diff --git a/notebooks/basics.ipynb b/notebooks/basics.ipynb
index 9f62f4f..ca10092 100644
--- a/notebooks/basics.ipynb
+++ b/notebooks/basics.ipynb
@@ -25,7 +25,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 15,
    "id": "63fb7d1a-cd49-4aac-8d4f-31bb54496a51",
    "metadata": {
     "tags": []
@@ -35,9 +35,9 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "-e git+https://github.com/vivarium-collective/bigraph-schema.git@a7010c1e2f137586078abfdc815eb27f25a6f886#egg=bigraph_schema\n",
-      "-e git+https://github.com/vivarium-collective/bigraph-viz.git@5eba77f4f72f164f54700d1f1b4d3c60d7777b0c#egg=bigraph_viz\n",
-      "-e git+https://github.com/vivarium-collective/process-bigraph.git@975b59fbed8800956cc163ac39cfeca152fb8515#egg=process_bigraph\n"
+      "-e git+https://github.com/vivarium-collective/bigraph-schema.git@6075161f7a063d2e2ccbff269d84e199b9418245#egg=bigraph_schema\n",
+      "-e git+https://github.com/vivarium-collective/bigraph-viz.git@cc41bb038afd6aaacd6f805e22db00196640d441#egg=bigraph_viz\n",
+      "-e git+https://github.com/vivarium-collective/process-bigraph.git@4bbb8c94185b6fbfe195b3edd92d602ba0d5fa25#egg=process_bigraph\n"
      ]
     }
    ],
@@ -57,7 +57,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 16,
    "id": "2ab3cb32-e007-45c4-807e-b1b442ac1608",
    "metadata": {
     "tags": []
@@ -98,7 +98,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 17,
    "id": "d711b952-089a-4938-817d-d1ccad9de56e",
    "metadata": {
     "tags": []
@@ -135,10 +135,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x10710af10>"
+       "<graphviz.graphs.Digraph at 0x121d6f5e0>"
       ]
      },
-     "execution_count": 3,
+     "execution_count": 17,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -160,7 +160,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 18,
    "id": "f3e5fa71-7ffc-4a8f-a1a0-dc547c886f84",
    "metadata": {},
    "outputs": [
@@ -190,16 +190,16 @@
        "<title>(&#39;store1&#39;,)</title>\n",
        "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"25.83\" cy=\"-25.83\" rx=\"25.83\" ry=\"25.83\"/>\n",
        "<text text-anchor=\"start\" x=\"11.16\" y=\"-28.23\" font-family=\"Times,serif\" font-size=\"12.00\">store1</text>\n",
-       "<text text-anchor=\"start\" x=\"11.16\" y=\"-16.23\" font-family=\"Times,serif\" font-size=\"12.00\">[float]</text>\n",
+       "<text text-anchor=\"start\" x=\"13.17\" y=\"-16.23\" font-family=\"Times,serif\" font-size=\"12.00\">[any]</text>\n",
        "</g>\n",
        "</g>\n",
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x1071c5700>"
+       "<graphviz.graphs.Digraph at 0x1263ff2b0>"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 18,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -225,7 +225,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 19,
    "id": "0f3f0824-f89d-4c6e-830e-2c5a321f7b33",
    "metadata": {},
    "outputs": [
@@ -326,10 +326,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x107168ca0>"
+       "<graphviz.graphs.Digraph at 0x122273c10>"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 19,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -369,7 +369,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 20,
    "id": "7c74237b-0d66-4e8f-a8ca-79174fadad8b",
    "metadata": {},
    "outputs": [
@@ -400,18 +400,18 @@
        "<polygon fill=\"none\" stroke=\"black\" stroke-width=\"2\" points=\"54,-53.58 0,-53.58 0,-17.58 54,-17.58 54,-53.58\"/>\n",
        "<text text-anchor=\"start\" x=\"6.01\" y=\"-31.98\" font-family=\"Times,serif\" font-size=\"12.00\">process1</text>\n",
        "</g>\n",
-       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;) -->\n",
-       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)&#45;&gt;(&#39;process1&#39;,) -->\n",
+       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)_input -->\n",
+       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)_input&#45;&gt;(&#39;process1&#39;,) -->\n",
        "<g id=\"edge1\" class=\"edge\">\n",
-       "<title>(&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)&#45;&gt;(&#39;process1&#39;,)</title>\n",
+       "<title>(&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)_input&#45;&gt;(&#39;process1&#39;,)</title>\n",
        "<path fill=\"none\" stroke=\"black\" stroke-dasharray=\"5,2\" d=\"M110.78,-55.47C99.18,-52.69 81.54,-48.45 65.52,-44.6\"/>\n",
