Add a simple simulation campaign using a subsampled circuit (#10)

This is needed to run the Jupyter notebooks in the documentation.

CHANGELOG.rst

@@ -8,7 +8,7 @@ Improvements
 ~~~~~~~~~~~~
 
 - Support relative paths in the simulation campaign config.
-
+- Add a simple simulation campaign using a subsampled circuit, to run the Jupyter notebooks in the documentation.
 
 Version 0.4.3
 -------------

doc/source/conf.py

@@ -89,7 +89,7 @@
 
 nb_execution_show_tb = True
 nb_execution_timeout = 60
-nb_execution_excludepatterns = ["02_features_basics.ipynb", "03_simulation_campaign.ipynb"]
+nb_execution_excludepatterns = []
 
 # generate the link to the notebooks on GitHub
 _base_url = "https://github.com/BlueBrain/blueetl"

doc/source/data/analysis/config.yaml

@@ -0,0 +1,34 @@
+# simple configuration with extraction and analysis, and combination of parameters
+version: 3
+simulation_campaign: ../simulation-campaign/config.json
+output: analysis_output
+analysis:
+  spikes:
+    extraction:
+      report:
+        type: spikes
+      neuron_classes:
+        Rt_EXC: {query: {layer: [Rt], synapse_class: [EXC]}}
+        VPL_EXC: {query: {layer: [VPL], synapse_class: [EXC]}}
+        Rt_INH: {query: {layer: [Rt], synapse_class: [INH]}}
+        VPL_INH: {query: {layer: [VPL], synapse_class: [INH]}}
+      limit: 1000
+      population: thalamus_neurons
+      node_set: null
+      windows:
+        w1: {bounds: [20, 90], window_type: spontaneous}
+        w2: {bounds: [10, 70], initial_offset: 10, n_trials: 3, trial_steps_value: 10}
+    features:
+    - type: multi
+      groupby: [simulation_id, circuit_id, neuron_class, window]
+      function: blueetl.external.bnac.calculate_features.calculate_features_multi
+      params:
+        export_all_neurons: true
+      params_product:
+        ratio: [0.25, 0.50, 0.75]
+        nested_example:
+        - params: {bin_size: 1}
+        - params: {bin_size: 2}
+      params_zip:
+        param1: [10, 20]
+        param2: [11, 21]

doc/source/data/circuit/circuit_config.json

@@ -0,0 +1,44 @@
+{
+  "version": 2,
+  "manifest": {
+    "$BASE_DIR": ".",
+    "$NETWORK_NODES_DIR": "$BASE_DIR/networks/nodes",
+    "$NETWORK_EDGES_DIR": "$BASE_DIR/networks/edges"
+  },
+  "node_sets_file": "$BASE_DIR/node_sets.json",
+  "networks": {
+    "nodes": [
+      {
+        "nodes_file": "$NETWORK_NODES_DIR/thalamus_neurons/nodes.h5",
+        "populations": {
+          "thalamus_neurons": {
+            "type": "biophysical",
+            "biophysical_neuron_models_dir": "emodels_hoc",
+            "alternate_morphologies": {
+              "neurolucida-asc": "morphologies/ASC",
+              "h5v1": "morphologies/h5v1"
+            }
+          }
+        }
+      }
+    ],
+    "edges": [
+      {
+        "edges_file": "$NETWORK_EDGES_DIR/thalamus_neurons__thalamus_neurons__chemical/edges.h5",
+        "populations": {
