It runs without errors (not working functionaltiy yet)

Cluster.cs

@@ -7,7 +7,8 @@ using static Unity.Mathematics.math;
 [System.Serializable]
 public class Cluster : INucleus {
     // The ScriptableObject asset from which the runtime object has been created
-    public readonly ClusterPrefab prefab;
+    [SerializeField]
+    public ClusterPrefab prefab;
 
     public ClusterPrefab cluster { get; set; }
 
@@ -18,9 +19,18 @@ public class Cluster : INucleus {
         set => _name = value;
     }
 
+    public Cluster(ClusterPrefab prefab) {
+        this.prefab = UnityEngine.Object.Instantiate(prefab);
+        this.name = prefab.name;
+        this.cluster = null;
+        if (this.cluster != null)
+            this.cluster.nuclei.Add(this);        
+    }
+
     // Hmm, a cluster instance can never be part of a scriptable object...(Cluster)
     public Cluster(ClusterPrefab parent, ClusterPrefab prefab) {
-        this.prefab = prefab;
+        this.prefab = prefab.Clone(); //UnityEngine.Object.Instantiate(prefab);
+        this.name = prefab.name;
         this.cluster = parent;
         if (this.cluster != null)
             this.cluster.nuclei.Add(this);
@@ -46,6 +56,8 @@ public class Cluster : INucleus {
         return clone;
     }
 
+    public INucleus output => prefab.output;
+
     // Not sure if this belongs here...
     [SerializeReference]
     private NucleusArray _array;

ClusterPrefab.cs

@@ -33,6 +33,12 @@ public class ClusterPrefab : ScriptableObject {
         }
     }
 
+    public virtual ClusterPrefab Clone() {
+        ClusterPrefab clone = Instantiate(this);
+        return clone;
+    }
+
+
     // Call this function to ensure that there is at least one nucleus
     // This is an invariant and should be ensured before the nucleus is used
     // because output requires it.

Receptor.cs

@@ -5,7 +5,7 @@ using static Unity.Mathematics.math;
 
 public class Receptor : IReceptor {
 
-    private ClusterPrefab cluster;
+    private Cluster cluster;
 
     [SerializeField]
     protected string _name;
@@ -14,25 +14,25 @@ public class Receptor : IReceptor {
         set => _name = value;
     }
 
-    public Receptor(ClusterPrefab cluster) {
+    public Receptor(Cluster cluster) {
         this.cluster = cluster;
         if (cluster != null)
-            cluster.nuclei.Add(this);
+            cluster.prefab.nuclei.Add(this);
     }
 
-    public Receptor(ClusterPrefab cluster, INucleus nucleus) {
+    public Receptor(Cluster cluster, INucleus nucleus) {
         this.cluster = cluster;
         if (cluster != null)
-            cluster.nuclei.Add(this);
+            cluster.prefab.nuclei.Add(this);
         this.AddReceiver(nucleus);
     }
 
-    public static Receptor CreateReceptor(ClusterPrefab cluster, string nucleusName) {
+    public static Receptor CreateReceptor(Cluster cluster, string nucleusName) {
         if (cluster == null)
             return null;
 
         Receptor receptor = new(cluster);
-        foreach (INucleus nucleus in cluster.inputs) {
+        foreach (INucleus nucleus in cluster.prefab.inputs) {
             if (nucleus != null && nucleus.name == nucleusName) {
                 // Receptor receptor = new(cluster, nucleus);
                 // return receptor;
@@ -45,7 +45,7 @@ public class Receptor : IReceptor {
             return receptor;
     }
 
-    public virtual IReceptor CloneTo(ClusterPrefab parent) {
+    public virtual IReceptor CloneTo(Cluster parent) {
         Receptor clone = new(parent);
 
         foreach (INucleus receiver in this.receivers) {

Velocity.asset

@@ -11,26 +11,20 @@ MonoBehaviour:
   m_EditorHideFlags: 0
   m_Script: {fileID: 11500000, guid: 60a957541c24c57e78018c202ebb1d9b, type: 3}
   m_Name: Velocity
-  m_EditorClassIdentifier: Assembly-CSharp::Cluster
+  m_EditorClassIdentifier: Assembly-CSharp::ClusterPrefab
   nuclei:
-  - rid: 2243601403683012671
+  - rid: 2243601420268863545
-  - rid: 2243601403683012676
   references:
     version: 2
     RefIds:
-    - rid: -2
+    - rid: 2243601420268863545
-      type: {class: , ns: , asm: }
-    - rid: 2243601403683012671
       type: {class: Neuron, ns: , asm: Assembly-CSharp}
       data:
         _name: Output
-        _synapses:
+        _synapses: []
-        - nucleus:
-            rid: -2
-          weight: 1
         _receivers: []
         _array:
-          rid: 2243601403683012672
+          rid: 2243601420268863546
         _curvePreset: 0
         curve:
           serializedVersion: 2
@@ -58,51 +52,9 @@ MonoBehaviour:
           m_RotationOrder: 4
         curveMax: 1
         average: 0
-    - rid: 2243601403683012672
+    - rid: 2243601420268863546
       type: {class: NucleusArray, ns: , asm: Assembly-CSharp}
       data:
         _nuclei:
-        - rid: 2243601403683012671
+        - rid: 2243601420268863545
         name: Output
-    - rid: 2243601403683012676
-      type: {class: Neuron, ns: , asm: Assembly-CSharp}
-      data:
-        _name: Position
-        _synapses: []
-        _receivers:
-        - rid: 2243601403683012671
-        _array:
-          rid: 2243601403683012677
-        _curvePreset: 0
-        curve:
-          serializedVersion: 2
-          m_Curve:
-          - serializedVersion: 3
-            time: 0
-            value: 0
-            inSlope: 0
-            outSlope: 1
-            tangentMode: 0
-            weightedMode: 0
-            inWeight: 0
-            outWeight: 0
-          - serializedVersion: 3
-            time: 1000
-            value: 1000
-            inSlope: 1
-            outSlope: 0
-            tangentMode: 0
-            weightedMode: 0
-            inWeight: 0
-            outWeight: 0
-          m_PreInfinity: 2
-          m_PostInfinity: 2
-          m_RotationOrder: 4
-        curveMax: 1
-        average: 0
-    - rid: 2243601403683012677
-      type: {class: NucleusArray, ns: , asm: Assembly-CSharp}
-      data:
-        _nuclei:
-        - rid: 2243601403683012676
-        name: New neuron

