad",
0.005,
0.1,
"uniform"
],
[
"ghdbar_hd",
1e-06,
0.0005,
"uniform"
],
[
"gcalbar_cal",
1e-06,
3e-05,
"uniform"
],
[
"gcanbar_can",
1e-06,
3e-05,
"uniform"
],
[
"gcatbar_cat",
1e-06,
3e-05,
"uniform"
],
[
"gbar_kca",
1e-06,
1e-05,
"uniform"
],
[
"gbar_cagk",
5e-06,
0.0003,
"uniform"
],
[
"Ra",
50,
400,
"secvar"
],
[
"g_pas",
1e-06,
0.0002,
"uniform"
],
[
"e_pas",
-120,
-80,
"uniform"
]
]
}
}
}
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