From 7da33a1c709d0697009bd5e7473eb11a0299e182 Mon Sep 17 00:00:00 2001 From: Eran Agmon Date: Tue, 22 Aug 2023 12:04:42 -0400 Subject: [PATCH] fix --- notebooks/basics.ipynb | 2024 ++++++++++++++++++---------------------- 1 file changed, 884 insertions(+), 1140 deletions(-) diff --git a/notebooks/basics.ipynb b/notebooks/basics.ipynb index f475d56..8c237a3 100644 --- a/notebooks/basics.ipynb +++ b/notebooks/basics.ipynb @@ -35,8 +35,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "bigraph-schema @ file:///Users/eranagmon/code/bigraph-schema\n", - "bigraph-viz @ file:///Users/eranagmon/code/bigraph-viz\n" + "bigraph-schema==0.0.17\n", + "bigraph-viz==0.0.30\n" ] } ], @@ -126,26 +126,26 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('store1',)\n", - "\n", - "store1\n", - "1.0\n", + "\n", + "store1\n", + "1.0\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 4, @@ -180,26 +180,26 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('store1',)\n", - "\n", - "store1\n", - "1.0::float\n", + "\n", + "store1\n", + "1.0::float\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 5, @@ -238,91 +238,91 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('store1',)\n", - "\n", - "store1\n", + "\n", + "store1\n", "\n", "\n", "\n", "('store1', 'store1.1')\n", - "\n", - "store1.1\n", + "\n", + "store1.1\n", "\n", "\n", "\n", "('store1',)->('store1', 'store1.1')\n", - "\n", + "\n", "\n", "\n", "\n", "('store1', 'store1.2')\n", - "\n", - "store1.2\n", + "\n", + "store1.2\n", "\n", "\n", "\n", "('store1',)->('store1', 'store1.2')\n", - "\n", + "\n", "\n", "\n", "\n", "('store1', 'store1.1', 'store1.1.1')\n", - "\n", - "store1.1.1\n", + "\n", + "store1.1.1\n", "\n", "\n", "\n", "('store1', 'store1.1')->('store1', 'store1.1', 'store1.1.1')\n", - "\n", + "\n", "\n", "\n", "\n", "('store1', 'store1.1', 'store1.1.2')\n", - "\n", - "store1.1.2\n", + "\n", + "store1.1.2\n", "\n", "\n", "\n", "('store1', 'store1.1')->('store1', 'store1.1', 'store1.1.2')\n", - "\n", + "\n", "\n", "\n", "\n", "('store1', 'store1.1', 'store1.1.3')\n", - "\n", - "store1.1.3\n", + "\n", + "store1.1.3\n", "\n", "\n", "\n", "('store1', 'store1.1')->('store1', 'store1.1', 'store1.1.3')\n", - "\n", + "\n", "\n", "\n", "\n", "('store1', 'store1.1', 'store1.1.3', 'store1.1.3.1')\n", - "\n", - "store1.1.3.1\n", + "\n", + "store1.1.3.1\n", "\n", "\n", "\n", "('store1', 'store1.1', 'store1.1.3')->('store1', 'store1.1', 'store1.1.3', 'store1.1.3.1')\n", - "\n", + "\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 6, @@ -375,41 +375,41 @@ "\n", "\n", - "\n", "\n", - "\n", + "\n", "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('process1',)\n", "\n", - "process1\n", + "process1\n", "\n", "\n", "\n", "\n", "('process1', 'port1')->('process1',)\n", - "\n", - "\n", - "port1\n", + "\n", + "\n", + "port1\n", "\n", "\n", "\n", "\n", "('process1', 'port2')->('process1',)\n", - "\n", - "\n", - "port2\n", + "\n", + "\n", + "port2\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 7, @@ -452,85 +452,85 