diff --git a/notebooks/basics.ipynb b/notebooks/basics.ipynb
index 8c237a3..ee719bc 100644
--- a/notebooks/basics.ipynb
+++ b/notebooks/basics.ipynb
@@ -25,7 +25,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 21,
    "id": "63fb7d1a-cd49-4aac-8d4f-31bb54496a51",
    "metadata": {
     "tags": []
@@ -56,7 +56,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 22,
    "id": "2ab3cb32-e007-45c4-807e-b1b442ac1608",
    "metadata": {
     "tags": []
@@ -64,7 +64,6 @@
    "outputs": [],
    "source": [
     "from bigraph_viz import plot_bigraph, plot_flow, plot_multitimestep, pf\n",
-    "from bigraph_schema import TypeSystem\n",
     "from bigraph_viz.dict_utils import replace_regex_recursive\n",
     "\n",
     "plot_settings = {'remove_process_place_edges': True}\n",
@@ -73,26 +72,6 @@
     "    plot_settings.update({'out_dir': 'out','dpi': '250'})"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "a3b85fe8-899d-4c61-8c75-0d572e44e493",
-   "metadata": {},
-   "source": [
-    "### Initialize Type System"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "id": "b1166de0-3811-4b35-90c1-3fbfa8343259",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "types = TypeSystem()"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "0e716c23-5fbe-4c08-a868-09611ca40ec4",
@@ -114,7 +93,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 23,
    "id": "d711b952-089a-4938-817d-d1ccad9de56e",
    "metadata": {
     "tags": []
@@ -145,10 +124,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106433b20>"
+       "<graphviz.graphs.Digraph at 0x1058c9550>"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 23,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -170,7 +149,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 24,
    "id": "f3e5fa71-7ffc-4a8f-a1a0-dc547c886f84",
    "metadata": {},
    "outputs": [
@@ -199,10 +178,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106433cd0>"
+       "<graphviz.graphs.Digraph at 0x1058c9460>"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 24,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -228,7 +207,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 25,
    "id": "0f3f0824-f89d-4c6e-830e-2c5a321f7b33",
    "metadata": {},
    "outputs": [
@@ -322,10 +301,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x1064491f0>"
+       "<graphviz.graphs.Digraph at 0x1058c9640>"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 25,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -365,7 +344,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 26,
    "id": "7c74237b-0d66-4e8f-a8ca-79174fadad8b",
    "metadata": {},
    "outputs": [
@@ -409,10 +388,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106449f70>"
+       "<graphviz.graphs.Digraph at 0x1058c9fd0>"
       ]
      },
-     "execution_count": 7,
+     "execution_count": 26,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -442,7 +421,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 27,
    "id": "8c2457a3-fc47-4850-8b9e-9ee98e81567d",
    "metadata": {},
    "outputs": [
@@ -530,10 +509,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106449160>"
+       "<graphviz.graphs.Digraph at 0x1058c9190>"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 27,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -567,7 +546,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 28,
    "id": "a6ecad5d-8948-4636-910c-79284a3e8679",
    "metadata": {},
    "outputs": [
@@ -634,10 +613,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106455490>"
+       "<graphviz.graphs.Digraph at 0x1032f1760>"
       ]
      },
-     "execution_count": 9,
+     "execution_count": 28,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -694,7 +673,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 29,
    "id": "781a84e6-bbe2-4708-b441-47efc611b46f",
    "metadata": {},
    "outputs": [
@@ -768,10 +747,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106449460>"
+       "<graphviz.graphs.Digraph at 0x1058c94c0>"
       ]
      },
-     "execution_count": 10,
+     "execution_count": 29,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -810,7 +789,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 30,
    "id": "701e759d-7f9b-41bb-911c-a8208c892462",
    "metadata": {},
    "outputs": [
@@ -915,10 +894,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106455e50>"
+       "<graphviz.graphs.Digraph at 0x1058062b0>"
       ]
      },
-     "execution_count": 11,