        "<polygon fill=\"black\" stroke=\"black\" points=\"66.8,-41.3 56.26,-42.37 65.17,-48.11 66.8,-41.3\"/>\n",
        "<text text-anchor=\"start\" x=\"72\" y=\"-52.58\" font-family=\"Times,serif\" font-size=\"10.00\">port1</text>\n",
        "</g>\n",
-       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;) -->\n",
-       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)&#45;&gt;(&#39;process1&#39;,) -->\n",
+       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)_input -->\n",
+       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)_input&#45;&gt;(&#39;process1&#39;,) -->\n",
        "<g id=\"edge2\" class=\"edge\">\n",
-       "<title>(&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)&#45;&gt;(&#39;process1&#39;,)</title>\n",
+       "<title>(&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)_input&#45;&gt;(&#39;process1&#39;,)</title>\n",
        "<path fill=\"none\" stroke=\"black\" stroke-dasharray=\"5,2\" d=\"M110.78,-16.54C99.29,-19.19 81.88,-23.19 65.99,-26.84\"/>\n",
        "<polygon fill=\"black\" stroke=\"black\" points=\"65.23,-23.43 56.26,-29.08 66.79,-30.25 65.23,-23.43\"/>\n",
        "<text text-anchor=\"start\" x=\"72\" y=\"-26.58\" font-family=\"Times,serif\" font-size=\"10.00\">port2</text>\n",
@@ -420,10 +420,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x10710afd0>"
+       "<graphviz.graphs.Digraph at 0x12640caf0>"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 20,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -451,7 +451,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 21,
    "id": "8c2457a3-fc47-4850-8b9e-9ee98e81567d",
    "metadata": {},
    "outputs": [
@@ -494,50 +494,50 @@
        "<polygon fill=\"none\" stroke=\"black\" stroke-width=\"2\" points=\"251.58,-109.15 197.58,-109.15 197.58,-73.15 251.58,-73.15 251.58,-109.15\"/>\n",
        "<text text-anchor=\"start\" x=\"203.58\" y=\"-87.55\" font-family=\"Times,serif\" font-size=\"12.00\">process3</text>\n",
        "</g>\n",
-       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;) -->\n",
-       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)&#45;&gt;(&#39;process1&#39;,) -->\n",
+       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)_input -->\n",
+       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)_input&#45;&gt;(&#39;process1&#39;,) -->\n",
        "<g id=\"edge1\" class=\"edge\">\n",
-       "<title>(&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)&#45;&gt;(&#39;process1&#39;,)</title>\n",
+       "<title>(&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)_input&#45;&gt;(&#39;process1&#39;,)</title>\n",
        "<path fill=\"none\" stroke=\"black\" stroke-dasharray=\"5,2\" d=\"M18.16,-27.29C21.26,-35.43 25.66,-46.13 30.47,-55.15 31.81,-57.68 33.29,-60.26 34.83,-62.82\"/>\n",
        "<polygon fill=\"black\" stroke=\"black\" points=\"31.78,-64.55 40.1,-71.11 37.69,-60.79 31.78,-64.55\"/>\n",
        "<text text-anchor=\"start\" x=\"30.58\" y=\"-47.15\" font-family=\"Times,serif\" font-size=\"10.00\">port1</text>\n",
        "</g>\n",
-       "<!-- (&#39;process2&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;) -->\n",
-       "<!-- (&#39;process2&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)&#45;&gt;(&#39;process2&#39;,) -->\n",
+       "<!-- (&#39;process2&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)_input -->\n",
+       "<!-- (&#39;process2&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)_input&#45;&gt;(&#39;process2&#39;,) -->\n",
        "<g id=\"edge2\" class=\"edge\">\n",
-       "<title>(&#39;process2&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)&#45;&gt;(&#39;process2&#39;,)</title>\n",
+       "<title>(&#39;process2&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)_input&#45;&gt;(&#39;process2&#39;,)</title>\n",
        "<path fill=\"none\" stroke=\"black\" stroke-dasharray=\"5,2\" d=\"M115.64,-27.61C117.72,-35.69 120.76,-46.2 124.47,-55.15 125.44,-57.49 126.52,-59.88 127.66,-62.25\"/>\n",
        "<polygon fill=\"black\" stroke=\"black\" points=\"124.49,-63.74 132.2,-71.01 130.71,-60.52 124.49,-63.74\"/>\n",
        "<text text-anchor=\"start\" x=\"123.58\" y=\"-47.15\" font-family=\"Times,serif\" font-size=\"10.00\">port1</text>\n",
        "</g>\n",
-       "<!-- (&#39;process3&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;) -->\n",