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('process1',)\n", - "\n", - "process1\n", + "\n", + "process1\n", "\n", "\n", "\n", "('process2',)\n", - "\n", - "process2\n", + "\n", + "process2\n", "\n", "\n", "\n", "('process3',)\n", - "\n", - "process3\n", + "\n", + "process3\n", "\n", "\n", "\n", "\n", "('process1', 'port1')->('process1',)\n", - "\n", - "\n", - "port1\n", + "\n", + "\n", + "port1\n", "\n", "\n", "\n", "\n", "('process1', 'port2')->('process1',)\n", - "\n", - "\n", - "port2\n", + "\n", + "\n", + "port2\n", "\n", "\n", "\n", "\n", "('process2', 'port1')->('process2',)\n", - "\n", - "\n", - "port1\n", + "\n", + "\n", + "port1\n", "\n", "\n", "\n", "\n", "('process2', 'port2')->('process2',)\n", - "\n", - "\n", - "port2\n", + "\n", + "\n", + "port2\n", "\n", "\n", "\n", "\n", "('process3', 'port1')->('process3',)\n", - "\n", - "\n", - "port1\n", + "\n", + "\n", + "port1\n", "\n", "\n", "\n", "\n", "('process3', 'port2')->('process3',)\n", - "\n", - "\n", - "port2\n", + "\n", + "\n", + "port2\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 8, @@ -577,64 +577,64 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('node1',)\n", - "\n", - "node1\n", + "\n", + "node1\n", "\n", "\n", "\n", "('process1',)\n", - "\n", - "process1\n", + "\n", + "process1\n", "\n", "\n", "\n", "('node1',)->('process1',)\n", - "\n", - "\n", - "port1\n", + "\n", + "\n", + "port1\n", "\n", "\n", "\n", "('node2',)\n", - "\n", - "node2\n", + "\n", + "node2\n", "\n", "\n", "\n", "('node2',)->('process1',)\n", - "\n", - "\n", - "port2\n", + "\n", + "\n", + "port2\n", "\n", "\n", "\n", "('node3',)\n", - "\n", - "node3\n", + "\n", + "node3\n", "\n", "\n", "\n", "('node3',)->('process1',)\n", - "\n", - "\n", - "port3\n", + "\n", + "\n", + "port3\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 9, @@ -704,71 +704,71 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('store1.1',)\n", - "\n", - "store1.1\n", + "\n", + "store1.1\n", "\n", "\n", "\n", "('process1',)\n", - "\n", - "process1\n", + "\n", + "process1\n", "\n", "\n", "\n", "('store1.1',)->('process1',)\n", - "\n", - "\n", - "port1\n", + "\n", + "\n", + "port1\n", "\n", "\n", "\n", "('process2',)\n", - "\n", - "process2\n", + "\n", + "process2\n", "\n", "\n", "\n", "('store1.1',)->('process2',)\n", - "\n", - "\n", - "port1\n", + "\n", + "\n", + "port1\n", "\n", "\n", "\n", "('store1.2',)\n", - "\n", - "store1.2\n", + "\n", + "store1.2\n", "\n", "\n", "\n", "('store1.2',)->('process1',)\n", - "\n", - "\n", - "port2\n", + "\n", + "\n", + "port2\n", "\n", "\n", "\n", "('store1.2',)->('process2',)\n", - "\n", - "\n", - "port2\n", + "\n", + "\n", + "port2\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 10, @@ -820,102 +820,102 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('store1',)\n", - "\n", - "store1\n", + "\n", + "store1\n", "\n", "\n", "\n", "('store1', 'store1.1')\n", - "\n", - "store1.1\n", + "\n", + "store1.1\n", "\n", "\n", "\n", "('store1',)->('store1', 'store1.1')\n", - "\n", + "\n", "\n", "\n", "\n", "('store1', 