+     "execution_count": 30,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -965,7 +944,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 31,
    "id": "638c5dc7-4cfd-46e4-b66a-8c42ca98ff1d",
    "metadata": {},
    "outputs": [
@@ -1088,10 +1067,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x1064339d0>"
+       "<graphviz.graphs.Digraph at 0x1058c98e0>"
       ]
      },
-     "execution_count": 12,
+     "execution_count": 31,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1129,388 +1108,6 @@
     "plot_bigraph(composite_process_spec, **plot_settings, filename='composite_process')"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "137bf506-d71c-447b-9bf3-7f310c26a5c5",
-   "metadata": {},
-   "source": [
-    "## Updates\n",
-    "\n",
-    "- state update\n",
-    "- structure update"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 13,
-   "id": "f28a8137-280e-4cd5-bfc3-d0d512684283",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "schemaa = {\n",
-    "    'base': {\n",
-    "        'a': {'_type': 'int'},\n",
-    "    },\n",
-    "\n",
-    "    # cannot override existing keys unless it is of a subtype\n",
-    "    'second': {\n",
-    "        'b': {'_type': 'int'},\n",
-    "        '_super': 'base',\n",
-    "    },\n",
-    "}\n",
-    "\n",
-    "types.type_registry.register_multiple(schemaa, force=True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 14,
-   "id": "1506f428-649d-4c38-aa47-9d85132faa99",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [
-    {
-     "data": {
-      "image/svg+xml": [
-       "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n",
-       "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n",
-       " \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n",
-       "<!-- Generated by graphviz version 8.1.0 (20230707.0739)\n",
-       " -->\n",
-       "<!-- Title: bigraph Pages: 1 -->\n",
-       "<svg width=\"123pt\" height=\"57pt\"\n",
-       " viewBox=\"0.00 0.00 126.49 58.49\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
-       "<g id=\"graph0\" class=\"graph\" transform=\"scale(0.972222 0.972222) rotate(0) translate(4 54.49)\">\n",
-       "<title>bigraph</title>\n",
-       "<polygon fill=\"white\" stroke=\"none\" points=\"-4,4 -4,-54.49 122.49,-54.49 122.49,4 -4,4\"/>\n",
-       "<!-- (&#39;a&#39;,) -->\n",
-       "<g id=\"node1\" class=\"node\">\n",
-       "<title>(&#39;a&#39;,)</title>\n",
-       "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"25.24\" cy=\"-25.24\" rx=\"25.24\" ry=\"25.24\"/>\n",
-       "<text text-anchor=\"start\" x=\"22.62\" y=\"-28.09\" font-family=\"Times,serif\" font-size=\"12.00\">a</text>\n",
-       "<text text-anchor=\"start\" x=\"19.24\" y=\"-13.84\" font-family=\"Times,serif\" font-size=\"12.00\">11</text>\n",
-       "</g>\n",
-       "<!-- (&#39;b&#39;,) -->\n",
-       "<g id=\"node2\" class=\"node\">\n",
-       "<title>(&#39;b&#39;,)</title>\n",
-       "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"93.24\" cy=\"-25.24\" rx=\"25.24\" ry=\"25.24\"/>\n",
-       "<text text-anchor=\"start\" x=\"90.24\" y=\"-28.09\" font-family=\"Times,serif\" font-size=\"12.00\">b</text>\n",
-       "<text text-anchor=\"start\" x=\"87.24\" y=\"-13.84\" font-family=\"Times,serif\" font-size=\"12.00\">13</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "</svg>\n"
-      ],
-      "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106449910>"
-      ]
-     },
-     "execution_count": 14,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "schema = {'_type': 'second'}\n",
-    "state = {\n",
-    "    'a': 11,\n",
-    "    'b': 13,\n",
-    "}\n",
-    "plot_bigraph(state, show_values=True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 15,
-   "id": "36f1fa08-5bb2-43c6-b9d8-3cba63646def",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "image/svg+xml": [
-       "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n",
-       "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n",
-       " \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n",
-       "<!-- Generated by graphviz version 8.1.0 (20230707.0739)\n",
-       " -->\n",
-       "<!-- Title: bigraph Pages: 1 -->\n",
-       "<svg width=\"123pt\" height=\"57pt\"\n",
-       " viewBox=\"0.00 0.00 126.49 58.49\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
-       "<g id=\"graph0\" class=\"graph\" transform=\"scale(0.972222 0.972222) rotate(0) translate(4 54.49)\">\n",
-       "<title>bigraph</title>\n",
-       "<polygon fill=\"white\" stroke=\"none\" points=\"-4,4 -4,-54.49 122.49,-54.49 122.49,4 -4,4\"/>\n",