-       "<!-- (&#39;process3&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)&#45;&gt;(&#39;process3&#39;,) -->\n",
+       "<!-- (&#39;process3&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)_input -->\n",
+       "<!-- (&#39;process3&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)_input&#45;&gt;(&#39;process3&#39;,) -->\n",
        "<g id=\"edge3\" class=\"edge\">\n",
-       "<title>(&#39;process3&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)&#45;&gt;(&#39;process3&#39;,)</title>\n",
+       "<title>(&#39;process3&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;1&#39;)_input&#45;&gt;(&#39;process3&#39;,)</title>\n",
        "<path fill=\"none\" stroke=\"black\" stroke-dasharray=\"5,2\" d=\"M205.92,-27.92C205.84,-35.92 206.3,-46.25 208.47,-55.15 209.02,-57.44 209.73,-59.76 210.54,-62.05\"/>\n",
        "<polygon fill=\"black\" stroke=\"black\" points=\"207.21,-63.16 214.26,-71.07 213.68,-60.49 207.21,-63.16\"/>\n",
        "<text text-anchor=\"start\" x=\"207.58\" y=\"-47.15\" font-family=\"Times,serif\" font-size=\"10.00\">port1</text>\n",
        "</g>\n",
-       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;) -->\n",
-       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)&#45;&gt;(&#39;process1&#39;,) -->\n",
+       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)_output -->\n",
+       "<!-- (&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)_output&#45;&gt;(&#39;process1&#39;,) -->\n",
        "<g id=\"edge4\" class=\"edge\">\n",
-       "<title>(&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)&#45;&gt;(&#39;process1&#39;,)</title>\n",
+       "<title>(&#39;process1&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)_output&#45;&gt;(&#39;process1&#39;,)</title>\n",
        "<path fill=\"none\" stroke=\"black\" stroke-dasharray=\"5,2\" d=\"M56.94,-39.31C56.23,-50.04 55.41,-62.38 54.76,-72.21\"/>\n",
        "<polygon fill=\"black\" stroke=\"black\" points=\"60.41,-39.81 57.58,-29.6 53.43,-39.35 60.41,-39.81\"/>\n",
        "<text text-anchor=\"start\" x=\"55.58\" y=\"-47.15\" font-family=\"Times,serif\" font-size=\"10.00\">port2</text>\n",
        "</g>\n",
-       "<!-- (&#39;process2&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;) -->\n",
-       "<!-- (&#39;process2&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)&#45;&gt;(&#39;process2&#39;,) -->\n",
+       "<!-- (&#39;process2&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)_output -->\n",
+       "<!-- (&#39;process2&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)_output&#45;&gt;(&#39;process2&#39;,) -->\n",
        "<g id=\"edge5\" class=\"edge\">\n",
-       "<title>(&#39;process2&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)&#45;&gt;(&#39;process2&#39;,)</title>\n",
+       "<title>(&#39;process2&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)_output&#45;&gt;(&#39;process2&#39;,)</title>\n",
        "<path fill=\"none\" stroke=\"black\" stroke-dasharray=\"5,2\" d=\"M153.05,-39.04C151.04,-49.88 148.72,-62.39 146.88,-72.33\"/>\n",
        "<polygon fill=\"black\" stroke=\"black\" points=\"156.48,-39.7 154.86,-29.23 149.6,-38.42 156.48,-39.7\"/>\n",
        "<text text-anchor=\"start\" x=\"151.58\" y=\"-47.15\" font-family=\"Times,serif\" font-size=\"10.00\">port2</text>\n",
        "</g>\n",
-       "<!-- (&#39;process3&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;) -->\n",
-       "<!-- (&#39;process3&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)&#45;&gt;(&#39;process3&#39;,) -->\n",
+       "<!-- (&#39;process3&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)_output -->\n",
+       "<!-- (&#39;process3&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)_output&#45;&gt;(&#39;process3&#39;,) -->\n",
        "<g id=\"edge6\" class=\"edge\">\n",
-       "<title>(&#39;process3&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)&#45;&gt;(&#39;process3&#39;,)</title>\n",
+       "<title>(&#39;process3&#39;, &#39;p&#39;, &#39;o&#39;, &#39;r&#39;, &#39;t&#39;, &#39;2&#39;)_output&#45;&gt;(&#39;process3&#39;,)</title>\n",
        "<path fill=\"none\" stroke=\"black\" stroke-dasharray=\"5,2\" d=\"M243.21,-37.99C239.28,-49 234.66,-61.93 231,-72.16\"/>\n",
        "<polygon fill=\"black\" stroke=\"black\" points=\"246.42,-39.42 246.49,-28.82 239.83,-37.06 246.42,-39.42\"/>\n",