'store1.2')\n", - "\n", - "store1.2\n", + "\n", + "store1.2\n", "\n", "\n", "\n", "('store1',)->('store1', 'store1.2')\n", - "\n", + "\n", "\n", "\n", "\n", "('store1', 'process1')\n", "\n", - "process1\n", + "process1\n", "\n", "\n", "\n", "\n", "('store1', 'process2')\n", "\n", - "process2\n", + "process2\n", "\n", "\n", "\n", "\n", "('process3',)\n", - "\n", - "process3\n", + "\n", + "process3\n", "\n", "\n", "\n", "('store1',)->('process3',)\n", - "\n", - "\n", - "port1\n", + "\n", + "\n", + "port1\n", "\n", "\n", "\n", "('store1', 'store1.1')->('store1', 'process1')\n", - "\n", - "\n", - "port1\n", + "\n", + "\n", + "port1\n", "\n", "\n", "\n", "('store1', 'store1.1')->('store1', 'process2')\n", - "\n", - "\n", - "port1\n", + "\n", + "\n", + "port1\n", "\n", "\n", "\n", "('store1', 'store1.2')->('store1', 'process1')\n", - "\n", - "\n", - "port2\n", + "\n", + "\n", + "port2\n", "\n", "\n", "\n", "('store1', 'store1.2')->('store1', 'process2')\n", - "\n", - "\n", - "port2\n", + "\n", + "\n", + "port2\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 11, @@ -975,96 +975,96 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('composite_process', 'store1.1')\n", - "\n", - "store1.1\n", + "\n", + "store1.1\n", "\n", "\n", "\n", "('composite_process', 'process1')\n", - "\n", - "process1\n", + "\n", + "process1\n", "\n", "\n", "\n", "('composite_process', 'store1.1')->('composite_process', 'process1')\n", - "\n", - "\n", - "port1\n", + "\n", + "\n", + "port1\n", "\n", "\n", "\n", "('composite_process', 'process2')\n", - "\n", - "process2\n", + "\n", + "process2\n", "\n", "\n", "\n", "('composite_process', 'store1.1')->('composite_process', 'process2')\n", - "\n", - "\n", - "port1\n", + "\n", + "\n", + "port1\n", "\n", "\n", "\n", "('composite_process', 'store1.2')\n", - "\n", - "store1.2\n", + "\n", + "store1.2\n", "\n", "\n", "\n", "('composite_process', 'store1.2')->('composite_process', 'process1')\n", - "\n", - "\n", - "port2\n", + "\n", + "\n", + "port2\n", "\n", "\n", "\n", "('composite_process', 'store1.2')->('composite_process', 'process2')\n", - "\n", - "\n", - "port2\n", + "\n", + "\n", + "port2\n", "\n", "\n", "\n", "('composite_process',)\n", - "\n", - "\n", - "composite_process\n", + "\n", + "\n", + "composite_process\n", "\n", "\n", "\n", "('composite_process',)->('composite_process', 'store1.1')\n", - "\n", + "\n", "\n", "\n", "\n", "('composite_process',)->('composite_process', 'store1.1')\n", - "\n", - "\n", - "tunnel port1\n", + "\n", + "\n", + "tunnel port1\n", "\n", "\n", "\n", "('composite_process',)->('composite_process', 'store1.2')\n", - "\n", + "\n", "\n", "\n", "\n", "('composite_process',)->('composite_process', 'store1.2')\n", - "\n", - "\n", - "tunnel port2\n", + "\n", + "\n", + "tunnel port2\n", "\n", "\n", "\n", @@ -1072,23 +1072,23 @@ "\n", "\n", "('composite_process', 'port1')->('composite_process',)\n", - "\n", - "\n", - "port1\n", + "\n", + "\n", + "port1\n", "\n", "\n", "\n", "\n", "('composite_process', 