-       "<!-- (&#39;a&#39;,) -->\n",
-       "<g id=\"node1\" class=\"node\">\n",
-       "<title>(&#39;a&#39;,)</title>\n",
-       "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"25.24\" cy=\"-25.24\" rx=\"25.24\" ry=\"25.24\"/>\n",
-       "<text text-anchor=\"start\" x=\"22.62\" y=\"-28.09\" font-family=\"Times,serif\" font-size=\"12.00\">a</text>\n",
-       "<text text-anchor=\"start\" x=\"19.24\" y=\"-13.84\" font-family=\"Times,serif\" font-size=\"12.00\">11</text>\n",
-       "</g>\n",
-       "<!-- (&#39;b&#39;,) -->\n",
-       "<g id=\"node2\" class=\"node\">\n",
-       "<title>(&#39;b&#39;,)</title>\n",
-       "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"93.24\" cy=\"-25.24\" rx=\"25.24\" ry=\"25.24\"/>\n",
-       "<text text-anchor=\"start\" x=\"90.24\" y=\"-28.09\" font-family=\"Times,serif\" font-size=\"12.00\">b</text>\n",
-       "<text text-anchor=\"start\" x=\"90.24\" y=\"-13.84\" font-family=\"Times,serif\" font-size=\"12.00\">8</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "</svg>\n"
-      ],
-      "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106455be0>"
-      ]
-     },
-     "execution_count": 15,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "update = {\n",
-    "    'b': -5\n",
-    "}\n",
-    "new_state = types.apply(\n",
-    "    schema,\n",
-    "    state,\n",
-    "    update\n",
-    ")\n",
-    "plot_bigraph(new_state, show_values=True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 16,
-   "id": "aa40b177-e9c6-4722-b996-1c1dba40eca4",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [
-    {
-     "data": {
-      "image/svg+xml": [
-       "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n",
-       "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n",
-       " \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n",
-       "<!-- Generated by graphviz version 8.1.0 (20230707.0739)\n",
-       " -->\n",
-       "<!-- Title: bigraph Pages: 1 -->\n",
-       "<svg width=\"123pt\" height=\"57pt\"\n",
-       " viewBox=\"0.00 0.00 126.49 58.49\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
-       "<g id=\"graph0\" class=\"graph\" transform=\"scale(0.972222 0.972222) rotate(0) translate(4 54.49)\">\n",
-       "<title>bigraph</title>\n",
-       "<polygon fill=\"white\" stroke=\"none\" points=\"-4,4 -4,-54.49 122.49,-54.49 122.49,4 -4,4\"/>\n",
-       "<!-- (&#39;a&#39;,) -->\n",
-       "<g id=\"node1\" class=\"node\">\n",
-       "<title>(&#39;a&#39;,)</title>\n",
-       "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"25.24\" cy=\"-25.24\" rx=\"25.24\" ry=\"25.24\"/>\n",
-       "<text text-anchor=\"start\" x=\"22.62\" y=\"-28.09\" font-family=\"Times,serif\" font-size=\"12.00\">a</text>\n",
-       "<text text-anchor=\"start\" x=\"19.24\" y=\"-13.84\" font-family=\"Times,serif\" font-size=\"12.00\">16</text>\n",
-       "</g>\n",
-       "<!-- (&#39;b&#39;,) -->\n",
-       "<g id=\"node2\" class=\"node\">\n",
-       "<title>(&#39;b&#39;,)</title>\n",
-       "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"93.24\" cy=\"-25.24\" rx=\"25.24\" ry=\"25.24\"/>\n",
-       "<text text-anchor=\"start\" x=\"90.24\" y=\"-28.09\" font-family=\"Times,serif\" font-size=\"12.00\">b</text>\n",
-       "<text text-anchor=\"start\" x=\"90.24\" y=\"-13.84\" font-family=\"Times,serif\" font-size=\"12.00\">8</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "</svg>\n"
-      ],
-      "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106455220>"
-      ]
-     },
-     "execution_count": 16,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "update = {\n",
-    "    'a': 5\n",
-    "}\n",
-    "new_state = types.apply(\n",
-    "    schema,\n",
-    "    new_state,\n",
-    "    update\n",
-    ")\n",
-    "plot_bigraph(new_state, show_values=True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 17,
-   "id": "be2541ae-d8a7-4926-8a18-6f9127f0744a",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "# from bigraph_schema.registry import apply_registry\n",
-    "from bigraph_viz.dict_utils import deep_merge\n",
-    "def apply_merge(current, update, bindings=None, types=None):\n",
-    "    assert isinstance(state, dict)\n",
-    "    assert isinstance(update, dict)\n",
-    "    updated = deep_merge(state, update)\n",
-    "    return updated\n",
-    "types.apply_registry.register('merge', apply_merge, force=True)\n",
-    "\n",
-    "schemab = {\n",
-    "    'merge_branch': {\n",
-    "        '_default': {'a1': 'any'},\n",