        "<text text-anchor=\"start\" x=\"239.58\" y=\"-47.15\" font-family=\"Times,serif\" font-size=\"10.00\">port2</text>\n",
@@ -546,10 +546,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x111d3f8e0>"
+       "<graphviz.graphs.Digraph at 0x12638faf0>"
       ]
      },
-     "execution_count": 7,
+     "execution_count": 21,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -584,7 +584,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 22,
    "id": "a6ecad5d-8948-4636-910c-79284a3e8679",
    "metadata": {},
    "outputs": [
@@ -658,10 +658,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x111d752b0>"
+       "<graphviz.graphs.Digraph at 0x12638fc40>"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 22,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -672,8 +672,8 @@
     "        '_type': 'edge',\n",
     "        '_inputs': {\n",
     "            'port1': 'float',\n",
-    "            'port2': 'int',\n",
-    "            'port3': 'int',\n",
+    "            'port2': 'integer',\n",
+    "            'port3': 'integer',\n",
     "        },\n",
     "        'inputs': {\n",
     "            'port1': ['node1'],\n",
@@ -682,8 +682,8 @@
     "        }\n",
     "    },\n",
     "    'node1': 'float',  # TODO -- shouldn't these fill?\n",
-    "    'node2': 'int',\n",
-    "    'node3': 'int',\n",
+    "    'node2': 'integer',\n",
+    "    'node3': 'integer',\n",
     "}\n",
     "plot_bigraph(connected_process_spec, **plot_settings, filename='wires')"
    ]
@@ -716,7 +716,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 23,
    "id": "781a84e6-bbe2-4708-b441-47efc611b46f",
    "metadata": {},
    "outputs": [
@@ -797,10 +797,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x111d75f70>"
+       "<graphviz.graphs.Digraph at 0x1263ff4f0>"
       ]
      },
-     "execution_count": 9,
+     "execution_count": 23,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -808,12 +808,12 @@
    "source": [
     "flat_composite_spec = {\n",
     "    'store1.1': 'float',\n",
-    "    'store1.2': 'int',\n",
+    "    'store1.2': 'integer',\n",
     "    'process1': {\n",
     "        '_type': 'process',\n",
     "        '_outputs': {\n",
     "            'port1': 'float',\n",
-    "            'port2': 'int',\n",
+    "            'port2': 'integer',\n",
     "        },\n",
     "        'outputs': {\n",
     "            'port1': ['store1.1'],\n",
@@ -824,7 +824,7 @@
     "        '_type': 'process',\n",
     "        '_inputs': {\n",
     "            'port1': 'float',\n",
-    "            'port2': 'int',\n",
+    "            'port2': 'integer',\n",
     "        },\n",
     "        'inputs': {\n",
     "            'port1': ['store1.1'],\n",
@@ -846,7 +846,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 38,
    "id": "701e759d-7f9b-41bb-911c-a8208c892462",
    "metadata": {},
    "outputs": [
@@ -966,10 +966,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x1071dfbe0>"
+       "<graphviz.graphs.Digraph at 0x1072af640>"
       ]
      },
-     "execution_count": 10,
+     "execution_count": 38,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -978,12 +978,12 @@
     "nested_composite_spec = {\n",
     "    'store1': {\n",
     "        'store1.1': 'float',\n",
-    "        'store1.2': 'int',\n",
+    "        'store1.2': 'integer',\n",
     "        'process1': {\n",
     "            '_type': 'process',\n",
     "            '_inputs': {\n",
     "                'port1': 'float',\n",
-    "                'port2': 'int',\n",
+    "                'port2': 'integer',\n",
     "            },\n",
     "            'inputs': {\n",
     "                'port1': ['store1.1'],\n",
@@ -994,7 +994,7 @@
     "            '_type': 'process',\n",
     "            '_outputs': {\n",
     "                'port1': 'float',\n",
-    "                'port2': 'int',\n",
+    "                'port2': 'integer',\n",
     "            },\n",
     "            'outputs': {\n",
     "                'port1': ['store1.1'],\n",
@@ -1028,7 +1028,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 25,
    "id": "638c5dc7-4cfd-46e4-b66a-8c42ca98ff1d",
    "metadata": {},
    "outputs": [
@@ -1127,10 +1127,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x1071df610>"
+       "<graphviz.graphs.Digraph at 0x121e9ccd0>"
       ]
      },
-     "execution_count": 11,