'port2')->('composite_process',)\n", - "\n", - "\n", - "port2\n", + "\n", + "\n", + "port2\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 12, @@ -1178,33 +1178,33 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('a',)\n", - "\n", - "a\n", - "11\n", + "\n", + "a\n", + "11\n", "\n", "\n", "\n", "('b',)\n", - "\n", - "b\n", - "13\n", + "\n", + "b\n", + "13\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 14, @@ -1233,33 +1233,33 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('a',)\n", - "\n", - "a\n", - "11\n", + "\n", + "a\n", + "11\n", "\n", "\n", "\n", "('b',)\n", - "\n", - "b\n", - "8\n", + "\n", + "b\n", + "8\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 15, @@ -1293,33 +1293,33 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('a',)\n", - "\n", - "a\n", - "16\n", + "\n", + "a\n", + "16\n", "\n", "\n", "\n", "('b',)\n", - "\n", - "b\n", - "8\n", + "\n", + "b\n", + "8\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 16, @@ -1388,37 +1388,37 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('a1',)\n", - "\n", - "a1\n", + "\n", + "a1\n", "\n", "\n", "\n", "('a1', 'a2')\n", - "\n", - "a2\n", - "11\n", + "\n", + "a2\n", + "11\n", "\n", "\n", "\n", "('a1',)->('a1', 'a2')\n", - "\n", + "\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 18, @@ -1448,49 +1448,49 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('a1',)\n", - "\n", - "a1\n", + "\n", + "a1\n", "\n", "\n", "\n", "('a1', 'a2')\n", - "\n", - "a2\n", - "11\n", + "\n", + "a2\n", + "11\n", "\n", "\n", "\n", "('a1',)->('a1', 'a2')\n", - "\n", + "\n", "\n", "\n", "\n", "('a1', 'a3')\n", - "\n", - "a3\n", - "-5\n", + "\n", + "a3\n", + "-5\n", "\n", "\n", "\n", "('a1',)->('a1', 'a3')\n", - "\n", + "\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 19, @@ -1556,169 +1556,169 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "flow\n", - "\n", + "\n", "\n", "\n", "('temporal<br/>process2',)\n", - "\n", - "temporal\n", - "process2\n", + "\n", + "temporal\n", + "process2\n", "\n", "\n", "\n", "('temporal<br/>process2',) 1.0\n", - "\n", - "1.0\n", + "\n", + "1.0\n", "\n", "\n", "\n", "('temporal<br/>process2',)->('temporal<br/>process2',) 1.0\n", - "\n", + "\n", "\n", "\n", "\n", "('temporal<br/>process2',) 2.0\n", - "\n", - "2.0\n", + "\n", + "2.0\n", "\n", "\n", "\n", "('temporal<br/>process2',) 1.0->('temporal<br/>process2',) 2.0\n", - "\n", + "\n", "\n", "\n", "\n", "('state',)\n", - "\n", - "state\n", + "\n", + "state\n", "\n", "\n", "\n", "('temporal<br/>process2',) 1.0->('state',)\n", - "\n", - "\n", - "\n", + "\n", + "\n", + "\n", "\n", "\n", "\n", "('temporal<br/>process2',) end\n", - "\n", + "\n", "\n", "\n", "\n", "('temporal<br/>process2',) 2.0->('temporal<br/>process2',) end\n", - "\n", - "\n", + "\n", + "\n", "\n", "\n", "\n", "('temporal<br/>process2',) 2.0->('state',)\n", - "\n", - "\n", - "\n", + "\n", + "\n", + "\n", "\n", "\n", "\n", "('temporal<br/>process1',)\n", - "\n", - "temporal\n", - "process1\n", + "\n", + "temporal\n", + "process1\n", "\n", "\n", "\n", "('temporal<br/>process1',) 