-    "        '_apply': 'merge',\n",
-    "        \n",
-    "    },\n",
-    "\n",
-    "    # cannot override existing keys unless it is of a subtype\n",
-    "    'second': {\n",
-    "        'a1': {'a2': 'any'},\n",
-    "        '_super': 'merge_branch',\n",
-    "    },\n",
-    "}\n",
-    "\n",
-    "types.type_registry.register_multiple(schemab, force=True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 18,
-   "id": "ed5c34bf-b357-4800-b126-73a32b6646c2",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [
-    {
-     "data": {
-      "image/svg+xml": [
-       "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n",
-       "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n",
-       " \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n",
-       "<!-- Generated by graphviz version 8.1.0 (20230707.0739)\n",
-       " -->\n",
-       "<!-- Title: bigraph Pages: 1 -->\n",
-       "<svg width=\"57pt\" height=\"127pt\"\n",
-       " viewBox=\"0.00 0.00 58.49 130.49\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
-       "<g id=\"graph0\" class=\"graph\" transform=\"scale(0.972222 0.972222) rotate(0) translate(4 126.49)\">\n",
-       "<title>bigraph</title>\n",
-       "<polygon fill=\"white\" stroke=\"none\" points=\"-4,4 -4,-126.49 54.49,-126.49 54.49,4 -4,4\"/>\n",
-       "<!-- (&#39;a1&#39;,) -->\n",
-       "<g id=\"node1\" class=\"node\">\n",
-       "<title>(&#39;a1&#39;,)</title>\n",
-       "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"25.24\" cy=\"-104.49\" rx=\"18\" ry=\"18\"/>\n",
-       "<text text-anchor=\"start\" x=\"19.62\" y=\"-100.21\" font-family=\"Times,serif\" font-size=\"12.00\">a1</text>\n",
-       "</g>\n",
-       "<!-- (&#39;a1&#39;, &#39;a2&#39;) -->\n",
-       "<g id=\"node2\" class=\"node\">\n",
-       "<title>(&#39;a1&#39;, &#39;a2&#39;)</title>\n",
-       "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"25.24\" cy=\"-25.24\" rx=\"25.24\" ry=\"25.24\"/>\n",
-       "<text text-anchor=\"start\" x=\"19.62\" y=\"-28.09\" font-family=\"Times,serif\" font-size=\"12.00\">a2</text>\n",
-       "<text text-anchor=\"start\" x=\"19.24\" y=\"-13.84\" font-family=\"Times,serif\" font-size=\"12.00\">11</text>\n",
-       "</g>\n",
-       "<!-- (&#39;a1&#39;,)&#45;&gt;(&#39;a1&#39;, &#39;a2&#39;) -->\n",
-       "<g id=\"edge1\" class=\"edge\">\n",
-       "<title>(&#39;a1&#39;,)&#45;&gt;(&#39;a1&#39;, &#39;a2&#39;)</title>\n",
-       "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M25.24,-85.57C25.24,-75.41 25.24,-62.53 25.24,-51.38\"/>\n",
-       "</g>\n",
-       "</g>\n",
-       "</svg>\n"
-      ],
-      "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106469070>"
-      ]
-     },
-     "execution_count": 18,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "schema = {'_type': 'merge_branch'}\n",
-    "state = {\n",
-    "    'a1': {'a2': 11},\n",
-    "}\n",
-    "plot_bigraph(state, show_values=True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 19,
-   "id": "072c2502-6fdd-4c10-af91-cf00e4de1656",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [
-    {
-     "data": {
-      "image/svg+xml": [
-       "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n",
-       "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n",
-       " \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n",
-       "<!-- Generated by graphviz version 8.1.0 (20230707.0739)\n",
-       " -->\n",
-       "<!-- Title: bigraph Pages: 1 -->\n",
-       "<svg width=\"123pt\" height=\"127pt\"\n",
-       " viewBox=\"0.00 0.00 126.49 130.49\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
-       "<g id=\"graph0\" class=\"graph\" transform=\"scale(0.972222 0.972222) rotate(0) translate(4 126.49)\">\n",
-       "<title>bigraph</title>\n",
-       "<polygon fill=\"white\" stroke=\"none\" points=\"-4,4 -4,-126.49 122.49,-126.49 122.49,4 -4,4\"/>\n",
-       "<!-- (&#39;a1&#39;,) -->\n",
-       "<g id=\"node1\" class=\"node\">\n",
-       "<title>(&#39;a1&#39;,)</title>\n",
-       "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"59.24\" cy=\"-104.49\" rx=\"18\" ry=\"18\"/>\n",
-       "<text text-anchor=\"start\" x=\"53.62\" y=\"-100.21\" font-family=\"Times,serif\" font-size=\"12.00\">a1</text>\n",
-       "</g>\n",
-       "<!-- (&#39;a1&#39;, &#39;a2&#39;) -->\n",
-       "<g id=\"node2\" class=\"node\">\n",
-       "<title>(&#39;a1&#39;, &#39;a2&#39;)</title>\n",
-       "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"25.24\" cy=\"-25.24\" rx=\"25.24\" ry=\"25.24\"/>\n",