Velocity.asset.meta

@@ -1,5 +1,5 @@
 fileFormatVersion: 2
-guid: dd622ac7ed09e70ea8edac595047ac82
+guid: c61aecac62c26de4aaefb2612bcc9a5d
 NativeFormatImporter:
   externalObjects: {}
   mainObjectFileID: 11400000

VisualEditor/Editor/BrainPickerWindow.cs

@@ -3,14 +3,14 @@ using UnityEngine;
 using System;
 using System.Linq;
 
-public class BrainPickerWindow : EditorWindow {
+public class ClusterPickerWindow : EditorWindow {
     private Vector2 scroll;
     private ClusterPrefab[] items = new ClusterPrefab[0];
     private Action<ClusterPrefab> onPicked;
     private string search = "";
 
     public static void ShowPicker(Action<ClusterPrefab> onPicked, string title = "Select Cluster") {
-        var w = CreateInstance<BrainPickerWindow>();
+        var w = CreateInstance<ClusterPickerWindow>();
         w.titleContent = new GUIContent(title);
         w.minSize = new Vector2(360, 320);
         w.onPicked = onPicked;
@@ -21,7 +21,7 @@ public class BrainPickerWindow : EditorWindow {
     private void OnEnable() => RefreshList();
 
     private void RefreshList() {
-        var guids = AssetDatabase.FindAssets("t:Cluster");
+        var guids = AssetDatabase.FindAssets("t:ClusterPrefab");
         items = guids
             .Select(g => AssetDatabase.LoadAssetAtPath<ClusterPrefab>(AssetDatabase.GUIDToAssetPath(g)))
             .Where(b => b != null)

VisualEditor/Editor/ClusterInspector.cs

@@ -617,7 +617,7 @@ public class ClusterInspector : Editor {
         }
 
         protected virtual void AddCluster(INucleus nucleus) {
-            BrainPickerWindow.ShowPicker(brain => OnClusterPicked(nucleus, brain), "Select Cluster");
+            ClusterPickerWindow.ShowPicker(brain => OnClusterPicked(nucleus, brain), "Select Cluster");
         }
 
         private void OnClusterPicked(INucleus nucleus, ClusterPrefab subCluster) {

VisualEditor/Editor/NanoBrainComponent_Editor.cs

@@ -23,7 +23,7 @@ public class NanoBrainComponent_Editor : Editor {
 
     public override VisualElement CreateInspectorGUI() {
         //NanoBrainComponent component = target as NanoBrainComponent;
-        ClusterPrefab brain = Application.isPlaying ? component.brain : component.defaultBrain;
+        ClusterPrefab brain = Application.isPlaying ? component.brain.prefab : component.defaultBrain;
 
         if (Application.isPlaying == false)
             serializedObject.Update();

VisualEditor/NanoBrainComponent.cs

@@ -2,13 +2,13 @@ using UnityEngine;
 
 public class NanoBrainComponent : MonoBehaviour {
     public ClusterPrefab defaultBrain;
-    private ClusterPrefab brainInstance;
+    private Cluster brainInstance;
 
-    public INucleus root => brainInstance.output;
+    //public INucleus root => brainInstance.output;
-    public ClusterPrefab brain {
+    public Cluster brain {
         get {
             if (brainInstance == null && defaultBrain != null) {
-                brainInstance = Instantiate(defaultBrain);
+                brainInstance = new Cluster(defaultBrain); //Instantiate(defaultBrain);
                 brainInstance.name = defaultBrain.name + " (Instance)";
 
                 SwarmControl sc = FindFirstObjectByType<SwarmControl>();
@@ -23,7 +23,7 @@ public class NanoBrainComponent : MonoBehaviour {
         }
     }
 
-    public static void UpdateWeight(ClusterPrefab brain, string name, float weight) {
+    public static void UpdateWeight(Cluster brain, string name, float weight) {
         INucleus root = brain.output;
         foreach (Synapse synapse in root.synapses) {
             if (synapse.nucleus.name == name) {