0.5\n", - "\n", - "0.5\n", + "\n", + "0.5\n", "\n", "\n", "\n", "('temporal<br/>process1',)->('temporal<br/>process1',) 0.5\n", - "\n", + "\n", "\n", "\n", "\n", "('temporal<br/>process1',) 1.0\n", - "\n", - "1.0\n", + "\n", + "1.0\n", "\n", "\n", "\n", "('temporal<br/>process1',) 0.5->('temporal<br/>process1',) 1.0\n", - "\n", + "\n", "\n", "\n", "\n", "('temporal<br/>process1',) 0.5->('state',)\n", - "\n", - "\n", - "\n", + "\n", + "\n", + "\n", "\n", "\n", "\n", "('temporal<br/>process1',) 1.5\n", - "\n", - "1.5\n", + "\n", + "1.5\n", "\n", "\n", "\n", "('temporal<br/>process1',) 1.0->('temporal<br/>process1',) 1.5\n", - "\n", + "\n", "\n", "\n", "\n", "('temporal<br/>process1',) 1.0->('state',)\n", - "\n", - "\n", - "\n", + "\n", + "\n", + "\n", "\n", "\n", "\n", "('temporal<br/>process1',) 2.0\n", - "\n", - "2.0\n", + "\n", + "2.0\n", "\n", "\n", "\n", "('temporal<br/>process1',) 1.5->('temporal<br/>process1',) 2.0\n", - "\n", + "\n", "\n", "\n", "\n", "('temporal<br/>process1',) 1.5->('state',)\n", - "\n", - "\n", - "\n", + "\n", + "\n", + "\n", "\n", "\n", "\n", "('temporal<br/>process1',) end\n", - "\n", + "\n", "\n", "\n", "\n", "('temporal<br/>process1',) 2.0->('temporal<br/>process1',) end\n", - "\n", - "\n", + "\n", + "\n", "\n", "\n", "\n", "('temporal<br/>process1',) 2.0->('state',)\n", - "\n", - "\n", - "\n", + "\n", + "\n", + "\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 21, @@ -1765,7 +1765,7 @@ "\n", "\n", - "\n", "\n", "\n", "('step1',)\n", "\n", - "step1\n", + "step1\n", "\n", "\n", "\n", "('step2',)\n", "\n", - "step2\n", + "step2\n", "\n", "\n", "\n", "('step1',)->('step2',)\n", "\n", - "\n", + "\n", "\n", "\n", "\n", "('step4',)\n", "\n", - "step4\n", + "step4\n", "\n", "\n", "\n", "('step2',)->('step4',)\n", "\n", - "\n", + "\n", "\n", "\n", "\n", "('step3',)\n", "\n", - "step3\n", + "step3\n", "\n", "\n", "\n", "('step3',)->('step4',)\n", "\n", - "\n", + "\n", "\n", "\n", "\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 22, @@ -1881,7 +1881,7 @@ }, { "cell_type": "code", - "execution_count": 37, + "execution_count": 23, "id": "47bdf8e5-0bdd-4cac-b57e-2449c75fa178", "metadata": { "tags": [] @@ -1893,588 +1893,588 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('cell',)\n", - "\n", - "cell\n", + "\n", + "cell\n", "\n", "\n", "\n", "('cell', 'cytoplasm')\n", - "\n", - "cytoplasm\n", + "\n", + "cytoplasm\n", "\n", "\n", "\n", "('cell',)->('cell', 'cytoplasm')\n", - "\n", + "\n", "\n", "\n", "\n", "('cell', 'nucleus')\n", - "\n", - "nucleus\n", + "\n", + "nucleus\n", "\n", "\n", "\n", "('cell',)->('cell', 'nucleus')\n", - "\n", + "\n", "\n", "\n", "\n", "('cell', 'cytoplasm', 'secretory<br/>organelles')\n", - "\n", - "secretory\n", - "organelles\n", + "\n", + "secretory\n", + "organelles\n", "\n", "\n", "\n", "('cell', 'cytoplasm')->('cell', 'cytoplasm', 'secretory<br/>organelles')\n", - "\n", + "\n", "\n", "\n", "\n", "('cell', 'cytoplasm', 