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hoc version of 472363762 model biophysics #107

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hoc version of 472363762 model biophysics #107

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@asanin-epfl asanin-epfl commented Aug 19, 2019

Hello, dear contributors of Sonata!

For my research I would need hoc templates for biophysics. Can you please check this file? It's a transformed version of Cell_472363762.cell.nml here in this repo. I have made it by hands according to SONATA_DEVELOPER_GUIDE.md#hoc-template. I am not sure about:

  • is the name L4PC472363762biophys fine for the template?
  • is the filename 472363762.hoc ok?
  • How do I reference the cell in the template? $o1?
  • Should I use $o1.distribute_channels?

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asanin-epfl commented Aug 19, 2019 •
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I've tried to run the 9cells network with this hoc file but unfortunately bmtk tried to load it as nml file and failed. In 9_cells/network/cortex_node_types.csv I replaced nml:nml/Cell_472363762.cell.nml with hoc:hoc/472363762.hoc

2019-08-19 11:18:55,403 [INFO] Created log file
NEURON mechanisms not found in ../shared_components/mechanisms.
2019-08-19 11:18:55,469 [INFO] Building cells.
Traceback (most recent call last):
  File "/home/sanin/workspace/sonata/examples/9_cells/run_bionet.py", line 16, in <module>
    run('config.json')
  File "/home/sanin/workspace/sonata/examples/9_cells/run_bionet.py", line 9, in run
    sim = bionet.BioSimulator.from_config(conf, network=net)
  File "/home/sanin/workspace/sonata/venv/lib/python3.6/site-packages/bmtk/simulator/bionet/biosimulator.py", line 281, in from_config
    network.build_nodes()
  File "/home/sanin/workspace/sonata/venv/lib/python3.6/site-packages/bmtk/simulator/bionet/bionetwork.py", line 145, in build_nodes
    cell = self._build_cell(node)
  File "/home/sanin/workspace/sonata/venv/lib/python3.6/site-packages/bmtk/simulator/bionet/bionetwork.py", line 128, in _build_cell
    cell = self._model_type_map[bionode.model_type](bionode, self)
  File "/home/sanin/workspace/sonata/venv/lib/python3.6/site-packages/bmtk/simulator/bionet/biocell.py", line 38, in __init__
    super(BioCell, self).__init__(node)
  File "/home/sanin/workspace/sonata/venv/lib/python3.6/site-packages/bmtk/simulator/bionet/cell.py", line 52, in __init__
    self._hobj = node.load_cell()
  File "/home/sanin/workspace/sonata/venv/lib/python3.6/site-packages/bmtk/simulator/bionet/sonata_adaptors.py", line 70, in load_cell
    hobj = cell_fnc(self, template_name, dynamics_params)
  File "/home/sanin/workspace/sonata/venv/lib/python3.6/site-packages/bmtk/simulator/bionet/default_setters/cell_models.py", line 429, in NMLLoad
    nml_params = NMLTree(nml_path)
  File "/home/sanin/workspace/sonata/venv/lib/python3.6/site-packages/bmtk/simulator/bionet/nml_reader.py", line 8, in __init__
    self._nml_root = ElementTree.parse(nml_path).getroot()
  File "/usr/lib/python3.6/xml/etree/ElementTree.py", line 1196, in parse
    tree.parse(source, parser)
  File "/usr/lib/python3.6/xml/etree/ElementTree.py", line 597, in parse
    self._root = parser._parse_whole(source)
xml.etree.ElementTree.ParseError: syntax error: line 1, column 0

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