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BlueBrain · Aug 27, 2024 · 3a92191 · 3a92191
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diff --git a/examples/README.md b/examples/README.md
@@ -4,7 +4,7 @@ This directory includes various examples demonstrating how to use BluePyEModel:
 
 - [**L5PC**](./L5PC/README.rst): Provides a guide for setting up and running the E-Model building pipeline locally on a personal computer or on a Slurm cluster. This is an example based on the juvenile (P14) rat somatosensory cortex layer 5 thick-tufted pyramidal cell (L5TPC) e-model optimisation of the [SSCxEModelExamples](https://github.com/BlueBrain/SSCxEModelExamples/tree/main/optimization) repository.
 
-- [**simplecell**](./simplecell/simplecell.ipynb): Demonstrates creating a single-compartment neuron model with two parameters using non-threshold optimization.
+- [**simplecell**](./simplecell/simplecell.ipynb): Demonstrates creating a single-compartment neuron model with two parameters using rheobase independent optimisation.
 
 - [**nexus**](./nexus/README.md): Demonstrates the use of BluePyEModel through the Nexus access point.
 

diff --git a/examples/simplecell/.gitignore b/examples/simplecell/.gitignore
@@ -16,5 +16,4 @@ recordings/
 __pycache__/
 ephys_data/
 myvenv/
-final.json
 final_tmp.json
diff --git a/examples/simplecell/config/extract_config/simplecell_config.json b/examples/simplecell/config/extract_config/simplecell_config.json
@@ -397,6 +397,39 @@
         "strict_stiminterval": true
       }
     },
+    {
+      "efeature": "Spikecount",
+      "protocol": "IDrest",
+      "amplitude": 0.4,
+      "tolerance": 0.1,
+      "efeature_name": null,
+      "weight": 1.0,
+      "efel_settings": {
+        "strict_stiminterval": true
+      }
+    },
+    {
+      "efeature": "mean_frequency",
+      "protocol": "IDrest",
+      "amplitude": 0.4,
+      "tolerance": 0.1,
+      "efeature_name": null,
+      "weight": 1.0,
+      "efel_settings": {
+        "strict_stiminterval": true
+      }
+    },
+    {
+      "efeature": "voltage_base",
+      "protocol": "IDrest",
+      "amplitude": 0.4,
+      "tolerance": 0.1,
+      "efeature_name": null,
+      "weight": 1.0,
+      "efel_settings": {
+        "strict_stiminterval": true
+      }
+    },
     {
       "efeature": "voltage_base",
       "protocol": "IV",

diff --git a/examples/simplecell/config/features/simplecell.json b/examples/simplecell/config/features/simplecell.json
@@ -5,84 +5,135 @@
       "protocol_name": "IDrest_0.256",
       "recording_name": "soma.v",
       "threshold_efeature_std": null,
-      "default_std_value": 0.01,
+      "default_std_value": 0.001,
       "mean": 6.6,
       "original_std": 4.5431266766402185,
       "sample_size": 5,
       "efeature_name": "Spikecount",
       "weight": 1.0,
       "efel_settings": {
+        "interp_step": 0.025,
         "strict_stiminterval": true,
-        "Threshold": -20.0,
-        "interp_step": 0.025
+        "Threshold": -50.11250305175781
       }
     },
     {
       "efel_feature_name": "mean_frequency",
       "protocol_name": "IDrest_0.256",
       "recording_name": "soma.v",
       "threshold_efeature_std": null,
-      "default_std_value": 0.01,
+      "default_std_value": 0.001,
       "mean": 4.6549665308108965,
       "original_std": 1.7066939148229534,
       "sample_size": 4,
       "efeature_name": "mean_frequency",
       "weight": 1.0,
       "efel_settings": {
+        "interp_step": 0.025,
         "strict_stiminterval": true,
-        "Threshold": -20.0,
-        "interp_step": 0.025
+        "Threshold": -50.11250305175781
       }
     },
     {
       "efel_feature_name": "voltage_base",
       "protocol_name": "IDrest_0.256",
       "recording_name": "soma.v",
       "threshold_efeature_std": null,
-      "default_std_value": 0.01,
+      "default_std_value": 0.001,
       "mean": -84.9396882128033,
       "original_std": 0.3331013733422112,
       "sample_size": 5,
       "efeature_name": "voltage_base",
       "weight": 1.0,
       "efel_settings": {
+        "interp_step": 0.025,
         "strict_stiminterval": true,
-        "Threshold": -20.0,
-        "interp_step": 0.025
+        "Threshold": -50.11250305175781
+      }
+    },
+    {
+      "efel_feature_name": "Spikecount",
+      "protocol_name": "IDrest_0.4",
+      "recording_name": "soma.v",
+      "threshold_efeature_std": null,
+      "default_std_value": 0.001,
+      "mean": 13.0,
+      "original_std": 0.001,
+      "sample_size": 1,
+      "efeature_name": "Spikecount",
+      "weight": 1.0,
+      "efel_settings": {
+        "interp_step": 0.025,
+        "strict_stiminterval": true,
+        "Threshold": -50.11250305175781
+      }
+    },
+    {
+      "efel_feature_name": "mean_frequency",
+      "protocol_name": "IDrest_0.4",
+      "recording_name": "soma.v",
+      "threshold_efeature_std": null,
+      "default_std_value": 0.001,
+      "mean": 6.888329580058474,
+      "original_std": 0.001,
+      "sample_size": 1,
+      "efeature_name": "mean_frequency",
+      "weight": 1.0,
+      "efel_settings": {
+        "interp_step": 0.025,
+        "strict_stiminterval": true,
+        "Threshold": -50.11250305175781
+      }
+    },
+    {
+      "efel_feature_name": "voltage_base",
+      "protocol_name": "IDrest_0.4",
+      "recording_name": "soma.v",
+      "threshold_efeature_std": null,
+      "default_std_value": 0.001,
+      "mean": -85.36351310593709,
+      "original_std": 0.001,
+      "sample_size": 1,
+      "efeature_name": "voltage_base",
+      "weight": 1.0,
+      "efel_settings": {
+        "interp_step": 0.025,
+        "strict_stiminterval": true,
+        "Threshold": -50.11250305175781
       }
     },
     {
       "efel_feature_name": "voltage_base",
       "protocol_name": "IV_-0.147",
       "recording_name": "soma.v",
       "threshold_efeature_std": null,
-      "default_std_value": 0.01,
+      "default_std_value": 0.001,
       "mean": -84.5937809414334,
       "original_std": 0.25958992541480197,
       "sample_size": 5,
       "efeature_name": "voltage_base",
       "weight": 1.0,
       "efel_settings": {
+        "interp_step": 0.025,
         "strict_stiminterval": true,
-        "Threshold": -20.0,
-        "interp_step": 0.025
+        "Threshold": -64.5374984741211
       }
     },
     {
       "efel_feature_name": "ohmic_input_resistance_vb_ssse",
       "protocol_name": "IV_-0.147",
       "recording_name": "soma.v",
       "threshold_efeature_std": null,
-      "default_std_value": 0.01,
+      "default_std_value": 0.001,
       "mean": 47.95114886552402,
       "original_std": 1.5928203273461563,
       "sample_size": 5,
       "efeature_name": "ohmic_input_resistance_vb_ssse",
       "weight": 1.0,
       "efel_settings": {
+        "interp_step": 0.025,
         "strict_stiminterval": true,
-        "Threshold": -20.0,
-        "interp_step": 0.025
+        "Threshold": -64.5374984741211
       }
     }
   ],
@@ -111,6 +162,30 @@
       "protocol_type": "Protocol",
       "stochasticity": false
     },
+    {
+      "name": "IDrest_0.4",
+      "stimuli": [
+        {
+          "delay": 700.0000000000001,
+          "amp": 0.3318749852478504,
+          "thresh_perc": null,
+          "duration": 2000.0,
+          "totduration": 3000.0,
+          "holding_current": -0.02656250074505806
+        }
+      ],
+      "recordings_from_config": [
+        {
+          "type": "CompRecording",
+          "name": "IDrest_0.4.soma.v",
+          "location": "soma",
+          "variable": "v"
+        }
+      ],
+      "validation": true,
+      "protocol_type": "Protocol",
+      "stochasticity": false
+    },
     {
       "name": "IV_-0.147",
       "stimuli": [