+     "execution_count": 25,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1144,7 +1144,7 @@
     "            '_type': 'process',\n",
     "            '_outputs': {\n",
     "                'port1': 'float',\n",
-    "                'port2': 'int',\n",
+    "                'port2': 'integer',\n",
     "            },\n",
     "            'outputs': {\n",
     "                'port1': ['store1.1'],\n",
@@ -1155,7 +1155,7 @@
     "            '_type': 'process',\n",
     "            '_outputs': {\n",
     "                'port1': 'float',\n",
-    "                'port2': 'int',\n",
+    "                'port2': 'integer',\n",
     "            },\n",
     "            'outputs': {\n",
     "                'port1': ['store1.1'],\n",
@@ -1188,7 +1188,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 26,
    "id": "e76c97a8-3037-464a-929e-ba4414c73c34",
    "metadata": {},
    "outputs": [],
@@ -1213,7 +1213,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 27,
    "id": "f0eff7b0-f0e2-4d56-8b16-ef0fc1ce5aba",
    "metadata": {},
    "outputs": [],
@@ -1246,7 +1246,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 28,
    "id": "db45c99b-b97b-47bc-a73e-c669882f3969",
    "metadata": {},
    "outputs": [],
@@ -1299,7 +1299,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 29,
    "id": "47bdf8e5-0bdd-4cac-b57e-2449c75fa178",
    "metadata": {
     "tags": []
@@ -1896,10 +1896,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x1071c5c40>"
+       "<graphviz.graphs.Digraph at 0x121eba460>"
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-     "execution_count": 15,
+     "execution_count": 29,
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@@ -1957,7 +1957,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 30,
    "id": "ab431982-d156-4b7a-9918-384a5ea5132a",
    "metadata": {
     "tags": []
@@ -1989,7 +1989,7 @@
        "   'nuclear transcriptional speckle': {'negative regulation of RNA biosynthesis process': {}}}}}"
       ]
      },
-     "execution_count": 16,
+     "execution_count": 30,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -2000,7 +2000,7 @@
   },
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-   "execution_count": 17,
+   "execution_count": 31,
    "id": "5a76608a-fff0-4005-9f32-c02afef39d9e",
    "metadata": {
     "tags": []
@@ -2771,10 +2771,10 @@
        "<text text-anchor=\"start\" x=\"1028.33\" y=\"-537.14\" font-family=\"Times,serif\" font-size=\"10.00\">negative</text>\n",
        "<text text-anchor=\"start\" x=\"1025\" y=\"-527.14\" font-family=\"Times,serif\" font-size=\"10.00\">regulation</text>\n",
        "</g>\n",
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-       "<!-- (&#39;cell&#39;, &#39;translation&#39;, &#39;m&#39;, &#39;e&#39;, &#39;m&#39;, &#39;b&#39;, &#39;r&#39;, &#39;a&#39;, &#39;n&#39;, &#39;e&#39;)&#45;&gt;(&#39;cell&#39;, &#39;translation&#39;) -->\n",
+       "<!-- (&#39;cell&#39;, &#39;translation&#39;, &#39;m&#39;, &#39;e&#39;, &#39;m&#39;, &#39;b&#39;, &#39;r&#39;, &#39;a&#39;, &#39;n&#39;, &#39;e&#39;)_output -->\n",
+       "<!-- (&#39;cell&#39;, &#39;translation&#39;, &#39;m&#39;, &#39;e&#39;, &#39;m&#39;, &#39;b&#39;, &#39;r&#39;, &#39;a&#39;, &#39;n&#39;, &#39;e&#39;)_output&#45;&gt;(&#39;cell&#39;, &#39;translation&#39;) -->\n",
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+       "<title>(&#39;cell&#39;, &#39;translation&#39;, &#39;m&#39;, &#39;e&#39;, &#39;m&#39;, &#39;b&#39;, &#39;r&#39;, &#39;a&#39;, &#39;n&#39;, &#39;e&#39;)_output&#45;&gt;(&#39;cell&#39;, &#39;translation&#39;)</title>\n",
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@@ -2783,10 +2783,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x1071c5cd0>"
+       "<graphviz.graphs.Digraph at 0x126427f70>"
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@@ -2931,7 +2931,7 @@
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+   "execution_count": 32,
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@@ -2965,17 +2965,17 @@
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+       "<!-- (&#39;hypothesized&lt;br/&gt;mechanism&#39;, &#39;1&#39;)_input -->\n",
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        "<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",
+       "<title>(&#39;hypothesized&lt;br/&gt;mechanism&#39;, &#39;1&#39;)_input&#45;&gt;(&#39;hypothesized&lt;br/&gt;mechanism&#39;,)</title>\n",