+          "thalamus_neurons__thalamus_neurons__chemical": {
+            "type": "chemical"
+          }
+        }
+      },
+      {
+        "edges_file": "$NETWORK_EDGES_DIR/thalamus_neurons__thalamus_neurons__electrical_synapse/edges.h5",
+        "populations": {
+          "thalamus_neurons__thalamus_neurons__electrical_synapse": {
+            "type": "electrical"
+          }
+        }
+      }
+    ]
+  }
+}

doc/source/data/circuit/node_sets.json

@@ -0,0 +1,149 @@
+{
+  "Mosaic": [
+    "All"
+  ],
+  "All": [
+    "thalamus_neurons"
+  ],
+  "thalamus_neurons": {
+    "population": "thalamus_neurons"
+  },
+  "thalamus_neurons": {
+    "population": "thalamus_neurons"
+  },
+  "Excitatory": {
+    "synapse_class": "EXC"
+  },
+  "Inhibitory": {
+    "synapse_class": "INH"
+  },
+  "Rt_RC": {
+    "mtype": "Rt_RC"
+  },
+  "VPL_IN": {
+    "mtype": "VPL_IN"
+  },
+  "VPL_TC": {
+    "mtype": "VPL_TC"
+  },
+  "bAC_IN": {
+    "etype": "bAC_IN"
+  },
+  "cAD_noscltb": {
+    "etype": "cAD_noscltb"
+  },
+  "cNAD_noscltb": {
+    "etype": "cNAD_noscltb"
+  },
+  "dAD_ltb": {
+    "etype": "dAD_ltb"
+  },
+  "dNAD_ltb": {
+    "etype": "dNAD_ltb"
+  },
+  "mc0;Rt": {
+    "region": "mc0;Rt"
+  },
+  "mc0;VPL": {
+    "region": "mc0;VPL"
+  },
+  "mc1;Rt": {
+    "region": "mc1;Rt"
+  },
+  "mc1;VPL": {
+    "region": "mc1;VPL"
+  },
+  "mc2;Rt": {
+    "region": "mc2;Rt"
+  },
+  "mc2;VPL": {
+    "region": "mc2;VPL"
+  },
+  "mc3;Rt": {
+    "region": "mc3;Rt"
+  },
+  "mc3;VPL": {
+    "region": "mc3;VPL"
+  },
+  "mc4;Rt": {
+    "region": "mc4;Rt"
+  },
+  "mc4;VPL": {
+    "region": "mc4;VPL"
+  },
+  "mc5;Rt": {
+    "region": "mc5;Rt"
+  },
+  "mc5;VPL": {
+    "region": "mc5;VPL"
+  },
+  "mc6;Rt": {
+    "region": "mc6;Rt"
+  },
+  "mc6;VPL": {
+    "region": "mc6;VPL"
+  },
+  "IN": {
+    "mtype": {
+      "$regex": ".*IN"
+    },
+    "region": {
+      "$regex": ".*"
+    }
+  },
+  "TC": {
+    "mtype": {
+      "$regex": ".*TC"
+    },
+    "region": {
+      "$regex": ".*"
+    }
+  },
+  "mc0_Column": {
+    "region": {
+      "$regex": "mc0.*"
+    }
+  },
+  "mc1_Column": {
+    "region": {
+      "$regex": "mc1.*"
+    }
+  },
+  "mc2_Column": {
+    "region": {
+      "$regex": "mc2.*"
+    }
+  },
+  "mc3_Column": {
+    "region": {
+      "$regex": "mc3.*"
+    }
+  },
+  "mc4_Column": {
+    "region": {
+      "$regex": "mc4.*"
+    }
+  },
+  "mc5_Column": {
+    "region": {
+      "$regex": "mc5.*"
+    }
+  },
+  "mc6_Column": {
+    "region": {
+      "$regex": "mc6.*"
+    }
+  },
+  "gapjunctions": [
+    "thalamus_neurons"
+  ],
+  "gap-junctions": [
+    "gapjunctions"
+  ],
+  "ML_afferents": {
+    "population": "MedialLemniscus_projections"
+  },
+  "CT_afferents": {
+    "population": "CorticoThalamic_projections"
+  }
+}

doc/source/data/simulation-campaign/0/reporting/populations_offset.dat

@@ -0,0 +1,2 @@
+ ::0:: 
+thalamus_neurons::0::thalamus_neurons