-       "<text text-anchor=\"start\" x=\"19.62\" y=\"-28.09\" font-family=\"Times,serif\" font-size=\"12.00\">a2</text>\n",
-       "<text text-anchor=\"start\" x=\"19.24\" y=\"-13.84\" font-family=\"Times,serif\" font-size=\"12.00\">11</text>\n",
-       "</g>\n",
-       "<!-- (&#39;a1&#39;,)&#45;&gt;(&#39;a1&#39;, &#39;a2&#39;) -->\n",
-       "<g id=\"edge1\" class=\"edge\">\n",
-       "<title>(&#39;a1&#39;,)&#45;&gt;(&#39;a1&#39;, &#39;a2&#39;)</title>\n",
-       "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M52.03,-87.11C47.2,-76.12 40.76,-61.5 35.41,-49.34\"/>\n",
-       "</g>\n",
-       "<!-- (&#39;a1&#39;, &#39;a3&#39;) -->\n",
-       "<g id=\"node3\" class=\"node\">\n",
-       "<title>(&#39;a1&#39;, &#39;a3&#39;)</title>\n",
-       "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"93.24\" cy=\"-25.24\" rx=\"25.24\" ry=\"25.24\"/>\n",
-       "<text text-anchor=\"start\" x=\"87.62\" y=\"-28.09\" font-family=\"Times,serif\" font-size=\"12.00\">a3</text>\n",
-       "<text text-anchor=\"start\" x=\"88.37\" y=\"-13.84\" font-family=\"Times,serif\" font-size=\"12.00\">&#45;5</text>\n",
-       "</g>\n",
-       "<!-- (&#39;a1&#39;,)&#45;&gt;(&#39;a1&#39;, &#39;a3&#39;) -->\n",
-       "<g id=\"edge2\" class=\"edge\">\n",
-       "<title>(&#39;a1&#39;,)&#45;&gt;(&#39;a1&#39;, &#39;a3&#39;)</title>\n",
-       "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M66.45,-87.11C71.29,-76.12 77.72,-61.5 83.08,-49.34\"/>\n",
-       "</g>\n",
-       "</g>\n",
-       "</svg>\n"
-      ],
-      "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106469490>"
-      ]
-     },
-     "execution_count": 19,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "update = {\n",
-    "    'a1': {'a3': -5},\n",
-    "}\n",
-    "new_state = types.apply(\n",
-    "    schema,\n",
-    "    state,\n",
-    "    update\n",
-    ")\n",
-    "# print(pf(new_state))\n",
-    "plot_bigraph(new_state, show_values=True)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "847cef26-65a1-4da6-9dd3-eb5839277970",
@@ -1521,7 +1118,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 32,
    "id": "e76c97a8-3037-464a-929e-ba4414c73c34",
    "metadata": {},
    "outputs": [],
@@ -1546,7 +1143,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 33,
    "id": "f0eff7b0-f0e2-4d56-8b16-ef0fc1ce5aba",
    "metadata": {},
    "outputs": [
@@ -1718,10 +1315,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106455f70>"
+       "<graphviz.graphs.Digraph at 0x1058f9070>"
       ]
      },
-     "execution_count": 21,
+     "execution_count": 33,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1755,7 +1352,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 34,
    "id": "db45c99b-b97b-47bc-a73e-c669882f3969",
    "metadata": {},
    "outputs": [
@@ -1819,20 +1416,15 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106469d60>"
+       "<graphviz.graphs.Digraph at 0x105806700>"
       ]
      },
-     "execution_count": 22,
+     "execution_count": 34,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "step_schema = {\n",
-    "    '_depends_on': 'list[string]',\n",
-    "}\n",
-    "types.type_registry.register('step_process', step_schema)\n",
-    "\n",
     "flow = {\n",
     "    'step1': {\n",
     "        '_type': 'step_process',\n",
@@ -1881,7 +1473,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 35,
    "id": "47bdf8e5-0bdd-4cac-b57e-2449c75fa178",
    "metadata": {
     "tags": []
@@ -2471,10 +2063,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106455b20>"
+       "<graphviz.graphs.Digraph at 0x1058f95e0>"
       ]
      },
-     "execution_count": 23,
+     "execution_count": 35,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -2532,7 +2124,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 36,
    "id": "ab431982-d156-4b7a-9918-384a5ea5132a",
    "metadata": {
     "tags": []
@@ -2564,7 +2156,7 @@
        "   'nuclear transcriptional speckle': {'negative regulation of RNA biosynthesis process': {}}}}}"
       ]
      },
-     "execution_count": 24,
+     "execution_count": 36,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -2575,7 +2167,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 37,
    "id": "5a76608a-fff0-4005-9f32-c02afef39d9e",
    "metadata": {
     "tags": []
@@ -3351,10 +2943,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x106469340>"
+       "<graphviz.graphs.Digraph at 0x103372d30>"
       ]
      },
-     "execution_count": 25,
+     "execution_count": 37,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -3500,19 +3092,57 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 38,