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+       "<!-- (&#39;hypothesized&lt;br/&gt;mechanism&#39;, &#39;2&#39;)_input -->\n",
+       "<!-- (&#39;hypothesized&lt;br/&gt;mechanism&#39;, &#39;2&#39;)_input&#45;&gt;(&#39;hypothesized&lt;br/&gt;mechanism&#39;,) -->\n",
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-       "<title>(&#39;hypothesized&lt;br/&gt;mechanism&#39;, &#39;2&#39;)&#45;&gt;(&#39;hypothesized&lt;br/&gt;mechanism&#39;,)</title>\n",
+       "<title>(&#39;hypothesized&lt;br/&gt;mechanism&#39;, &#39;2&#39;)_input&#45;&gt;(&#39;hypothesized&lt;br/&gt;mechanism&#39;,)</title>\n",
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@@ -2983,10 +2983,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x111d3f7c0>"
+       "<graphviz.graphs.Digraph at 0x12638f5b0>"
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-     "execution_count": 18,
+     "execution_count": 32,
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@@ -3025,7 +3025,7 @@
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   {
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-   "execution_count": 19,
+   "execution_count": 33,
    "id": "b39417ce-d9a1-4985-abce-ce22df816897",
    "metadata": {
     "tags": []
@@ -3047,60 +3047,49 @@
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-       " viewBox=\"0.00 0.00 687.63 682.51\" 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(4 678.51)\">\n",
+       "<svg width=\"669pt\" height=\"658pt\"\n",
+       " viewBox=\"0.00 0.00 687.63 676.98\" 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(4 672.98)\">\n",
        "<title>bigraph</title>\n",
-       "<polygon fill=\"white\" stroke=\"none\" points=\"-4,4 -4,-678.51 683.63,-678.51 683.63,4 -4,4\"/>\n",
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@@ -3111,7 +3100,7 @@
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@@ -3122,17 +3111,17 @@
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        "<polygon fill=\"black\" stroke=\"black\" points=\"37.2,-352.43 39.76,-362.72 44.17,-353.09 37.2,-352.43\"/>\n",
@@ -3147,7 +3136,7 @@
        "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;)&#45;&gt;(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;metabolites&#39;) -->\n",
        "<g id=\"edge6\" class=\"edge\">\n",
        "<title>(&#39;cell&#39;, &#39;cytoplasm&#39;)&#45;&gt;(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;metabolites&#39;)</title>\n",
-       "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M343.25,-547.03C321.71,-533.87 292.86,-513.82 272.74,-490.6 259.23,-475.01 248.21,-454.77 240.35,-437.76\"/>\n",
+       "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M343.22,-545.13C321.66,-532.58 292.81,-513.34 272.74,-490.6 259.09,-475.13 248.06,-454.9 240.24,-437.87\"/>\n",
        "</g>\n",
        "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;ribosomal complexes&#39;) -->\n",
        "<g id=\"node7\" class=\"node\">\n",
@@ -3158,7 +3147,7 @@
        "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;)&#45;&gt;(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;ribosomal complexes&#39;) -->\n",
        "<g id=\"edge7\" class=\"edge\">\n",
        "<title>(&#39;cell&#39;, &#39;cytoplasm&#39;)&#45;&gt;(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;ribosomal complexes&#39;)</title>\n",
-       "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M364.14,-531.48C361.16,-518.84 358.21,-504.14 356.74,-490.6 348.33,-413.04 341.46,-391.57 356.74,-315.06 358.27,-307.38 360.55,-299.51 363.2,-291.84\"/>\n",
+       "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M363.88,-528.9C360.99,-516.98 358.17,-503.27 356.74,-490.6 348.02,-413.07 341.46,-391.57 356.74,-315.06 358.27,-307.38 360.55,-299.51 363.2,-291.84\"/>\n",
        "</g>\n",
        "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;transcript regulation complex&#39;) -->\n",
        "<g id=\"node8\" class=\"node\">\n",
@@ -3169,24 +3158,24 @@
        "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;)&#45;&gt;(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;transcript regulation complex&#39;) -->\n",
        "<g id=\"edge8\" class=\"edge\">\n",
        "<title>(&#39;cell&#39;, &#39;cytoplasm&#39;)&#45;&gt;(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;transcript regulation complex&#39;)</title>\n",
