Circuit Configuration File Nodes and Edges Out of Order

[mwstroud]

The build_env_bionet() function seems to be building the circuit_config.json incorrectly. In the "networks" section, the nodes and edges are listed out of order. The code block below shows how this function generates the nodes and edges incorrectly. The Edrive_nodes are virtual cells and the network_nodes are biophysical cells. This ordering in both the nodes and edges breaks the simulation.

  "networks": {
    "nodes": [
      {
        "nodes_file": "$NETWORK_DIR\\Edrive_nodes.h5",
        "node_types_file": "$NETWORK_DIR\\Edrive_node_types.csv"
      },
      {
        "nodes_file": "$NETWORK_DIR\\network_nodes.h5",
        "node_types_file": "$NETWORK_DIR\\network_node_types.csv"
      }
    ],
    "edges": [
      {
        "edges_file": "$NETWORK_DIR\\Edrive_network_edges.h5",
        "edge_types_file": "$NETWORK_DIR\\Edrive_network_edge_types.csv"
      },
      {
        "edges_file": "$NETWORK_DIR\\network_network_edges.h5",
        "edge_types_file": "$NETWORK_DIR\\network_network_edge_types.csv"
      }
    ],
    "gap_juncs": []
  }

Importantly, build_env_bionet() writes biophysical nodes last when they should be listed first. If the ordering is changed such that biophysical cells are listed first, the simulation runs correctly.

  "networks": {
    "nodes": [
      {
        "nodes_file": "$NETWORK_DIR\\network_nodes.h5",
        "node_types_file": "$NETWORK_DIR\\network_node_types.csv"
      },
      {
        "nodes_file": "$NETWORK_DIR\\Edrive_nodes.h5",
        "node_types_file": "$NETWORK_DIR\\Edrive_node_types.csv"
      }
    ],
    "edges": [
      {
        "edges_file": "$NETWORK_DIR\\network_network_edges.h5",
        "edge_types_file": "$NETWORK_DIR\\network_network_edge_types.csv"
      },
      {
        "edges_file": "$NETWORK_DIR\\Edrive_network_edges.h5",
        "edge_types_file": "$NETWORK_DIR\\Edrive_network_edge_types.csv"
      }
    ],
    "gap_juncs": []
  }

Here are raster plots showing the effects of this error using a different network:
Raster plot with incorrect circuit_config.json ordering:

Raster plot with correct circuit_config.json ordering:

As is shown, the effects are large from this ordering issue. It has been identified that biophysical to biophysical edges break as a result of this issue.
Setup:

• BMTK 0.0.9
• NEURON 8.0

[mwstroud]

Kael Dai has resolved this issue in an update to the develop branch. There seemed to be a mix up in a local variable node_id and NEURON's variable gid, but this has been fixed.

Thanks Kael Dai!