    "id": "fe3008ad-498e-449f-8521-6ea29fd903f1",
    "metadata": {
     "tags": []
    },
    "outputs": [
     {
-     "ename": "SyntaxError",
-     "evalue": "invalid syntax (754939450.py, line 7)",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;36m  Cell \u001b[0;32mIn[26], line 7\u001b[0;36m\u001b[0m\n\u001b[0;31m    }s\u001b[0m\n\u001b[0m     ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
-     ]
+     "data": {
+      "image/svg+xml": [
+       "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n",
+       "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n",
+       " \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n",
+       "<!-- Generated by graphviz version 8.1.0 (20230707.0739)\n",
+       " -->\n",
+       "<!-- Title: bigraph Pages: 1 -->\n",
+       "<svg width=\"72pt\" height=\"113pt\"\n",
+       " viewBox=\"0.00 0.00 74.57 116.00\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
+       "<g id=\"graph0\" class=\"graph\" transform=\"scale(0.972222 0.972222) rotate(0) translate(4 112)\">\n",
+       "<title>bigraph</title>\n",
+       "<polygon fill=\"white\" stroke=\"none\" points=\"-4,4 -4,-112 70.57,-112 70.57,4 -4,4\"/>\n",
+       "<!-- (&#39;hypothesized&lt;br/&gt;mechanism&#39;,) -->\n",
+       "<g id=\"node1\" class=\"node\">\n",
+       "<title>(&#39;hypothesized&lt;br/&gt;mechanism&#39;,)</title>\n",
+       "<polygon fill=\"none\" stroke=\"blue\" stroke-width=\"2\" points=\"66.57,-36 0,-36 0,0 66.57,0 66.57,-36\"/>\n",
+       "<text text-anchor=\"start\" x=\"2.16\" y=\"-20.85\" font-family=\"Times,serif\" font-size=\"12.00\">hypothesized</text>\n",
+       "<text text-anchor=\"start\" x=\"6.66\" y=\"-6.6\" font-family=\"Times,serif\" font-size=\"12.00\">mechanism</text>\n",
+       "</g>\n",
+       "<!-- (&#39;hypothesized&lt;br/&gt;mechanism&#39;, &#39;1&#39;) -->\n",
+       "<!-- (&#39;hypothesized&lt;br/&gt;mechanism&#39;, &#39;1&#39;)&#45;&gt;(&#39;hypothesized&lt;br/&gt;mechanism&#39;,) -->\n",
+       "<g id=\"edge1\" class=\"edge\">\n",
+       "<title>(&#39;hypothesized&lt;br/&gt;mechanism&#39;, &#39;1&#39;)&#45;&gt;(&#39;hypothesized&lt;br/&gt;mechanism&#39;,)</title>\n",
+       "<path fill=\"none\" stroke=\"black\" stroke-dasharray=\"5,2\" d=\"M25.61,-78.67C26.86,-69 28.76,-54.22 30.35,-41.79\"/>\n",
+       "<ellipse fill=\"black\" stroke=\"black\" cx=\"30.65\" cy=\"-39.46\" rx=\"2\" ry=\"2\"/>\n",
+       "</g>\n",
+       "<!-- (&#39;hypothesized&lt;br/&gt;mechanism&#39;, &#39;2&#39;) -->\n",
+       "<!-- (&#39;hypothesized&lt;br/&gt;mechanism&#39;, &#39;2&#39;)&#45;&gt;(&#39;hypothesized&lt;br/&gt;mechanism&#39;,) -->\n",
+       "<g id=\"edge2\" class=\"edge\">\n",
+       "<title>(&#39;hypothesized&lt;br/&gt;mechanism&#39;, &#39;2&#39;)&#45;&gt;(&#39;hypothesized&lt;br/&gt;mechanism&#39;,)</title>\n",
+       "<path fill=\"none\" stroke=\"black\" stroke-dasharray=\"5,2\" d=\"M41.94,-79.56C40.55,-69.85 38.34,-54.38 36.5,-41.51\"/>\n",
+       "<ellipse fill=\"black\" stroke=\"black\" cx=\"36.2\" cy=\"-39.37\" rx=\"2\" ry=\"2\"/>\n",
+       "</g>\n",
+       "</g>\n",
+       "</svg>\n"
+      ],
+      "text/plain": [
+       "<graphviz.graphs.Digraph at 0x105820ee0>"
+      ]
+     },
+     "execution_count": 38,
+     "metadata": {},
+     "output_type": "execute_result"
     }
    ],
    "source": [
@@ -3522,7 +3152,7 @@
     "            '1': 'Any',\n",
     "            '2': 'Any',\n",
     "        }\n",
-    "    }s\n",
+    "    }\n",
     "}\n",
     "\n",
     "new_process = replace_regex_recursive(new_process)\n",
@@ -3549,12 +3179,222 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 39,
    "id": "b39417ce-d9a1-4985-abce-ce22df816897",
    "metadata": {
     "tags": []
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Writing out/cell\n"
+     ]
+    },
+    {
+     "data": {
+      "image/svg+xml": [
+       "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n",
+       "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n",
+       " \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n",
+       "<!-- Generated by graphviz version 8.1.0 (20230707.0739)\n",
+       " -->\n",
+       "<!-- Title: bigraph Pages: 1 -->\n",
+       "<svg width=\"651pt\" height=\"670pt\"\n",
+       " viewBox=\"0.00 0.00 669.87 689.62\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
+       "<g id=\"graph0\" class=\"graph\" transform=\"scale(0.972222 0.972222) rotate(0) translate(4 685.62)\">\n",
+       "<title>bigraph</title>\n",
+       "<polygon fill=\"white\" stroke=\"none\" points=\"-4,4 -4,-685.62 665.87,-685.62 665.87,4 -4,4\"/>\n",
+       "<!-- (&#39;cell&#39;,) -->\n",
+       "<g id=\"node1\" class=\"node\">\n",
+       "<title>(&#39;cell&#39;,)</title>\n",
+       "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"349.57\" cy=\"-663.62\" rx=\"18\" ry=\"18\"/>\n",
+       "<text text-anchor=\"start\" x=\"341.32\" y=\"-659.34\" font-family=\"Times,serif\" font-size=\"12.00\">cell</text>\n",
+       "</g>\n",
+       "<!-- (&#39;cell&#39;, &#39;membrane&#39;) -->\n",
+       "<g id=\"node2\" class=\"node\">\n",
+       "<title>(&#39;cell&#39;, &#39;membrane&#39;)</title>\n",
+       "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"139.57\" cy=\"-573.32\" rx=\"35.3\" ry=\"35.3\"/>\n",
+       "<text text-anchor=\"start\" x=\"114.82\" y=\"-569.04\" font-family=\"Times,serif\" font-size=\"12.00\">membrane</text>\n",
+       "</g>\n",
+       "<!-- (&#39;cell&#39;,)&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;) -->\n",
+       "<g id=\"edge11\" class=\"edge\">\n",
+       "<title>(&#39;cell&#39;,)&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;)</title>\n",
+       "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M332.74,-655.54C297.99,-640.93 217.79,-607.21 172.41,-588.13\"/>\n",
+       "</g>\n",
+       "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;) -->\n",
+       "<g id=\"node5\" class=\"node\">\n",
+       "<title>(&#39;cell&#39;, &#39;cytoplasm&#39;)</title>\n",
+       "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"349.57\" cy=\"-573.32\" rx=\"34.37\" ry=\"34.37\"/>\n",
+       "<text text-anchor=\"start\" x=\"325.57\" y=\"-569.04\" font-family=\"Times,serif\" font-size=\"12.00\">cytoplasm</text>\n",
+       "</g>\n",
+       "<!-- (&#39;cell&#39;,)&#45;&gt;(&#39;cell&#39;, &#39;cytoplasm&#39;) -->\n",
+       "<g id=\"edge12\" class=\"edge\">\n",
+       "<title>(&#39;cell&#39;,)&#45;&gt;(&#39;cell&#39;, &#39;cytoplasm&#39;)</title>\n",
+       "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M349.57,-644.75C349.57,-634.37 349.57,-620.94 349.57,-608.59\"/>\n",
+       "</g>\n",
+       "<!-- (&#39;cell&#39;, &#39;nucleoid&#39;) -->\n",
+       "<g id=\"node10\" class=\"node\">\n",
+       "<title>(&#39;cell&#39;, &#39;nucleoid&#39;)</title>\n",
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+       "<text text-anchor=\"start\" x=\"500.32\" y=\"-569.04\" font-family=\"Times,serif\" font-size=\"12.00\">nucleoid</text>\n",
+       "</g>\n",
+       "<!-- (&#39;cell&#39;,)&#45;&gt;(&#39;cell&#39;, &#39;nucleoid&#39;) -->\n",
+       "<g id=\"edge13\" class=\"edge\">\n",
+       "<title>(&#39;cell&#39;,)&#45;&gt;(&#39;cell&#39;, &#39;nucleoid&#39;)</title>\n",
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+       "</g>\n",
+       "<!-- (&#39;cell&#39;, &#39;membrane&#39;, &#39;transporters&#39;) -->\n",
+       "<g id=\"node3\" class=\"node\">\n",
+       "<title>(&#39;cell&#39;, &#39;membrane&#39;, &#39;transporters&#39;)</title>\n",
+       "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"38.57\" cy=\"-411.08\" rx=\"38.57\" ry=\"38.57\"/>\n",
+       "<text text-anchor=\"start\" x=\"11.19\" y=\"-406.81\" font-family=\"Times,serif\" font-size=\"12.00\">transporters</text>\n",
+       "</g>\n",
+       "<!-- (&#39;cell&#39;, &#39;membrane&#39;)&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;, &#39;transporters&#39;) -->\n",
+       "<g id=\"edge1\" class=\"edge\">\n",
+       "<title>(&#39;cell&#39;, &#39;membrane&#39;)&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;, &#39;transporters&#39;)</title>\n",
+       "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M117.46,-544.53C107.56,-531.61 96.01,-515.85 86.57,-501.02 75.45,-483.55 64.38,-463.3 55.68,-446.53\"/>\n",
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+       "<!-- (&#39;cell&#39;, &#39;membrane&#39;, &#39;lipids&#39;) -->\n",
+       "<g id=\"node4\" class=\"node\">\n",
+       "<title>(&#39;cell&#39;, &#39;membrane&#39;, &#39;lipids&#39;)</title>\n",
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+       "<text text-anchor=\"start\" x=\"102.82\" y=\"-406.81\" font-family=\"Times,serif\" font-size=\"12.00\">lipids</text>\n",
+       "</g>\n",
+       "<!-- (&#39;cell&#39;, &#39;membrane&#39;)&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;, &#39;lipids&#39;) -->\n",
+       "<g id=\"edge2\" class=\"edge\">\n",