diff --git a/examples/simplecell/config/recipes.json b/examples/simplecell/config/recipes.json
@@ -11,26 +11,13 @@
         "features": "config/features/simplecell.json",
         "pipeline_settings": {
             "path_extract_config": "config/extract_config/simplecell_config.json",
-            "plot_extraction": true,
-            "default_std_value": 0.01,
             "extract_absolute_amplitudes": true,
-            "efel_settings":{
-                "strict_stiminterval": true,
-                "Threshold": -20.0,
-                "interp_step": 0.025
-            },
-            "optimisation_timeout": 300,
             "optimiser": "SO-CMA",
             "max_ngen": 5,
             "optimisation_params": {
                 "offspring_size": 20
             },
-            "validation_threshold": 100,
-            "plot_currentscape": true,
-            "currentscape_config": {
-                "title": "simplecell"
-            },
-            "validation_protocols": [],
+            "validation_protocols": ["IDrest_0.4"],
             "morph_modifiers": []
         }
     }

diff --git a/examples/simplecell/final.json b/examples/simplecell/final.json
@@ -0,0 +1,42 @@
+{
+  "simplecell__1": {
+    "emodel": "simplecell",
+    "etype": "cADpyr",
+    "ttype": null,
+    "mtype": null,
+    "species": "rat",
+    "brain_region": "SSCX",
+    "iteration": null,
+    "synapse_class": null,
+    "allen_notation": null,
+    "score": 1257.8671455915864,
+    "parameters": {
+      "gnabar_hh.somatic": 0.10623315844384061,
+      "gkbar_hh.somatic": 0.026127548830000066
+    },
+    "fitness": {
+      "IDrest_0.256.soma.v.Spikecount": 0.1320676359488435,
+      "IDrest_0.256.soma.v.mean_frequency": 250.0,
+      "IDrest_0.256.soma.v.voltage_base": 6.755673681284991,
+      "IV_-0.147.soma.v.voltage_base": 0.979404274352486,
+      "IV_-0.147.soma.v.ohmic_input_resistance_vb_ssse": 250.0,
+      "IDrest_0.4.soma.v.Spikecount": 250.0,
+      "IDrest_0.4.soma.v.mean_frequency": 250.0,
+      "IDrest_0.4.soma.v.voltage_base": 250.0
+    },
+    "features": {
+      "IDrest_0.256.soma.v.Spikecount": 6.0,
+      "IDrest_0.256.soma.v.mean_frequency": 1105.990783485126,
+      "IDrest_0.256.soma.v.voltage_base": -82.68936403171544,
+      "IDrest_0.4.soma.v.Spikecount": 4.0,
+      "IDrest_0.4.soma.v.mean_frequency": 1333.3333334958297,
+      "IDrest_0.4.soma.v.voltage_base": -82.5609583626679,
+      "IV_-0.147.soma.v.voltage_base": -84.8480244239635,
+      "IV_-0.147.soma.v.ohmic_input_resistance_vb_ssse": 1060.9623644880035
+    },
+    "validation_fitness": {},
+    "validated": false,
+    "seed": 1,
+    "pdfs": []
+  }
+}