-       "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M387.79,-533.89C395.29,-519.09 404.75,-500.43 414.15,-481.9\"/>\n",
+       "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M387.98,-531.27C395.26,-517.15 404.37,-499.51 413.45,-481.9\"/>\n",
        "</g>\n",
        "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;translation&#39;) -->\n",
-       "<g id=\"node15\" class=\"node\">\n",
+       "<g id=\"node14\" class=\"node\">\n",
        "<title>(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;translation&#39;)</title>\n",
        "<polygon fill=\"none\" stroke=\"black\" stroke-width=\"2\" points=\"499.67,-36 441.81,-36 441.81,0 499.67,0 499.67,-36\"/>\n",
        "<text text-anchor=\"start\" x=\"445.41\" y=\"-14.4\" font-family=\"Times,serif\" font-size=\"12.00\">translation</text>\n",
        "</g>\n",
        "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;)&#45;&gt;(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;translation&#39;) -->\n",
        "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;metabolites&#39;)&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;) -->\n",
-       "<g id=\"edge16\" class=\"edge\">\n",
+       "<g id=\"edge15\" class=\"edge\">\n",
        "<title>(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;metabolites&#39;)&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;)</title>\n",
        "<path fill=\"none\" stroke=\"black\" stroke-dasharray=\"5,2\" d=\"M218.75,-354.37C207.89,-289.89 188.99,-177.69 181.72,-134.48\"/>\n",
        "<polygon fill=\"black\" stroke=\"black\" points=\"215.25,-354.67 220.36,-363.95 222.15,-353.51 215.25,-354.67\"/>\n",
        "<text text-anchor=\"start\" x=\"208.74\" y=\"-229.33\" font-family=\"Times,serif\" font-size=\"10.00\">internal</text>\n",
        "</g>\n",
        "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;ribosomal complexes&#39;)&#45;&gt;(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;translation&#39;) -->\n",
-       "<g id=\"edge17\" class=\"edge\">\n",
+       "<g id=\"edge16\" class=\"edge\">\n",
        "<title>(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;ribosomal complexes&#39;)&#45;&gt;(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;translation&#39;)</title>\n",
        "<path fill=\"none\" stroke=\"black\" stroke-dasharray=\"5,2\" d=\"M396.67,-155.61C400.58,-131.28 407.05,-104.75 417.74,-82 425.82,-64.79 439.81,-48.46 451.39,-36.74\"/>\n",
        "<polygon fill=\"black\" stroke=\"black\" points=\"393.21,-155.09 395.22,-165.49 400.14,-156.1 393.21,-155.09\"/>\n",
@@ -3204,14 +3193,14 @@
        "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M458.96,-314.38C462.26,-258.9 466.36,-190.27 468.75,-150.23\"/>\n",
        "</g>\n",
        "<!-- (&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;transcript regulation complex&#39;, &#39;transcripts&#39;)&#45;&gt;(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;translation&#39;) -->\n",
-       "<g id=\"edge18\" class=\"edge\">\n",
+       "<g id=\"edge17\" class=\"edge\">\n",
        "<title>(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;transcript regulation complex&#39;, &#39;transcripts&#39;)&#45;&gt;(&#39;cell&#39;, &#39;cytoplasm&#39;, &#39;translation&#39;)</title>\n",
        "<path fill=\"none\" stroke=\"black\" stroke-dasharray=\"5,2\" d=\"M470.74,-69.6C470.74,-58.01 470.74,-46.2 470.74,-36.91\"/>\n",
        "<polygon fill=\"black\" stroke=\"black\" points=\"467.24,-69.51 470.74,-79.51 474.24,-69.51 467.24,-69.51\"/>\n",
        "<text text-anchor=\"start\" x=\"470.74\" y=\"-56\" font-family=\"Times,serif\" font-size=\"10.00\">p2</text>\n",
        "</g>\n",
        "<!-- (&#39;cell&#39;, &#39;nucleoid&#39;, &#39;chromosome&#39;) -->\n",
-       "<g id=\"node12\" class=\"node\">\n",
+       "<g id=\"node11\" class=\"node\">\n",
        "<title>(&#39;cell&#39;, &#39;nucleoid&#39;, &#39;chromosome&#39;)</title>\n",
        "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"638.74\" cy=\"-402.83\" rx=\"40.89\" ry=\"40.89\"/>\n",
        "<text text-anchor=\"start\" x=\"607.75\" y=\"-399.23\" font-family=\"Times,serif\" font-size=\"12.00\">chromosome</text>\n",
@@ -3219,10 +3208,10 @@
        "<!-- (&#39;cell&#39;, &#39;nucleoid&#39;)&#45;&gt;(&#39;cell&#39;, &#39;nucleoid&#39;, &#39;chromosome&#39;) -->\n",
        "<g id=\"edge10\" class=\"edge\">\n",