'cytoplasmic<br/>organelles')\n", - "\n", - "cytoplasmic\n", - "organelles\n", + "\n", + "cytoplasmic\n", + "organelles\n", "\n", "\n", "\n", "('cell', 'cytoplasm')->('cell', 'cytoplasm', 'cytoplasmic<br/>organelles')\n", - "\n", + "\n", "\n", "\n", "\n", "('cell', 'cytoplasm', 'transcriptional<br/>regulation<br/>complex<br/>family')\n", - "\n", - "transcriptional\n", - "regulation\n", - "complex\n", - "family\n", + "\n", + "transcriptional\n", + "regulation\n", + "complex\n", + "family\n", "\n", "\n", "\n", "('cell', 'cytoplasm')->('cell', 'cytoplasm', 'transcriptional<br/>regulation<br/>complex<br/>family')\n", - "\n", + "\n", "\n", "\n", "\n", "('cell', 'cytoplasm', 'secretory<br/>organelles', 'transmembrane<br/>transport<br/>systems')\n", - "\n", - "transmembrane\n", - "transport\n", - "systems\n", + "\n", + "transmembrane\n", + "transport\n", + "systems\n", "\n", "\n", "\n", "('cell', 'cytoplasm', 'secretory<br/>organelles')->('cell', 'cytoplasm', 'secretory<br/>organelles', 'transmembrane<br/>transport<br/>systems')\n", - "\n", + "\n", "\n", "\n", "\n", "('cell', 'cytoplasm', 'secretory<br/>organelles', 'transmembrane<br/>transport<br/>systems', 'ion<br/>transmembrane<br/>transport<br/>systems')\n", - "\n", - "ion\n", - "transmembrane\n", - "transport\n", - "systems\n", + "\n", + "ion\n", + "transmembrane\n", + "transport\n", + "systems\n", "\n", "\n", "\n", "('cell', 'cytoplasm', 'secretory<br/>organelles', 'transmembrane<br/>transport<br/>systems')->('cell', 'cytoplasm', 'secretory<br/>organelles', 'transmembrane<br/>transport<br/>systems', 'ion<br/>transmembrane<br/>transport<br/>systems')\n", - 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"\n", + "\n", "\n", "\n", "\n", "('cell', 'cytoplasm', 'cytoplasmic<br/>organelles', 'subgroup<br/>of<br/>cytoplasmic<br/>organelles', 'metabolic<br/>organelles', 'mitochondrion')\n", - "\n", - "mitochondrion\n", + "\n", + "mitochondrion\n", "\n", "\n", "\n", "('cell', 'cytoplasm', 'cytoplasmic<br/>organelles', 'subgroup<br/>of<br/>cytoplasmic<br/>organelles', 'metabolic<br/>organelles')->('cell', 'cytoplasm', 'cytoplasmic<br/>organelles', 'subgroup<br/>of<br/>cytoplasmic<br/>organelles', 'metabolic<br/>organelles', 'mitochondrion')\n", - "\n", + "\n", "\n", "\n", "\n", "('cell', 'cytoplasm', 'cytoplasmic<br/>organelles', 'subgroup<br/>of<br/>cytoplasmic<br/>organelles', 'ribonucleoprotein<br/>complex<br/>family', 'RNA<br/>processing<br/>complex<br/>1')\n", - "\n", - "RNA\n", - "processing\n", - "complex\n", - "1\n", + "\n", + "RNA\n", + "processing\n", + "complex\n", + "1\n", "\n", "\n", "\n", "('cell', 'cytoplasm', 'cytoplasmic<br/>organelles', 'subgroup<br/>of<br/>cytoplasmic<br/>organelles', 'ribonucleoprotein<br/>complex<br/>family')->('cell', 'cytoplasm', 'cytoplasmic<br/>organelles', 'subgroup<br/>of<br/>cytoplasmic<br/>organelles', 'ribonucleoprotein<br/>complex<br/>family', 'RNA<br/>processing<br/>complex<br/>1')\n", - 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"" + "" ] }, - "execution_count": 37, + "execution_count": 23, "metadata": {}, "output_type": "execute_result" } @@ -2575,7 +2575,7 @@ }, { "cell_type": "code", - "execution_count": 45, + "execution_count": 25, "id": "5a76608a-fff0-4005-9f32-c02afef39d9e", "metadata": { "tags": [] @@ -2587,774 +2587,774 @@ "\n", "\n", - "\n", "\n", - "\n", - "\n", + "\n", + "\n", "bigraph\n", - "\n", + "\n", "\n", "\n", "('cell',)\n", - "\n", - "cell\n", + "\n", + "cell\n", "\n", "\n", "\n", "('cell', 'cytoplasm')\n", - "\n", - "cytoplasm\n", + "\n", + "cytoplasm\n", "\n", "\n", "\n", "('cell',)->('cell', 'cytoplasm')\n", - "\n", + "\n", "\n", "\n", "\n", "('cell', 'nucleus')\n", - "\n", - "nucleus\n", + "\n", + "nucleus\n", "\n", "\n", "\n", "('cell',)->('cell', 'nucleus')\n", - "\n", + "\n", "\n", "\n", "\n", "('cell', 'transcription')\n", - "\n", - "transcription\n", + "\n", + "transcription\n", "\n", "\n", "\n", "\n", "('cell', 'translation')\n", - "\n", - "translation\n", + "\n", + "translation\n", "\n", "\n", "\n", "\n", "('cell', 'metabolism')\n", - 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"execution_count": 60, + "execution_count": 26, "id": "fe3008ad-498e-449f-8521-6ea29fd903f1", "metadata": { "tags": [] }, "outputs": [ { - "data": { - "image/svg+xml": [ - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "bigraph\n", - "\n", - "\n", - "\n", - "('hypothesized<br/>mechanism',)\n", - "\n", - "hypothesized\n", - "mechanism\n", - "\n", - "\n", - "\n", - "\n", - "('hypothesized<br/>mechanism', '1')->('hypothesized<br/>mechanism',)\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "('hypothesized<br/>mechanism', '2')->('hypothesized<br/>mechanism',)\n", - "\n", - "\n", - "\n", - "\n", - "\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 60, - "metadata": {}, - "output_type": "execute_result" + "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" + ] } ], "source": [ @@ -3587,222 +3549,12 @@ }, { "cell_type": "code", - "execution_count": 26, + "execution_count": null, "id": "b39417ce-d9a1-4985-abce-ce22df816897", "metadata": { "tags": [] }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Writing out/cell\n" - ] - }, - { - "data": { - "image/svg+xml": [ - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "bigraph\n", - "\n", - "\n", - "\n", - "('cell',)\n", - "\n", - "cell\n", - "\n", - "\n", - "\n", - "('cell', 'membrane')\n", - "\n", - "membrane\n", - "\n", - "\n", - "\n", - "('cell',)->('cell', 'membrane')\n", - "\n", - "\n", - "\n", - "\n", - "('cell', 'cytoplasm')\n", - "\n", - "cytoplasm\n", - "\n", - "\n", - "\n", - "('cell',)->('cell', 'cytoplasm')\n", - "\n", - "\n", - "\n", - "\n", - "('cell', 'nucleoid')\n", - "\n", - "nucleoid\n", - "\n", - "\n", - "\n", - "('cell',)->('cell', 'nucleoid')\n", - "\n", - "\n", - "\n", - "\n", - "('cell', 'membrane', 'transporters')\n", - "\n", - "transporters\n", - "\n", - "\n", - "\n", - "('cell', 'membrane')->('cell', 'membrane', 'transporters')\n", - "\n", - "\n", - "\n", - "\n", - "('cell', 'membrane', 'lipids')\n", - "\n", - "lipids\n", - "\n", - "\n", - "\n", - "('cell', 'membrane')->('cell', 'membrane', 'lipids')\n", - "\n", - "\n", - "\n", - "\n", - "('cell', 'membrane', 'transmembrane transport')\n", - "\n", - "transmembrane transport\n", - "\n", - "\n", - "\n", - "\n", - "('cell', 'membrane', 'transporters')->('cell', 'membrane', 'transmembrane transport')\n", - "\n", - "\n", - "transporters\n", - "\n", - "\n", - "\n", - "('cell', 'cytoplasm', 'metabolites')\n", - "\n", - "metabolites\n", - "\n", - "\n", - "\n", - "('cell', 'cytoplasm')->('cell', 'cytoplasm', 'metabolites')\n", - "\n", - "\n", - "\n", - "\n", - "('cell', 'cytoplasm', 'ribosomal complexes')\n", - "\n", - "ribosomal complexes\n", - "\n", - "\n", - "\n", - "('cell', 'cytoplasm')->('cell', 'cytoplasm', 'ribosomal complexes')\n", - "\n", - "\n", - "\n", - "\n", - "('cell', 'cytoplasm', 'transcript regulation complex')\n", - "\n", - "transcript regulation complex\n", - "\n", - "\n", - "\n", - "('cell', 'cytoplasm')->('cell', 'cytoplasm', 'transcript regulation complex')\n", - "\n", - "\n", - "\n", - "\n", - "('cell', 'cytoplasm', 'translation')\n", - "\n", - "translation\n", - "\n", - "\n", - "\n", - "\n", - "('cell', 'cytoplasm', 'metabolites')->('cell', 'membrane', 'transmembrane transport')\n", - "\n", - "\n", - "internal\n", - "\n", - "\n", - "\n", - "('cell', 'cytoplasm', 'ribosomal complexes')->('cell', 'cytoplasm', 'translation')\n", - "\n", - "\n", - "p1\n", - "\n", - "\n", - "\n", - "('cell', 'cytoplasm', 'transcript regulation complex', 'transcripts')\n", - "\n", - "transcripts\n", - "\n", - "\n", - "\n", - "('cell', 'cytoplasm', 'transcript regulation complex')->('cell', 'cytoplasm', 'transcript regulation complex', 'transcripts')\n", - "\n", - "\n", - "\n", - "\n", - "('cell', 'cytoplasm', 'transcript regulation complex', 'transcripts')->('cell', 'cytoplasm', 'translation')\n", - "\n", - "\n", - "p2\n", - "\n", - "\n", - "\n", - "('cell', 'nucleoid', 'chromosome')\n", - "\n", - "chromosome\n", - "\n", - "\n", - "\n", - "('cell', 'nucleoid')->('cell', 'nucleoid', 'chromosome')\n", - "\n", - "\n", - "\n", - "\n", - "('cell', 'nucleoid', 'chromosome', 'genes')\n", - "\n", - "genes\n", - "\n", - "\n", - "\n", - "('cell', 'nucleoid', 'chromosome')->('cell', 'nucleoid', 'chromosome', 'genes')\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "('cell', 'membrane', 'transmembrane transport', 'external')->('cell', 'membrane', 'transmembrane transport')\n", - "\n", - "\n", - "external\n", - "\n", - "\n", - "\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 26, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "cell_struct_func = {\n", " 'cell': {\n", @@ -3866,20 +3618,12 @@ }, { "cell_type": "code", - "execution_count": 27, + "execution_count": null, "id": "16960d1b-6e35-421e-bb7d-3efe5052e4fc", "metadata": { "tags": [] }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Writing out/ecoli\n" - ] - } - ], + "outputs": [], "source": [ "ecoli = { \n", " 'chromosome-structure': { \n", @@ -4077,7 +3821,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.13" + "version": "3.9.6" } }, "nbformat": 4,