+       "<title>(&#39;cell&#39;, &#39;membrane&#39;)&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;, &#39;lipids&#39;)</title>\n",
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+       "</g>\n",
+       "<!-- (&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;) -->\n",
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+       "<title>(&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;)</title>\n",
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+       "<!-- (&#39;cell&#39;, &#39;membrane&#39;)&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;) -->\n",
+       "<!-- (&#39;cell&#39;, &#39;membrane&#39;, &#39;transporters&#39;)&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;) -->\n",
+       "<g id=\"edge14\" class=\"edge\">\n",
+       "<title>(&#39;cell&#39;, &#39;membrane&#39;, &#39;transporters&#39;)&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;)</title>\n",
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+       "</g>\n",
+       "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;metabolites&#39;) -->\n",
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+       "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;ribosomal complexes&#39;) -->\n",
+       "<g id=\"node7\" class=\"node\">\n",
+       "<title>(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;ribosomal complexes&#39;)</title>\n",
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+       "</g>\n",
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+       "</g>\n",
+       "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;transcript regulation complex&#39;) -->\n",
+       "<g id=\"node8\" class=\"node\">\n",
+       "<title>(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;transcript regulation complex&#39;)</title>\n",
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+       "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;translation&#39;) -->\n",
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+       "<title>(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;translation&#39;)</title>\n",
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+       "</g>\n",
+       "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;)&#45;&gt;(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;translation&#39;) -->\n",
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+       "<g id=\"edge15\" class=\"edge\">\n",
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+       "</g>\n",
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+       "</g>\n",
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+       "<g id=\"node9\" class=\"node\">\n",
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+       "</g>\n",
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+       "</g>\n",
+       "<!-- (&#39;cell&#39;, &#39;nucleoid&#39;, &#39;chromosome&#39;) -->\n",
+       "<g id=\"node11\" class=\"node\">\n",
+       "<title>(&#39;cell&#39;, &#39;nucleoid&#39;, &#39;chromosome&#39;)</title>\n",
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+       "</g>\n",
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+       "<g id=\"edge9\" class=\"edge\">\n",
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+       "<!-- (&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;, &#39;external&#39;) -->\n",
+       "<!-- (&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;, &#39;external&#39;)&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;) -->\n",
+       "<g id=\"edge18\" class=\"edge\">\n",
+       "<title>(&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;, &#39;external&#39;)&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;)</title>\n",
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+       "<ellipse fill=\"black\" stroke=\"black\" cx=\"219.7\" cy=\"-138.1\" rx=\"2\" ry=\"2\"/>\n",
+       "<text text-anchor=\"start\" x=\"277.57\" y=\"-232.69\" font-family=\"Times,serif\" font-size=\"10.00\">external</text>\n",
+       "</g>\n",
+       "</g>\n",
+       "</svg>\n"
+      ],
+      "text/plain": [
+       "<graphviz.graphs.Digraph at 0x105a38190>"
+      ]
+     },
+     "execution_count": 39,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "cell_struct_func = {\n",
     "    'cell': {\n",
@@ -3618,12 +3458,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 40,
    "id": "16960d1b-6e35-421e-bb7d-3efe5052e4fc",
    "metadata": {
     "tags": []
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Writing out/ecoli\n"
+     ]
+    }
+   ],
    "source": [
     "ecoli = { \n",
     "    'chromosome-structure': { \n",