        "<title>(&#39;cell&#39;, &#39;nucleoid&#39;)&#45;&gt;(&#39;cell&#39;, &#39;nucleoid&#39;, &#39;chromosome&#39;)</title>\n",
-       "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M596.39,-536.46C604.6,-510.74 617.04,-471.8 626.31,-442.76\"/>\n",
+       "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M560.25,-539.69C568.03,-530.76 576.78,-520.02 583.74,-509.6 598.34,-487.75 611.99,-461.54 622.04,-440.69\"/>\n",
        "</g>\n",
        "<!-- (&#39;cell&#39;, &#39;nucleoid&#39;, &#39;chromosome&#39;, &#39;genes&#39;) -->\n",
-       "<g id=\"node13\" class=\"node\">\n",
+       "<g id=\"node12\" class=\"node\">\n",
        "<title>(&#39;cell&#39;, &#39;nucleoid&#39;, &#39;chromosome&#39;, &#39;genes&#39;)</title>\n",
        "<ellipse fill=\"none\" stroke=\"black\" stroke-width=\"2\" cx=\"638.74\" cy=\"-115.8\" rx=\"20.41\" ry=\"20.41\"/>\n",
        "<text text-anchor=\"start\" x=\"625.08\" y=\"-112.2\" font-family=\"Times,serif\" font-size=\"12.00\">genes</text>\n",
@@ -3232,10 +3221,10 @@
        "<title>(&#39;cell&#39;, &#39;nucleoid&#39;, &#39;chromosome&#39;)&#45;&gt;(&#39;cell&#39;, &#39;nucleoid&#39;, &#39;chromosome&#39;, &#39;genes&#39;)</title>\n",
        "<path fill=\"none\" stroke=\"black\" stroke-width=\"2\" d=\"M638.74,-360.99C638.74,-299.11 638.74,-183.87 638.74,-137.2\"/>\n",
        "</g>\n",
-       "<!-- (&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;, &#39;e&#39;, &#39;x&#39;, &#39;t&#39;, &#39;e&#39;, &#39;r&#39;, &#39;n&#39;, &#39;a&#39;, &#39;l&#39;) -->\n",
-       "<!-- (&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;, &#39;e&#39;, &#39;x&#39;, &#39;t&#39;, &#39;e&#39;, &#39;r&#39;, &#39;n&#39;, &#39;a&#39;, &#39;l&#39;)&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;) -->\n",
-       "<g id=\"edge19\" class=\"edge\">\n",
-       "<title>(&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;, &#39;e&#39;, &#39;x&#39;, &#39;t&#39;, &#39;e&#39;, &#39;r&#39;, &#39;n&#39;, &#39;a&#39;, &#39;l&#39;)&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;)</title>\n",
+       "<!-- (&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;, &#39;e&#39;, &#39;x&#39;, &#39;t&#39;, &#39;e&#39;, &#39;r&#39;, &#39;n&#39;, &#39;a&#39;, &#39;l&#39;)_output -->\n",
+       "<!-- (&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;, &#39;e&#39;, &#39;x&#39;, &#39;t&#39;, &#39;e&#39;, &#39;r&#39;, &#39;n&#39;, &#39;a&#39;, &#39;l&#39;)_output&#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;e&#39;, &#39;x&#39;, &#39;t&#39;, &#39;e&#39;, &#39;r&#39;, &#39;n&#39;, &#39;a&#39;, &#39;l&#39;)_output&#45;&gt;(&#39;cell&#39;, &#39;membrane&#39;, &#39;transmembrane transport&#39;)</title>\n",
        "<path fill=\"none\" stroke=\"black\" stroke-dasharray=\"5,2\" d=\"M292.45,-377.41C285.02,-324.8 265.86,-202.66 243.74,-167.6 235.41,-154.4 222.39,-143.23 210.18,-134.76\"/>\n",
        "<polygon fill=\"black\" stroke=\"black\" points=\"288.96,-377.72 293.8,-387.15 295.89,-376.76 288.96,-377.72\"/>\n",
        "<text text-anchor=\"start\" x=\"279.74\" y=\"-229.33\" font-family=\"Times,serif\" font-size=\"10.00\">external</text>\n",
@@ -3244,10 +3233,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.graphs.Digraph at 0x111db1ee0>"
+       "<graphviz.graphs.Digraph at 0x10729ddc0>"
       ]
      },
-     "execution_count": 19,
+     "execution_count": 33,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -3324,7 +3313,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 34,
    "id": "16960d1b-6e35-421e-bb7d-3efe5052e4fc",
    "metadata": {
     "tags": []
diff --git a/notebooks/bigraph_example.ipynb b/notebooks/bigraph_example.ipynb
index 685040c..2d0913c 100644
--- a/notebooks/bigraph_example.ipynb
+++ b/notebooks/bigraph_example.ipynb
@@ -883,7 +883,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.9.6"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/ecoli.ipynb b/notebooks/ecoli.ipynb
index b8fc395..d2e9974 100644
--- a/notebooks/ecoli.ipynb
+++ b/notebooks/ecoli.ipynb
@@ -2128,7 +2128,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.9.6"
   }
  },
  "nbformat": 4,
diff --git a/setup.py b/setup.py
index 1dc5dca..f0a8a31 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 from setuptools import setup, find_packages
 
 
-VERSION = '0.0.33'
+VERSION = '0.0.34'
 
 
 with open("README.md", "r") as readme: