From 0c58d4194d462315663e78f4c7eb76587b168903 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Sun, 12 May 2024 09:45:29 +0000 Subject: [PATCH] Update docs for branch main --- .../base.ipynb | 883 ++++++ .../base.ipynb | 1806 +++++++++++ ...5a69a6aefb567140fed800290f7e312bf398ca.svg | 2802 +++++++++++++++++ ...c4dc0c510c4e41d0fe34fa9dfae3bc662b2bb2.svg | 131 + ...cfd857934e3a7c2731577a6acf2f279d44b8b3.svg | 170 + ...ecadb3e0ff5a4bd81ae225a115f4bf9e56ae53.svg | 210 ++ ...7f6b4d57dbccbd0120e59abc2f30407c7dfed9.svg | 210 ++ ...e59f6202431263bc98d2b38ab5d3e0881995b8.svg | 2802 +++++++++++++++++ ...3dfc3ddab9d41d7f88310804f0f80d84116ddc.svg | 58 + ...4a2f8125974cc83a7f80508687554b10f489ef.svg | 339 ++ ...325f80b19a3d0487cc439bf3c02c3ed740686c.svg | 2802 +++++++++++++++++ ...31bc12efabe34882770aed1ced1bdbd70dde75.svg | 2802 +++++++++++++++++ ...c6e1d4f2ee9377e328cb7bd41292044252c803.svg | 125 + ...5a69a6aefb567140fed800290f7e312bf398ca.svg | 2802 +++++++++++++++++ ...c4dc0c510c4e41d0fe34fa9dfae3bc662b2bb2.svg | 131 + ...cfd857934e3a7c2731577a6acf2f279d44b8b3.svg | 170 + ...ecadb3e0ff5a4bd81ae225a115f4bf9e56ae53.svg | 210 ++ ...7f6b4d57dbccbd0120e59abc2f30407c7dfed9.svg | 210 ++ ...e59f6202431263bc98d2b38ab5d3e0881995b8.svg | 2802 +++++++++++++++++ ...3dfc3ddab9d41d7f88310804f0f80d84116ddc.svg | 58 + ...4a2f8125974cc83a7f80508687554b10f489ef.svg | 339 ++ ...325f80b19a3d0487cc439bf3c02c3ed740686c.svg | 2802 +++++++++++++++++ ...31bc12efabe34882770aed1ced1bdbd70dde75.svg | 2802 +++++++++++++++++ ...c6e1d4f2ee9377e328cb7bd41292044252c803.svg | 125 + ...5a69a6aefb567140fed800290f7e312bf398ca.svg | 2802 +++++++++++++++++ ...c4dc0c510c4e41d0fe34fa9dfae3bc662b2bb2.svg | 131 + ...cfd857934e3a7c2731577a6acf2f279d44b8b3.svg | 170 + ...ecadb3e0ff5a4bd81ae225a115f4bf9e56ae53.svg | 210 ++ ...7f6b4d57dbccbd0120e59abc2f30407c7dfed9.svg | 210 ++ ...e59f6202431263bc98d2b38ab5d3e0881995b8.svg | 2802 +++++++++++++++++ ...3dfc3ddab9d41d7f88310804f0f80d84116ddc.svg | 58 + ...4a2f8125974cc83a7f80508687554b10f489ef.svg | 339 ++ ...325f80b19a3d0487cc439bf3c02c3ed740686c.svg | 2802 +++++++++++++++++ ...31bc12efabe34882770aed1ced1bdbd70dde75.svg | 2802 +++++++++++++++++ ...c6e1d4f2ee9377e328cb7bd41292044252c803.svg | 125 + 35 files changed, 40042 insertions(+) create mode 100644 docs/_build/html/.jupyter_cache/executed/89154b67f99973a42898921123bb5bc5/base.ipynb create mode 100644 docs/_build/html/.jupyter_cache/executed/a1c94afe4498dab82a8d54f8976a4430/base.ipynb create mode 100644 docs/_build/html/jupyter_execute/2a38f2d0d5b8c60309d55a245b5a69a6aefb567140fed800290f7e312bf398ca.svg create mode 100644 docs/_build/html/jupyter_execute/2c64097f5da14ea3c688e1a93dc4dc0c510c4e41d0fe34fa9dfae3bc662b2bb2.svg create mode 100644 docs/_build/html/jupyter_execute/443cf7bd4db35676d58fdb902fcfd857934e3a7c2731577a6acf2f279d44b8b3.svg create mode 100644 docs/_build/html/jupyter_execute/5b572f011bdaf826106697ae16ecadb3e0ff5a4bd81ae225a115f4bf9e56ae53.svg create mode 100644 docs/_build/html/jupyter_execute/7d51afb160f63cb72df323a55c7f6b4d57dbccbd0120e59abc2f30407c7dfed9.svg create mode 100644 docs/_build/html/jupyter_execute/868a4c4ff4d416d677b3e548cce59f6202431263bc98d2b38ab5d3e0881995b8.svg create mode 100644 docs/_build/html/jupyter_execute/a18af31210c20b9afdc10fc3443dfc3ddab9d41d7f88310804f0f80d84116ddc.svg create mode 100644 docs/_build/html/jupyter_execute/a611717058041567090a4563f14a2f8125974cc83a7f80508687554b10f489ef.svg create mode 100644 docs/_build/html/jupyter_execute/aa13e66ecb35e387e408e46e79325f80b19a3d0487cc439bf3c02c3ed740686c.svg create mode 100644 docs/_build/html/jupyter_execute/cec93c0a71c17db5062ee6115e31bc12efabe34882770aed1ced1bdbd70dde75.svg create mode 100644 docs/_build/html/jupyter_execute/d2fa409fe9ed28e8a79df8ed63c6e1d4f2ee9377e328cb7bd41292044252c803.svg create mode 100644 docs/_build/html/main/_images/2a38f2d0d5b8c60309d55a245b5a69a6aefb567140fed800290f7e312bf398ca.svg create mode 100644 docs/_build/html/main/_images/2c64097f5da14ea3c688e1a93dc4dc0c510c4e41d0fe34fa9dfae3bc662b2bb2.svg create mode 100644 docs/_build/html/main/_images/443cf7bd4db35676d58fdb902fcfd857934e3a7c2731577a6acf2f279d44b8b3.svg create mode 100644 docs/_build/html/main/_images/5b572f011bdaf826106697ae16ecadb3e0ff5a4bd81ae225a115f4bf9e56ae53.svg create mode 100644 docs/_build/html/main/_images/7d51afb160f63cb72df323a55c7f6b4d57dbccbd0120e59abc2f30407c7dfed9.svg create mode 100644 docs/_build/html/main/_images/868a4c4ff4d416d677b3e548cce59f6202431263bc98d2b38ab5d3e0881995b8.svg create mode 100644 docs/_build/html/main/_images/a18af31210c20b9afdc10fc3443dfc3ddab9d41d7f88310804f0f80d84116ddc.svg create mode 100644 docs/_build/html/main/_images/a611717058041567090a4563f14a2f8125974cc83a7f80508687554b10f489ef.svg create mode 100644 docs/_build/html/main/_images/aa13e66ecb35e387e408e46e79325f80b19a3d0487cc439bf3c02c3ed740686c.svg create mode 100644 docs/_build/html/main/_images/cec93c0a71c17db5062ee6115e31bc12efabe34882770aed1ced1bdbd70dde75.svg create mode 100644 docs/_build/html/main/_images/d2fa409fe9ed28e8a79df8ed63c6e1d4f2ee9377e328cb7bd41292044252c803.svg create mode 100644 main/_images/2a38f2d0d5b8c60309d55a245b5a69a6aefb567140fed800290f7e312bf398ca.svg create mode 100644 main/_images/2c64097f5da14ea3c688e1a93dc4dc0c510c4e41d0fe34fa9dfae3bc662b2bb2.svg create mode 100644 main/_images/443cf7bd4db35676d58fdb902fcfd857934e3a7c2731577a6acf2f279d44b8b3.svg create mode 100644 main/_images/5b572f011bdaf826106697ae16ecadb3e0ff5a4bd81ae225a115f4bf9e56ae53.svg create mode 100644 main/_images/7d51afb160f63cb72df323a55c7f6b4d57dbccbd0120e59abc2f30407c7dfed9.svg create mode 100644 main/_images/868a4c4ff4d416d677b3e548cce59f6202431263bc98d2b38ab5d3e0881995b8.svg create mode 100644 main/_images/a18af31210c20b9afdc10fc3443dfc3ddab9d41d7f88310804f0f80d84116ddc.svg create mode 100644 main/_images/a611717058041567090a4563f14a2f8125974cc83a7f80508687554b10f489ef.svg create mode 100644 main/_images/aa13e66ecb35e387e408e46e79325f80b19a3d0487cc439bf3c02c3ed740686c.svg create mode 100644 main/_images/cec93c0a71c17db5062ee6115e31bc12efabe34882770aed1ced1bdbd70dde75.svg create mode 100644 main/_images/d2fa409fe9ed28e8a79df8ed63c6e1d4f2ee9377e328cb7bd41292044252c803.svg diff --git a/docs/_build/html/.jupyter_cache/executed/89154b67f99973a42898921123bb5bc5/base.ipynb b/docs/_build/html/.jupyter_cache/executed/89154b67f99973a42898921123bb5bc5/base.ipynb new file mode 100644 index 00000000..14783941 --- /dev/null +++ b/docs/_build/html/.jupyter_cache/executed/89154b67f99973a42898921123bb5bc5/base.ipynb @@ -0,0 +1,883 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "a1684e94", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [], + "text/plain": [] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
\n", + " \n", + " \n", + " \n", + " \n", + "
Installed version:v1.0.0.dev0 (up to date)
Available backends:CVXPY v1.5.1, PICOS v2.4.17
Default backend (corneto.opt):CVXPY
Installed solvers:CLARABEL, CVXOPT, ECOS, ECOS_BB, GLPK, GLPK_MI, OSQP, SCIP, SCIPY, SCS
Graphviz version:v0.20.3
Repository:https://github.com/saezlab/corneto
\n", + "
" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "import corneto as cn\n", + "\n", + "cn.info()" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "4512c595", + "metadata": {}, + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "%3\n", + "\n", + "\n", + "\n", + "1\n", + "\n", + "1\n", + "\n", + "\n", + "\n", + "2\n", + "\n", + "2\n", + "\n", + "\n", + "\n", + "1->2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "3\n", + "\n", + "3\n", + "\n", + "\n", + "\n", + "1->3\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "2->3\n", + "\n", + "\n", + "\n", + "\n", + "\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "G = cn.Graph()\n", + "G.add_edge(1, 2)\n", + "G.add_edge(2, 3)\n", + "G.add_edge(1, 3)\n", + "G.plot()" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "ad64bcb7", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "3\n" + ] + }, + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "%3\n", + "\n", + "\n", + "\n", + "1\n", + "\n", + "1\n", + "\n", + "\n", + "\n", + "2\n", + "\n", + "2\n", + "\n", + "\n", + "\n", + "1->2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "3\n", + "\n", + "3\n", + "\n", + "\n", + "\n", + "1->3\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "2->3\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "4\n", + "\n", + "4\n", + "\n", + "\n", + "\n", + "3->4\n", + "\n", + "\n", + "\n", + "\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "idx = G.add_edge(3, 4, cn.EdgeType.UNDIRECTED)\n", + "print(idx)\n", + "G.plot()" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "d87919e0", + "metadata": {}, + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "%3\n", + "\n", + "\n", + "\n", + "1\n", + "\n", + "1\n", + "\n", + "\n", + "\n", + "2\n", + "\n", + "2\n", + "\n", + "\n", + "\n", + "1->2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "3\n", + "\n", + "3\n", + "\n", + "\n", + "\n", + "1->3\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "2->3\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "4\n", + "\n", + "4\n", + "\n", + "\n", + "\n", + "3->4\n", + "\n", + "\n", + "\n", + "\n", + "3->4\n", + "\n", + "\n", + "\n", + "\n", + "3->4\n", + "\n", + "\n", + "\n", + "\n", + "\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "G.add_edge(3, 4, cn.EdgeType.UNDIRECTED)\n", + "G.add_edge(3, 4)\n", + "G.plot()" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "cfc44e12", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'__edge_type': 'directed',\n", + " 'weight': 0.5,\n", + " 'label': 'E(3->4)',\n", + " '__source_attr': {3: {'__value': {}}},\n", + " '__target_attr': {4: {'__value': {}}}}" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "idx = G.add_edge(3, 4, weight=0.5, label=\"E(3->4)\")\n", + "attr = G.get_attr_edge(idx)\n", + "attr" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "990951f4", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "0.5" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "attr.weight" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "fe14480b", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'__edge_type': 'directed',\n", + " 'weight': 0.5,\n", + " 'label': 'E(3->4)',\n", + " '__source_attr': {3: {'__value': {}}},\n", + " '__target_attr': {4: {'__value': {}}}}" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "G.get_attr_edge(idx)" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "215eebcf", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[6]" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "list(G.get_edges_by_attr(\"label\", \"E(3->4)\"))" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "58cc1998", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(frozenset({3}), frozenset({4}))" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "edge = G.get_edge(idx)\n", + "edge" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "281142cf", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{3: {'__value': {}}}" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "attr = G.get_attr_edge(idx)\n", + "attr.get_attr(cn.Attr.SOURCE_ATTR)" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "9c1df45f", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{3: {'__value': {}}}" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "attr.__source_attr" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "d5b8730c", + "metadata": {}, + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "%3\n", + "\n", + "\n", + "\n", + "A\n", + "\n", + "A\n", + "\n", + "\n", + "\n", + "B\n", + "\n", + "B\n", + "\n", + "\n", + "\n", + "A->B\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "C\n", + "\n", + "C\n", + "\n", + "\n", + "\n", + "A->C\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "sif_graph = cn.Graph.from_sif_tuples([(\"A\", 1, \"B\"), (\"A\", -1, \"C\")])\n", + "sif_graph.plot()" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "558c4a7e", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[{'__edge_type': 'directed',\n", + " 'interaction': 1,\n", + " '__source_attr': {'A': {'__value': {}}},\n", + " '__target_attr': {'B': {'__value': {}}}},\n", + " {'__edge_type': 'directed',\n", + " 'interaction': -1,\n", + " '__source_attr': {'A': {'__value': {}}},\n", + " '__target_attr': {'C': {'__value': {}}}}]" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "sif_graph.get_attr_edges()" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "id": "c3310b77", + "metadata": {}, + "outputs": [], + "source": [ + "# cn.Graph.from_sif_file()" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "d29ddc6e", + "metadata": {}, + "outputs": [], + "source": [ + "G.save(\"my_graph\")" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "id": "035d04d4", + "metadata": {}, + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "%3\n", + "\n", + "\n", + "\n", + "1\n", + "\n", + "1\n", + "\n", + "\n", + "\n", + "2\n", + "\n", + "2\n", + "\n", + "\n", + "\n", + "1->2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "3\n", + "\n", + "3\n", + "\n", + "\n", + "\n", + "1->3\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "2->3\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "4\n", + "\n", + "4\n", + "\n", + "\n", + "\n", + "3->4\n", + "\n", + "\n", + "\n", + "\n", + "3->4\n", + "\n", + "\n", + "\n", + "\n", + "3->4\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "3->4\n", + "\n", + "\n", + "\n", + "\n", + "\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "G_c = cn.Graph.load(\"my_graph.pkl.xz\")\n", + "G_c.plot()" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "id": "20ebd58d", + "metadata": {}, + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "%3\n", + "\n", + "\n", + "\n", + "A\n", + "\n", + "A\n", + "\n", + "\n", + "\n", + "e_0_center\n", + "\n", + "\n", + "\n", + "\n", + "A->e_0_center\n", + "\n", + "\n", + "\n", + "\n", + "B\n", + "\n", + "B\n", + "\n", + "\n", + "\n", + "B->e_0_center\n", + "\n", + "\n", + "\n", + "\n", + "C\n", + "\n", + "C\n", + "\n", + "\n", + "\n", + "e_4_target\n", + "\n", + "\n", + "\n", + "\n", + "C->e_4_target\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "D\n", + "\n", + "D\n", + "\n", + "\n", + "\n", + "e_1_center\n", + "\n", + "\n", + "\n", + "\n", + "D->e_1_center\n", + "\n", + "\n", + "\n", + "\n", + "e_0_center->C\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "e_0_center->D\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "F\n", + "\n", + "F\n", + "\n", + "\n", + "\n", + "E\n", + "\n", + "E\n", + "\n", + "\n", + "\n", + "e_1_center->F\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "e_1_center->E\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "e_2_source\n", + "\n", + "\n", + "\n", + "\n", + "e_2_source->A\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "e_3_source\n", + "\n", + "\n", + "\n", + "\n", + "e_3_source->B\n", + "\n", + "\n", + "\n", + "\n", + "\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "G = cn.Graph()\n", + "G.add_edge({\"A\", \"B\"}, {\"C\", \"D\"})\n", + "G.add_edge(\"D\", {\"E\", \"F\"})\n", + "G.add_edge((), \"A\")\n", + "G.add_edge((), \"B\")\n", + "G.add_edge(\"C\", ())\n", + "G.plot()" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.9" + }, + "toc": { + "base_numbering": 1, + "nav_menu": {}, + "number_sections": true, + "sideBar": true, + "skip_h1_title": false, + "title_cell": "Table of Contents", + "title_sidebar": "Contents", + "toc_cell": false, + "toc_position": {}, + "toc_section_display": true, + "toc_window_display": false + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} \ No newline at end of file diff --git a/docs/_build/html/.jupyter_cache/executed/a1c94afe4498dab82a8d54f8976a4430/base.ipynb b/docs/_build/html/.jupyter_cache/executed/a1c94afe4498dab82a8d54f8976a4430/base.ipynb new file mode 100644 index 00000000..3db41e54 --- /dev/null +++ b/docs/_build/html/.jupyter_cache/executed/a1c94afe4498dab82a8d54f8976a4430/base.ipynb @@ -0,0 +1,1806 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "a1684e94", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [], + "text/plain": [] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
\n", + " \n", + " \n", + " \n", + " \n", + "
Installed version:v1.0.0.dev0 (up to date)
Available backends:CVXPY v1.5.1, PICOS v2.4.17
Default backend (corneto.opt):CVXPY
Installed solvers:CLARABEL, CVXOPT, ECOS, ECOS_BB, GLPK, GLPK_MI, OSQP, SCIP, SCIPY, SCS
Graphviz version:v0.20.3
Repository:https://github.com/saezlab/corneto
\n", + "
" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "import corneto as cn\n", + "\n", + "cn.info()" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "2a193cb0", + "metadata": {}, + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "%3\n", + "\n", + "\n", + "\n", + "I1\n", + "\n", + "I1\n", + "\n", + "\n", + "\n", + "N1\n", + "\n", + "N1\n", + "\n", + "\n", + "\n", + "I1->N1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "M1\n", + "\n", + "M1\n", + "\n", + "\n", + "\n", + "N1->M1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "M2\n", + "\n", + "M2\n", + "\n", + "\n", + "\n", + "N1->M2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "I2\n", + "\n", + "I2\n", + "\n", + "\n", + "\n", + "N2\n", + "\n", + "N2\n", + "\n", + "\n", + "\n", + "I2->N2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "N2->M1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "N2->M2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "G = cn.Graph.from_sif_tuples(\n", + " [\n", + " (\"I1\", 1, \"N1\"), # I1 activates N1\n", + " (\"N1\", 1, \"M1\"), # N1 activates M1\n", + " (\"N1\", 1, \"M2\"), # N1 activaes M2\n", + " (\"I2\", -1, \"N2\"), # I2 inhibits N2\n", + " (\"N2\", -1, \"M2\"), # N2 inhibits M2\n", + " (\"N2\", -1, \"M1\"), # N2 inhibits M1\n", + " ]\n", + ")\n", + "G.plot()" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "176d8ced", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CORNETO) May 12 09:45:18 AM - INFO : 2/2 inputs mapped to the graph\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CORNETO) May 12 09:45:18 AM - INFO : 2/2 outputs mapped to the graph\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CORNETO) May 12 09:45:18 AM - INFO : Pruning the graph with size: V x E = (6, 6)...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CORNETO) May 12 09:45:18 AM - INFO : Finished. Final size: V x E = (6, 6).\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CORNETO) May 12 09:45:18 AM - INFO : 2/2 inputs after pruning.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CORNETO) May 12 09:45:18 AM - INFO : 2/2 outputs after pruning.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CORNETO) May 12 09:45:18 AM - INFO : Converting into a flow graph...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CORNETO) May 12 09:45:18 AM - INFO : Creating a network flow problem...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CORNETO) May 12 09:45:18 AM - INFO : Preprocess completed.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "===============================================================================\n", + " CVXPY \n", + " v1.5.1 \n", + "===============================================================================\n", + "(CVXPY) May 12 09:45:18 AM: Your problem has 86 variables, 197 constraints, and 0 parameters.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CVXPY) May 12 09:45:18 AM: It is compliant with the following grammars: DCP, DQCP\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CVXPY) May 12 09:45:18 AM: (If you need to solve this problem multiple times, but with different data, consider using parameters.)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CVXPY) May 12 09:45:18 AM: CVXPY will first compile your problem; then, it will invoke a numerical solver to obtain a solution.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CVXPY) May 12 09:45:18 AM: Your problem is compiled with the CPP canonicalization backend.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "-------------------------------------------------------------------------------\n", + " Compilation \n", + "-------------------------------------------------------------------------------\n", + "(CVXPY) May 12 09:45:18 AM: Compiling problem (target solver=SCIP).\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CVXPY) May 12 09:45:18 AM: Reduction chain: Dcp2Cone -> CvxAttr2Constr -> ConeMatrixStuffing -> SCIP\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CVXPY) May 12 09:45:18 AM: Applying reduction Dcp2Cone\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CVXPY) May 12 09:45:18 AM: Applying reduction CvxAttr2Constr\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CVXPY) May 12 09:45:18 AM: Applying reduction ConeMatrixStuffing\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CVXPY) May 12 09:45:18 AM: Applying reduction SCIP\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CVXPY) May 12 09:45:18 AM: Finished problem compilation (took 3.057e-02 seconds).\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "-------------------------------------------------------------------------------\n", + " Numerical solver \n", + "-------------------------------------------------------------------------------\n", + "(CVXPY) May 12 09:45:18 AM: Invoking solver SCIP to obtain a solution.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "presolving:\n", + "(round 1, fast) 36 del vars, 95 del conss, 0 add conss, 48 chg bounds, 1 chg sides, 23 chg coeffs, 0 upgd conss, 0 impls, 28 clqs\n", + "(round 2, fast) 54 del vars, 129 del conss, 0 add conss, 52 chg bounds, 9 chg sides, 31 chg coeffs, 0 upgd conss, 0 impls, 20 clqs\n", + "(round 3, fast) 63 del vars, 145 del conss, 0 add conss, 52 chg bounds, 11 chg sides, 33 chg coeffs, 0 upgd conss, 0 impls, 18 clqs\n", + "(round 4, fast) 65 del vars, 147 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 0 upgd conss, 0 impls, 18 clqs\n", + "(round 5, fast) 67 del vars, 151 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 0 upgd conss, 0 impls, 18 clqs\n", + "(round 6, exhaustive) 67 del vars, 151 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 40 upgd conss, 0 impls, 18 clqs\n", + " (0.0s) probing cycle finished: starting next cycle\n", + "(round 7, exhaustive) 69 del vars, 151 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 40 upgd conss, 28 impls, 46 clqs\n", + "(round 8, medium) 69 del vars, 155 del conss, 0 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 40 upgd conss, 28 impls, 46 clqs\n", + " (0.0s) probing cycle finished: starting next cycle\n", + " (0.0s) symmetry computation started: requiring (bin +, int +, cont +), (fixed: bin -, int -, cont -)\n", + " (0.0s) symmetry computation finished: 2 generators found (max: 1500, log10 of symmetry group size: 0.6) (symcode time: 0.00)\n", + "dynamic symmetry handling statistics:\n", + " orbitopal reduction: no components\n", + " orbital reduction: no components\n", + " lexicographic reduction: no permutations\n", + "handled 1 out of 1 symmetry components\n", + "(round 9, exhaustive) 69 del vars, 155 del conss, 3 add conss, 52 chg bounds, 15 chg sides, 37 chg coeffs, 40 upgd conss, 28 impls, 46 clqs\n", + "presolving (10 rounds: 10 fast, 5 medium, 4 exhaustive):\n", + " 69 deleted vars, 155 deleted constraints, 3 added constraints, 52 tightened bounds, 0 added holes, 15 changed sides, 37 changed coefficients\n", + " 28 implications, 46 cliques\n", + "presolved problem has 27 variables (19 bin, 0 int, 0 impl, 8 cont) and 45 constraints\n", + " 16 constraints of type \n", + " 18 constraints of type \n", + " 9 constraints of type \n", + " 2 constraints of type \n", + "transformed objective value is always integral (scale: 0.1)\n", + "Presolving Time: 0.00\n", + "\n", + " time | node | left |LP iter|LP it/n|mem/heur|mdpt |vars |cons |rows |cuts |sepa|confs|strbr| dualbound | primalbound | gap | compl. \n", + "p 0.0s| 1 | 0 | 0 | - | clique| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 | 1.000000e-01 | Inf | unknown\n", + "p 0.0s| 1 | 0 | 0 | - | locks| 0 | 27 | 45 | 42 | 0 | 0 | 0 | 0 |-3.500000e+00 |-6.000000e-01 | 483.33%| unknown\n", + "p 0.0s| 1 | 0 | 0 | - | vbounds| 0 | 27 | 46 | 42 | 0 | 0 | 1 | 0 |-3.500000e+00 |-1.600000e+00 | 118.75%| unknown\n", + "p 0.0s| 1 | 0 | 0 | - | vbounds| 0 | 27 | 48 | 42 | 0 | 0 | 3 | 0 |-3.500000e+00 |-3.200000e+00 | 9.37%| unknown\n", + " 0.0s| 1 | 0 | 23 | - | 1784k | 0 | 27 | 49 | 42 | 0 | 0 | 8 | 0 |-3.300000e+00 |-3.200000e+00 | 3.13%| unknown\n", + "r 0.0s| 1 | 0 | 23 | - |rounding| 0 | 27 | 49 | 39 | 0 | 0 | 8 | 0 |-3.300000e+00 |-3.300000e+00 | 0.00%| unknown\n", + " 0.0s| 1 | 0 | 23 | - | 1784k | 0 | 27 | 49 | 39 | 0 | 0 | 8 | 0 |-3.300000e+00 |-3.300000e+00 | 0.00%| unknown\n", + " 0.0s| 1 | 0 | 23 | - | 1784k | 0 | 27 | 49 | 39 | 0 | 0 | 8 | 0 |-3.300000e+00 |-3.300000e+00 | 0.00%| unknown\n", + "\n", + "SCIP Status : problem is solved [optimal solution found]\n", + "Solving Time (sec) : 0.01\n", + "Solving Nodes : 1\n", + "Primal Bound : -3.30000000000000e+00 (5 solutions)\n", + "Dual Bound : -3.30000000000000e+00\n", + "Gap : 0.00 %\n", + "-------------------------------------------------------------------------------\n", + " Summary \n", + "-------------------------------------------------------------------------------\n", + "(CVXPY) May 12 09:45:18 AM: Problem status: optimal\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CVXPY) May 12 09:45:18 AM: Optimal value: 7.000e-01\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CVXPY) May 12 09:45:18 AM: Compilation took 3.057e-02 seconds\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CVXPY) May 12 09:45:18 AM: Solver (including time spent in interface) took 2.116e-02 seconds\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(CORNETO) May 12 09:45:18 AM - INFO : Finished in 0.07 s.\n" + ] + } + ], + "source": [ + "from corneto.methods import runVanillaCarnival\n", + "\n", + "# These are the measurements (e.g. TF activity from Decoupler).\n", + "# Positive values correspond to up-regulation and negative values\n", + "# with down-regulation. The bigger the absolute value is,\n", + "# the bigger the importance is\n", + "measurements = {\"M1\": 1, \"M2\": 1}\n", + "\n", + "# Perturbations are the upstream nodes were the signal originates on,\n", + "# for example, ligands or receptors.\n", + "perturbations = {\"I1\": 1, \"I2\": 1}\n", + "\n", + "# We run the `standard` carnival problem. This interface is similar\n", + "# to the old R function https://saezlab.github.io/CARNIVAL/reference/runVanillaCarnival.html\n", + "P, Gf = runVanillaCarnival(perturbations, measurements, G, betaWeight=0.1)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "8b03e08d", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([0.])" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# We can check the error. Values larger than 0 indicate that\n", + "# some TF or measurement was not selected.\n", + "P.objectives[0].value" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "00d86874", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'_flow': Variable((14,), _flow),\n", + " '_flow_ipos': Variable((14,), _flow_ipos, boolean=True),\n", + " 'species_inhibited_c0': Variable((10,), species_inhibited_c0, boolean=True),\n", + " 'reaction_sends_inhibition_c0': Variable((14,), reaction_sends_inhibition_c0, boolean=True),\n", + " 'species_activated_c0': Variable((10,), species_activated_c0, boolean=True),\n", + " 'reaction_sends_activation_c0': Variable((14,), reaction_sends_activation_c0, boolean=True),\n", + " 'dag_layer_position_c0': Variable((10,), dag_layer_position_c0),\n", + " 'flow': Variable((14,), _flow),\n", + " 'edge_values_c0': Expression(AFFINE, UNKNOWN, (14,)),\n", + " 'vertex_values_c0': Expression(AFFINE, UNKNOWN, (10,))}" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Variables that are defined by CARNIVAL\n", + "P.expr" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "a1b0e7ec", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Warning: node '_pert_c0', graph '%3' size too small for label\n", + "Warning: node '_meas_c0', graph '%3' size too small for label\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Warning: node '_pert_c0', graph '%3' size too small for label\n", + "Warning: node '_meas_c0', graph '%3' size too small for label\n" + ] + }, + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "%3\n", + "\n", + "\n", + "\n", + "I1\n", + "\n", + "I1\n", + "\n", + "\n", + "\n", + "N1\n", + "\n", + "N1\n", + "\n", + "\n", + "\n", + "I1->N1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "M1\n", + "\n", + "M1\n", + "\n", + "\n", + "\n", + "N1->M1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "M2\n", + "\n", + "M2\n", + "\n", + "\n", + "\n", + "N1->M2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "_meas_c0\n", + "\n", + "_meas_c0\n", + "\n", + "\n", + "\n", + "M1->_meas_c0\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "M2->_meas_c0\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "I2\n", + "\n", + "I2\n", + "\n", + "\n", + "\n", + "N2\n", + "\n", + "N2\n", + "\n", + "\n", + "\n", + "I2->N2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "N2->M1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "N2->M2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "_s\n", + "\n", + "_s\n", + "\n", + "\n", + "\n", + "_pert_c0\n", + "\n", + "_pert_c0\n", + "\n", + "\n", + "\n", + "_s->_pert_c0\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "_pert_c0->I1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "_pert_c0->I2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "_t\n", + "\n", + "_t\n", + "\n", + "\n", + "\n", + "_meas_c0->_t\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "e_13_target\n", + "\n", + "\n", + "\n", + "\n", + "_t->e_13_target\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "e_12_source\n", + "\n", + "\n", + "\n", + "\n", + "e_12_source->_s\n", + "\n", + "\n", + "\n", + "\n", + "\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "Gf.plot_values(vertex_values=P.expr.vertex_values_c0, edge_values=P.expr.edge_values_c0)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "c8be26ab", + "metadata": {}, + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "%3\n", + "\n", + "\n", + "\n", + "I1\n", + "\n", + "I1\n", + "\n", + "\n", + "\n", + "N1\n", + "\n", + "N1\n", + "\n", + "\n", + "\n", + "I1->N1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "M1\n", + "\n", + "M1\n", + "\n", + "\n", + "\n", + "N1->M1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "M2\n", + "\n", + "M2\n", + "\n", + "\n", + "\n", + "N1->M2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "I2\n", + "\n", + "I2\n", + "\n", + "\n", + "\n", + "N2\n", + "\n", + "N2\n", + "\n", + "\n", + "\n", + "I2->N2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "N2->M1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "N2->M2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "G.plot(\n", + " custom_edge_attr=cn.pl.edge_style(P, edge_var=\"edge_values_c0\"),\n", + " custom_vertex_attr=cn.pl.vertex_style(P, Gf, vertex_var=\"vertex_values_c0\"),\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "a7b0d803", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
Vvalue
0M21.0
1I21.0
2I11.0
3N10.0
4M11.0
5N2-1.0
6_s1.0
7_pert_c01.0
8_meas_c00.0
9_t0.0
\n", + "
" + ], + "text/plain": [ + " V value\n", + "0 M2 1.0\n", + "1 I2 1.0\n", + "2 I1 1.0\n", + "3 N1 0.0\n", + "4 M1 1.0\n", + "5 N2 -1.0\n", + "6 _s 1.0\n", + "7 _pert_c0 1.0\n", + "8 _meas_c0 0.0\n", + "9 _t 0.0" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import pandas as pd\n", + "\n", + "from corneto.methods.carnival import get_result, get_selected_edges\n", + "\n", + "V, E = get_result(P, Gf)\n", + "pd.DataFrame(V)" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "7ff44c27", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
Evalue
0((I1), (N1))0.0
1((N1), (M1))0.0
2((N1), (M2))0.0
3((I2), (N2))-1.0
4((N2), (M2))1.0
5((N2), (M1))1.0
6((_s), (_pert_c0))1.0
7((_pert_c0), (I1))1.0
8((_pert_c0), (I2))1.0
9((M1), (_meas_c0))1.0
10((M2), (_meas_c0))1.0
11((_meas_c0), (_t))0.0
12((), (_s))1.0
13((_t), ())0.0
\n", + "
" + ], + "text/plain": [ + " E value\n", + "0 ((I1), (N1)) 0.0\n", + "1 ((N1), (M1)) 0.0\n", + "2 ((N1), (M2)) 0.0\n", + "3 ((I2), (N2)) -1.0\n", + "4 ((N2), (M2)) 1.0\n", + "5 ((N2), (M1)) 1.0\n", + "6 ((_s), (_pert_c0)) 1.0\n", + "7 ((_pert_c0), (I1)) 1.0\n", + "8 ((_pert_c0), (I2)) 1.0\n", + "9 ((M1), (_meas_c0)) 1.0\n", + "10 ((M2), (_meas_c0)) 1.0\n", + "11 ((_meas_c0), (_t)) 0.0\n", + "12 ((), (_s)) 1.0\n", + "13 ((_t), ()) 0.0" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "pd.DataFrame(E)" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "548f868d", + "metadata": {}, + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "%3\n", + "\n", + "\n", + "\n", + "I2\n", + "\n", + "I2\n", + "\n", + "\n", + "\n", + "N2\n", + "\n", + "N2\n", + "\n", + "\n", + "\n", + "I2->N2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "M2\n", + "\n", + "M2\n", + "\n", + "\n", + "\n", + "N2->M2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "M1\n", + "\n", + "M1\n", + "\n", + "\n", + "\n", + "N2->M1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "G_sol = Gf.edge_subgraph(get_selected_edges(P, Gf))\n", + "G_sol.plot()" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "ac0d1daa", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(4931, 13157)" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "from corneto.methods import fast_carnival\n", + "from corneto.methods.carnival import read_dataset\n", + "\n", + "G, dict_data = read_dataset(\"carnival_example.zip\")\n", + "G.shape" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "0ae90239", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'EGFR': ('P', -1),\n", + " 'AEBP1': ('M', -1),\n", + " 'CREB3': ('M', 1),\n", + " 'EGR3': ('M', -1),\n", + " 'ELK1': ('M', -1),\n", + " 'FOSL2': ('M', -1),\n", + " 'FOXA3': ('M', 1),\n", + " 'FOXE1': ('M', 1),\n", + " 'HIPK2': ('M', 1),\n", + " 'HOXA2': ('M', 1),\n", + " 'HOXB7': ('M', -1),\n", + " 'HOXD3': ('M', 1),\n", + " 'KDM5C': ('M', -1),\n", + " 'KDM5D': ('M', 1),\n", + " 'KLF2': ('M', -1),\n", + " 'NEUROD1': ('M', -1),\n", + " 'NFATC4': ('M', -1),\n", + " 'NFYB': ('M', -1),\n", + " 'NHLH2': ('M', 1),\n", + " 'PLAGL2': ('M', -1),\n", + " 'RUNX2': ('M', -1),\n", + " 'SIRT1': ('M', 1),\n", + " 'SUPT20H': ('M', 1),\n", + " 'TBX20': ('M', -1),\n", + " 'TET1': ('M', 1),\n", + " 'ZBTB4': ('M', -1)}" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "dict_data" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "0ad5157f", + "metadata": {}, + "outputs": [], + "source": [ + "c_inputs = {k: v[1] for k, v in dict_data.items() if v[0] == \"P\"}\n", + "c_outputs = {k: v[1] for k, v in dict_data.items() if v[0] == \"M\"}" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "id": "437b70c6", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "1/1 inputs mapped to the graph\n", + "16/25 outputs mapped to the graph\n", + "Pruning the graph with size: V x E = (4931, 13157)...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Finished. Final size: V x E = (1182, 5789).\n", + "ELK1 (L3), NEUROD1 (L4), SIRT1 (L3), NFYB (L3), HOXB7 (L4), RUNX2 (L3), AEBP1 (L3), HIPK2 (L3), NFATC4 (L3), ZBTB4 (L4)\n", + "L1 : 1 iters, 0.00 s.\n", + "L2 : 41 iters, 0.00 s.\n", + " > -EGFR -> +CRK -> +MAPK8 -> +SIRT1\n", + " > -EGFR -> +CRK -> +MAPK8 -> -NFATC4\n", + " > -EGFR -> -PTPN1 -> +ABL1 -> +HIPK2\n", + " > -EGFR -> -PRKDC -> -MAPK8 -> -ELK1\n", + " ! conflict: -EGFR/-MAPK8 != -EGFR/+MAPK8\n", + " > -EGFR -> -MAP2K1 -> -MAPK1 -> -ELK1\n", + " > -EGFR -> -MAP2K1 -> -MAPK1 -> -AEBP1\n", + " > -EGFR -> -MAP2K1 -> -MAPK3 -> -RUNX2\n", + "L3 : 316 iters, 0.01 s.\n", + " > -EGFR -> -STAT1 -> +CREBBP -> ... -> -NFYB\n", + " > -EGFR -> -PIK3R1 -> -RAC1 -> ... -> -NEUROD1\n", + " > -EGFR -> -PTPN1 -> +ABL1 -> ... -> -ZBTB4\n", + " > -EGFR -> -ERBB2 -> +CDK1 -> ... -> -HOXB7\n", + "Finished (0.18 s)\n", + " > Number of selected edges: 26\n", + " > Total iterations: 2287\n", + " > Detected loops: 255\n", + " > Conflicts: 1\n", + "Total error: 15\n", + "Number of selected edges: 26\n" + ] + } + ], + "source": [ + "Gc, selected_edges, paths, stats, errors = fast_carnival(\n", + " G, c_inputs, c_outputs, restricted_search=False\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "5288e16b", + "metadata": {}, + "outputs": [], + "source": [ + "node_values = {}\n", + "for p in paths:\n", + " for k, v in p[1].items():\n", + " node_values[k] = v[1]\n", + "\n", + "G_sol = Gc.edge_subgraph(selected_edges)\n", + "\n", + "V = G_sol.V\n", + "vertex_values = [node_values.get(v, 0) for v in V]" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "id": "88af4853", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'AEBP1': 0,\n", + " 'CREB3': 1,\n", + " 'EGR3': 1,\n", + " 'ELK1': 0,\n", + " 'FOSL2': 1,\n", + " 'FOXA3': 1,\n", + " 'FOXE1': 1,\n", + " 'HIPK2': 0,\n", + " 'HOXA2': 1,\n", + " 'HOXB7': 0,\n", + " 'HOXD3': 1,\n", + " 'KDM5C': 1,\n", + " 'KDM5D': 1,\n", + " 'KLF2': 1,\n", + " 'NEUROD1': 0,\n", + " 'NFATC4': 0,\n", + " 'NFYB': 0,\n", + " 'NHLH2': 1,\n", + " 'PLAGL2': 1,\n", + " 'RUNX2': 0,\n", + " 'SIRT1': 0,\n", + " 'SUPT20H': 1,\n", + " 'TBX20': 1,\n", + " 'TET1': 1,\n", + " 'ZBTB4': 0}" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "errors" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "id": "8410ac74", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Warning: node 'EGFR', graph '%3' size too small for label\n", + "Warning: node 'STAT1', graph '%3' size too small for label\n", + "Warning: node 'MAPK8', graph '%3' size too small for label\n", + "Warning: node 'SIRT1', graph '%3' size too small for label\n", + "Warning: node 'ERBB2', graph '%3' size too small for label\n", + "Warning: node 'MAP2K1', graph '%3' size too small for label\n", + "Warning: node 'MAPK1', graph '%3' size too small for label\n", + "Warning: node 'CREBBP', graph '%3' size too small for label\n", + "Warning: node 'CSNK2A1', graph '%3' size too small for label\n", + "Warning: node 'HOXB7', graph '%3' size too small for label\n", + "Warning: node 'ABL1', graph '%3' size too small for label\n", + "Warning: node 'HIPK2', graph '%3' size too small for label\n", + "Warning: node 'ELK1', graph '%3' size too small for label\n", + "Warning: node 'PIK3R1', graph '%3' size too small for label\n", + "Warning: node 'RAC1', graph '%3' size too small for label\n", + "Warning: node 'MAPK3', graph '%3' size too small for label\n", + "Warning: node 'RUNX2', graph '%3' size too small for label\n", + "Warning: node 'ZBTB4', graph '%3' size too small for label\n", + "Warning: node 'AEBP1', graph '%3' size too small for label\n", + "Warning: node 'PTPN1', graph '%3' size too small for label\n", + "Warning: node 'TP53', graph '%3' size too small for label\n", + "Warning: node 'NFYB', graph '%3' size too small for label\n", + "Warning: node 'CDK1', graph '%3' size too small for label\n", + "Warning: node 'MAP3K10', graph '%3' size too small for label\n", + "Warning: node 'NFATC4', graph '%3' size too small for label\n", + "Warning: node 'NEUROD1', graph '%3' size too small for label\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Warning: node 'EGFR', graph '%3' size too small for label\n", + "Warning: node 'STAT1', graph '%3' size too small for label\n", + "Warning: node 'MAPK8', graph '%3' size too small for label\n", + "Warning: node 'SIRT1', graph '%3' size too small for label\n", + "Warning: node 'ERBB2', graph '%3' size too small for label\n", + "Warning: node 'MAP2K1', graph '%3' size too small for label\n", + "Warning: node 'MAPK1', graph '%3' size too small for label\n", + "Warning: node 'CREBBP', graph '%3' size too small for label\n", + "Warning: node 'CSNK2A1', graph '%3' size too small for label\n", + "Warning: node 'HOXB7', graph '%3' size too small for label\n", + "Warning: node 'ABL1', graph '%3' size too small for label\n", + "Warning: node 'HIPK2', graph '%3' size too small for label\n", + "Warning: node 'ELK1', graph '%3' size too small for label\n", + "Warning: node 'PIK3R1', graph '%3' size too small for label\n", + "Warning: node 'RAC1', graph '%3' size too small for label\n", + "Warning: node 'MAPK3', graph '%3' size too small for label\n", + "Warning: node 'RUNX2', graph '%3' size too small for label\n", + "Warning: node 'ZBTB4', graph '%3' size too small for label\n", + "Warning: node 'AEBP1', graph '%3' size too small for label\n", + "Warning: node 'PTPN1', graph '%3' size too small for label\n", + "Warning: node 'TP53', graph '%3' size too small for label\n", + "Warning: node 'NFYB', graph '%3' size too small for label\n", + "Warning: node 'CDK1', graph '%3' size too small for label\n", + "Warning: node 'MAP3K10', graph '%3' size too small for label\n", + "Warning: node 'NFATC4', graph '%3' size too small for label\n", + "Warning: node 'NEUROD1', graph '%3' size too small for label\n" + ] + }, + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "%3\n", + "\n", + "\n", + "\n", + "EGFR\n", + "\n", + "EGFR\n", + "\n", + "\n", + "\n", + "STAT1\n", + "\n", + "STAT1\n", + "\n", + "\n", + "\n", + "EGFR->STAT1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "ERBB2\n", + "\n", + "ERBB2\n", + "\n", + "\n", + "\n", + "EGFR->ERBB2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "MAP2K1\n", + "\n", + "MAP2K1\n", + "\n", + "\n", + "\n", + "EGFR->MAP2K1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "PIK3R1\n", + "\n", + "PIK3R1\n", + "\n", + "\n", + "\n", + "EGFR->PIK3R1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "CRK\n", + "\n", + "CRK\n", + "\n", + "\n", + "\n", + "EGFR->CRK\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "PTPN1\n", + "\n", + "PTPN1\n", + "\n", + "\n", + "\n", + "EGFR->PTPN1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "CREBBP\n", + "\n", + "CREBBP\n", + "\n", + "\n", + "\n", + "STAT1->CREBBP\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "MAPK8\n", + "\n", + "MAPK8\n", + "\n", + "\n", + "\n", + "SIRT1\n", + "\n", + "SIRT1\n", + "\n", + "\n", + "\n", + "MAPK8->SIRT1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "NFATC4\n", + "\n", + "NFATC4\n", + "\n", + "\n", + "\n", + "MAPK8->NFATC4\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "CDK1\n", + "\n", + "CDK1\n", + "\n", + "\n", + "\n", + "ERBB2->CDK1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "MAPK1\n", + "\n", + "MAPK1\n", + "\n", + "\n", + "\n", + "MAP2K1->MAPK1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "MAPK3\n", + "\n", + "MAPK3\n", + "\n", + "\n", + "\n", + "MAP2K1->MAPK3\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "ELK1\n", + "\n", + "ELK1\n", + "\n", + "\n", + "\n", + "MAPK1->ELK1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "AEBP1\n", + "\n", + "AEBP1\n", + "\n", + "\n", + "\n", + "MAPK1->AEBP1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "TP53\n", + "\n", + "TP53\n", + "\n", + "\n", + "\n", + "CREBBP->TP53\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "CSNK2A1\n", + "\n", + "CSNK2A1\n", + "\n", + "\n", + "\n", + "HOXB7\n", + "\n", + "HOXB7\n", + "\n", + "\n", + "\n", + "CSNK2A1->HOXB7\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "ABL1\n", + "\n", + "ABL1\n", + "\n", + "\n", + "\n", + "HIPK2\n", + "\n", + "HIPK2\n", + "\n", + "\n", + "\n", + "ABL1->HIPK2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "ZBTB4\n", + "\n", + "ZBTB4\n", + "\n", + "\n", + "\n", + "HIPK2->ZBTB4\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "RAC1\n", + "\n", + "RAC1\n", + "\n", + "\n", + "\n", + "PIK3R1->RAC1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "MAP3K10\n", + "\n", + "MAP3K10\n", + "\n", + "\n", + "\n", + "RAC1->MAP3K10\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "RUNX2\n", + "\n", + "RUNX2\n", + "\n", + "\n", + "\n", + "MAPK3->RUNX2\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "CRK->MAPK8\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "PTPN1->ABL1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "NFYB\n", + "\n", + "NFYB\n", + "\n", + "\n", + "\n", + "TP53->NFYB\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "CDK1->CSNK2A1\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "NEUROD1\n", + "\n", + "NEUROD1\n", + "\n", + "\n", + "\n", + "MAP3K10->NEUROD1\n", + "\n", + "\n", + "\n", + "\n", + "\n" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "G_sol.plot_values(vertex_values=vertex_values)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.9" + }, + "toc": { + "base_numbering": 1, + "nav_menu": {}, + "number_sections": true, + "sideBar": true, + "skip_h1_title": false, + "title_cell": "Table of Contents", + "title_sidebar": "Contents", + "toc_cell": false, + "toc_position": {}, + "toc_section_display": true, + "toc_window_display": false + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} \ No newline at end of file diff --git a/docs/_build/html/jupyter_execute/2a38f2d0d5b8c60309d55a245b5a69a6aefb567140fed800290f7e312bf398ca.svg b/docs/_build/html/jupyter_execute/2a38f2d0d5b8c60309d55a245b5a69a6aefb567140fed800290f7e312bf398ca.svg new file mode 100644 index 00000000..8e5a4820 --- /dev/null +++ b/docs/_build/html/jupyter_execute/2a38f2d0d5b8c60309d55a245b5a69a6aefb567140fed800290f7e312bf398ca.svg @@ -0,0 +1,2802 @@ + + + + + + +%3 + + + +acald_c + +acald_c + + + +e_0_center + + + + +acald_c->e_0_center + + + + +nad_c + +nad_c + + + +nad_c->e_0_center + + + + +e_7_center + + + + +nad_c->e_7_center + + + + +e_9_center + + + + +nad_c->e_9_center + + + + +e_12_center + + + + +nad_c->e_12_center + + + + +e_48_center + + + + +nad_c->e_48_center + + + + +e_60_center + + + + +nad_c->e_60_center + + + + +e_63_center + + + + +nad_c->e_63_center + + + + +e_64_center + + + + +nad_c->e_64_center + + + + +e_67_center + + + + +nad_c->e_67_center + + + + +e_70_center + + + + +nad_c->e_70_center + + + + +coa_c + +coa_c + + + +coa_c->e_0_center + + + + +coa_c->e_7_center + + + + +coa_c->e_70_center + + + + +e_72_center + + + + +coa_c->e_72_center + + + + +e_89_center + + + + +coa_c->e_89_center + + + + +accoa_c + +accoa_c + + + +accoa_c->e_12_center + + + + +e_14_center + + + + +accoa_c->e_14_center + + + + +e_61_center + + + + +accoa_c->e_61_center + + + + +e_81_center + + + + +accoa_c->e_81_center + + + + +h_c + +h_c + + + +e_15_center + + + + +h_c->e_15_center + + + + +e_54_center + + + + +h_c->e_54_center + + + + +e_66_center + + + + +h_c->e_66_center + + + + +e_82_center + + + + +h_c->e_82_center + + + + +nadh_c + +nadh_c + + + +nadh_c->e_66_center + + + + +e_91_center + + + + +nadh_c->e_91_center + + + + +e_0_center->accoa_c + + + + + +e_0_center->h_c + + + + + +e_0_center->nadh_c + + + + + +acald_e + +acald_e + + + +acald_e->acald_c + + + + + +e_20_target + + + + +acald_e->e_20_target + + + + + +atp_c + +atp_c + + + +e_2_center + + + + +atp_c->e_2_center + + + + +e_6_center + + + + +atp_c->e_6_center + + + + +e_10_center + + + + +atp_c->e_10_center + + + + +atp_c->e_12_center + + + + +e_50_center + + + + +atp_c->e_50_center + + + + +e_51_center + + + + +atp_c->e_51_center + + + + +e_71_center + + + + +atp_c->e_71_center + + + + +e_74_center + + + + +atp_c->e_74_center + + + + +e_79_center + + + + +atp_c->e_79_center + + + + +e_80_center + + + + +atp_c->e_80_center + + + + +atp_c->e_89_center + + + + +ac_c + +ac_c + + + +ac_c->e_2_center + + + + +actp_c + +actp_c + + + +adp_c + +adp_c + + + +e_11_center + + + + +adp_c->e_11_center + + + + +adp_c->e_82_center + + + + +e_2_center->actp_c + + + + + +e_2_center->adp_c + + + + + +cit_c + +cit_c + + + +e_3_center + + + + +cit_c->e_3_center + + + + +acon_C_c + +acon_C_c + + + +e_4_center + + + + +acon_C_c->e_4_center + + + + +h2o_c + +h2o_c + + + +h2o_c->e_4_center + + + + +h2o_c->e_10_center + + + + +h2o_c->e_12_center + + + + +h2o_c->e_14_center + + + + +e_40_center + + + + +h2o_c->e_40_center + + + + +e_45_center + + + + +h2o_c->e_45_center + + + + +h2o_c->e_51_center + + + + +e_52_center + + + + +h2o_c->e_52_center + + + + +e_53_center + + + + +h2o_c->e_53_center + + + + +h2o_c->e_61_center + + + + +e_75_center + + + + +h2o_c->e_75_center + + + + +e_78_center + + + + +h2o_c->e_78_center + + + + +h2o_c->e_80_center + + + + +e_3_center->acon_C_c + + + + + +e_3_center->h2o_c + + + + + +icit_c + +icit_c + + + +e_58_center + + + + +icit_c->e_58_center + + + + +e_59_center + + + + +icit_c->e_59_center + + + + +e_4_center->icit_c + + + + + +ac_e + +ac_e + + + +e_5_center + + + + +ac_e->e_5_center + + + + +e_19_target + + + + +ac_e->e_19_target + + + + + +h_e + +h_e + + + +h_e->e_5_center + + + + +e_8_center + + + + +h_e->e_8_center + + + + +h_e->e_11_center + + + + +e_16_center + + + + +h_e->e_16_center + + + + +e_18_center + + + + +h_e->e_18_center + + + + +e_30_target + + + + +h_e->e_30_target + + + + + +e_41_center + + + + +h_e->e_41_center + + + + +e_46_center + + + + +h_e->e_46_center + + + + +e_55_center + + + + +h_e->e_55_center + + + + +e_62_center + + + + +h_e->e_62_center + + + + +e_77_center + + + + +h_e->e_77_center + + + + +e_83_center + + + + +h_e->e_83_center + + + + +e_86_center + + + + +h_e->e_86_center + + + + +e_87_center + + + + +h_e->e_87_center + + + + +h_e->e_91_center + + + + +e_5_center->h_c + + + + + +e_5_center->ac_c + + + + + +amp_c + +amp_c + + + +amp_c->e_6_center + + + + +e_6_center->adp_c + + + + + +akg_c + +akg_c + + + +akg_c->e_7_center + + + + +akg_c->e_54_center + + + + +co2_c + +co2_c + + + +co2_c->e_78_center + + + + +succoa_c + +succoa_c + + + +e_7_center->nadh_c + + + + + +e_7_center->co2_c + + + + + +e_7_center->succoa_c + + + + + +akg_e + +akg_e + + + +akg_e->e_8_center + + + + +e_21_target + + + + +akg_e->e_21_target + + + + + +e_8_center->h_c + + + + + +e_8_center->akg_c + + + + + +etoh_c + +etoh_c + + + +etoh_c->e_9_center + + + + +e_9_center->acald_c + + + + + +e_9_center->h_c + + + + + +e_9_center->nadh_c + + + + + +pi_c + +pi_c + + + +pi_c->e_11_center + + + + +pi_c->e_48_center + + + + +pi_c->e_81_center + + + + +e_10_center->h_c + + + + + +e_10_center->adp_c + + + + + +e_10_center->pi_c + + + + + +e_11_center->h_c + + + + + +e_11_center->atp_c + + + + + +e_11_center->h2o_c + + + + + +r5p_c + +r5p_c + + + +r5p_c->e_12_center + + + + +ru5p__D_c + +ru5p__D_c + + + +r5p_c->ru5p__D_c + + + + + +e_92_center + + + + +r5p_c->e_92_center + + + + +nadph_c + +nadph_c + + + +nadph_c->e_12_center + + + + +nadph_c->e_54_center + + + + +nadph_c->e_67_center + + + + +oaa_c + +oaa_c + + + +oaa_c->e_12_center + + + + +oaa_c->e_14_center + + + + +oaa_c->e_79_center + + + + +glu__L_c + +glu__L_c + + + +glu__L_c->e_12_center + + + + +glu__L_c->e_50_center + + + + +glu__L_c->e_52_center + + + + +g3p_c + +g3p_c + + + +g3p_c->e_12_center + + + + +g3p_c->e_48_center + + + + +e_90_center + + + + +g3p_c->e_90_center + + + + +3pg_c + +3pg_c + + + +3pg_c->e_12_center + + + + +3pg_c->e_74_center + + + + +pyr_c + +pyr_c + + + +pyr_c->e_12_center + + + + +pyr_c->e_70_center + + + + +pyr_c->e_72_center + + + + +pyr_c->e_80_center + + + + +pep_c + +pep_c + + + +pep_c->e_12_center + + + + +e_44_center + + + + +pep_c->e_44_center + + + + +e_49_center + + + + +pep_c->e_49_center + + + + +pep_c->e_78_center + + + + +pep_c->e_82_center + + + + +f6p_c + +f6p_c + + + +f6p_c->e_12_center + + + + +f6p_c->e_71_center + + + + +g6p_c + +g6p_c + + + +g6p_c->f6p_c + + + + + +g6p_c->e_12_center + + + + +e_47_center + + + + +g6p_c->e_47_center + + + + +e4p_c + +e4p_c + + + +e4p_c->e_12_center + + + + +e_93_center + + + + +e4p_c->e_93_center + + + + +gln__L_c + +gln__L_c + + + +gln__L_c->e_12_center + + + + +gln__L_c->e_53_center + + + + +gln__L_c->e_54_center + + + + +nadp_c + +nadp_c + + + +nadp_c->e_47_center + + + + +nadp_c->e_52_center + + + + +e_56_center + + + + +nadp_c->e_56_center + + + + +nadp_c->e_58_center + + + + +e_65_center + + + + +nadp_c->e_65_center + + + + +nadp_c->e_91_center + + + + +e_12_center->coa_c + + + + + +e_12_center->h_c + + + + + +e_12_center->nadh_c + + + + + +e_12_center->adp_c + + + + + +e_12_center->akg_c + + + + + +e_12_center->pi_c + + + + + +e_12_center->nadp_c + + + + + +co2_e + +co2_e + + + +co2_e->co2_c + + + + + +e_22_target + + + + +co2_e->e_22_target + + + + + +e_14_center->coa_c + + + + + +e_14_center->h_c + + + + + +e_14_center->cit_c + + + + + +o2_c + +o2_c + + + +o2_c->e_15_center + + + + +q8h2_c + +q8h2_c + + + +q8h2_c->e_15_center + + + + +e_43_center + + + + +q8h2_c->e_43_center + + + + +q8_c + +q8_c + + + +q8_c->e_66_center + + + + +e_88_center + + + + +q8_c->e_88_center + + + + +e_15_center->h2o_c + + + + + +e_15_center->h_e + + + + + +e_15_center->q8_c + + + + + +lac__D_e + +lac__D_e + + + +lac__D_e->e_16_center + + + + +e_32_target + + + + +lac__D_e->e_32_target + + + + + +lac__D_c + +lac__D_c + + + +lac__D_c->e_60_center + + + + +e_16_center->h_c + + + + + +e_16_center->lac__D_c + + + + + +2pg_c + +2pg_c + + + +2pg_c->3pg_c + + + + + +e_17_center + + + + +2pg_c->e_17_center + + + + +e_17_center->h2o_c + + + + + +e_17_center->pep_c + + + + + +etoh_e + +etoh_e + + + +etoh_e->e_18_center + + + + +e_23_target + + + + +etoh_e->e_23_target + + + + + +e_18_center->h_c + + + + + +e_18_center->etoh_c + + + + + +e_24_target + + + + +for_e + +for_e + + + +for_e->e_24_target + + + + + +for_e->e_41_center + + + + +e_25_target + + + + +fru_e + +fru_e + + + +fru_e->e_25_target + + + + + +fru_e->e_44_center + + + + +e_26_target + + + + +fum_e + +fum_e + + + +fum_e->e_26_target + + + + + +fum_e->e_46_center + + + + +e_27_target + + + + +glc__D_e + +glc__D_e + + + +glc__D_e->e_27_target + + + + + +glc__D_e->e_49_center + + + + +e_28_target + + + + +gln__L_e + +gln__L_e + + + +gln__L_e->e_28_target + + + + + +gln__L_e->e_51_center + + + + +e_29_target + + + + +glu__L_e + +glu__L_e + + + +glu__L_e->e_29_target + + + + + +glu__L_e->e_55_center + + + + +e_31_target + + + + +h2o_e + +h2o_e + + + +h2o_e->h2o_c + + + + + +h2o_e->e_31_target + + + + + +e_33_target + + + + +mal__L_e + +mal__L_e + + + +mal__L_e->e_33_target + + + + + +mal__L_e->e_62_center + + + + +e_34_target + + + + +nh4_e + +nh4_e + + + +nh4_e->e_34_target + + + + + +nh4_c + +nh4_c + + + +nh4_e->nh4_c + + + + + +e_35_target + + + + +o2_e + +o2_e + + + +o2_e->o2_c + + + + + +o2_e->e_35_target + + + + + +e_36_target + + + + +pi_e + +pi_e + + + +pi_e->e_36_target + + + + + +pi_e->e_77_center + + + + +e_37_target + + + + +pyr_e + +pyr_e + + + +pyr_e->e_37_target + + + + + +pyr_e->e_83_center + + + + +e_38_target + + + + +succ_e + +succ_e + + + +succ_e->e_38_target + + + + + +succ_e->e_86_center + + + + +fdp_c + +fdp_c + + + +e_39_center + + + + +fdp_c->e_39_center + + + + +fdp_c->e_40_center + + + + +dhap_c + +dhap_c + + + +dhap_c->g3p_c + + + + + +e_39_center->g3p_c + + + + + +e_39_center->dhap_c + + + + + +e_40_center->pi_c + + + + + +e_40_center->f6p_c + + + + + +for_c + +for_c + + + +for_c->for_e + + + + + +e_41_center->h_c + + + + + +e_41_center->for_c + + + + + +fum_c + +fum_c + + + +fum_c->e_43_center + + + + +fum_c->e_45_center + + + + +succ_c + +succ_c + + + +succ_c->e_87_center + + + + +succ_c->e_88_center + + + + +succ_c->e_89_center + + + + +e_43_center->q8_c + + + + + +e_43_center->succ_c + + + + + +e_44_center->pyr_c + + + + + +e_44_center->f6p_c + + + + + +mal__L_c + +mal__L_c + + + +mal__L_c->e_63_center + + + + +mal__L_c->e_64_center + + + + +mal__L_c->e_65_center + + + + +e_45_center->mal__L_c + + + + + +e_46_center->h_c + + + + + +e_46_center->fum_c + + + + + +6pgl_c + +6pgl_c + + + +6pgl_c->e_75_center + + + + +e_47_center->h_c + + + + + +e_47_center->nadph_c + + + + + +e_47_center->6pgl_c + + + + + +13dpg_c + +13dpg_c + + + +e_48_center->h_c + + + + + +e_48_center->nadh_c + + + + + +e_48_center->13dpg_c + + + + + +e_49_center->pyr_c + + + + + +e_49_center->g6p_c + + + + + +nh4_c->e_50_center + + + + +e_50_center->h_c + + + + + +e_50_center->adp_c + + + + + +e_50_center->pi_c + + + + + +e_50_center->gln__L_c + + + + + +e_51_center->h_c + + + + + +e_51_center->adp_c + + + + + +e_51_center->pi_c + + + + + +e_51_center->gln__L_c + + + + + +e_52_center->h_c + + + + + +e_52_center->akg_c + + + + + +e_52_center->nadph_c + + + + + +e_52_center->nh4_c + + + + + +e_53_center->glu__L_c + + + + + +e_53_center->nh4_c + + + + + +e_54_center->glu__L_c + + + + + +e_54_center->nadp_c + + + + + +e_55_center->h_c + + + + + +e_55_center->glu__L_c + + + + + +6pgc_c + +6pgc_c + + + +6pgc_c->e_56_center + + + + +xu5p__D_c + +xu5p__D_c + + + +ru5p__D_c->xu5p__D_c + + + + + +e_56_center->co2_c + + + + + +e_56_center->nadph_c + + + + + +e_56_center->ru5p__D_c + + + + + +e_58_center->akg_c + + + + + +e_58_center->co2_c + + + + + +e_58_center->nadph_c + + + + + +glx_c + +glx_c + + + +glx_c->e_61_center + + + + +e_59_center->succ_c + + + + + +e_59_center->glx_c + + + + + +e_60_center->h_c + + + + + +e_60_center->nadh_c + + + + + +e_60_center->pyr_c + + + + + +e_61_center->coa_c + + + + + +e_61_center->h_c + + + + + +e_61_center->mal__L_c + + + + + +e_62_center->h_c + + + + + +e_62_center->mal__L_c + + + + + +e_63_center->h_c + + + + + +e_63_center->nadh_c + + + + + +e_63_center->oaa_c + + + + + +e_64_center->nadh_c + + + + + +e_64_center->co2_c + + + + + +e_64_center->pyr_c + + + + + +e_65_center->co2_c + + + + + +e_65_center->nadph_c + + + + + +e_65_center->pyr_c + + + + + +e_66_center->nad_c + + + + + +e_66_center->h_e + + + + + +e_66_center->q8h2_c + + + + + +e_67_center->nadh_c + + + + + +e_67_center->nadp_c + + + + + +e_70_center->accoa_c + + + + + +e_70_center->nadh_c + + + + + +e_70_center->co2_c + + + + + +e_71_center->h_c + + + + + +e_71_center->adp_c + + + + + +e_71_center->fdp_c + + + + + +e_72_center->accoa_c + + + + + +e_72_center->for_c + + + + + +e_74_center->adp_c + + + + + +e_74_center->13dpg_c + + + + + +e_75_center->h_c + + + + + +e_75_center->6pgc_c + + + + + +e_77_center->h_c + + + + + +e_77_center->pi_c + + + + + +e_78_center->h_c + + + + + +e_78_center->pi_c + + + + + +e_78_center->oaa_c + + + + + +e_79_center->adp_c + + + + + +e_79_center->co2_c + + + + + +e_79_center->pep_c + + + + + +e_80_center->h_c + + + + + +e_80_center->amp_c + + + + + +e_80_center->pi_c + + + + + +e_80_center->pep_c + + + + + +e_81_center->coa_c + + + + + +e_81_center->actp_c + + + + + +e_82_center->atp_c + + + + + +e_82_center->pyr_c + + + + + +e_83_center->h_c + + + + + +e_83_center->pyr_c + + + + + +xu5p__D_c->e_92_center + + + + +xu5p__D_c->e_93_center + + + + +e_86_center->h_c + + + + + +e_86_center->succ_c + + + + + +e_87_center->h_c + + + + + +e_87_center->succ_e + + + + + +e_88_center->q8h2_c + + + + + +e_88_center->fum_c + + + + + +e_89_center->adp_c + + + + + +e_89_center->succoa_c + + + + + +e_89_center->pi_c + + + + + +s7p_c + +s7p_c + + + +s7p_c->e_90_center + + + + +e_90_center->f6p_c + + + + + +e_90_center->e4p_c + + + + + +e_91_center->nad_c + + + + + +e_91_center->h_c + + + + + +e_91_center->nadph_c + + + + + +e_92_center->g3p_c + + + + + +e_92_center->s7p_c + + + + + +e_93_center->g3p_c + + + + + +e_93_center->f6p_c + + + + + \ No newline at end of file diff --git a/docs/_build/html/jupyter_execute/2c64097f5da14ea3c688e1a93dc4dc0c510c4e41d0fe34fa9dfae3bc662b2bb2.svg b/docs/_build/html/jupyter_execute/2c64097f5da14ea3c688e1a93dc4dc0c510c4e41d0fe34fa9dfae3bc662b2bb2.svg new file mode 100644 index 00000000..f48a01f9 --- /dev/null +++ b/docs/_build/html/jupyter_execute/2c64097f5da14ea3c688e1a93dc4dc0c510c4e41d0fe34fa9dfae3bc662b2bb2.svg @@ -0,0 +1,131 @@ + + + + + + +%3 + + + +A + +A + + + +e_0_center + + + + +A->e_0_center + + + + +B + +B + + + +B->e_0_center + + + + +C + +C + + + +e_4_target + + + + +C->e_4_target + + + + + +D + +D + + + +e_1_center + + + + +D->e_1_center + + + + +e_0_center->C + + + + + +e_0_center->D + + + + + +F + +F + + + +E + +E + + + +e_1_center->F + + + + + +e_1_center->E + + + + + +e_2_source + + + + +e_2_source->A + + + + + +e_3_source + + + + +e_3_source->B + + + + + \ No newline at end of file diff --git a/docs/_build/html/jupyter_execute/443cf7bd4db35676d58fdb902fcfd857934e3a7c2731577a6acf2f279d44b8b3.svg b/docs/_build/html/jupyter_execute/443cf7bd4db35676d58fdb902fcfd857934e3a7c2731577a6acf2f279d44b8b3.svg new file mode 100644 index 00000000..1319a462 --- /dev/null +++ b/docs/_build/html/jupyter_execute/443cf7bd4db35676d58fdb902fcfd857934e3a7c2731577a6acf2f279d44b8b3.svg @@ -0,0 +1,170 @@ + + + + + + +%3 + + + +I1 + +I1 + + + +N1 + +N1 + + + +I1->N1 + + + + + +M1 + +M1 + + + +N1->M1 + + + + + +M2 + +M2 + + + +N1->M2 + + + + + +_meas_c0 + +_meas_c0 + + + +M1->_meas_c0 + + + + + +M2->_meas_c0 + + + + + +I2 + +I2 + + + +N2 + +N2 + + + +I2->N2 + + + + + + +N2->M1 + + + + + + +N2->M2 + + + + + + +_s + +_s + + + +_pert_c0 + +_pert_c0 + + + +_s->_pert_c0 + + + + + +_pert_c0->I1 + + + + + +_pert_c0->I2 + + + + + +_t + +_t + + + +_meas_c0->_t + + + + + +e_13_target + + + + +_t->e_13_target + + + + + +e_12_source + + + + +e_12_source->_s + + + + + \ No newline at end of file diff --git a/docs/_build/html/jupyter_execute/5b572f011bdaf826106697ae16ecadb3e0ff5a4bd81ae225a115f4bf9e56ae53.svg b/docs/_build/html/jupyter_execute/5b572f011bdaf826106697ae16ecadb3e0ff5a4bd81ae225a115f4bf9e56ae53.svg new file mode 100644 index 00000000..e2fdfd18 --- /dev/null +++ b/docs/_build/html/jupyter_execute/5b572f011bdaf826106697ae16ecadb3e0ff5a4bd81ae225a115f4bf9e56ae53.svg @@ -0,0 +1,210 @@ + + + + + + +%3 + + + +M1 + +M1 + + + +e_0_center + + + + +M1->e_0_center + + + + +M4 + +M4 + + + +M1->M4 + + + + + +M2 + +M2 + + + +M2->e_0_center + + + + +M5 + +M5 + + + +e_7_target + + + + +M5->e_7_target + + + + + +M6 + +M6 + + + +M9 + +M9 + + + +M6->M9 + + + + + +e_0_center->M5 + + + + + +e_0_center->M6 + + + + + +e_2_center + + + + +M4->e_2_center + + + + +M3 + +M3 + + + +M3->e_2_center + + + + +M8 + +M8 + + + +e_9_target + + + + +M8->e_9_target + + + + + +M7 + +M7 + + + +e_8_target + + + + +M7->e_8_target + + + + + +e_2_center->M8 + + + + + +e_2_center->M7 + + + + + +e_10_target + + + + +M9->e_10_target + + + + + +e_4_source + + + + +e_4_source->M1 + + + + + +e_5_source + + + + +e_5_source->M2 + + + + + +e_6_source + + + + +e_6_source->M3 + + + + + \ No newline at end of file diff --git a/docs/_build/html/jupyter_execute/7d51afb160f63cb72df323a55c7f6b4d57dbccbd0120e59abc2f30407c7dfed9.svg b/docs/_build/html/jupyter_execute/7d51afb160f63cb72df323a55c7f6b4d57dbccbd0120e59abc2f30407c7dfed9.svg new file mode 100644 index 00000000..b7c17409 --- /dev/null +++ b/docs/_build/html/jupyter_execute/7d51afb160f63cb72df323a55c7f6b4d57dbccbd0120e59abc2f30407c7dfed9.svg @@ -0,0 +1,210 @@ + + + + + + +%3 + + + +M1 + +M1 + + + +e_0_center + + + + +M1->e_0_center + + + + +M4 + +M4 + + + +M1->M4 + + + + + +M2 + +M2 + + + +M2->e_0_center + + + + +M5 + +M5 + + + +e_7_target + + + + +M5->e_7_target + + + + + +M6 + +M6 + + + +M9 + +M9 + + + +M6->M9 + + + + + +e_0_center->M5 + + + + + +e_0_center->M6 + + + + + +e_2_center + + + + +M4->e_2_center + + + + +M3 + +M3 + + + +M3->e_2_center + + + + +M8 + +M8 + + + +e_9_target + + + + +M8->e_9_target + + + + + +M7 + +M7 + + + +e_8_target + + + + +M7->e_8_target + + + + + +e_2_center->M8 + + + + + +e_2_center->M7 + + + + + +e_10_target + + + + +M9->e_10_target + + + + + +e_4_source + + + + +e_4_source->M1 + + + + + +e_5_source + + + + +e_5_source->M2 + + + + + +e_6_source + + + + +e_6_source->M3 + + + + + \ No newline at end of file diff --git a/docs/_build/html/jupyter_execute/868a4c4ff4d416d677b3e548cce59f6202431263bc98d2b38ab5d3e0881995b8.svg b/docs/_build/html/jupyter_execute/868a4c4ff4d416d677b3e548cce59f6202431263bc98d2b38ab5d3e0881995b8.svg new file mode 100644 index 00000000..08ee5d59 --- /dev/null +++ b/docs/_build/html/jupyter_execute/868a4c4ff4d416d677b3e548cce59f6202431263bc98d2b38ab5d3e0881995b8.svg @@ -0,0 +1,2802 @@ + + + + + + +%3 + + + +nad_c + +nad_c + + + +e_0_center + + + + +nad_c->e_0_center + + + + +e_7_center + + + + +nad_c->e_7_center + + + + +e_9_center + + + + +nad_c->e_9_center + + + + +e_12_center + + + + +nad_c->e_12_center + + + + +e_48_center + + + + +nad_c->e_48_center + + + + +e_60_center + + + + +nad_c->e_60_center + + + + +e_63_center + + + + +nad_c->e_63_center + + + + +e_64_center + + + + +nad_c->e_64_center + + + + +e_67_center + + + + +nad_c->e_67_center + + + + +e_70_center + + + + +nad_c->e_70_center + + + + +acald_c + +acald_c + + + +acald_c->e_0_center + + + + +coa_c + +coa_c + + + +coa_c->e_0_center + + + + +coa_c->e_7_center + + + + +coa_c->e_70_center + + + + +e_72_center + + + + +coa_c->e_72_center + + + + +e_89_center + + + + +coa_c->e_89_center + + + + +h_c + +h_c + + + +e_15_center + + + + +h_c->e_15_center + + + + +e_54_center + + + + +h_c->e_54_center + + + + +e_66_center + + + + +h_c->e_66_center + + + + +e_82_center + + + + +h_c->e_82_center + + + + +nadh_c + +nadh_c + + + +nadh_c->e_66_center + + + + +e_91_center + + + + +nadh_c->e_91_center + + + + +accoa_c + +accoa_c + + + +accoa_c->e_12_center + + + + +e_14_center + + + + +accoa_c->e_14_center + + + + +e_61_center + + + + +accoa_c->e_61_center + + + + +e_81_center + + + + +accoa_c->e_81_center + + + + +e_0_center->h_c + + + + + +e_0_center->nadh_c + + + + + +e_0_center->accoa_c + + + + + +acald_e + +acald_e + + + +acald_e->acald_c + + + + + +e_20_target + + + + +acald_e->e_20_target + + + + + +ac_c + +ac_c + + + +e_2_center + + + + +ac_c->e_2_center + + + + +atp_c + +atp_c + + + +atp_c->e_2_center + + + + +e_6_center + + + + +atp_c->e_6_center + + + + +e_10_center + + + + +atp_c->e_10_center + + + + +atp_c->e_12_center + + + + +e_50_center + + + + +atp_c->e_50_center + + + + +e_51_center + + + + +atp_c->e_51_center + + + + +e_71_center + + + + +atp_c->e_71_center + + + + +e_74_center + + + + +atp_c->e_74_center + + + + +e_79_center + + + + +atp_c->e_79_center + + + + +e_80_center + + + + +atp_c->e_80_center + + + + +atp_c->e_89_center + + + + +adp_c + +adp_c + + + +e_11_center + + + + +adp_c->e_11_center + + + + +adp_c->e_82_center + + + + +actp_c + +actp_c + + + +e_2_center->adp_c + + + + + +e_2_center->actp_c + + + + + +cit_c + +cit_c + + + +e_3_center + + + + +cit_c->e_3_center + + + + +h2o_c + +h2o_c + + + +e_4_center + + + + +h2o_c->e_4_center + + + + +h2o_c->e_10_center + + + + +h2o_c->e_12_center + + + + +h2o_c->e_14_center + + + + +e_40_center + + + + +h2o_c->e_40_center + + + + +e_45_center + + + + +h2o_c->e_45_center + + + + +h2o_c->e_51_center + + + + +e_52_center + + + + +h2o_c->e_52_center + + + + +e_53_center + + + + +h2o_c->e_53_center + + + + +h2o_c->e_61_center + + + + +e_75_center + + + + +h2o_c->e_75_center + + + + +e_78_center + + + + +h2o_c->e_78_center + + + + +h2o_c->e_80_center + + + + +acon_C_c + +acon_C_c + + + +acon_C_c->e_4_center + + + + +e_3_center->h2o_c + + + + + +e_3_center->acon_C_c + + + + + +icit_c + +icit_c + + + +e_58_center + + + + +icit_c->e_58_center + + + + +e_59_center + + + + +icit_c->e_59_center + + + + +e_4_center->icit_c + + + + + +ac_e + +ac_e + + + +e_5_center + + + + +ac_e->e_5_center + + + + +e_19_target + + + + +ac_e->e_19_target + + + + + +h_e + +h_e + + + +h_e->e_5_center + + + + +e_8_center + + + + +h_e->e_8_center + + + + +h_e->e_11_center + + + + +e_16_center + + + + +h_e->e_16_center + + + + +e_18_center + + + + +h_e->e_18_center + + + + +e_30_target + + + + +h_e->e_30_target + + + + + +e_41_center + + + + +h_e->e_41_center + + + + +e_46_center + + + + +h_e->e_46_center + + + + +e_55_center + + + + +h_e->e_55_center + + + + +e_62_center + + + + +h_e->e_62_center + + + + +e_77_center + + + + +h_e->e_77_center + + + + +e_83_center + + + + +h_e->e_83_center + + + + +e_86_center + + + + +h_e->e_86_center + + + + +e_87_center + + + + +h_e->e_87_center + + + + +h_e->e_91_center + + + + +e_5_center->h_c + + + + + +e_5_center->ac_c + + + + + +amp_c + +amp_c + + + +amp_c->e_6_center + + + + +e_6_center->adp_c + + + + + +akg_c + +akg_c + + + +akg_c->e_7_center + + + + +akg_c->e_54_center + + + + +co2_c + +co2_c + + + +co2_c->e_78_center + + + + +succoa_c + +succoa_c + + + +e_7_center->nadh_c + + + + + +e_7_center->co2_c + + + + + +e_7_center->succoa_c + + + + + +akg_e + +akg_e + + + +akg_e->e_8_center + + + + +e_21_target + + + + +akg_e->e_21_target + + + + + +e_8_center->h_c + + + + + +e_8_center->akg_c + + + + + +etoh_c + +etoh_c + + + +etoh_c->e_9_center + + + + +e_9_center->acald_c + + + + + +e_9_center->h_c + + + + + +e_9_center->nadh_c + + + + + +pi_c + +pi_c + + + +pi_c->e_11_center + + + + +pi_c->e_48_center + + + + +pi_c->e_81_center + + + + +e_10_center->h_c + + + + + +e_10_center->adp_c + + + + + +e_10_center->pi_c + + + + + +e_11_center->h_c + + + + + +e_11_center->atp_c + + + + + +e_11_center->h2o_c + + + + + +gln__L_c + +gln__L_c + + + +gln__L_c->e_12_center + + + + +gln__L_c->e_53_center + + + + +gln__L_c->e_54_center + + + + +pep_c + +pep_c + + + +pep_c->e_12_center + + + + +e_44_center + + + + +pep_c->e_44_center + + + + +e_49_center + + + + +pep_c->e_49_center + + + + +pep_c->e_78_center + + + + +pep_c->e_82_center + + + + +glu__L_c + +glu__L_c + + + +glu__L_c->e_12_center + + + + +glu__L_c->e_50_center + + + + +glu__L_c->e_52_center + + + + +oaa_c + +oaa_c + + + +oaa_c->e_12_center + + + + +oaa_c->e_14_center + + + + +oaa_c->e_79_center + + + + +nadph_c + +nadph_c + + + +nadph_c->e_12_center + + + + +nadph_c->e_54_center + + + + +nadph_c->e_67_center + + + + +f6p_c + +f6p_c + + + +f6p_c->e_12_center + + + + +f6p_c->e_71_center + + + + +g3p_c + +g3p_c + + + +g3p_c->e_12_center + + + + +g3p_c->e_48_center + + + + +e_90_center + + + + +g3p_c->e_90_center + + + + +pyr_c + +pyr_c + + + +pyr_c->e_12_center + + + + +pyr_c->e_70_center + + + + +pyr_c->e_72_center + + + + +pyr_c->e_80_center + + + + +g6p_c + +g6p_c + + + +g6p_c->f6p_c + + + + + +g6p_c->e_12_center + + + + +e_47_center + + + + +g6p_c->e_47_center + + + + +e4p_c + +e4p_c + + + +e4p_c->e_12_center + + + + +e_93_center + + + + +e4p_c->e_93_center + + + + +3pg_c + +3pg_c + + + +3pg_c->e_12_center + + + + +3pg_c->e_74_center + + + + +r5p_c + +r5p_c + + + +r5p_c->e_12_center + + + + +ru5p__D_c + +ru5p__D_c + + + +r5p_c->ru5p__D_c + + + + + +e_92_center + + + + +r5p_c->e_92_center + + + + +nadp_c + +nadp_c + + + +nadp_c->e_47_center + + + + +nadp_c->e_52_center + + + + +e_56_center + + + + +nadp_c->e_56_center + + + + +nadp_c->e_58_center + + + + +e_65_center + + + + +nadp_c->e_65_center + + + + +nadp_c->e_91_center + + + + +e_12_center->coa_c + + + + + +e_12_center->h_c + + + + + +e_12_center->nadh_c + + + + + +e_12_center->adp_c + + + + + +e_12_center->akg_c + + + + + +e_12_center->pi_c + + + + + +e_12_center->nadp_c + + + + + +co2_e + +co2_e + + + +co2_e->co2_c + + + + + +e_22_target + + + + +co2_e->e_22_target + + + + + +e_14_center->coa_c + + + + + +e_14_center->h_c + + + + + +e_14_center->cit_c + + + + + +o2_c + +o2_c + + + +o2_c->e_15_center + + + + +q8h2_c + +q8h2_c + + + +q8h2_c->e_15_center + + + + +e_43_center + + + + +q8h2_c->e_43_center + + + + +q8_c + +q8_c + + + +q8_c->e_66_center + + + + +e_88_center + + + + +q8_c->e_88_center + + + + +e_15_center->h2o_c + + + + + +e_15_center->h_e + + + + + +e_15_center->q8_c + + + + + +lac__D_e + +lac__D_e + + + +lac__D_e->e_16_center + + + + +e_32_target + + + + +lac__D_e->e_32_target + + + + + +lac__D_c + +lac__D_c + + + +lac__D_c->e_60_center + + + + +e_16_center->h_c + + + + + +e_16_center->lac__D_c + + + + + +2pg_c + +2pg_c + + + +2pg_c->3pg_c + + + + + +e_17_center + + + + +2pg_c->e_17_center + + + + +e_17_center->h2o_c + + + + + +e_17_center->pep_c + + + + + +etoh_e + +etoh_e + + + +etoh_e->e_18_center + + + + +e_23_target + + + + +etoh_e->e_23_target + + + + + +e_18_center->h_c + + + + + +e_18_center->etoh_c + + + + + +e_24_target + + + + +for_e + +for_e + + + +for_e->e_24_target + + + + + +for_e->e_41_center + + + + +e_25_target + + + + +fru_e + +fru_e + + + +fru_e->e_25_target + + + + + +fru_e->e_44_center + + + + +e_26_target + + + + +fum_e + +fum_e + + + +fum_e->e_26_target + + + + + +fum_e->e_46_center + + + + +e_27_target + + + + +glc__D_e + +glc__D_e + + + +glc__D_e->e_27_target + + + + + +glc__D_e->e_49_center + + + + +e_28_target + + + + +gln__L_e + +gln__L_e + + + +gln__L_e->e_28_target + + + + + +gln__L_e->e_51_center + + + + +e_29_target + + + + +glu__L_e + +glu__L_e + + + +glu__L_e->e_29_target + + + + + +glu__L_e->e_55_center + + + + +e_31_target + + + + +h2o_e + +h2o_e + + + +h2o_e->h2o_c + + + + + +h2o_e->e_31_target + + + + + +e_33_target + + + + +mal__L_e + +mal__L_e + + + +mal__L_e->e_33_target + + + + + +mal__L_e->e_62_center + + + + +e_34_target + + + + +nh4_e + +nh4_e + + + +nh4_e->e_34_target + + + + + +nh4_c + +nh4_c + + + +nh4_e->nh4_c + + + + + +e_35_target + + + + +o2_e + +o2_e + + + +o2_e->o2_c + + + + + +o2_e->e_35_target + + + + + +e_36_target + + + + +pi_e + +pi_e + + + +pi_e->e_36_target + + + + + +pi_e->e_77_center + + + + +e_37_target + + + + +pyr_e + +pyr_e + + + +pyr_e->e_37_target + + + + + +pyr_e->e_83_center + + + + +e_38_target + + + + +succ_e + +succ_e + + + +succ_e->e_38_target + + + + + +succ_e->e_86_center + + + + +fdp_c + +fdp_c + + + +e_39_center + + + + +fdp_c->e_39_center + + + + +fdp_c->e_40_center + + + + +dhap_c + +dhap_c + + + +dhap_c->g3p_c + + + + + +e_39_center->g3p_c + + + + + +e_39_center->dhap_c + + + + + +e_40_center->pi_c + + + + + +e_40_center->f6p_c + + + + + +for_c + +for_c + + + +for_c->for_e + + + + + +e_41_center->h_c + + + + + +e_41_center->for_c + + + + + +fum_c + +fum_c + + + +fum_c->e_43_center + + + + +fum_c->e_45_center + + + + +succ_c + +succ_c + + + +succ_c->e_87_center + + + + +succ_c->e_88_center + + + + +succ_c->e_89_center + + + + +e_43_center->q8_c + + + + + +e_43_center->succ_c + + + + + +e_44_center->f6p_c + + + + + +e_44_center->pyr_c + + + + + +mal__L_c + +mal__L_c + + + +mal__L_c->e_63_center + + + + +mal__L_c->e_64_center + + + + +mal__L_c->e_65_center + + + + +e_45_center->mal__L_c + + + + + +e_46_center->h_c + + + + + +e_46_center->fum_c + + + + + +6pgl_c + +6pgl_c + + + +6pgl_c->e_75_center + + + + +e_47_center->h_c + + + + + +e_47_center->nadph_c + + + + + +e_47_center->6pgl_c + + + + + +13dpg_c + +13dpg_c + + + +e_48_center->h_c + + + + + +e_48_center->nadh_c + + + + + +e_48_center->13dpg_c + + + + + +e_49_center->pyr_c + + + + + +e_49_center->g6p_c + + + + + +nh4_c->e_50_center + + + + +e_50_center->h_c + + + + + +e_50_center->adp_c + + + + + +e_50_center->pi_c + + + + + +e_50_center->gln__L_c + + + + + +e_51_center->h_c + + + + + +e_51_center->adp_c + + + + + +e_51_center->pi_c + + + + + +e_51_center->gln__L_c + + + + + +e_52_center->h_c + + + + + +e_52_center->akg_c + + + + + +e_52_center->nadph_c + + + + + +e_52_center->nh4_c + + + + + +e_53_center->glu__L_c + + + + + +e_53_center->nh4_c + + + + + +e_54_center->glu__L_c + + + + + +e_54_center->nadp_c + + + + + +e_55_center->h_c + + + + + +e_55_center->glu__L_c + + + + + +6pgc_c + +6pgc_c + + + +6pgc_c->e_56_center + + + + +xu5p__D_c + +xu5p__D_c + + + +ru5p__D_c->xu5p__D_c + + + + + +e_56_center->co2_c + + + + + +e_56_center->nadph_c + + + + + +e_56_center->ru5p__D_c + + + + + +e_58_center->akg_c + + + + + +e_58_center->co2_c + + + + + +e_58_center->nadph_c + + + + + +glx_c + +glx_c + + + +glx_c->e_61_center + + + + +e_59_center->succ_c + + + + + +e_59_center->glx_c + + + + + +e_60_center->h_c + + + + + +e_60_center->nadh_c + + + + + +e_60_center->pyr_c + + + + + +e_61_center->coa_c + + + + + +e_61_center->h_c + + + + + +e_61_center->mal__L_c + + + + + +e_62_center->h_c + + + + + +e_62_center->mal__L_c + + + + + +e_63_center->h_c + + + + + +e_63_center->nadh_c + + + + + +e_63_center->oaa_c + + + + + +e_64_center->nadh_c + + + + + +e_64_center->co2_c + + + + + +e_64_center->pyr_c + + + + + +e_65_center->co2_c + + + + + +e_65_center->nadph_c + + + + + +e_65_center->pyr_c + + + + + +e_66_center->nad_c + + + + + +e_66_center->h_e + + + + + +e_66_center->q8h2_c + + + + + +e_67_center->nadh_c + + + + + +e_67_center->nadp_c + + + + + +e_70_center->nadh_c + + + + + +e_70_center->accoa_c + + + + + +e_70_center->co2_c + + + + + +e_71_center->h_c + + + + + +e_71_center->adp_c + + + + + +e_71_center->fdp_c + + + + + +e_72_center->accoa_c + + + + + +e_72_center->for_c + + + + + +e_74_center->adp_c + + + + + +e_74_center->13dpg_c + + + + + +e_75_center->h_c + + + + + +e_75_center->6pgc_c + + + + + +e_77_center->h_c + + + + + +e_77_center->pi_c + + + + + +e_78_center->h_c + + + + + +e_78_center->pi_c + + + + + +e_78_center->oaa_c + + + + + +e_79_center->adp_c + + + + + +e_79_center->co2_c + + + + + +e_79_center->pep_c + + + + + +e_80_center->h_c + + + + + +e_80_center->amp_c + + + + + +e_80_center->pi_c + + + + + +e_80_center->pep_c + + + + + +e_81_center->coa_c + + + + + +e_81_center->actp_c + + + + + +e_82_center->atp_c + + + + + +e_82_center->pyr_c + + + + + +e_83_center->h_c + + + + + +e_83_center->pyr_c + + + + + +xu5p__D_c->e_92_center + + + + +xu5p__D_c->e_93_center + + + + +e_86_center->h_c + + + + + +e_86_center->succ_c + + + + + +e_87_center->h_c + + + + + +e_87_center->succ_e + + + + + +e_88_center->q8h2_c + + + + + +e_88_center->fum_c + + + + + +e_89_center->adp_c + + + + + +e_89_center->succoa_c + + + + + +e_89_center->pi_c + + + + + +s7p_c + +s7p_c + + + +s7p_c->e_90_center + + + + +e_90_center->f6p_c + + + + + +e_90_center->e4p_c + + + + + +e_91_center->nad_c + + + + + +e_91_center->h_c + + + + + +e_91_center->nadph_c + + + + + +e_92_center->g3p_c + + + + + +e_92_center->s7p_c + + + + + +e_93_center->f6p_c + + + + + +e_93_center->g3p_c + + + + + \ No newline at end of file diff --git a/docs/_build/html/jupyter_execute/a18af31210c20b9afdc10fc3443dfc3ddab9d41d7f88310804f0f80d84116ddc.svg b/docs/_build/html/jupyter_execute/a18af31210c20b9afdc10fc3443dfc3ddab9d41d7f88310804f0f80d84116ddc.svg new file mode 100644 index 00000000..abb919aa --- /dev/null +++ b/docs/_build/html/jupyter_execute/a18af31210c20b9afdc10fc3443dfc3ddab9d41d7f88310804f0f80d84116ddc.svg @@ -0,0 +1,58 @@ + + + + + + +%3 + + + +I2 + +I2 + + + +N2 + +N2 + + + +I2->N2 + + + + + + +M2 + +M2 + + + +N2->M2 + + + + + + +M1 + +M1 + + + +N2->M1 + + + + + + \ No newline at end of file diff --git a/docs/_build/html/jupyter_execute/a611717058041567090a4563f14a2f8125974cc83a7f80508687554b10f489ef.svg b/docs/_build/html/jupyter_execute/a611717058041567090a4563f14a2f8125974cc83a7f80508687554b10f489ef.svg new file mode 100644 index 00000000..06648725 --- /dev/null +++ b/docs/_build/html/jupyter_execute/a611717058041567090a4563f14a2f8125974cc83a7f80508687554b10f489ef.svg @@ -0,0 +1,339 @@ + + + + + + +%3 + + + +EGFR + +EGFR + + + +STAT1 + +STAT1 + + + +EGFR->STAT1 + + + + + +ERBB2 + +ERBB2 + + + +EGFR->ERBB2 + + + + + +MAP2K1 + +MAP2K1 + + + +EGFR->MAP2K1 + + + + + +PIK3R1 + +PIK3R1 + + + +EGFR->PIK3R1 + + + + + +CRK + +CRK + + + +EGFR->CRK + + + + + + +PTPN1 + +PTPN1 + + + +EGFR->PTPN1 + + + + + +CREBBP + +CREBBP + + + +STAT1->CREBBP + + + + + + +MAPK8 + +MAPK8 + + + +SIRT1 + +SIRT1 + + + +MAPK8->SIRT1 + + + + + +NFATC4 + +NFATC4 + + + +MAPK8->NFATC4 + + + + + + +CDK1 + +CDK1 + + + +ERBB2->CDK1 + + + + + + +MAPK1 + +MAPK1 + + + +MAP2K1->MAPK1 + + + + + +MAPK3 + +MAPK3 + + + +MAP2K1->MAPK3 + + + + + +ELK1 + +ELK1 + + + +MAPK1->ELK1 + + + + + +AEBP1 + +AEBP1 + + + +MAPK1->AEBP1 + + + + + +TP53 + +TP53 + + + +CREBBP->TP53 + + + + + +CSNK2A1 + +CSNK2A1 + + + +HOXB7 + +HOXB7 + + + +CSNK2A1->HOXB7 + + + + + + +ABL1 + +ABL1 + + + +HIPK2 + +HIPK2 + + + +ABL1->HIPK2 + + + + + +ZBTB4 + +ZBTB4 + + + +HIPK2->ZBTB4 + + + + + + +RAC1 + +RAC1 + + + +PIK3R1->RAC1 + + + + + +MAP3K10 + +MAP3K10 + + + +RAC1->MAP3K10 + + + + + +RUNX2 + +RUNX2 + + + +MAPK3->RUNX2 + + + + + +CRK->MAPK8 + + + + + +PTPN1->ABL1 + + + + + + +NFYB + +NFYB + + + +TP53->NFYB + + + + + + +CDK1->CSNK2A1 + + + + + +NEUROD1 + +NEUROD1 + + + +MAP3K10->NEUROD1 + + + + + \ No newline at end of file diff --git a/docs/_build/html/jupyter_execute/aa13e66ecb35e387e408e46e79325f80b19a3d0487cc439bf3c02c3ed740686c.svg b/docs/_build/html/jupyter_execute/aa13e66ecb35e387e408e46e79325f80b19a3d0487cc439bf3c02c3ed740686c.svg new file mode 100644 index 00000000..f8836717 --- /dev/null +++ b/docs/_build/html/jupyter_execute/aa13e66ecb35e387e408e46e79325f80b19a3d0487cc439bf3c02c3ed740686c.svg @@ -0,0 +1,2802 @@ + + + + + + +%3 + + + +acald_c + +acald_c + + + +e_0_center + + + + +acald_c->e_0_center + + + + +nad_c + +nad_c + + + +nad_c->e_0_center + + + + +e_7_center + + + + +nad_c->e_7_center + + + + +e_9_center + + + + +nad_c->e_9_center + + + + +e_12_center + + + + +nad_c->e_12_center + + + + +e_48_center + + + + +nad_c->e_48_center + + + + +e_60_center + + + + +nad_c->e_60_center + + + + +e_63_center + + + + +nad_c->e_63_center + + + + +e_64_center + + + + +nad_c->e_64_center + + + + +e_67_center + + + + +nad_c->e_67_center + + + + +e_70_center + + + + +nad_c->e_70_center + + + + +coa_c + +coa_c + + + +coa_c->e_0_center + + + + +coa_c->e_7_center + + + + +coa_c->e_70_center + + + + +e_72_center + + + + +coa_c->e_72_center + + + + +e_89_center + + + + +coa_c->e_89_center + + + + +accoa_c + +accoa_c + + + +accoa_c->e_12_center + + + + +e_14_center + + + + +accoa_c->e_14_center + + + + +e_61_center + + + + +accoa_c->e_61_center + + + + +e_81_center + + + + +accoa_c->e_81_center + + + + +h_c + +h_c + + + +e_15_center + + + + +h_c->e_15_center + + + + +e_54_center + + + + +h_c->e_54_center + + + + +e_66_center + + + + +h_c->e_66_center + + + + +e_82_center + + + + +h_c->e_82_center + + + + +nadh_c + +nadh_c + + + +nadh_c->e_66_center + + + + +e_91_center + + + + +nadh_c->e_91_center + + + + +e_0_center->accoa_c + + + + + +e_0_center->h_c + + + + + +e_0_center->nadh_c + + + + + +acald_e + +acald_e + + + +acald_e->acald_c + + + + + +e_20_target + + + + +acald_e->e_20_target + + + + + +atp_c + +atp_c + + + +e_2_center + + + + +atp_c->e_2_center + + + + +e_6_center + + + + +atp_c->e_6_center + + + + +e_10_center + + + + +atp_c->e_10_center + + + + +atp_c->e_12_center + + + + +e_50_center + + + + +atp_c->e_50_center + + + + +e_51_center + + + + +atp_c->e_51_center + + + + +e_71_center + + + + +atp_c->e_71_center + + + + +e_74_center + + + + +atp_c->e_74_center + + + + +e_79_center + + + + +atp_c->e_79_center + + + + +e_80_center + + + + +atp_c->e_80_center + + + + +atp_c->e_89_center + + + + +ac_c + +ac_c + + + +ac_c->e_2_center + + + + +actp_c + +actp_c + + + +adp_c + +adp_c + + + +e_11_center + + + + +adp_c->e_11_center + + + + +adp_c->e_82_center + + + + +e_2_center->actp_c + + + + + +e_2_center->adp_c + + + + + +cit_c + +cit_c + + + +e_3_center + + + + +cit_c->e_3_center + + + + +acon_C_c + +acon_C_c + + + +e_4_center + + + + +acon_C_c->e_4_center + + + + +h2o_c + +h2o_c + + + +h2o_c->e_4_center + + + + +h2o_c->e_10_center + + + + +h2o_c->e_12_center + + + + +h2o_c->e_14_center + + + + +e_40_center + + + + +h2o_c->e_40_center + + + + +e_45_center + + + + +h2o_c->e_45_center + + + + +h2o_c->e_51_center + + + + +e_52_center + + + + +h2o_c->e_52_center + + + + +e_53_center + + + + +h2o_c->e_53_center + + + + +h2o_c->e_61_center + + + + +e_75_center + + + + +h2o_c->e_75_center + + + + +e_78_center + + + + +h2o_c->e_78_center + + + + +h2o_c->e_80_center + + + + +e_3_center->acon_C_c + + + + + +e_3_center->h2o_c + + + + + +icit_c + +icit_c + + + +e_58_center + + + + +icit_c->e_58_center + + + + +e_59_center + + + + +icit_c->e_59_center + + + + +e_4_center->icit_c + + + + + +ac_e + +ac_e + + + +e_5_center + + + + +ac_e->e_5_center + + + + +e_19_target + + + + +ac_e->e_19_target + + + + + +h_e + +h_e + + + +h_e->e_5_center + + + + +e_8_center + + + + +h_e->e_8_center + + + + +h_e->e_11_center + + + + +e_16_center + + + + +h_e->e_16_center + + + + +e_18_center + + + + +h_e->e_18_center + + + + +e_30_target + + + + +h_e->e_30_target + + + + + +e_41_center + + + + +h_e->e_41_center + + + + +e_46_center + + + + +h_e->e_46_center + + + + +e_55_center + + + + +h_e->e_55_center + + + + +e_62_center + + + + +h_e->e_62_center + + + + +e_77_center + + + + +h_e->e_77_center + + + + +e_83_center + + + + +h_e->e_83_center + + + + +e_86_center + + + + +h_e->e_86_center + + + + +e_87_center + + + + +h_e->e_87_center + + + + +h_e->e_91_center + + + + +e_5_center->h_c + + + + + +e_5_center->ac_c + + + + + +amp_c + +amp_c + + + +amp_c->e_6_center + + + + +e_6_center->adp_c + + + + + +akg_c + +akg_c + + + +akg_c->e_7_center + + + + +akg_c->e_54_center + + + + +co2_c + +co2_c + + + +co2_c->e_78_center + + + + +succoa_c + +succoa_c + + + +e_7_center->nadh_c + + + + + +e_7_center->co2_c + + + + + +e_7_center->succoa_c + + + + + +akg_e + +akg_e + + + +akg_e->e_8_center + + + + +e_21_target + + + + +akg_e->e_21_target + + + + + +e_8_center->h_c + + + + + +e_8_center->akg_c + + + + + +etoh_c + +etoh_c + + + +etoh_c->e_9_center + + + + +e_9_center->acald_c + + + + + +e_9_center->h_c + + + + + +e_9_center->nadh_c + + + + + +pi_c + +pi_c + + + +pi_c->e_11_center + + + + +pi_c->e_48_center + + + + +pi_c->e_81_center + + + + +e_10_center->h_c + + + + + +e_10_center->adp_c + + + + + +e_10_center->pi_c + + + + + +e_11_center->h_c + + + + + +e_11_center->atp_c + + + + + +e_11_center->h2o_c + + + + + +r5p_c + +r5p_c + + + +r5p_c->e_12_center + + + + +ru5p__D_c + +ru5p__D_c + + + +r5p_c->ru5p__D_c + + + + + +e_92_center + + + + +r5p_c->e_92_center + + + + +nadph_c + +nadph_c + + + +nadph_c->e_12_center + + + + +nadph_c->e_54_center + + + + +nadph_c->e_67_center + + + + +oaa_c + +oaa_c + + + +oaa_c->e_12_center + + + + +oaa_c->e_14_center + + + + +oaa_c->e_79_center + + + + +glu__L_c + +glu__L_c + + + +glu__L_c->e_12_center + + + + +glu__L_c->e_50_center + + + + +glu__L_c->e_52_center + + + + +g3p_c + +g3p_c + + + +g3p_c->e_12_center + + + + +g3p_c->e_48_center + + + + +e_90_center + + + + +g3p_c->e_90_center + + + + +3pg_c + +3pg_c + + + +3pg_c->e_12_center + + + + +3pg_c->e_74_center + + + + +pyr_c + +pyr_c + + + +pyr_c->e_12_center + + + + +pyr_c->e_70_center + + + + +pyr_c->e_72_center + + + + +pyr_c->e_80_center + + + + +pep_c + +pep_c + + + +pep_c->e_12_center + + + + +e_44_center + + + + +pep_c->e_44_center + + + + +e_49_center + + + + +pep_c->e_49_center + + + + +pep_c->e_78_center + + + + +pep_c->e_82_center + + + + +f6p_c + +f6p_c + + + +f6p_c->e_12_center + + + + +f6p_c->e_71_center + + + + +g6p_c + +g6p_c + + + +g6p_c->f6p_c + + + + + +g6p_c->e_12_center + + + + +e_47_center + + + + +g6p_c->e_47_center + + + + +e4p_c + +e4p_c + + + +e4p_c->e_12_center + + + + +e_93_center + + + + +e4p_c->e_93_center + + + + +gln__L_c + +gln__L_c + + + +gln__L_c->e_12_center + + + + +gln__L_c->e_53_center + + + + +gln__L_c->e_54_center + + + + +nadp_c + +nadp_c + + + +nadp_c->e_47_center + + + + +nadp_c->e_52_center + + + + +e_56_center + + + + +nadp_c->e_56_center + + + + +nadp_c->e_58_center + + + + +e_65_center + + + + +nadp_c->e_65_center + + + + +nadp_c->e_91_center + + + + +e_12_center->coa_c + + + + + +e_12_center->h_c + + + + + +e_12_center->nadh_c + + + + + +e_12_center->adp_c + + + + + +e_12_center->akg_c + + + + + +e_12_center->pi_c + + + + + +e_12_center->nadp_c + + + + + +co2_e + +co2_e + + + +co2_e->co2_c + + + + + +e_22_target + + + + +co2_e->e_22_target + + + + + +e_14_center->coa_c + + + + + +e_14_center->h_c + + + + + +e_14_center->cit_c + + + + + +o2_c + +o2_c + + + +o2_c->e_15_center + + + + +q8h2_c + +q8h2_c + + + +q8h2_c->e_15_center + + + + +e_43_center + + + + +q8h2_c->e_43_center + + + + +q8_c + +q8_c + + + +q8_c->e_66_center + + + + +e_88_center + + + + +q8_c->e_88_center + + + + +e_15_center->h2o_c + + + + + +e_15_center->h_e + + + + + +e_15_center->q8_c + + + + + +lac__D_e + +lac__D_e + + + +lac__D_e->e_16_center + + + + +e_32_target + + + + +lac__D_e->e_32_target + + + + + +lac__D_c + +lac__D_c + + + +lac__D_c->e_60_center + + + + +e_16_center->h_c + + + + + +e_16_center->lac__D_c + + + + + +2pg_c + +2pg_c + + + +2pg_c->3pg_c + + + + + +e_17_center + + + + +2pg_c->e_17_center + + + + +e_17_center->h2o_c + + + + + +e_17_center->pep_c + + + + + +etoh_e + +etoh_e + + + +etoh_e->e_18_center + + + + +e_23_target + + + + +etoh_e->e_23_target + + + + + +e_18_center->h_c + + + + + +e_18_center->etoh_c + + + + + +e_24_target + + + + +for_e + +for_e + + + +for_e->e_24_target + + + + + +for_e->e_41_center + + + + +e_25_target + + + + +fru_e + +fru_e + + + +fru_e->e_25_target + + + + + +fru_e->e_44_center + + + + +e_26_target + + + + +fum_e + +fum_e + + + +fum_e->e_26_target + + + + + +fum_e->e_46_center + + + + +e_27_target + + + + +glc__D_e + +glc__D_e + + + +glc__D_e->e_27_target + + + + + +glc__D_e->e_49_center + + + + +e_28_target + + + + +gln__L_e + +gln__L_e + + + +gln__L_e->e_28_target + + + + + +gln__L_e->e_51_center + + + + +e_29_target + + + + +glu__L_e + +glu__L_e + + + +glu__L_e->e_29_target + + + + + +glu__L_e->e_55_center + + + + +e_31_target + + + + +h2o_e + +h2o_e + + + +h2o_e->h2o_c + + + + + +h2o_e->e_31_target + + + + + +e_33_target + + + + +mal__L_e + +mal__L_e + + + +mal__L_e->e_33_target + + + + + +mal__L_e->e_62_center + + + + +e_34_target + + + + +nh4_e + +nh4_e + + + +nh4_e->e_34_target + + + + + +nh4_c + +nh4_c + + + +nh4_e->nh4_c + + + + + +e_35_target + + + + +o2_e + +o2_e + + + +o2_e->o2_c + + + + + +o2_e->e_35_target + + + + + +e_36_target + + + + +pi_e + +pi_e + + + +pi_e->e_36_target + + + + + +pi_e->e_77_center + + + + +e_37_target + + + + +pyr_e + +pyr_e + + + +pyr_e->e_37_target + + + + + +pyr_e->e_83_center + + + + +e_38_target + + + + +succ_e + +succ_e + + + +succ_e->e_38_target + + + + + +succ_e->e_86_center + + + + +fdp_c + +fdp_c + + + +e_39_center + + + + +fdp_c->e_39_center + + + + +fdp_c->e_40_center + + + + +dhap_c + +dhap_c + + + +dhap_c->g3p_c + + + + + +e_39_center->g3p_c + + + + + +e_39_center->dhap_c + + + + + +e_40_center->pi_c + + + + + +e_40_center->f6p_c + + + + + +for_c + +for_c + + + +for_c->for_e + + + + + +e_41_center->h_c + + + + + +e_41_center->for_c + + + + + +fum_c + +fum_c + + + +fum_c->e_43_center + + + + +fum_c->e_45_center + + + + +succ_c + +succ_c + + + +succ_c->e_87_center + + + + +succ_c->e_88_center + + + + +succ_c->e_89_center + + + + +e_43_center->q8_c + + + + + +e_43_center->succ_c + + + + + +e_44_center->pyr_c + + + + + +e_44_center->f6p_c + + + + + +mal__L_c + +mal__L_c + + + +mal__L_c->e_63_center + + + + +mal__L_c->e_64_center + + + + +mal__L_c->e_65_center + + + + +e_45_center->mal__L_c + + + + + +e_46_center->h_c + + + + + +e_46_center->fum_c + + + + + +6pgl_c + +6pgl_c + + + +6pgl_c->e_75_center + + + + +e_47_center->h_c + + + + + +e_47_center->nadph_c + + + + + +e_47_center->6pgl_c + + + + + +13dpg_c + +13dpg_c + + + +e_48_center->h_c + + + + + +e_48_center->nadh_c + + + + + +e_48_center->13dpg_c + + + + + +e_49_center->pyr_c + + + + + +e_49_center->g6p_c + + + + + +nh4_c->e_50_center + + + + +e_50_center->h_c + + + + + +e_50_center->adp_c + + + + + +e_50_center->pi_c + + + + + +e_50_center->gln__L_c + + + + + +e_51_center->h_c + + + + + +e_51_center->adp_c + + + + + +e_51_center->pi_c + + + + + +e_51_center->gln__L_c + + + + + +e_52_center->h_c + + + + + +e_52_center->akg_c + + + + + +e_52_center->nadph_c + + + + + +e_52_center->nh4_c + + + + + +e_53_center->glu__L_c + + + + + +e_53_center->nh4_c + + + + + +e_54_center->glu__L_c + + + + + +e_54_center->nadp_c + + + + + +e_55_center->h_c + + + + + +e_55_center->glu__L_c + + + + + +6pgc_c + +6pgc_c + + + +6pgc_c->e_56_center + + + + +xu5p__D_c + +xu5p__D_c + + + +ru5p__D_c->xu5p__D_c + + + + + +e_56_center->co2_c + + + + + +e_56_center->nadph_c + + + + + +e_56_center->ru5p__D_c + + + + + +e_58_center->akg_c + + + + + +e_58_center->co2_c + + + + + +e_58_center->nadph_c + + + + + +glx_c + +glx_c + + + +glx_c->e_61_center + + + + +e_59_center->succ_c + + + + + +e_59_center->glx_c + + + + + +e_60_center->h_c + + + + + +e_60_center->nadh_c + + + + + +e_60_center->pyr_c + + + + + +e_61_center->coa_c + + + + + +e_61_center->h_c + + + + + +e_61_center->mal__L_c + + + + + +e_62_center->h_c + + + + + +e_62_center->mal__L_c + + + + + +e_63_center->h_c + + + + + +e_63_center->nadh_c + + + + + +e_63_center->oaa_c + + + + + +e_64_center->nadh_c + + + + + +e_64_center->co2_c + + + + + +e_64_center->pyr_c + + + + + +e_65_center->co2_c + + + + + +e_65_center->nadph_c + + + + + +e_65_center->pyr_c + + + + + +e_66_center->nad_c + + + + + +e_66_center->h_e + + + + + +e_66_center->q8h2_c + + + + + +e_67_center->nadh_c + + + + + +e_67_center->nadp_c + + + + + +e_70_center->accoa_c + + + + + +e_70_center->nadh_c + + + + + +e_70_center->co2_c + + + + + +e_71_center->h_c + + + + + +e_71_center->adp_c + + + + + +e_71_center->fdp_c + + + + + +e_72_center->accoa_c + + + + + +e_72_center->for_c + + + + + +e_74_center->adp_c + + + + + +e_74_center->13dpg_c + + + + + +e_75_center->h_c + + + + + +e_75_center->6pgc_c + + + + + +e_77_center->h_c + + + + + +e_77_center->pi_c + + + + + +e_78_center->h_c + + + + + +e_78_center->pi_c + + + + + +e_78_center->oaa_c + + + + + +e_79_center->adp_c + + + + + +e_79_center->co2_c + + + + + +e_79_center->pep_c + + + + + +e_80_center->h_c + + + + + +e_80_center->amp_c + + + + + +e_80_center->pi_c + + + + + +e_80_center->pep_c + + + + + +e_81_center->coa_c + + + + + +e_81_center->actp_c + + + + + +e_82_center->atp_c + + + + + +e_82_center->pyr_c + + + + + +e_83_center->h_c + + + + + +e_83_center->pyr_c + + + + + +xu5p__D_c->e_92_center + + + + +xu5p__D_c->e_93_center + + + + +e_86_center->h_c + + + + + +e_86_center->succ_c + + + + + +e_87_center->h_c + + + + + +e_87_center->succ_e + + + + + +e_88_center->q8h2_c + + + + + +e_88_center->fum_c + + + + + +e_89_center->adp_c + + + + + +e_89_center->succoa_c + + + + + +e_89_center->pi_c + + + + + +s7p_c + +s7p_c + + + +s7p_c->e_90_center + + + + +e_90_center->f6p_c + + + + + +e_90_center->e4p_c + + + + + +e_91_center->nad_c + + + + + +e_91_center->h_c + + + + + +e_91_center->nadph_c + + + + + +e_92_center->g3p_c + + + + + +e_92_center->s7p_c + + + + + +e_93_center->g3p_c + + + + + +e_93_center->f6p_c + + + + + \ No newline at end of file diff --git a/docs/_build/html/jupyter_execute/cec93c0a71c17db5062ee6115e31bc12efabe34882770aed1ced1bdbd70dde75.svg b/docs/_build/html/jupyter_execute/cec93c0a71c17db5062ee6115e31bc12efabe34882770aed1ced1bdbd70dde75.svg new file mode 100644 index 00000000..93548619 --- /dev/null +++ b/docs/_build/html/jupyter_execute/cec93c0a71c17db5062ee6115e31bc12efabe34882770aed1ced1bdbd70dde75.svg @@ -0,0 +1,2802 @@ + + + + + + +%3 + + + +nad_c + +nad_c + + + +e_0_center + + + + +nad_c->e_0_center + + + + +e_7_center + + + + +nad_c->e_7_center + + + + +e_9_center + + + + +nad_c->e_9_center + + + + +e_12_center + + + + +nad_c->e_12_center + + + + +e_48_center + + + + +nad_c->e_48_center + + + + +e_60_center + + + + +nad_c->e_60_center + + + + +e_63_center + + + + +nad_c->e_63_center + + + + +e_64_center + + + + +nad_c->e_64_center + + + + +e_67_center + + + + +nad_c->e_67_center + + + + +e_70_center + + + + +nad_c->e_70_center + + + + +acald_c + +acald_c + + + +acald_c->e_0_center + + + + +coa_c + +coa_c + + + +coa_c->e_0_center + + + + +coa_c->e_7_center + + + + +coa_c->e_70_center + + + + +e_72_center + + + + +coa_c->e_72_center + + + + +e_89_center + + + + +coa_c->e_89_center + + + + +h_c + +h_c + + + +e_15_center + + + + +h_c->e_15_center + + + + +e_54_center + + + + +h_c->e_54_center + + + + +e_66_center + + + + +h_c->e_66_center + + + + +e_82_center + + + + +h_c->e_82_center + + + + +nadh_c + +nadh_c + + + +nadh_c->e_66_center + + + + +e_91_center + + + + +nadh_c->e_91_center + + + + +accoa_c + +accoa_c + + + +accoa_c->e_12_center + + + + +e_14_center + + + + +accoa_c->e_14_center + + + + +e_61_center + + + + +accoa_c->e_61_center + + + + +e_81_center + + + + +accoa_c->e_81_center + + + + +e_0_center->h_c + + + + + +e_0_center->nadh_c + + + + + +e_0_center->accoa_c + + + + + +acald_e + +acald_e + + + +acald_e->acald_c + + + + + +e_20_target + + + + +acald_e->e_20_target + + + + + +ac_c + +ac_c + + + +e_2_center + + + + +ac_c->e_2_center + + + + +atp_c + +atp_c + + + +atp_c->e_2_center + + + + +e_6_center + + + + +atp_c->e_6_center + + + + +e_10_center + + + + +atp_c->e_10_center + + + + +atp_c->e_12_center + + + + +e_50_center + + + + +atp_c->e_50_center + + + + +e_51_center + + + + +atp_c->e_51_center + + + + +e_71_center + + + + +atp_c->e_71_center + + + + +e_74_center + + + + +atp_c->e_74_center + + + + +e_79_center + + + + +atp_c->e_79_center + + + + +e_80_center + + + + +atp_c->e_80_center + + + + +atp_c->e_89_center + + + + +adp_c + +adp_c + + + +e_11_center + + + + +adp_c->e_11_center + + + + +adp_c->e_82_center + + + + +actp_c + +actp_c + + + +e_2_center->adp_c + + + + + +e_2_center->actp_c + + + + + +cit_c + +cit_c + + + +e_3_center + + + + +cit_c->e_3_center + + + + +h2o_c + +h2o_c + + + +e_4_center + + + + +h2o_c->e_4_center + + + + +h2o_c->e_10_center + + + + +h2o_c->e_12_center + + + + +h2o_c->e_14_center + + + + +e_40_center + + + + +h2o_c->e_40_center + + + + +e_45_center + + + + +h2o_c->e_45_center + + + + +h2o_c->e_51_center + + + + +e_52_center + + + + +h2o_c->e_52_center + + + + +e_53_center + + + + +h2o_c->e_53_center + + + + +h2o_c->e_61_center + + + + +e_75_center + + + + +h2o_c->e_75_center + + + + +e_78_center + + + + +h2o_c->e_78_center + + + + +h2o_c->e_80_center + + + + +acon_C_c + +acon_C_c + + + +acon_C_c->e_4_center + + + + +e_3_center->h2o_c + + + + + +e_3_center->acon_C_c + + + + + +icit_c + +icit_c + + + +e_58_center + + + + +icit_c->e_58_center + + + + +e_59_center + + + + +icit_c->e_59_center + + + + +e_4_center->icit_c + + + + + +ac_e + +ac_e + + + +e_5_center + + + + +ac_e->e_5_center + + + + +e_19_target + + + + +ac_e->e_19_target + + + + + +h_e + +h_e + + + +h_e->e_5_center + + + + +e_8_center + + + + +h_e->e_8_center + + + + +h_e->e_11_center + + + + +e_16_center + + + + +h_e->e_16_center + + + + +e_18_center + + + + +h_e->e_18_center + + + + +e_30_target + + + + +h_e->e_30_target + + + + + +e_41_center + + + + +h_e->e_41_center + + + + +e_46_center + + + + +h_e->e_46_center + + + + +e_55_center + + + + +h_e->e_55_center + + + + +e_62_center + + + + +h_e->e_62_center + + + + +e_77_center + + + + +h_e->e_77_center + + + + +e_83_center + + + + +h_e->e_83_center + + + + +e_86_center + + + + +h_e->e_86_center + + + + +e_87_center + + + + +h_e->e_87_center + + + + +h_e->e_91_center + + + + +e_5_center->h_c + + + + + +e_5_center->ac_c + + + + + +amp_c + +amp_c + + + +amp_c->e_6_center + + + + +e_6_center->adp_c + + + + + +akg_c + +akg_c + + + +akg_c->e_7_center + + + + +akg_c->e_54_center + + + + +co2_c + +co2_c + + + +co2_c->e_78_center + + + + +succoa_c + +succoa_c + + + +e_7_center->nadh_c + + + + + +e_7_center->co2_c + + + + + +e_7_center->succoa_c + + + + + +akg_e + +akg_e + + + +akg_e->e_8_center + + + + +e_21_target + + + + +akg_e->e_21_target + + + + + +e_8_center->h_c + + + + + +e_8_center->akg_c + + + + + +etoh_c + +etoh_c + + + +etoh_c->e_9_center + + + + +e_9_center->acald_c + + + + + +e_9_center->h_c + + + + + +e_9_center->nadh_c + + + + + +pi_c + +pi_c + + + +pi_c->e_11_center + + + + +pi_c->e_48_center + + + + +pi_c->e_81_center + + + + +e_10_center->h_c + + + + + +e_10_center->adp_c + + + + + +e_10_center->pi_c + + + + + +e_11_center->h_c + + + + + +e_11_center->atp_c + + + + + +e_11_center->h2o_c + + + + + +gln__L_c + +gln__L_c + + + +gln__L_c->e_12_center + + + + +gln__L_c->e_53_center + + + + +gln__L_c->e_54_center + + + + +pep_c + +pep_c + + + +pep_c->e_12_center + + + + +e_44_center + + + + +pep_c->e_44_center + + + + +e_49_center + + + + +pep_c->e_49_center + + + + +pep_c->e_78_center + + + + +pep_c->e_82_center + + + + +glu__L_c + +glu__L_c + + + +glu__L_c->e_12_center + + + + +glu__L_c->e_50_center + + + + +glu__L_c->e_52_center + + + + +oaa_c + +oaa_c + + + +oaa_c->e_12_center + + + + +oaa_c->e_14_center + + + + +oaa_c->e_79_center + + + + +nadph_c + +nadph_c + + + +nadph_c->e_12_center + + + + +nadph_c->e_54_center + + + + +nadph_c->e_67_center + + + + +f6p_c + +f6p_c + + + +f6p_c->e_12_center + + + + +f6p_c->e_71_center + + + + +g3p_c + +g3p_c + + + +g3p_c->e_12_center + + + + +g3p_c->e_48_center + + + + +e_90_center + + + + +g3p_c->e_90_center + + + + +pyr_c + +pyr_c + + + +pyr_c->e_12_center + + + + +pyr_c->e_70_center + + + + +pyr_c->e_72_center + + + + +pyr_c->e_80_center + + + + +g6p_c + +g6p_c + + + +g6p_c->f6p_c + + + + + +g6p_c->e_12_center + + + + +e_47_center + + + + +g6p_c->e_47_center + + + + +e4p_c + +e4p_c + + + +e4p_c->e_12_center + + + + +e_93_center + + + + +e4p_c->e_93_center + + + + +3pg_c + +3pg_c + + + +3pg_c->e_12_center + + + + +3pg_c->e_74_center + + + + +r5p_c + +r5p_c + + + +r5p_c->e_12_center + + + + +ru5p__D_c + +ru5p__D_c + + + +r5p_c->ru5p__D_c + + + + + +e_92_center + + + + +r5p_c->e_92_center + + + + +nadp_c + +nadp_c + + + +nadp_c->e_47_center + + + + +nadp_c->e_52_center + + + + +e_56_center + + + + +nadp_c->e_56_center + + + + +nadp_c->e_58_center + + + + +e_65_center + + + + +nadp_c->e_65_center + + + + +nadp_c->e_91_center + + + + +e_12_center->coa_c + + + + + +e_12_center->h_c + + + + + +e_12_center->nadh_c + + + + + +e_12_center->adp_c + + + + + +e_12_center->akg_c + + + + + +e_12_center->pi_c + + + + + +e_12_center->nadp_c + + + + + +co2_e + +co2_e + + + +co2_e->co2_c + + + + + +e_22_target + + + + +co2_e->e_22_target + + + + + +e_14_center->coa_c + + + + + +e_14_center->h_c + + + + + +e_14_center->cit_c + + + + + +o2_c + +o2_c + + + +o2_c->e_15_center + + + + +q8h2_c + +q8h2_c + + + +q8h2_c->e_15_center + + + + +e_43_center + + + + +q8h2_c->e_43_center + + + + +q8_c + +q8_c + + + +q8_c->e_66_center + + + + +e_88_center + + + + +q8_c->e_88_center + + + + +e_15_center->h2o_c + + + + + +e_15_center->h_e + + + + + +e_15_center->q8_c + + + + + +lac__D_e + +lac__D_e + + + +lac__D_e->e_16_center + + + + +e_32_target + + + + +lac__D_e->e_32_target + + + + + +lac__D_c + +lac__D_c + + + +lac__D_c->e_60_center + + + + +e_16_center->h_c + + + + + +e_16_center->lac__D_c + + + + + +2pg_c + +2pg_c + + + +2pg_c->3pg_c + + + + + +e_17_center + + + + +2pg_c->e_17_center + + + + +e_17_center->h2o_c + + + + + +e_17_center->pep_c + + + + + +etoh_e + +etoh_e + + + +etoh_e->e_18_center + + + + +e_23_target + + + + +etoh_e->e_23_target + + + + + +e_18_center->h_c + + + + + +e_18_center->etoh_c + + + + + +e_24_target + + + + +for_e + +for_e + + + +for_e->e_24_target + + + + + +for_e->e_41_center + + + + +e_25_target + + + + +fru_e + +fru_e + + + +fru_e->e_25_target + + + + + +fru_e->e_44_center + + + + +e_26_target + + + + +fum_e + +fum_e + + + +fum_e->e_26_target + + + + + +fum_e->e_46_center + + + + +e_27_target + + + + +glc__D_e + +glc__D_e + + + +glc__D_e->e_27_target + + + + + +glc__D_e->e_49_center + + + + +e_28_target + + + + +gln__L_e + +gln__L_e + + + +gln__L_e->e_28_target + + + + + +gln__L_e->e_51_center + + + + +e_29_target + + + + +glu__L_e + +glu__L_e + + + +glu__L_e->e_29_target + + + + + +glu__L_e->e_55_center + + + + +e_31_target + + + + +h2o_e + +h2o_e + + + +h2o_e->h2o_c + + + + + +h2o_e->e_31_target + + + + + +e_33_target + + + + +mal__L_e + +mal__L_e + + + +mal__L_e->e_33_target + + + + + +mal__L_e->e_62_center + + + + +e_34_target + + + + +nh4_e + +nh4_e + + + +nh4_e->e_34_target + + + + + +nh4_c + +nh4_c + + + +nh4_e->nh4_c + + + + + +e_35_target + + + + +o2_e + +o2_e + + + +o2_e->o2_c + + + + + +o2_e->e_35_target + + + + + +e_36_target + + + + +pi_e + +pi_e + + + +pi_e->e_36_target + + + + + +pi_e->e_77_center + + + + +e_37_target + + + + +pyr_e + +pyr_e + + + +pyr_e->e_37_target + + + + + +pyr_e->e_83_center + + + + +e_38_target + + + + +succ_e + +succ_e + + + +succ_e->e_38_target + + + + + +succ_e->e_86_center + + + + +fdp_c + +fdp_c + + + +e_39_center + + + + +fdp_c->e_39_center + + + + +fdp_c->e_40_center + + + + +dhap_c + +dhap_c + + + +dhap_c->g3p_c + + + + + +e_39_center->g3p_c + + + + + +e_39_center->dhap_c + + + + + +e_40_center->pi_c + + + + + +e_40_center->f6p_c + + + + + +for_c + +for_c + + + +for_c->for_e + + + + + +e_41_center->h_c + + + + + +e_41_center->for_c + + + + + +fum_c + +fum_c + + + +fum_c->e_43_center + + + + +fum_c->e_45_center + + + + +succ_c + +succ_c + + + +succ_c->e_87_center + + + + +succ_c->e_88_center + + + + +succ_c->e_89_center + + + + +e_43_center->q8_c + + + + + +e_43_center->succ_c + + + + + +e_44_center->f6p_c + + + + + +e_44_center->pyr_c + + + + + +mal__L_c + +mal__L_c + + + +mal__L_c->e_63_center + + + + +mal__L_c->e_64_center + + + + +mal__L_c->e_65_center + + + + +e_45_center->mal__L_c + + + + + +e_46_center->h_c + + + + + +e_46_center->fum_c + + + + + +6pgl_c + +6pgl_c + + + +6pgl_c->e_75_center + + + + +e_47_center->h_c + + + + + +e_47_center->nadph_c + + + + + +e_47_center->6pgl_c + + + + + +13dpg_c + +13dpg_c + + + +e_48_center->h_c + + + + + +e_48_center->nadh_c + + + + + +e_48_center->13dpg_c + + + + + +e_49_center->pyr_c + + + + + +e_49_center->g6p_c + + + + + +nh4_c->e_50_center + + + + +e_50_center->h_c + + + + + +e_50_center->adp_c + + + + + +e_50_center->pi_c + + + + + +e_50_center->gln__L_c + + + + + +e_51_center->h_c + + + + + +e_51_center->adp_c + + + + + +e_51_center->pi_c + + + + + +e_51_center->gln__L_c + + + + + +e_52_center->h_c + + + + + +e_52_center->akg_c + + + + + +e_52_center->nadph_c + + + + + +e_52_center->nh4_c + + + + + +e_53_center->glu__L_c + + + + + +e_53_center->nh4_c + + + + + +e_54_center->glu__L_c + + + + + +e_54_center->nadp_c + + + + + +e_55_center->h_c + + + + + +e_55_center->glu__L_c + + + + + +6pgc_c + +6pgc_c + + + +6pgc_c->e_56_center + + + + +xu5p__D_c + +xu5p__D_c + + + +ru5p__D_c->xu5p__D_c + + + + + +e_56_center->co2_c + + + + + +e_56_center->nadph_c + + + + + +e_56_center->ru5p__D_c + + + + + +e_58_center->akg_c + + + + + +e_58_center->co2_c + + + + + +e_58_center->nadph_c + + + + + +glx_c + +glx_c + + + +glx_c->e_61_center + + + + +e_59_center->succ_c + + + + + +e_59_center->glx_c + + + + + +e_60_center->h_c + + + + + +e_60_center->nadh_c + + + + + +e_60_center->pyr_c + + + + + +e_61_center->coa_c + + + + + +e_61_center->h_c + + + + + +e_61_center->mal__L_c + + + + + +e_62_center->h_c + + + + + +e_62_center->mal__L_c + + + + + +e_63_center->h_c + + + + + +e_63_center->nadh_c + + + + + +e_63_center->oaa_c + + + + + +e_64_center->nadh_c + + + + + +e_64_center->co2_c + + + + + +e_64_center->pyr_c + + + + + +e_65_center->co2_c + + + + + +e_65_center->nadph_c + + + + + +e_65_center->pyr_c + + + + + +e_66_center->nad_c + + + + + +e_66_center->h_e + + + + + +e_66_center->q8h2_c + + + + + +e_67_center->nadh_c + + + + + +e_67_center->nadp_c + + + + + +e_70_center->nadh_c + + + + + +e_70_center->accoa_c + + + + + +e_70_center->co2_c + + + + + +e_71_center->h_c + + + + + +e_71_center->adp_c + + + + + +e_71_center->fdp_c + + + + + +e_72_center->accoa_c + + + + + +e_72_center->for_c + + + + + +e_74_center->adp_c + + + + + +e_74_center->13dpg_c + + + + + +e_75_center->h_c + + + + + +e_75_center->6pgc_c + + + + + +e_77_center->h_c + + + + + +e_77_center->pi_c + + + + + +e_78_center->h_c + + + + + +e_78_center->pi_c + + + + + +e_78_center->oaa_c + + + + + +e_79_center->adp_c + + + + + +e_79_center->co2_c + + + + + +e_79_center->pep_c + + + + + +e_80_center->h_c + + + + + +e_80_center->amp_c + + + + + +e_80_center->pi_c + + + + + +e_80_center->pep_c + + + + + +e_81_center->coa_c + + + + + +e_81_center->actp_c + + + + + +e_82_center->atp_c + + + + + +e_82_center->pyr_c + + + + + +e_83_center->h_c + + + + + +e_83_center->pyr_c + + + + + +xu5p__D_c->e_92_center + + + + +xu5p__D_c->e_93_center + + + + +e_86_center->h_c + + + + + +e_86_center->succ_c + + + + + +e_87_center->h_c + + + + + +e_87_center->succ_e + + + + + +e_88_center->q8h2_c + + + + + +e_88_center->fum_c + + + + + +e_89_center->adp_c + + + + + +e_89_center->succoa_c + + + + + +e_89_center->pi_c + + + + + +s7p_c + +s7p_c + + + +s7p_c->e_90_center + + + + +e_90_center->f6p_c + + + + + +e_90_center->e4p_c + + + + + +e_91_center->nad_c + + + + + +e_91_center->h_c + + + + + +e_91_center->nadph_c + + + + + +e_92_center->g3p_c + + + + + +e_92_center->s7p_c + + + + + +e_93_center->f6p_c + + + + + +e_93_center->g3p_c + + + + + \ No newline at end of file diff --git a/docs/_build/html/jupyter_execute/d2fa409fe9ed28e8a79df8ed63c6e1d4f2ee9377e328cb7bd41292044252c803.svg b/docs/_build/html/jupyter_execute/d2fa409fe9ed28e8a79df8ed63c6e1d4f2ee9377e328cb7bd41292044252c803.svg new file mode 100644 index 00000000..7466718a --- /dev/null +++ b/docs/_build/html/jupyter_execute/d2fa409fe9ed28e8a79df8ed63c6e1d4f2ee9377e328cb7bd41292044252c803.svg @@ -0,0 +1,125 @@ + + + + + + +%3 + + + +4554 + +4554 + + + +7 + +7 + + + +4554->7 + + + + + +113 + +113 + + + +7->113 + + + + + +4107 + +4107 + + + +113->4107 + + + + + +1440 + +1440 + + + +4107->1440 + + + + + +e_2_target + + + + +4047 + +4047 + + + +4047->e_2_target + + + + + +3498 + +3498 + + + +1338 + +1338 + + + +3498->1338 + + + + + +1338->4554 + + + + + +1440->4047 + + + + + +e_7_source + + + + +e_7_source->3498 + + + + + \ No newline at end of file diff --git a/docs/_build/html/main/_images/2a38f2d0d5b8c60309d55a245b5a69a6aefb567140fed800290f7e312bf398ca.svg b/docs/_build/html/main/_images/2a38f2d0d5b8c60309d55a245b5a69a6aefb567140fed800290f7e312bf398ca.svg new file mode 100644 index 00000000..8e5a4820 --- /dev/null +++ b/docs/_build/html/main/_images/2a38f2d0d5b8c60309d55a245b5a69a6aefb567140fed800290f7e312bf398ca.svg @@ -0,0 +1,2802 @@ + + + + + + +%3 + + + +acald_c + +acald_c + + + +e_0_center + + + + +acald_c->e_0_center + + + + +nad_c + +nad_c + + + +nad_c->e_0_center + + + + +e_7_center + + + + +nad_c->e_7_center + + + + +e_9_center + + + + +nad_c->e_9_center + + + + +e_12_center + + + + +nad_c->e_12_center + + + + +e_48_center + + + + +nad_c->e_48_center + + + + +e_60_center + + + + +nad_c->e_60_center + + + + +e_63_center + + + + +nad_c->e_63_center + + + + +e_64_center + + + + +nad_c->e_64_center + + + + +e_67_center + + + + +nad_c->e_67_center + + + + +e_70_center + + + + +nad_c->e_70_center + + + + +coa_c + +coa_c + + + +coa_c->e_0_center + + + + +coa_c->e_7_center + + + + +coa_c->e_70_center + + + + +e_72_center + + + + +coa_c->e_72_center + + + + +e_89_center + + + + +coa_c->e_89_center + + + + +accoa_c + +accoa_c + + + +accoa_c->e_12_center + + + + +e_14_center + + + + +accoa_c->e_14_center + + + + +e_61_center + + + + +accoa_c->e_61_center + + + + +e_81_center + + + + +accoa_c->e_81_center + + + + +h_c + +h_c + + + +e_15_center + + + + +h_c->e_15_center + + + + +e_54_center + + + + +h_c->e_54_center + + + + +e_66_center + + + + +h_c->e_66_center + + + + +e_82_center + + + + +h_c->e_82_center + + + + +nadh_c + +nadh_c + + + +nadh_c->e_66_center + + + + +e_91_center + + + + +nadh_c->e_91_center + + + + +e_0_center->accoa_c + + + + + +e_0_center->h_c + + + + + +e_0_center->nadh_c + + + + + +acald_e + +acald_e + + + +acald_e->acald_c + + + + + +e_20_target + + + + +acald_e->e_20_target + + + + + +atp_c + +atp_c + + + +e_2_center + + + + +atp_c->e_2_center + + + + +e_6_center + + + + +atp_c->e_6_center + + + + +e_10_center + + + + +atp_c->e_10_center + + + + +atp_c->e_12_center + + + + +e_50_center + + + + +atp_c->e_50_center + + + + +e_51_center + + + + +atp_c->e_51_center + + + + +e_71_center + + + + +atp_c->e_71_center + + + + +e_74_center + + + + +atp_c->e_74_center + + + + +e_79_center + + + + +atp_c->e_79_center + + + + +e_80_center + + + + +atp_c->e_80_center + + + + +atp_c->e_89_center + + + + +ac_c + +ac_c + + + +ac_c->e_2_center + + + + +actp_c + +actp_c + + + +adp_c + +adp_c + + + +e_11_center + + + + +adp_c->e_11_center + + + + +adp_c->e_82_center + + + + +e_2_center->actp_c + + + + + +e_2_center->adp_c + + + + + +cit_c + +cit_c + + + +e_3_center + + + + +cit_c->e_3_center + + + + +acon_C_c + +acon_C_c + + + +e_4_center + + + + +acon_C_c->e_4_center + + + + +h2o_c + +h2o_c + + + +h2o_c->e_4_center + + + + +h2o_c->e_10_center + + + + +h2o_c->e_12_center + + + + +h2o_c->e_14_center + + + + +e_40_center + + + + +h2o_c->e_40_center + + + + +e_45_center + + + + +h2o_c->e_45_center + + + + +h2o_c->e_51_center + + + + +e_52_center + + + + +h2o_c->e_52_center + + + + +e_53_center + + + + +h2o_c->e_53_center + + + + +h2o_c->e_61_center + + + + +e_75_center + + + + +h2o_c->e_75_center + + + + +e_78_center + + + + +h2o_c->e_78_center + + + + +h2o_c->e_80_center + + + + +e_3_center->acon_C_c + + + + + +e_3_center->h2o_c + + + + + +icit_c + +icit_c + + + +e_58_center + + + + +icit_c->e_58_center + + + + +e_59_center + + + + +icit_c->e_59_center + + + + +e_4_center->icit_c + + + + + +ac_e + +ac_e + + + +e_5_center + + + + +ac_e->e_5_center + + + + +e_19_target + + + + +ac_e->e_19_target + + + + + +h_e + +h_e + + + +h_e->e_5_center + + + + +e_8_center + + + + +h_e->e_8_center + + + + +h_e->e_11_center + + + + +e_16_center + + + + +h_e->e_16_center + + + + +e_18_center + + + + +h_e->e_18_center + + + + +e_30_target + + + + +h_e->e_30_target + + + + + +e_41_center + + + + +h_e->e_41_center + + + + +e_46_center + + + + +h_e->e_46_center + + + + +e_55_center + + + + +h_e->e_55_center + + + + +e_62_center + + + + +h_e->e_62_center + + + + +e_77_center + + + + +h_e->e_77_center + + + + +e_83_center + + + + +h_e->e_83_center + + + + +e_86_center + + + + +h_e->e_86_center + + + + +e_87_center + + + + +h_e->e_87_center + + + + +h_e->e_91_center + + + + +e_5_center->h_c + + + + + +e_5_center->ac_c + + + + + +amp_c + +amp_c + + + +amp_c->e_6_center + + + + +e_6_center->adp_c + + + + + +akg_c + +akg_c + + + +akg_c->e_7_center + + + + +akg_c->e_54_center + + + + +co2_c + +co2_c + + + +co2_c->e_78_center + + + + +succoa_c + +succoa_c + + + +e_7_center->nadh_c + + + + + +e_7_center->co2_c + + + + + +e_7_center->succoa_c + + + + + +akg_e + +akg_e + + + +akg_e->e_8_center + + + + +e_21_target + + + + +akg_e->e_21_target + + + + + +e_8_center->h_c + + + + + +e_8_center->akg_c + + + + + +etoh_c + +etoh_c + + + +etoh_c->e_9_center + + + + +e_9_center->acald_c + + + + + +e_9_center->h_c + + + + + +e_9_center->nadh_c + + + + + +pi_c + +pi_c + + + +pi_c->e_11_center + + + + +pi_c->e_48_center + + + + +pi_c->e_81_center + + + + +e_10_center->h_c + + + + + +e_10_center->adp_c + + + + + +e_10_center->pi_c + + + + + +e_11_center->h_c + + + + + +e_11_center->atp_c + + + + + +e_11_center->h2o_c + + + + + +r5p_c + +r5p_c + + + +r5p_c->e_12_center + + + + +ru5p__D_c + +ru5p__D_c + + + +r5p_c->ru5p__D_c + + + + + +e_92_center + + + + +r5p_c->e_92_center + + + + +nadph_c + +nadph_c + + + +nadph_c->e_12_center + + + + +nadph_c->e_54_center + + + + +nadph_c->e_67_center + + + + +oaa_c + +oaa_c + + + +oaa_c->e_12_center + + + + +oaa_c->e_14_center + + + + +oaa_c->e_79_center + + + + +glu__L_c + +glu__L_c + + + +glu__L_c->e_12_center + + + + +glu__L_c->e_50_center + + + + +glu__L_c->e_52_center + + + + +g3p_c + +g3p_c + + + +g3p_c->e_12_center + + + + +g3p_c->e_48_center + + + + +e_90_center + + + + +g3p_c->e_90_center + + + + +3pg_c + +3pg_c + + + +3pg_c->e_12_center + + + + +3pg_c->e_74_center + + + + +pyr_c + +pyr_c + + + +pyr_c->e_12_center + + + + +pyr_c->e_70_center + + + + +pyr_c->e_72_center + + + + +pyr_c->e_80_center + + + + +pep_c + +pep_c + + + +pep_c->e_12_center + + + + +e_44_center + + + + +pep_c->e_44_center + + + + +e_49_center + + + + +pep_c->e_49_center + + + + +pep_c->e_78_center + + + + +pep_c->e_82_center + + + + +f6p_c + +f6p_c + + + +f6p_c->e_12_center + + + + +f6p_c->e_71_center + + + + +g6p_c + +g6p_c + + + +g6p_c->f6p_c + + + + + +g6p_c->e_12_center + + + + +e_47_center + + + + +g6p_c->e_47_center + + + + +e4p_c + +e4p_c + + + +e4p_c->e_12_center + + + + +e_93_center + + + + +e4p_c->e_93_center + + + + +gln__L_c + +gln__L_c + + + +gln__L_c->e_12_center + + + + +gln__L_c->e_53_center + + + + +gln__L_c->e_54_center + + + + +nadp_c + +nadp_c + + + +nadp_c->e_47_center + + + + +nadp_c->e_52_center + + + + +e_56_center + + + + +nadp_c->e_56_center + + + + +nadp_c->e_58_center + + + + +e_65_center + + + + +nadp_c->e_65_center + + + + +nadp_c->e_91_center + + + + +e_12_center->coa_c + + + + + +e_12_center->h_c + + + + + +e_12_center->nadh_c + + + + + +e_12_center->adp_c + + + + + +e_12_center->akg_c + + + + + +e_12_center->pi_c + + + + + +e_12_center->nadp_c + + + + + +co2_e + +co2_e + + + +co2_e->co2_c + + + + + +e_22_target + + + + +co2_e->e_22_target + + + + + +e_14_center->coa_c + + + + + +e_14_center->h_c + + + + + +e_14_center->cit_c + + + + + +o2_c + +o2_c + + + +o2_c->e_15_center + + + + +q8h2_c + +q8h2_c + + + +q8h2_c->e_15_center + + + + +e_43_center + + + + +q8h2_c->e_43_center + + + + +q8_c + +q8_c + + + +q8_c->e_66_center + + + + +e_88_center + + + + +q8_c->e_88_center + + + + +e_15_center->h2o_c + + + + + +e_15_center->h_e + + + + + +e_15_center->q8_c + + + + + +lac__D_e + +lac__D_e + + + +lac__D_e->e_16_center + + + + +e_32_target + + + + +lac__D_e->e_32_target + + + + + +lac__D_c + +lac__D_c + + + +lac__D_c->e_60_center + + + + +e_16_center->h_c + + + + + +e_16_center->lac__D_c + + + + + +2pg_c + +2pg_c + + + +2pg_c->3pg_c + + + + + +e_17_center + + + + +2pg_c->e_17_center + + + + +e_17_center->h2o_c + + + + + +e_17_center->pep_c + + + + + +etoh_e + +etoh_e + + + +etoh_e->e_18_center + + + + +e_23_target + + + + +etoh_e->e_23_target + + + + + +e_18_center->h_c + + + + + +e_18_center->etoh_c + + + + + +e_24_target + + + + +for_e + +for_e + + + +for_e->e_24_target + + + + + +for_e->e_41_center + + + + +e_25_target + + + + +fru_e + +fru_e + + + +fru_e->e_25_target + + + + + +fru_e->e_44_center + + + + +e_26_target + + + + +fum_e + +fum_e + + + +fum_e->e_26_target + + + + + +fum_e->e_46_center + + + + +e_27_target + + + + +glc__D_e + +glc__D_e + + + +glc__D_e->e_27_target + + + + + +glc__D_e->e_49_center + + + + +e_28_target + + + + +gln__L_e + +gln__L_e + + + +gln__L_e->e_28_target + + + + + +gln__L_e->e_51_center + + + + +e_29_target + + + + +glu__L_e + +glu__L_e + + + +glu__L_e->e_29_target + + + + + +glu__L_e->e_55_center + + + + +e_31_target + + + + +h2o_e + +h2o_e + + + +h2o_e->h2o_c + + + + + +h2o_e->e_31_target + + + + + +e_33_target + + + + +mal__L_e + +mal__L_e + + + +mal__L_e->e_33_target + + + + + +mal__L_e->e_62_center + + + + +e_34_target + + + + +nh4_e + +nh4_e + + + +nh4_e->e_34_target + + + + + +nh4_c + +nh4_c + + + +nh4_e->nh4_c + + + + + +e_35_target + + + + +o2_e + +o2_e + + + +o2_e->o2_c + + + + + +o2_e->e_35_target + + + + + +e_36_target + + + + +pi_e + +pi_e + + + +pi_e->e_36_target + + + + + +pi_e->e_77_center + + + + +e_37_target + + + + +pyr_e + +pyr_e + + + +pyr_e->e_37_target + + + + + +pyr_e->e_83_center + + + + +e_38_target + + + + +succ_e + +succ_e + + + +succ_e->e_38_target + + + + + +succ_e->e_86_center + + + + +fdp_c + +fdp_c + + + +e_39_center + + + + +fdp_c->e_39_center + + + + +fdp_c->e_40_center + + + + +dhap_c + +dhap_c + + + +dhap_c->g3p_c + + + + + +e_39_center->g3p_c + + + + + +e_39_center->dhap_c + + + + + +e_40_center->pi_c + + + + + +e_40_center->f6p_c + + + + + +for_c + +for_c + + + +for_c->for_e + + + + + +e_41_center->h_c + + + + + +e_41_center->for_c + + + + + +fum_c + +fum_c + + + +fum_c->e_43_center + + + + +fum_c->e_45_center + + + + +succ_c + +succ_c + + + +succ_c->e_87_center + + + + +succ_c->e_88_center + + + + +succ_c->e_89_center + + + + +e_43_center->q8_c + + + + + +e_43_center->succ_c + + + + + +e_44_center->pyr_c + + + + + +e_44_center->f6p_c + + + + + +mal__L_c + +mal__L_c + + + +mal__L_c->e_63_center + + + + +mal__L_c->e_64_center + + + + +mal__L_c->e_65_center + + + + +e_45_center->mal__L_c + + + + + +e_46_center->h_c + + + + + +e_46_center->fum_c + + + + + +6pgl_c + +6pgl_c + + + +6pgl_c->e_75_center + + + + +e_47_center->h_c + + + + + +e_47_center->nadph_c + + + + + +e_47_center->6pgl_c + + + + + +13dpg_c + +13dpg_c + + + +e_48_center->h_c + + + + + +e_48_center->nadh_c + + + + + +e_48_center->13dpg_c + + + + + +e_49_center->pyr_c + + + + + +e_49_center->g6p_c + + + + + +nh4_c->e_50_center + + + + +e_50_center->h_c + + + + + +e_50_center->adp_c + + + + + +e_50_center->pi_c + + + + + +e_50_center->gln__L_c + + + + + +e_51_center->h_c + + + + + +e_51_center->adp_c + + + + + +e_51_center->pi_c + + + + + +e_51_center->gln__L_c + + + + + +e_52_center->h_c + + + + + +e_52_center->akg_c + + + + + +e_52_center->nadph_c + + + + + +e_52_center->nh4_c + + + + + +e_53_center->glu__L_c + + + + + +e_53_center->nh4_c + + + + + +e_54_center->glu__L_c + + + + + +e_54_center->nadp_c + + + + + +e_55_center->h_c + + + + + +e_55_center->glu__L_c + + + + + +6pgc_c + +6pgc_c + + + +6pgc_c->e_56_center + + + + +xu5p__D_c + +xu5p__D_c + + + +ru5p__D_c->xu5p__D_c + + + + + +e_56_center->co2_c + + + + + +e_56_center->nadph_c + + + + + +e_56_center->ru5p__D_c + + + + + +e_58_center->akg_c + + + + + +e_58_center->co2_c + + + + + +e_58_center->nadph_c + + + + + +glx_c + +glx_c + + + +glx_c->e_61_center + + + + +e_59_center->succ_c + + + + + +e_59_center->glx_c + + + + + +e_60_center->h_c + + + + + +e_60_center->nadh_c + + + + + +e_60_center->pyr_c + + + + + +e_61_center->coa_c + + + + + +e_61_center->h_c + + + + + +e_61_center->mal__L_c + + + + + +e_62_center->h_c + + + + + +e_62_center->mal__L_c + + + + + +e_63_center->h_c + + + + + +e_63_center->nadh_c + + + + + +e_63_center->oaa_c + + + + + +e_64_center->nadh_c + + + + + +e_64_center->co2_c + + + + + +e_64_center->pyr_c + + + + + +e_65_center->co2_c + + + + + +e_65_center->nadph_c + + + + + +e_65_center->pyr_c + + + + + +e_66_center->nad_c + + + + + +e_66_center->h_e + + + + + +e_66_center->q8h2_c + + + + + +e_67_center->nadh_c + + + + + +e_67_center->nadp_c + + + + + +e_70_center->accoa_c + + + + + +e_70_center->nadh_c + + + + + +e_70_center->co2_c + + + + + +e_71_center->h_c + + + + + +e_71_center->adp_c + + + + + +e_71_center->fdp_c + + + + + +e_72_center->accoa_c + + + + + +e_72_center->for_c + + + + + +e_74_center->adp_c + + + + + +e_74_center->13dpg_c + + + + + +e_75_center->h_c + + + + + +e_75_center->6pgc_c + + + + + +e_77_center->h_c + + + + + +e_77_center->pi_c + + + + + +e_78_center->h_c + + + + + +e_78_center->pi_c + + + + + +e_78_center->oaa_c + + + + + +e_79_center->adp_c + + + + + +e_79_center->co2_c + + + + + +e_79_center->pep_c + + + + + +e_80_center->h_c + + + + + +e_80_center->amp_c + + + + + +e_80_center->pi_c + + + + + +e_80_center->pep_c + + + + + +e_81_center->coa_c + + + + + +e_81_center->actp_c + + + + + +e_82_center->atp_c + + + + + +e_82_center->pyr_c + + + + + +e_83_center->h_c + + + + + +e_83_center->pyr_c + + + + + +xu5p__D_c->e_92_center + + + + +xu5p__D_c->e_93_center + + + + +e_86_center->h_c + + + + + +e_86_center->succ_c + + + + + +e_87_center->h_c + + + + + +e_87_center->succ_e + + + + + +e_88_center->q8h2_c + + + + + +e_88_center->fum_c + + + + + +e_89_center->adp_c + + + + + +e_89_center->succoa_c + + + + + +e_89_center->pi_c + + + + + +s7p_c + +s7p_c + + + +s7p_c->e_90_center + + + + +e_90_center->f6p_c + + + + + +e_90_center->e4p_c + + + + + +e_91_center->nad_c + + + + + +e_91_center->h_c + + + + + +e_91_center->nadph_c + + + + + +e_92_center->g3p_c + + + + + +e_92_center->s7p_c + + + + + +e_93_center->g3p_c + + + + + +e_93_center->f6p_c + + + + + \ No newline at end of file diff --git a/docs/_build/html/main/_images/2c64097f5da14ea3c688e1a93dc4dc0c510c4e41d0fe34fa9dfae3bc662b2bb2.svg b/docs/_build/html/main/_images/2c64097f5da14ea3c688e1a93dc4dc0c510c4e41d0fe34fa9dfae3bc662b2bb2.svg new file mode 100644 index 00000000..f48a01f9 --- /dev/null +++ b/docs/_build/html/main/_images/2c64097f5da14ea3c688e1a93dc4dc0c510c4e41d0fe34fa9dfae3bc662b2bb2.svg @@ -0,0 +1,131 @@ + + + + + + +%3 + + + +A + +A + + + +e_0_center + + + + +A->e_0_center + + + + +B + +B + + + +B->e_0_center + + + + +C + +C + + + +e_4_target + + + + +C->e_4_target + + + + + +D + +D + + + +e_1_center + + + + +D->e_1_center + + + + +e_0_center->C + + + + + +e_0_center->D + + + + + +F + +F + + + +E + +E + + + +e_1_center->F + + + + + +e_1_center->E + + + + + +e_2_source + + + + +e_2_source->A + + + + + +e_3_source + + + + +e_3_source->B + + + + + \ No newline at end of file diff --git a/docs/_build/html/main/_images/443cf7bd4db35676d58fdb902fcfd857934e3a7c2731577a6acf2f279d44b8b3.svg b/docs/_build/html/main/_images/443cf7bd4db35676d58fdb902fcfd857934e3a7c2731577a6acf2f279d44b8b3.svg new file mode 100644 index 00000000..1319a462 --- /dev/null +++ b/docs/_build/html/main/_images/443cf7bd4db35676d58fdb902fcfd857934e3a7c2731577a6acf2f279d44b8b3.svg @@ -0,0 +1,170 @@ + + + + + + +%3 + + + +I1 + +I1 + + + +N1 + +N1 + + + +I1->N1 + + + + + +M1 + +M1 + + + +N1->M1 + + + + + +M2 + +M2 + + + +N1->M2 + + + + + +_meas_c0 + +_meas_c0 + + + +M1->_meas_c0 + + + + + +M2->_meas_c0 + + + + + +I2 + +I2 + + + +N2 + +N2 + + + +I2->N2 + + + + + + +N2->M1 + + + + + + +N2->M2 + + + + + + +_s + +_s + + + +_pert_c0 + +_pert_c0 + + + +_s->_pert_c0 + + + + + +_pert_c0->I1 + + + + + +_pert_c0->I2 + + + + + +_t + +_t + + + +_meas_c0->_t + + + + + +e_13_target + + + + +_t->e_13_target + + + + + +e_12_source + + + + +e_12_source->_s + + + + + \ No newline at end of file diff --git a/docs/_build/html/main/_images/5b572f011bdaf826106697ae16ecadb3e0ff5a4bd81ae225a115f4bf9e56ae53.svg b/docs/_build/html/main/_images/5b572f011bdaf826106697ae16ecadb3e0ff5a4bd81ae225a115f4bf9e56ae53.svg new file mode 100644 index 00000000..e2fdfd18 --- /dev/null +++ b/docs/_build/html/main/_images/5b572f011bdaf826106697ae16ecadb3e0ff5a4bd81ae225a115f4bf9e56ae53.svg @@ -0,0 +1,210 @@ + + + + + + +%3 + + + +M1 + +M1 + + + +e_0_center + + + + +M1->e_0_center + + + + +M4 + +M4 + + + +M1->M4 + + + + + +M2 + +M2 + + + +M2->e_0_center + + + + +M5 + +M5 + + + +e_7_target + + + + +M5->e_7_target + + + + + +M6 + +M6 + + + +M9 + +M9 + + + +M6->M9 + + + + + +e_0_center->M5 + + + + + +e_0_center->M6 + + + + + +e_2_center + + + + +M4->e_2_center + + + + +M3 + +M3 + + + +M3->e_2_center + + + + +M8 + +M8 + + + +e_9_target + + + + +M8->e_9_target + + + + + +M7 + +M7 + + + +e_8_target + + + + +M7->e_8_target + + + + + +e_2_center->M8 + + + + + +e_2_center->M7 + + + + + +e_10_target + + + + +M9->e_10_target + + + + + +e_4_source + + + + +e_4_source->M1 + + + + + +e_5_source + + + + +e_5_source->M2 + + + + + +e_6_source + + + + +e_6_source->M3 + + + + + \ No newline at end of file diff --git a/docs/_build/html/main/_images/7d51afb160f63cb72df323a55c7f6b4d57dbccbd0120e59abc2f30407c7dfed9.svg b/docs/_build/html/main/_images/7d51afb160f63cb72df323a55c7f6b4d57dbccbd0120e59abc2f30407c7dfed9.svg new file mode 100644 index 00000000..b7c17409 --- /dev/null +++ b/docs/_build/html/main/_images/7d51afb160f63cb72df323a55c7f6b4d57dbccbd0120e59abc2f30407c7dfed9.svg @@ -0,0 +1,210 @@ + + + + + + +%3 + + + +M1 + +M1 + + + +e_0_center + + + + +M1->e_0_center + + + + +M4 + +M4 + + + +M1->M4 + + + + + +M2 + +M2 + + + +M2->e_0_center + + + + +M5 + +M5 + + + +e_7_target + + + + +M5->e_7_target + + + + + +M6 + +M6 + + + +M9 + +M9 + + + +M6->M9 + + + + + +e_0_center->M5 + + + + + +e_0_center->M6 + + + + + +e_2_center + + + + +M4->e_2_center + + + + +M3 + +M3 + + + +M3->e_2_center + + + + +M8 + +M8 + + + +e_9_target + + + + +M8->e_9_target + + + + + +M7 + +M7 + + + +e_8_target + + + + +M7->e_8_target + + + + + +e_2_center->M8 + + + + + +e_2_center->M7 + + + + + +e_10_target + + + + +M9->e_10_target + + + + + +e_4_source + + + + +e_4_source->M1 + + + + + +e_5_source + + + + +e_5_source->M2 + + + + + +e_6_source + + + + +e_6_source->M3 + + + + + \ No newline at end of file diff --git a/docs/_build/html/main/_images/868a4c4ff4d416d677b3e548cce59f6202431263bc98d2b38ab5d3e0881995b8.svg b/docs/_build/html/main/_images/868a4c4ff4d416d677b3e548cce59f6202431263bc98d2b38ab5d3e0881995b8.svg new file mode 100644 index 00000000..08ee5d59 --- /dev/null +++ b/docs/_build/html/main/_images/868a4c4ff4d416d677b3e548cce59f6202431263bc98d2b38ab5d3e0881995b8.svg @@ -0,0 +1,2802 @@ + + + + + + +%3 + + + +nad_c + +nad_c + + + +e_0_center + + + + +nad_c->e_0_center + + + + +e_7_center + + + + +nad_c->e_7_center + + + + +e_9_center + + + + +nad_c->e_9_center + + + + +e_12_center + + + + +nad_c->e_12_center + + + + +e_48_center + + + + +nad_c->e_48_center + + + + +e_60_center + + + + +nad_c->e_60_center + + + + +e_63_center + + + + +nad_c->e_63_center + + + + +e_64_center + + + + +nad_c->e_64_center + + + + +e_67_center + + + + +nad_c->e_67_center + + + + +e_70_center + + + + +nad_c->e_70_center + + + + +acald_c + +acald_c + + + +acald_c->e_0_center + + + + +coa_c + +coa_c + + + +coa_c->e_0_center + + + + +coa_c->e_7_center + + + + +coa_c->e_70_center + + + + +e_72_center + + + + +coa_c->e_72_center + + + + +e_89_center + + + + +coa_c->e_89_center + + + + +h_c + +h_c + + + +e_15_center + + + + +h_c->e_15_center + + + + +e_54_center + + + + +h_c->e_54_center + + + + +e_66_center + + + + +h_c->e_66_center + + + + +e_82_center + + + + +h_c->e_82_center + + + + +nadh_c + +nadh_c + + + +nadh_c->e_66_center + + + + +e_91_center + + + + +nadh_c->e_91_center + + + + +accoa_c + +accoa_c + + + +accoa_c->e_12_center + + + + +e_14_center + + + + +accoa_c->e_14_center + + + + +e_61_center + + + + +accoa_c->e_61_center + + + + +e_81_center + + + + +accoa_c->e_81_center + + + + +e_0_center->h_c + + + + + +e_0_center->nadh_c + + + + + +e_0_center->accoa_c + + + + + +acald_e + +acald_e + + + +acald_e->acald_c + + + + + +e_20_target + + + + +acald_e->e_20_target + + + + + +ac_c + +ac_c + + + +e_2_center + + + + +ac_c->e_2_center + + + + +atp_c + +atp_c + + + +atp_c->e_2_center + + + + +e_6_center + + + + +atp_c->e_6_center + + + + +e_10_center + + + + +atp_c->e_10_center + + + + +atp_c->e_12_center + + + + +e_50_center + + + + +atp_c->e_50_center + + + + +e_51_center + + + + +atp_c->e_51_center + + + + +e_71_center + + + + +atp_c->e_71_center + + + + +e_74_center + + + + +atp_c->e_74_center + + + + +e_79_center + + + + +atp_c->e_79_center + + + + +e_80_center + + + + +atp_c->e_80_center + + + + +atp_c->e_89_center + + + + +adp_c + +adp_c + + + +e_11_center + + + + +adp_c->e_11_center + + + + +adp_c->e_82_center + + + + +actp_c + +actp_c + + + +e_2_center->adp_c + + + + + +e_2_center->actp_c + + + + + +cit_c + +cit_c + + + +e_3_center + + + + +cit_c->e_3_center + + + + +h2o_c + +h2o_c + + + +e_4_center + + + + +h2o_c->e_4_center + + + + +h2o_c->e_10_center + + + + +h2o_c->e_12_center + + + + +h2o_c->e_14_center + + + + +e_40_center + + + + +h2o_c->e_40_center + + + + +e_45_center + + + + +h2o_c->e_45_center + + + + +h2o_c->e_51_center + + + + +e_52_center + + + + +h2o_c->e_52_center + + + + +e_53_center + + + + +h2o_c->e_53_center + + + + +h2o_c->e_61_center + + + + +e_75_center + + + + +h2o_c->e_75_center + + + + +e_78_center + + + + +h2o_c->e_78_center + + + + +h2o_c->e_80_center + + + + +acon_C_c + +acon_C_c + + + +acon_C_c->e_4_center + + + + +e_3_center->h2o_c + + + + + +e_3_center->acon_C_c + + + + + +icit_c + +icit_c + + + +e_58_center + + + + +icit_c->e_58_center + + + + +e_59_center + + + + +icit_c->e_59_center + + + + +e_4_center->icit_c + + + + + +ac_e + +ac_e + + + +e_5_center + + + + +ac_e->e_5_center + + + + +e_19_target + + + + +ac_e->e_19_target + + + + + +h_e + +h_e + + + +h_e->e_5_center + + + + +e_8_center + + + + +h_e->e_8_center + + + + +h_e->e_11_center + + + + +e_16_center + + + + +h_e->e_16_center + + + + +e_18_center + + + + +h_e->e_18_center + + + + +e_30_target + + + + +h_e->e_30_target + + + + + +e_41_center + + + + +h_e->e_41_center + + + + +e_46_center + + + + +h_e->e_46_center + + + + +e_55_center + + + + +h_e->e_55_center + + + + +e_62_center + + + + +h_e->e_62_center + + + + +e_77_center + + + + +h_e->e_77_center + + + + +e_83_center + + + + +h_e->e_83_center + + + + +e_86_center + + + + +h_e->e_86_center + + + + +e_87_center + + + + +h_e->e_87_center + + + + +h_e->e_91_center + + + + +e_5_center->h_c + + + + + +e_5_center->ac_c + + + + + +amp_c + +amp_c + + + +amp_c->e_6_center + + + + +e_6_center->adp_c + + + + + +akg_c + +akg_c + + + +akg_c->e_7_center + + + + +akg_c->e_54_center + + + + +co2_c + +co2_c + + + +co2_c->e_78_center + + + + +succoa_c + +succoa_c + + + +e_7_center->nadh_c + + + + + +e_7_center->co2_c + + + + + +e_7_center->succoa_c + + + + + +akg_e + +akg_e + + + +akg_e->e_8_center + + + + +e_21_target + + + + +akg_e->e_21_target + + + + + +e_8_center->h_c + + + + + +e_8_center->akg_c + + + + + +etoh_c + +etoh_c + + + +etoh_c->e_9_center + + + + +e_9_center->acald_c + + + + + +e_9_center->h_c + + + + + +e_9_center->nadh_c + + + + + +pi_c + +pi_c + + + +pi_c->e_11_center + + + + +pi_c->e_48_center + + + + +pi_c->e_81_center + + + + +e_10_center->h_c + + + + + +e_10_center->adp_c + + + + + +e_10_center->pi_c + + + + + +e_11_center->h_c + + + + + +e_11_center->atp_c + + + + + +e_11_center->h2o_c + + + + + +gln__L_c + +gln__L_c + + + +gln__L_c->e_12_center + + + + +gln__L_c->e_53_center + + + + +gln__L_c->e_54_center + + + + +pep_c + +pep_c + + + +pep_c->e_12_center + + + + +e_44_center + + + + +pep_c->e_44_center + + + + +e_49_center + + + + +pep_c->e_49_center + + + + +pep_c->e_78_center + + + + +pep_c->e_82_center + + + + +glu__L_c + +glu__L_c + + + +glu__L_c->e_12_center + + + + +glu__L_c->e_50_center + + + + +glu__L_c->e_52_center + + + + +oaa_c + +oaa_c + + + +oaa_c->e_12_center + + + + +oaa_c->e_14_center + + + + +oaa_c->e_79_center + + + + +nadph_c + +nadph_c + + + +nadph_c->e_12_center + + + + +nadph_c->e_54_center + + + + +nadph_c->e_67_center + + + + +f6p_c + +f6p_c + + + +f6p_c->e_12_center + + + + +f6p_c->e_71_center + + + + +g3p_c + +g3p_c + + + +g3p_c->e_12_center + + + + +g3p_c->e_48_center + + + + +e_90_center + + + + +g3p_c->e_90_center + + + + +pyr_c + +pyr_c + + + +pyr_c->e_12_center + + + + +pyr_c->e_70_center + + + + +pyr_c->e_72_center + + + + +pyr_c->e_80_center + + + + +g6p_c + +g6p_c + + + +g6p_c->f6p_c + + + + + +g6p_c->e_12_center + + + + +e_47_center + + + + +g6p_c->e_47_center + + + + +e4p_c + +e4p_c + + + +e4p_c->e_12_center + + + + +e_93_center + + + + +e4p_c->e_93_center + + + + +3pg_c + +3pg_c + + + +3pg_c->e_12_center + + + + +3pg_c->e_74_center + + + + +r5p_c + +r5p_c + + + +r5p_c->e_12_center + + + + +ru5p__D_c + +ru5p__D_c + + + +r5p_c->ru5p__D_c + + + + + +e_92_center + + + + +r5p_c->e_92_center + + + + +nadp_c + +nadp_c + + + +nadp_c->e_47_center + + + + +nadp_c->e_52_center + + + + +e_56_center + + + + +nadp_c->e_56_center + + + + +nadp_c->e_58_center + + + + +e_65_center + + + + +nadp_c->e_65_center + + + + +nadp_c->e_91_center + + + + +e_12_center->coa_c + + + + + +e_12_center->h_c + + + + + +e_12_center->nadh_c + + + + + +e_12_center->adp_c + + + + + +e_12_center->akg_c + + + + + +e_12_center->pi_c + + + + + +e_12_center->nadp_c + + + + + +co2_e + +co2_e + + + +co2_e->co2_c + + + + + +e_22_target + + + + +co2_e->e_22_target + + + + + +e_14_center->coa_c + + + + + +e_14_center->h_c + + + + + +e_14_center->cit_c + + + + + +o2_c + +o2_c + + + +o2_c->e_15_center + + + + +q8h2_c + +q8h2_c + + + +q8h2_c->e_15_center + + + + +e_43_center + + + + +q8h2_c->e_43_center + + + + +q8_c + +q8_c + + + +q8_c->e_66_center + + + + +e_88_center + + + + +q8_c->e_88_center + + + + +e_15_center->h2o_c + + + + + +e_15_center->h_e + + + + + +e_15_center->q8_c + + + + + +lac__D_e + +lac__D_e + + + +lac__D_e->e_16_center + + + + +e_32_target + + + + +lac__D_e->e_32_target + + + + + +lac__D_c + +lac__D_c + + + +lac__D_c->e_60_center + + + + +e_16_center->h_c + + + + + +e_16_center->lac__D_c + + + + + +2pg_c + +2pg_c + + + +2pg_c->3pg_c + + + + + +e_17_center + + + + +2pg_c->e_17_center + + + + +e_17_center->h2o_c + + + + + +e_17_center->pep_c + + + + + +etoh_e + +etoh_e + + + +etoh_e->e_18_center + + + + +e_23_target + + + + +etoh_e->e_23_target + + + + + +e_18_center->h_c + + + + + +e_18_center->etoh_c + + + + + +e_24_target + + + + +for_e + +for_e + + + +for_e->e_24_target + + + + + +for_e->e_41_center + + + + +e_25_target + + + + +fru_e + +fru_e + + + +fru_e->e_25_target + + + + + +fru_e->e_44_center + + + + +e_26_target + + + + +fum_e + +fum_e + + + +fum_e->e_26_target + + + + + +fum_e->e_46_center + + + + +e_27_target + + + + +glc__D_e + +glc__D_e + + + +glc__D_e->e_27_target + + + + + +glc__D_e->e_49_center + + + + +e_28_target + + + + +gln__L_e + +gln__L_e + + + +gln__L_e->e_28_target + + + + + +gln__L_e->e_51_center + + + + +e_29_target + + + + +glu__L_e + +glu__L_e + + + +glu__L_e->e_29_target + + + + + +glu__L_e->e_55_center + + + + +e_31_target + + + + +h2o_e + +h2o_e + + + +h2o_e->h2o_c + + + + + +h2o_e->e_31_target + + + + + +e_33_target + + + + +mal__L_e + +mal__L_e + + + +mal__L_e->e_33_target + + + + + +mal__L_e->e_62_center + + + + +e_34_target + + + + +nh4_e + +nh4_e + + + +nh4_e->e_34_target + + + + + +nh4_c + +nh4_c + + + +nh4_e->nh4_c + + + + + +e_35_target + + + + +o2_e + +o2_e + + + +o2_e->o2_c + + + + + +o2_e->e_35_target + + + + + +e_36_target + + + + +pi_e + +pi_e + + + +pi_e->e_36_target + + + + + +pi_e->e_77_center + + + + +e_37_target + + + + +pyr_e + +pyr_e + + + +pyr_e->e_37_target + + + + + +pyr_e->e_83_center + + + + +e_38_target + + + + +succ_e + +succ_e + + + +succ_e->e_38_target + + + + + +succ_e->e_86_center + + + + +fdp_c + +fdp_c + + + +e_39_center + + + + +fdp_c->e_39_center + + + + +fdp_c->e_40_center + + + + +dhap_c + +dhap_c + + + +dhap_c->g3p_c + + + + + +e_39_center->g3p_c + + + + + +e_39_center->dhap_c + + + + + +e_40_center->pi_c + + + + + +e_40_center->f6p_c + + + + + +for_c + +for_c + + + +for_c->for_e + + + + + +e_41_center->h_c + + + + + +e_41_center->for_c + + + + + +fum_c + +fum_c + + + +fum_c->e_43_center + + + + +fum_c->e_45_center + + + + +succ_c + +succ_c + + + +succ_c->e_87_center + + + + +succ_c->e_88_center + + + + +succ_c->e_89_center + + + + +e_43_center->q8_c + + + + + +e_43_center->succ_c + + + + + +e_44_center->f6p_c + + + + + +e_44_center->pyr_c + + + + + +mal__L_c + +mal__L_c + + + +mal__L_c->e_63_center + + + + +mal__L_c->e_64_center + + + + +mal__L_c->e_65_center + + + + +e_45_center->mal__L_c + + + + + +e_46_center->h_c + + + + + +e_46_center->fum_c + + + + + +6pgl_c + +6pgl_c + + + +6pgl_c->e_75_center + + + + +e_47_center->h_c + + + + + +e_47_center->nadph_c + + + + + +e_47_center->6pgl_c + + + + + +13dpg_c + +13dpg_c + + + +e_48_center->h_c + + + + + +e_48_center->nadh_c + + + + + +e_48_center->13dpg_c + + + + + +e_49_center->pyr_c + + + + + +e_49_center->g6p_c + + + + + +nh4_c->e_50_center + + + + +e_50_center->h_c + + + + + +e_50_center->adp_c + + + + + +e_50_center->pi_c + + + + + +e_50_center->gln__L_c + + + + + +e_51_center->h_c + + + + + +e_51_center->adp_c + + + + + +e_51_center->pi_c + + + + + +e_51_center->gln__L_c + + + + + +e_52_center->h_c + + + + + +e_52_center->akg_c + + + + + +e_52_center->nadph_c + + + + + +e_52_center->nh4_c + + + + + +e_53_center->glu__L_c + + + + + +e_53_center->nh4_c + + + + + +e_54_center->glu__L_c + + + + + +e_54_center->nadp_c + + + + + +e_55_center->h_c + + + + + +e_55_center->glu__L_c + + + + + +6pgc_c + +6pgc_c + + + +6pgc_c->e_56_center + + + + +xu5p__D_c + +xu5p__D_c + + + +ru5p__D_c->xu5p__D_c + + + + + +e_56_center->co2_c + + + + + +e_56_center->nadph_c + + + + + +e_56_center->ru5p__D_c + + + + + +e_58_center->akg_c + + + + + +e_58_center->co2_c + + + + + +e_58_center->nadph_c + + + + + +glx_c + +glx_c + + + +glx_c->e_61_center + + + + +e_59_center->succ_c + + + + + +e_59_center->glx_c + + + + + +e_60_center->h_c + + + + + +e_60_center->nadh_c + + + + + +e_60_center->pyr_c + + + + + +e_61_center->coa_c + + + + + +e_61_center->h_c + + + + + +e_61_center->mal__L_c + + + + + +e_62_center->h_c + + + + + +e_62_center->mal__L_c + + + + + +e_63_center->h_c + + + + + +e_63_center->nadh_c + + + + + +e_63_center->oaa_c + + + + + +e_64_center->nadh_c + + + + + +e_64_center->co2_c + + + + + +e_64_center->pyr_c + + + + + +e_65_center->co2_c + + + + + +e_65_center->nadph_c + + + + + +e_65_center->pyr_c + + + + + +e_66_center->nad_c + + + + + +e_66_center->h_e + + + + + +e_66_center->q8h2_c + + + + + +e_67_center->nadh_c + + + + + +e_67_center->nadp_c + + + + + +e_70_center->nadh_c + + + + + +e_70_center->accoa_c + + + + + +e_70_center->co2_c + + + + + +e_71_center->h_c + + + + + +e_71_center->adp_c + + + + + +e_71_center->fdp_c + + + + + +e_72_center->accoa_c + + + + + +e_72_center->for_c + + + + + +e_74_center->adp_c + + + + + +e_74_center->13dpg_c + + + + + +e_75_center->h_c + + + + + +e_75_center->6pgc_c + + + + + +e_77_center->h_c + + + + + +e_77_center->pi_c + + + + + +e_78_center->h_c + + + + + +e_78_center->pi_c + + + + + +e_78_center->oaa_c + + + + + +e_79_center->adp_c + + + + + +e_79_center->co2_c + + + + + +e_79_center->pep_c + + + + + +e_80_center->h_c + + + + + +e_80_center->amp_c + + + + + +e_80_center->pi_c + + + + + +e_80_center->pep_c + + + + + +e_81_center->coa_c + + + + + +e_81_center->actp_c + + + + + +e_82_center->atp_c + + + + + +e_82_center->pyr_c + + + + + +e_83_center->h_c + + + + + +e_83_center->pyr_c + + + + + +xu5p__D_c->e_92_center + + + + +xu5p__D_c->e_93_center + + + + +e_86_center->h_c + + + + + +e_86_center->succ_c + + + + + +e_87_center->h_c + + + + + +e_87_center->succ_e + + + + + +e_88_center->q8h2_c + + + + + +e_88_center->fum_c + + + + + +e_89_center->adp_c + + + + + +e_89_center->succoa_c + + + + + +e_89_center->pi_c + + + + + +s7p_c + +s7p_c + + + +s7p_c->e_90_center + + + + +e_90_center->f6p_c + + + + + +e_90_center->e4p_c + + + + + +e_91_center->nad_c + + + + + +e_91_center->h_c + + + + + +e_91_center->nadph_c + + + + + +e_92_center->g3p_c + + + + + +e_92_center->s7p_c + + + + + +e_93_center->f6p_c + + + + + +e_93_center->g3p_c + + + + + \ No newline at end of file diff --git a/docs/_build/html/main/_images/a18af31210c20b9afdc10fc3443dfc3ddab9d41d7f88310804f0f80d84116ddc.svg b/docs/_build/html/main/_images/a18af31210c20b9afdc10fc3443dfc3ddab9d41d7f88310804f0f80d84116ddc.svg new file mode 100644 index 00000000..abb919aa --- /dev/null +++ b/docs/_build/html/main/_images/a18af31210c20b9afdc10fc3443dfc3ddab9d41d7f88310804f0f80d84116ddc.svg @@ -0,0 +1,58 @@ + + + + + + +%3 + + + +I2 + +I2 + + + +N2 + +N2 + + + +I2->N2 + + + + + + +M2 + +M2 + + + +N2->M2 + + + + + + +M1 + +M1 + + + +N2->M1 + + + + + + \ No newline at end of file diff --git a/docs/_build/html/main/_images/a611717058041567090a4563f14a2f8125974cc83a7f80508687554b10f489ef.svg b/docs/_build/html/main/_images/a611717058041567090a4563f14a2f8125974cc83a7f80508687554b10f489ef.svg new file mode 100644 index 00000000..06648725 --- /dev/null +++ b/docs/_build/html/main/_images/a611717058041567090a4563f14a2f8125974cc83a7f80508687554b10f489ef.svg @@ -0,0 +1,339 @@ + + + + + + +%3 + + + +EGFR + +EGFR + + + +STAT1 + +STAT1 + + + +EGFR->STAT1 + + + + + +ERBB2 + +ERBB2 + + + +EGFR->ERBB2 + + + + + +MAP2K1 + +MAP2K1 + + + +EGFR->MAP2K1 + + + + + +PIK3R1 + +PIK3R1 + + + +EGFR->PIK3R1 + + + + + +CRK + +CRK + + + +EGFR->CRK + + + + + + +PTPN1 + +PTPN1 + + + +EGFR->PTPN1 + + + + + +CREBBP + +CREBBP + + + +STAT1->CREBBP + + + + + + +MAPK8 + +MAPK8 + + + +SIRT1 + +SIRT1 + + + +MAPK8->SIRT1 + + + + + +NFATC4 + +NFATC4 + + + +MAPK8->NFATC4 + + + + + + +CDK1 + +CDK1 + + + +ERBB2->CDK1 + + + + + + +MAPK1 + +MAPK1 + + + +MAP2K1->MAPK1 + + + + + +MAPK3 + +MAPK3 + + + +MAP2K1->MAPK3 + + + + + +ELK1 + +ELK1 + + + +MAPK1->ELK1 + + + + + +AEBP1 + +AEBP1 + + + +MAPK1->AEBP1 + + + + + +TP53 + +TP53 + + + +CREBBP->TP53 + + + + + +CSNK2A1 + +CSNK2A1 + + + +HOXB7 + +HOXB7 + + + +CSNK2A1->HOXB7 + + + + + + +ABL1 + +ABL1 + + + +HIPK2 + +HIPK2 + + + +ABL1->HIPK2 + + + + + +ZBTB4 + +ZBTB4 + + + +HIPK2->ZBTB4 + + + + + + +RAC1 + +RAC1 + + + +PIK3R1->RAC1 + + + + + +MAP3K10 + +MAP3K10 + + + +RAC1->MAP3K10 + + + + + +RUNX2 + +RUNX2 + + + +MAPK3->RUNX2 + + + + + +CRK->MAPK8 + + + + + +PTPN1->ABL1 + + + + + + +NFYB + +NFYB + + + +TP53->NFYB + + + + + + +CDK1->CSNK2A1 + + + + + +NEUROD1 + +NEUROD1 + + + +MAP3K10->NEUROD1 + + + + + \ No newline at end of file diff --git a/docs/_build/html/main/_images/aa13e66ecb35e387e408e46e79325f80b19a3d0487cc439bf3c02c3ed740686c.svg b/docs/_build/html/main/_images/aa13e66ecb35e387e408e46e79325f80b19a3d0487cc439bf3c02c3ed740686c.svg new file mode 100644 index 00000000..f8836717 --- /dev/null +++ b/docs/_build/html/main/_images/aa13e66ecb35e387e408e46e79325f80b19a3d0487cc439bf3c02c3ed740686c.svg @@ -0,0 +1,2802 @@ + + + + + + +%3 + + + +acald_c + +acald_c + + + +e_0_center + + + + +acald_c->e_0_center + + + + +nad_c + +nad_c + + + +nad_c->e_0_center + + + + +e_7_center + + + + +nad_c->e_7_center + + + + +e_9_center + + + + +nad_c->e_9_center + + + + +e_12_center + + + + +nad_c->e_12_center + + + + +e_48_center + + + + +nad_c->e_48_center + + + + +e_60_center + + + + +nad_c->e_60_center + + + + +e_63_center + + + + +nad_c->e_63_center + + + + +e_64_center + + + + +nad_c->e_64_center + + + + +e_67_center + + + + +nad_c->e_67_center + + + + +e_70_center + + + + +nad_c->e_70_center + + + + +coa_c + +coa_c + + + +coa_c->e_0_center + + + + +coa_c->e_7_center + + + + +coa_c->e_70_center + + + + +e_72_center + + + + +coa_c->e_72_center + + + + +e_89_center + + + + +coa_c->e_89_center + + + + +accoa_c + +accoa_c + + + +accoa_c->e_12_center + + + + +e_14_center + + + + +accoa_c->e_14_center + + + + +e_61_center + + + + +accoa_c->e_61_center + + + + +e_81_center + + + + +accoa_c->e_81_center + + + + +h_c + +h_c + + + +e_15_center + + + + +h_c->e_15_center + + + + +e_54_center + + + + +h_c->e_54_center + + + + +e_66_center + + + + +h_c->e_66_center + + + + +e_82_center + + + + +h_c->e_82_center + + + + +nadh_c + +nadh_c + + + +nadh_c->e_66_center + + + + +e_91_center + + + + +nadh_c->e_91_center + + + + +e_0_center->accoa_c + + + + + +e_0_center->h_c + + + + + +e_0_center->nadh_c + + + + + +acald_e + +acald_e + + + +acald_e->acald_c + + + + + +e_20_target + + + + +acald_e->e_20_target + + + + + +atp_c + +atp_c + + + +e_2_center + + + + +atp_c->e_2_center + + + + +e_6_center + + + + +atp_c->e_6_center + + + + +e_10_center + + + + +atp_c->e_10_center + + + + +atp_c->e_12_center + + + + +e_50_center + + + + +atp_c->e_50_center + + + + +e_51_center + + + + +atp_c->e_51_center + + + + +e_71_center + + + + +atp_c->e_71_center + + + + +e_74_center + + + + +atp_c->e_74_center + + + + +e_79_center + + + + +atp_c->e_79_center + + + + +e_80_center + + + + +atp_c->e_80_center + + + + +atp_c->e_89_center + + + + +ac_c + +ac_c + + + +ac_c->e_2_center + + + + +actp_c + +actp_c + + + +adp_c + +adp_c + + + +e_11_center + + + + +adp_c->e_11_center + + + + +adp_c->e_82_center + + + + +e_2_center->actp_c + + + + + +e_2_center->adp_c + + + + + +cit_c + +cit_c + + + +e_3_center + + + + +cit_c->e_3_center + + + + +acon_C_c + +acon_C_c + + + +e_4_center + + + + +acon_C_c->e_4_center + + + + +h2o_c + +h2o_c + + + +h2o_c->e_4_center + + + + +h2o_c->e_10_center + + + + +h2o_c->e_12_center + + + + +h2o_c->e_14_center + + + + +e_40_center + + + + +h2o_c->e_40_center + + + + +e_45_center + + + + +h2o_c->e_45_center + + + + +h2o_c->e_51_center + + + + +e_52_center + + + + +h2o_c->e_52_center + + + + +e_53_center + + + + +h2o_c->e_53_center + + + + +h2o_c->e_61_center + + + + +e_75_center + + + + +h2o_c->e_75_center + + + + +e_78_center + + + + +h2o_c->e_78_center + + + + +h2o_c->e_80_center + + + + +e_3_center->acon_C_c + + + + + +e_3_center->h2o_c + + + + + +icit_c + +icit_c + + + +e_58_center + + + + +icit_c->e_58_center + + + + +e_59_center + + + + +icit_c->e_59_center + + + + +e_4_center->icit_c + + + + + +ac_e + +ac_e + + + +e_5_center + + + + +ac_e->e_5_center + + + + +e_19_target + + + + +ac_e->e_19_target + + + + + +h_e + +h_e + + + +h_e->e_5_center + + + + +e_8_center + + + + +h_e->e_8_center + + + + +h_e->e_11_center + + + + +e_16_center + + + + +h_e->e_16_center + + + + +e_18_center + + + + +h_e->e_18_center + + + + +e_30_target + + + + +h_e->e_30_target + + + + + +e_41_center + + + + +h_e->e_41_center + + + + +e_46_center + + + + +h_e->e_46_center + + + + +e_55_center + + + + +h_e->e_55_center + + + + +e_62_center + + + + +h_e->e_62_center + + + + +e_77_center + + + + +h_e->e_77_center + + + + +e_83_center + + + + +h_e->e_83_center + + + + +e_86_center + + + + +h_e->e_86_center + + + + +e_87_center + + + + +h_e->e_87_center + + + + +h_e->e_91_center + + + + +e_5_center->h_c + + + + + +e_5_center->ac_c + + + + + +amp_c + +amp_c + + + +amp_c->e_6_center + + + + +e_6_center->adp_c + + + + + +akg_c + +akg_c + + + +akg_c->e_7_center + + + + +akg_c->e_54_center + + + + +co2_c + +co2_c + + + +co2_c->e_78_center + + + + +succoa_c + +succoa_c + + + +e_7_center->nadh_c + + + + + +e_7_center->co2_c + + + + + +e_7_center->succoa_c + + + + + +akg_e + +akg_e + + + +akg_e->e_8_center + + + + +e_21_target + + + + +akg_e->e_21_target + + + + + +e_8_center->h_c + + + + + +e_8_center->akg_c + + + + + +etoh_c + +etoh_c + + + +etoh_c->e_9_center + + + + +e_9_center->acald_c + + + + + +e_9_center->h_c + + + + + +e_9_center->nadh_c + + + + + +pi_c + +pi_c + + + +pi_c->e_11_center + + + + +pi_c->e_48_center + + + + +pi_c->e_81_center + + + + +e_10_center->h_c + + + + + +e_10_center->adp_c + + + + + +e_10_center->pi_c + + + + + +e_11_center->h_c + + + + + +e_11_center->atp_c + + + + + +e_11_center->h2o_c + + + + + +r5p_c + +r5p_c + + + +r5p_c->e_12_center + + + + +ru5p__D_c + +ru5p__D_c + + + +r5p_c->ru5p__D_c + + + + + +e_92_center + + + + +r5p_c->e_92_center + + + + +nadph_c + +nadph_c + + + +nadph_c->e_12_center + + + + +nadph_c->e_54_center + + + + +nadph_c->e_67_center + + + + +oaa_c + +oaa_c + + + +oaa_c->e_12_center + + + + +oaa_c->e_14_center + + + + +oaa_c->e_79_center + + + + +glu__L_c + +glu__L_c + + + +glu__L_c->e_12_center + + + + +glu__L_c->e_50_center + + + + +glu__L_c->e_52_center + + + + +g3p_c + +g3p_c + + + +g3p_c->e_12_center + + + + +g3p_c->e_48_center + + + + +e_90_center + + + + +g3p_c->e_90_center + + + + +3pg_c + +3pg_c + + + +3pg_c->e_12_center + + + + +3pg_c->e_74_center + + + + +pyr_c + +pyr_c + + + +pyr_c->e_12_center + + + + +pyr_c->e_70_center + + + + +pyr_c->e_72_center + + + + +pyr_c->e_80_center + + + + +pep_c + +pep_c + + + +pep_c->e_12_center + + + + +e_44_center + + + + +pep_c->e_44_center + + + + +e_49_center + + + + +pep_c->e_49_center + + + + +pep_c->e_78_center + + + + +pep_c->e_82_center + + + + +f6p_c + +f6p_c + + + +f6p_c->e_12_center + + + + +f6p_c->e_71_center + + + + +g6p_c + +g6p_c + + + +g6p_c->f6p_c + + + + + +g6p_c->e_12_center + + + + +e_47_center + + + + +g6p_c->e_47_center + + + + +e4p_c + +e4p_c + + + +e4p_c->e_12_center + + + + +e_93_center + + + + +e4p_c->e_93_center + + + + +gln__L_c + +gln__L_c + + + +gln__L_c->e_12_center + + + + +gln__L_c->e_53_center + + + + +gln__L_c->e_54_center + + + + +nadp_c + +nadp_c + + + +nadp_c->e_47_center + + + + +nadp_c->e_52_center + + + + +e_56_center + + + + +nadp_c->e_56_center + + + + +nadp_c->e_58_center + + + + +e_65_center + + + + +nadp_c->e_65_center + + + + +nadp_c->e_91_center + + + + +e_12_center->coa_c + + + + + +e_12_center->h_c + + + + + +e_12_center->nadh_c + + + + + +e_12_center->adp_c + + + + + +e_12_center->akg_c + + + + + +e_12_center->pi_c + + + + + +e_12_center->nadp_c + + + + + +co2_e + +co2_e + + + +co2_e->co2_c + + + + + +e_22_target + + + + +co2_e->e_22_target + + + + + +e_14_center->coa_c + + + + + +e_14_center->h_c + + + + + +e_14_center->cit_c + + + + + +o2_c + +o2_c + + + +o2_c->e_15_center + + + + +q8h2_c + +q8h2_c + + + +q8h2_c->e_15_center + + + + +e_43_center + + + + +q8h2_c->e_43_center + + + + +q8_c + +q8_c + + + +q8_c->e_66_center + + + + +e_88_center + + + + +q8_c->e_88_center + + + + +e_15_center->h2o_c + + + + + +e_15_center->h_e + + + + + +e_15_center->q8_c + + + + + +lac__D_e + +lac__D_e + + + +lac__D_e->e_16_center + + + + +e_32_target + + + + +lac__D_e->e_32_target + + + + + +lac__D_c + +lac__D_c + + + +lac__D_c->e_60_center + + + + +e_16_center->h_c + + + + + +e_16_center->lac__D_c + + + + + +2pg_c + +2pg_c + + + +2pg_c->3pg_c + + + + + +e_17_center + + + + +2pg_c->e_17_center + + + + +e_17_center->h2o_c + + + + + +e_17_center->pep_c + + + + + +etoh_e + +etoh_e + + + +etoh_e->e_18_center + + + + +e_23_target + + + + +etoh_e->e_23_target + + + + + +e_18_center->h_c + + + + + +e_18_center->etoh_c + + + + + +e_24_target + + + + +for_e + +for_e + + + +for_e->e_24_target + + + + + +for_e->e_41_center + + + + +e_25_target + + + + +fru_e + +fru_e + + + +fru_e->e_25_target + + + + + +fru_e->e_44_center + + + + +e_26_target + + + + +fum_e + +fum_e + + + +fum_e->e_26_target + + + + + +fum_e->e_46_center + + + + +e_27_target + + + + +glc__D_e + +glc__D_e + + + +glc__D_e->e_27_target + + + + + +glc__D_e->e_49_center + + + + +e_28_target + + + + +gln__L_e + +gln__L_e + + + +gln__L_e->e_28_target + + + + + +gln__L_e->e_51_center + + + + +e_29_target + + + + +glu__L_e + +glu__L_e + + + +glu__L_e->e_29_target + + + + + +glu__L_e->e_55_center + + + + +e_31_target + + + + +h2o_e + +h2o_e + + + +h2o_e->h2o_c + + + + + +h2o_e->e_31_target + + + + + +e_33_target + + + + +mal__L_e + +mal__L_e + + + +mal__L_e->e_33_target + + + + + +mal__L_e->e_62_center + + + + +e_34_target + + + + +nh4_e + +nh4_e + + + +nh4_e->e_34_target + + + + + +nh4_c + +nh4_c + + + +nh4_e->nh4_c + + + + + +e_35_target + + + + +o2_e + +o2_e + + + +o2_e->o2_c + + + + + +o2_e->e_35_target + + + + + +e_36_target + + + + +pi_e + +pi_e + + + +pi_e->e_36_target + + + + + +pi_e->e_77_center + + + + +e_37_target + + + + +pyr_e + +pyr_e + + + +pyr_e->e_37_target + + + + + +pyr_e->e_83_center + + + + +e_38_target + + + + +succ_e + +succ_e + + + +succ_e->e_38_target + + + + + +succ_e->e_86_center + + + + +fdp_c + +fdp_c + + + +e_39_center + + + + +fdp_c->e_39_center + + + + +fdp_c->e_40_center + + + + +dhap_c + +dhap_c + + + +dhap_c->g3p_c + + + + + +e_39_center->g3p_c + + + + + +e_39_center->dhap_c + + + + + +e_40_center->pi_c + + + + + +e_40_center->f6p_c + + + + + +for_c + +for_c + + + +for_c->for_e + + + + + +e_41_center->h_c + + + + + +e_41_center->for_c + + + + + +fum_c + +fum_c + + + +fum_c->e_43_center + + + + +fum_c->e_45_center + + + + +succ_c + +succ_c + + + +succ_c->e_87_center + + + + +succ_c->e_88_center + + + + +succ_c->e_89_center + + + + +e_43_center->q8_c + + + + + +e_43_center->succ_c + + + + + +e_44_center->pyr_c + + + + + +e_44_center->f6p_c + + + + + +mal__L_c + +mal__L_c + + + +mal__L_c->e_63_center + + + + +mal__L_c->e_64_center + + + + +mal__L_c->e_65_center + + + + +e_45_center->mal__L_c + + + + + +e_46_center->h_c + + + + + +e_46_center->fum_c + + + + + +6pgl_c + +6pgl_c + + + +6pgl_c->e_75_center + + + + +e_47_center->h_c + + + + + +e_47_center->nadph_c + + + + + +e_47_center->6pgl_c + + + + + +13dpg_c + +13dpg_c + + + +e_48_center->h_c + + + + + +e_48_center->nadh_c + + + + + +e_48_center->13dpg_c + + + + + +e_49_center->pyr_c + + + + + +e_49_center->g6p_c + + + + + +nh4_c->e_50_center + + + + +e_50_center->h_c + + + + + +e_50_center->adp_c + + + + + +e_50_center->pi_c + + + + + +e_50_center->gln__L_c + + + + + +e_51_center->h_c + + + + + +e_51_center->adp_c + + + + + +e_51_center->pi_c + + + + + +e_51_center->gln__L_c + + + + + +e_52_center->h_c + + + + + +e_52_center->akg_c + + + + + +e_52_center->nadph_c + + + + + +e_52_center->nh4_c + + + + + +e_53_center->glu__L_c + + + + + +e_53_center->nh4_c + + + + + +e_54_center->glu__L_c + + + + + +e_54_center->nadp_c + + + + + +e_55_center->h_c + + + + + +e_55_center->glu__L_c + + + + + +6pgc_c + +6pgc_c + + + +6pgc_c->e_56_center + + + + +xu5p__D_c + +xu5p__D_c + + + +ru5p__D_c->xu5p__D_c + + + + + +e_56_center->co2_c + + + + + +e_56_center->nadph_c + + + + + +e_56_center->ru5p__D_c + + + + + +e_58_center->akg_c + + + + + +e_58_center->co2_c + + + + + +e_58_center->nadph_c + + + + + +glx_c + +glx_c + + + +glx_c->e_61_center + + + + +e_59_center->succ_c + + + + + +e_59_center->glx_c + + + + + +e_60_center->h_c + + + + + +e_60_center->nadh_c + + + + + +e_60_center->pyr_c + + + + + +e_61_center->coa_c + + + + + +e_61_center->h_c + + + + + +e_61_center->mal__L_c + + + + + +e_62_center->h_c + + + + + +e_62_center->mal__L_c + + + + + +e_63_center->h_c + + + + + +e_63_center->nadh_c + + + + + +e_63_center->oaa_c + + + + + +e_64_center->nadh_c + + + + + +e_64_center->co2_c + + + + + +e_64_center->pyr_c + + + + + +e_65_center->co2_c + + + + + +e_65_center->nadph_c + + + + + +e_65_center->pyr_c + + + + + +e_66_center->nad_c + + + + + +e_66_center->h_e + + + + + +e_66_center->q8h2_c + + + + + +e_67_center->nadh_c + + + + + +e_67_center->nadp_c + + + + + +e_70_center->accoa_c + + + + + +e_70_center->nadh_c + + + + + +e_70_center->co2_c + + + + + +e_71_center->h_c + + + + + +e_71_center->adp_c + + + + + +e_71_center->fdp_c + + + + + +e_72_center->accoa_c + + + + + +e_72_center->for_c + + + + + +e_74_center->adp_c + + + + + +e_74_center->13dpg_c + + + + + +e_75_center->h_c + + + + + +e_75_center->6pgc_c + + + + + +e_77_center->h_c + + + + + +e_77_center->pi_c + + + + + +e_78_center->h_c + + + + + +e_78_center->pi_c + + + + + +e_78_center->oaa_c + + + + + +e_79_center->adp_c + + + + + +e_79_center->co2_c + + + + + +e_79_center->pep_c + + + + + +e_80_center->h_c + + + + + +e_80_center->amp_c + + + + + +e_80_center->pi_c + + + + + +e_80_center->pep_c + + + + + +e_81_center->coa_c + + + + + +e_81_center->actp_c + + + + + +e_82_center->atp_c + + + + + +e_82_center->pyr_c + + + + + +e_83_center->h_c + + + + + +e_83_center->pyr_c + + + + + +xu5p__D_c->e_92_center + + + + +xu5p__D_c->e_93_center + + + + +e_86_center->h_c + + + + + +e_86_center->succ_c + + + + + +e_87_center->h_c + + + + + +e_87_center->succ_e + + + + + +e_88_center->q8h2_c + + + + + +e_88_center->fum_c + + + + + +e_89_center->adp_c + + + + + +e_89_center->succoa_c + + + + + +e_89_center->pi_c + + + + + +s7p_c + +s7p_c + + + +s7p_c->e_90_center + + + + +e_90_center->f6p_c + + + + + +e_90_center->e4p_c + + + + + +e_91_center->nad_c + + + + + +e_91_center->h_c + + + + + +e_91_center->nadph_c + + + + + +e_92_center->g3p_c + + + + + +e_92_center->s7p_c + + + + + +e_93_center->g3p_c + + + + + +e_93_center->f6p_c + + + + + \ No newline at end of file diff --git a/docs/_build/html/main/_images/cec93c0a71c17db5062ee6115e31bc12efabe34882770aed1ced1bdbd70dde75.svg b/docs/_build/html/main/_images/cec93c0a71c17db5062ee6115e31bc12efabe34882770aed1ced1bdbd70dde75.svg new file mode 100644 index 00000000..93548619 --- /dev/null +++ b/docs/_build/html/main/_images/cec93c0a71c17db5062ee6115e31bc12efabe34882770aed1ced1bdbd70dde75.svg @@ -0,0 +1,2802 @@ + + + + + + +%3 + + + +nad_c + +nad_c + + + +e_0_center + + + + +nad_c->e_0_center + + + + +e_7_center + + + + +nad_c->e_7_center + + + + +e_9_center + + + + +nad_c->e_9_center + + + + +e_12_center + + + + +nad_c->e_12_center + + + + +e_48_center + + + + +nad_c->e_48_center + + + + +e_60_center + + + + +nad_c->e_60_center + + + + +e_63_center + + + + +nad_c->e_63_center + + + + +e_64_center + + + + +nad_c->e_64_center + + + + +e_67_center + + + + +nad_c->e_67_center + + + + +e_70_center + + + + +nad_c->e_70_center + + + + +acald_c + +acald_c + + + +acald_c->e_0_center + + + + +coa_c + +coa_c + + + +coa_c->e_0_center + + + + +coa_c->e_7_center + + + + +coa_c->e_70_center + + + + +e_72_center + + + + +coa_c->e_72_center + + + + +e_89_center + + + + +coa_c->e_89_center + + + + +h_c + +h_c + + + +e_15_center + + + + +h_c->e_15_center + + + + +e_54_center + + + + +h_c->e_54_center + + + + +e_66_center + + + + +h_c->e_66_center + + + + +e_82_center + + + + +h_c->e_82_center + + + + +nadh_c + +nadh_c + + + +nadh_c->e_66_center + + + + +e_91_center + + + + +nadh_c->e_91_center + + + + +accoa_c + +accoa_c + + + +accoa_c->e_12_center + + + + +e_14_center + + + + +accoa_c->e_14_center + + + + +e_61_center + + + + +accoa_c->e_61_center + + + + +e_81_center + + + + +accoa_c->e_81_center + + + + +e_0_center->h_c + + + + + +e_0_center->nadh_c + + + + + +e_0_center->accoa_c + + + + + +acald_e + +acald_e + + + +acald_e->acald_c + + + + + +e_20_target + + + + +acald_e->e_20_target + + + + + +ac_c + +ac_c + + + +e_2_center + + + + +ac_c->e_2_center + + + + +atp_c + +atp_c + + + +atp_c->e_2_center + + + + +e_6_center + + + + +atp_c->e_6_center + + + + +e_10_center + + + + +atp_c->e_10_center + + + + +atp_c->e_12_center + + + + +e_50_center + + + + +atp_c->e_50_center + + + + +e_51_center + + + + +atp_c->e_51_center + + + + +e_71_center + + + + +atp_c->e_71_center + + + + +e_74_center + + + + +atp_c->e_74_center + + + + +e_79_center + + + + +atp_c->e_79_center + + + + +e_80_center + + + + +atp_c->e_80_center + + + + +atp_c->e_89_center + + + + +adp_c + +adp_c + + + +e_11_center + + + + +adp_c->e_11_center + + + + +adp_c->e_82_center + + + + +actp_c + +actp_c + + + +e_2_center->adp_c + + + + + +e_2_center->actp_c + + + + + +cit_c + +cit_c + + + +e_3_center + + + + +cit_c->e_3_center + + + + +h2o_c + +h2o_c + + + +e_4_center + + + + +h2o_c->e_4_center + + + + +h2o_c->e_10_center + + + + +h2o_c->e_12_center + + + + +h2o_c->e_14_center + + + + +e_40_center + + + + +h2o_c->e_40_center + + + + +e_45_center + + + + +h2o_c->e_45_center + + + + +h2o_c->e_51_center + + + + +e_52_center + + + + +h2o_c->e_52_center + + + + +e_53_center + + + + +h2o_c->e_53_center + + + + +h2o_c->e_61_center + + + + +e_75_center + + + + +h2o_c->e_75_center + + + + +e_78_center + + + + +h2o_c->e_78_center + + + + +h2o_c->e_80_center + + + + +acon_C_c + +acon_C_c + + + +acon_C_c->e_4_center + + + + +e_3_center->h2o_c + + + + + +e_3_center->acon_C_c + + + + + +icit_c + +icit_c + + + +e_58_center + + + + +icit_c->e_58_center + + + + +e_59_center + + + + +icit_c->e_59_center + + + + +e_4_center->icit_c + + + + + +ac_e + +ac_e + + + +e_5_center + + + + +ac_e->e_5_center + + + + +e_19_target + + + + +ac_e->e_19_target + + + + + +h_e + +h_e + + + +h_e->e_5_center + + + + +e_8_center + + + + +h_e->e_8_center + + + + +h_e->e_11_center + + + + +e_16_center + + + + +h_e->e_16_center + + + + +e_18_center + + + + +h_e->e_18_center + + + + +e_30_target + + + + +h_e->e_30_target + + + + + +e_41_center + + + + +h_e->e_41_center + + + + +e_46_center + + + + +h_e->e_46_center + + + + +e_55_center + + + + +h_e->e_55_center + + + + +e_62_center + + + + +h_e->e_62_center + + + + +e_77_center + + + + +h_e->e_77_center + + + + +e_83_center + + + + +h_e->e_83_center + + + + +e_86_center + + + + +h_e->e_86_center + + + + +e_87_center + + + + +h_e->e_87_center + + + + +h_e->e_91_center + + + + +e_5_center->h_c + + + + + +e_5_center->ac_c + + + + + +amp_c + +amp_c + + + +amp_c->e_6_center + + + + +e_6_center->adp_c + + + + + +akg_c + +akg_c + + + +akg_c->e_7_center + + + + +akg_c->e_54_center + + + + +co2_c + +co2_c + + + +co2_c->e_78_center + + + + +succoa_c + +succoa_c + + + +e_7_center->nadh_c + + + + + +e_7_center->co2_c + + + + + +e_7_center->succoa_c + + + + + +akg_e + +akg_e + + + +akg_e->e_8_center + + + + +e_21_target + + + + +akg_e->e_21_target + + + + + +e_8_center->h_c + + + + + +e_8_center->akg_c + + + + + +etoh_c + +etoh_c + + + +etoh_c->e_9_center + + + + +e_9_center->acald_c + + + + + +e_9_center->h_c + + + + + +e_9_center->nadh_c + + + + + +pi_c + +pi_c + + + +pi_c->e_11_center + + + + +pi_c->e_48_center + + + + +pi_c->e_81_center + + + + +e_10_center->h_c + + + + + +e_10_center->adp_c + + + + + +e_10_center->pi_c + + + + + +e_11_center->h_c + + + + + +e_11_center->atp_c + + + + + +e_11_center->h2o_c + + + + + +gln__L_c + +gln__L_c + + + +gln__L_c->e_12_center + + + + +gln__L_c->e_53_center + + + + +gln__L_c->e_54_center + + + + +pep_c + +pep_c + + + +pep_c->e_12_center + + + + +e_44_center + + + + +pep_c->e_44_center + + + + +e_49_center + + + + +pep_c->e_49_center + + + + +pep_c->e_78_center + + + + +pep_c->e_82_center + + + + +glu__L_c + +glu__L_c + + + +glu__L_c->e_12_center + + + + +glu__L_c->e_50_center + + + + +glu__L_c->e_52_center + + + + +oaa_c + +oaa_c + + + +oaa_c->e_12_center + + + + +oaa_c->e_14_center + + + + +oaa_c->e_79_center + + + + +nadph_c + +nadph_c + + + +nadph_c->e_12_center + + + + +nadph_c->e_54_center + + + + +nadph_c->e_67_center + + + + +f6p_c + +f6p_c + + + +f6p_c->e_12_center + + + + +f6p_c->e_71_center + + + + +g3p_c + +g3p_c + + + +g3p_c->e_12_center + + + + +g3p_c->e_48_center + + + + +e_90_center + + + + +g3p_c->e_90_center + + + + +pyr_c + +pyr_c + + + +pyr_c->e_12_center + + + + +pyr_c->e_70_center + + + + +pyr_c->e_72_center + + + + +pyr_c->e_80_center + + + + +g6p_c + +g6p_c + + + +g6p_c->f6p_c + + + + + +g6p_c->e_12_center + + + + +e_47_center + + + + +g6p_c->e_47_center + + + + +e4p_c + +e4p_c + + + +e4p_c->e_12_center + + + + +e_93_center + + + + +e4p_c->e_93_center + + + + +3pg_c + +3pg_c + + + +3pg_c->e_12_center + + + + +3pg_c->e_74_center + + + + +r5p_c + +r5p_c + + + +r5p_c->e_12_center + + + + +ru5p__D_c + +ru5p__D_c + + + +r5p_c->ru5p__D_c + + + + + +e_92_center + + + + +r5p_c->e_92_center + + + + +nadp_c + +nadp_c + + + +nadp_c->e_47_center + + + + +nadp_c->e_52_center + + + + +e_56_center + + + + +nadp_c->e_56_center + + + + +nadp_c->e_58_center + + + + +e_65_center + + + + +nadp_c->e_65_center + + + + +nadp_c->e_91_center + + + + +e_12_center->coa_c + + + + + +e_12_center->h_c + + + + + +e_12_center->nadh_c + + + + + +e_12_center->adp_c + + + + + +e_12_center->akg_c + + + + + +e_12_center->pi_c + + + + + +e_12_center->nadp_c + + + + + +co2_e + +co2_e + + + +co2_e->co2_c + + + + + +e_22_target + + + + +co2_e->e_22_target + + + + + +e_14_center->coa_c + + + + + +e_14_center->h_c + + + + + +e_14_center->cit_c + + + + + +o2_c + +o2_c + + + +o2_c->e_15_center + + + + +q8h2_c + +q8h2_c + + + +q8h2_c->e_15_center + + + + +e_43_center + + + + +q8h2_c->e_43_center + + + + +q8_c + +q8_c + + + +q8_c->e_66_center + + + + +e_88_center + + + + +q8_c->e_88_center + + + + +e_15_center->h2o_c + + + + + +e_15_center->h_e + + + + + +e_15_center->q8_c + + + + + +lac__D_e + +lac__D_e + + + +lac__D_e->e_16_center + + + + +e_32_target + + + + +lac__D_e->e_32_target + + + + + +lac__D_c + +lac__D_c + + + +lac__D_c->e_60_center + + + + +e_16_center->h_c + + + + + +e_16_center->lac__D_c + + + + + +2pg_c + +2pg_c + + + +2pg_c->3pg_c + + + + + +e_17_center + + + + +2pg_c->e_17_center + + + + +e_17_center->h2o_c + + + + + +e_17_center->pep_c + + + + + +etoh_e + +etoh_e + + + +etoh_e->e_18_center + + + + +e_23_target + + + + +etoh_e->e_23_target + + + + + +e_18_center->h_c + + + + + +e_18_center->etoh_c + + + + + +e_24_target + + + + +for_e + +for_e + + + +for_e->e_24_target + + + + + +for_e->e_41_center + + + + +e_25_target + + + + +fru_e + +fru_e + + + +fru_e->e_25_target + + + + + +fru_e->e_44_center + + + + +e_26_target + + + + +fum_e + +fum_e + + + +fum_e->e_26_target + + + + + +fum_e->e_46_center + + + + +e_27_target + + + + +glc__D_e + +glc__D_e + + + +glc__D_e->e_27_target + + + + + +glc__D_e->e_49_center + + + + +e_28_target + + + + +gln__L_e + +gln__L_e + + + +gln__L_e->e_28_target + + + + + +gln__L_e->e_51_center + + + + +e_29_target + + + + +glu__L_e + +glu__L_e + + + +glu__L_e->e_29_target + + + + + +glu__L_e->e_55_center + + + + +e_31_target + + + + +h2o_e + +h2o_e + + + +h2o_e->h2o_c + + + + + +h2o_e->e_31_target + + + + + +e_33_target + + + + +mal__L_e + +mal__L_e + + + +mal__L_e->e_33_target + + + + + +mal__L_e->e_62_center + + + + +e_34_target + + + + +nh4_e + +nh4_e + + + +nh4_e->e_34_target + + + + + +nh4_c + +nh4_c + + + +nh4_e->nh4_c + + + + + +e_35_target + + + + +o2_e + +o2_e + + + +o2_e->o2_c + + + + + +o2_e->e_35_target + + + + + +e_36_target + + + + +pi_e + +pi_e + + + +pi_e->e_36_target + + + + + +pi_e->e_77_center + + + + +e_37_target + + + + +pyr_e + +pyr_e + + + +pyr_e->e_37_target + + + + + +pyr_e->e_83_center + + + + +e_38_target + + + + +succ_e + +succ_e + + + +succ_e->e_38_target + + + + + +succ_e->e_86_center + + + + +fdp_c + +fdp_c + + + +e_39_center + + + + +fdp_c->e_39_center + + + + +fdp_c->e_40_center + + + + +dhap_c + +dhap_c + + + +dhap_c->g3p_c + + + + + +e_39_center->g3p_c + + + + + +e_39_center->dhap_c + + + + + +e_40_center->pi_c + + + + + +e_40_center->f6p_c + + + + + +for_c + +for_c + + + +for_c->for_e + + + + + +e_41_center->h_c + + + + + +e_41_center->for_c + + + + + +fum_c + +fum_c + + + +fum_c->e_43_center + + + + +fum_c->e_45_center + + + + +succ_c + +succ_c + + + +succ_c->e_87_center + + + + +succ_c->e_88_center + + + + +succ_c->e_89_center + + + + +e_43_center->q8_c + + + + + +e_43_center->succ_c + + + + + +e_44_center->f6p_c + + + + + +e_44_center->pyr_c + + + + + +mal__L_c + +mal__L_c + + + +mal__L_c->e_63_center + + + + +mal__L_c->e_64_center + + + + +mal__L_c->e_65_center + + + + +e_45_center->mal__L_c + + + + + +e_46_center->h_c + + + + + +e_46_center->fum_c + + + + + +6pgl_c + +6pgl_c + + + +6pgl_c->e_75_center + + + + +e_47_center->h_c + + + + + +e_47_center->nadph_c + + + + + +e_47_center->6pgl_c + + + + + +13dpg_c + +13dpg_c + + + +e_48_center->h_c + + + + + +e_48_center->nadh_c + + + + + +e_48_center->13dpg_c + + + + + +e_49_center->pyr_c + + + + + +e_49_center->g6p_c + + + + + +nh4_c->e_50_center + + + + +e_50_center->h_c + + + + + +e_50_center->adp_c + + + + + +e_50_center->pi_c + + + + + +e_50_center->gln__L_c + + + + + +e_51_center->h_c + + + + + +e_51_center->adp_c + + + + + +e_51_center->pi_c + + + + + +e_51_center->gln__L_c + + + + + +e_52_center->h_c + + + + + +e_52_center->akg_c + + + + + +e_52_center->nadph_c + + + + + +e_52_center->nh4_c + + + + + +e_53_center->glu__L_c + + + + + +e_53_center->nh4_c + + + + + +e_54_center->glu__L_c + + + + + +e_54_center->nadp_c + + + + + +e_55_center->h_c + + + + + +e_55_center->glu__L_c + + + + + +6pgc_c + +6pgc_c + + + +6pgc_c->e_56_center + + + + +xu5p__D_c + +xu5p__D_c + + + +ru5p__D_c->xu5p__D_c + + + + + +e_56_center->co2_c + + + + + +e_56_center->nadph_c + + + + + +e_56_center->ru5p__D_c + + + + + +e_58_center->akg_c + + + + + +e_58_center->co2_c + + + + + +e_58_center->nadph_c + + + + + +glx_c + +glx_c + + + +glx_c->e_61_center + + + + +e_59_center->succ_c + + + + + +e_59_center->glx_c + + + + + +e_60_center->h_c + + + + + +e_60_center->nadh_c + + + + + +e_60_center->pyr_c + + + + + +e_61_center->coa_c + + + + + +e_61_center->h_c + + + + + +e_61_center->mal__L_c + + + + + +e_62_center->h_c + + + + + +e_62_center->mal__L_c + + + + + +e_63_center->h_c + + + + + +e_63_center->nadh_c + + + + + +e_63_center->oaa_c + + + + + +e_64_center->nadh_c + + + + + +e_64_center->co2_c + + + + + +e_64_center->pyr_c + + + + + +e_65_center->co2_c + + + + + +e_65_center->nadph_c + + + + + +e_65_center->pyr_c + + + + + +e_66_center->nad_c + + + + + +e_66_center->h_e + + + + + +e_66_center->q8h2_c + + + + + +e_67_center->nadh_c + + + + + +e_67_center->nadp_c + + + + + +e_70_center->nadh_c + + + + + +e_70_center->accoa_c + + + + + +e_70_center->co2_c + + + + + +e_71_center->h_c + + + + + +e_71_center->adp_c + + + + + +e_71_center->fdp_c + + + + + +e_72_center->accoa_c + + + + + +e_72_center->for_c + + + + + +e_74_center->adp_c + + + + + +e_74_center->13dpg_c + + + + + +e_75_center->h_c + + + + + +e_75_center->6pgc_c + + + + + +e_77_center->h_c + + + + + +e_77_center->pi_c + + + + + +e_78_center->h_c + + + + + +e_78_center->pi_c + + + + + +e_78_center->oaa_c + + + + + +e_79_center->adp_c + + + + + +e_79_center->co2_c + + + + + +e_79_center->pep_c + + + + + +e_80_center->h_c + + + + + +e_80_center->amp_c + + + + + +e_80_center->pi_c + + + + + +e_80_center->pep_c + + + + + +e_81_center->coa_c + + + + + +e_81_center->actp_c + + + + + +e_82_center->atp_c + + + + + +e_82_center->pyr_c + + + + + +e_83_center->h_c + + + + + +e_83_center->pyr_c + + + + + +xu5p__D_c->e_92_center + + + + +xu5p__D_c->e_93_center + + + + +e_86_center->h_c + + + + + +e_86_center->succ_c + + + + + +e_87_center->h_c + + + + + +e_87_center->succ_e + + + + + +e_88_center->q8h2_c + + + + + +e_88_center->fum_c + + + + + +e_89_center->adp_c + + + + + +e_89_center->succoa_c + + + + + +e_89_center->pi_c + + + + + +s7p_c + +s7p_c + + + +s7p_c->e_90_center + + + + +e_90_center->f6p_c + + + + + +e_90_center->e4p_c + + + + + +e_91_center->nad_c + + + + + +e_91_center->h_c + + + + + +e_91_center->nadph_c + + + + + +e_92_center->g3p_c + + + + + +e_92_center->s7p_c + + + + + +e_93_center->f6p_c + + + + + +e_93_center->g3p_c + + + + + \ No newline at end of file diff --git a/docs/_build/html/main/_images/d2fa409fe9ed28e8a79df8ed63c6e1d4f2ee9377e328cb7bd41292044252c803.svg b/docs/_build/html/main/_images/d2fa409fe9ed28e8a79df8ed63c6e1d4f2ee9377e328cb7bd41292044252c803.svg new file mode 100644 index 00000000..7466718a --- /dev/null +++ b/docs/_build/html/main/_images/d2fa409fe9ed28e8a79df8ed63c6e1d4f2ee9377e328cb7bd41292044252c803.svg @@ -0,0 +1,125 @@ + + + + + + +%3 + + + +4554 + +4554 + + + +7 + +7 + + + +4554->7 + + + + + +113 + +113 + + + +7->113 + + + + + +4107 + +4107 + + + +113->4107 + + + + + +1440 + +1440 + + + +4107->1440 + + + + + +e_2_target + + + + +4047 + +4047 + + + +4047->e_2_target + + + + + +3498 + +3498 + + + +1338 + +1338 + + + +3498->1338 + + + + + +1338->4554 + + + + + +1440->4047 + + + + + +e_7_source + + + + +e_7_source->3498 + + + + + \ No newline at end of file diff --git a/main/_images/2a38f2d0d5b8c60309d55a245b5a69a6aefb567140fed800290f7e312bf398ca.svg b/main/_images/2a38f2d0d5b8c60309d55a245b5a69a6aefb567140fed800290f7e312bf398ca.svg new file mode 100644 index 00000000..8e5a4820 --- /dev/null +++ b/main/_images/2a38f2d0d5b8c60309d55a245b5a69a6aefb567140fed800290f7e312bf398ca.svg @@ -0,0 +1,2802 @@ + + + + + + +%3 + + + +acald_c + +acald_c + + + +e_0_center + + + + +acald_c->e_0_center + + + + +nad_c + +nad_c + + + +nad_c->e_0_center + + + + +e_7_center + + + + +nad_c->e_7_center + + + + +e_9_center + + + + +nad_c->e_9_center + + + + +e_12_center + + + + +nad_c->e_12_center + + + + +e_48_center + + + + +nad_c->e_48_center + + + + +e_60_center + + + + +nad_c->e_60_center + + + + +e_63_center + + + + +nad_c->e_63_center + + + + +e_64_center + + + + +nad_c->e_64_center + + + + +e_67_center + + + + +nad_c->e_67_center + + + + +e_70_center + + + + +nad_c->e_70_center + + + + +coa_c + +coa_c + + + +coa_c->e_0_center + + + + +coa_c->e_7_center + + + + +coa_c->e_70_center + + + + +e_72_center + + + + +coa_c->e_72_center + + + + +e_89_center + + + + +coa_c->e_89_center + + + + +accoa_c + +accoa_c + + + +accoa_c->e_12_center + + + + +e_14_center + + + + +accoa_c->e_14_center + + + + +e_61_center + + + + +accoa_c->e_61_center + + + + +e_81_center + + + + +accoa_c->e_81_center + + + + +h_c + +h_c + + + +e_15_center + + + + +h_c->e_15_center + + + + +e_54_center + + + + +h_c->e_54_center + + + + +e_66_center + + + + +h_c->e_66_center + + + + +e_82_center + + + + +h_c->e_82_center + + + + +nadh_c + +nadh_c + + + +nadh_c->e_66_center + + + + +e_91_center + + + + +nadh_c->e_91_center + + + + +e_0_center->accoa_c + + + + + +e_0_center->h_c + + + + + +e_0_center->nadh_c + + + + + +acald_e + +acald_e + + + +acald_e->acald_c + + + + + +e_20_target + + + + +acald_e->e_20_target + + + + + +atp_c + +atp_c + + + +e_2_center + + + + +atp_c->e_2_center + + + + +e_6_center + + + + +atp_c->e_6_center + + + + +e_10_center + + + + +atp_c->e_10_center + + + + +atp_c->e_12_center + + + + +e_50_center + + + + +atp_c->e_50_center + + + + +e_51_center + + + + +atp_c->e_51_center + + + + +e_71_center + + + + +atp_c->e_71_center + + + + +e_74_center + + + + +atp_c->e_74_center + + + + +e_79_center + + + + +atp_c->e_79_center + + + + +e_80_center + + + + +atp_c->e_80_center + + + + +atp_c->e_89_center + + + + +ac_c + +ac_c + + + +ac_c->e_2_center + + + + +actp_c + +actp_c + + + +adp_c + +adp_c + + + +e_11_center + + + + +adp_c->e_11_center + + + + +adp_c->e_82_center + + + + +e_2_center->actp_c + + + + + +e_2_center->adp_c + + + + + +cit_c + +cit_c + + + +e_3_center + + + + +cit_c->e_3_center + + + + +acon_C_c + +acon_C_c + + + +e_4_center + + + + +acon_C_c->e_4_center + + + + +h2o_c + +h2o_c + + + +h2o_c->e_4_center + + + + +h2o_c->e_10_center + + + + +h2o_c->e_12_center + + + + +h2o_c->e_14_center + + + + +e_40_center + + + + +h2o_c->e_40_center + + + + +e_45_center + + + + +h2o_c->e_45_center + + + + +h2o_c->e_51_center + + + + +e_52_center + + + + +h2o_c->e_52_center + + + + +e_53_center + + + + +h2o_c->e_53_center + + + + +h2o_c->e_61_center + + + + +e_75_center + + + + +h2o_c->e_75_center + + + + +e_78_center + + + + +h2o_c->e_78_center + + + + +h2o_c->e_80_center + + + + +e_3_center->acon_C_c + + + + + +e_3_center->h2o_c + + + + + +icit_c + +icit_c + + + +e_58_center + + + + +icit_c->e_58_center + + + + +e_59_center + + + + +icit_c->e_59_center + + + + +e_4_center->icit_c + + + + + +ac_e + +ac_e + + + +e_5_center + + + + +ac_e->e_5_center + + + + +e_19_target + + + + +ac_e->e_19_target + + + + + +h_e + +h_e + + + +h_e->e_5_center + + + + +e_8_center + + + + +h_e->e_8_center + + + + +h_e->e_11_center + + + + +e_16_center + + + + +h_e->e_16_center + + + + +e_18_center + + + + +h_e->e_18_center + + + + +e_30_target + + + + +h_e->e_30_target + + + + + +e_41_center + + + + +h_e->e_41_center + + + + +e_46_center + + + + +h_e->e_46_center + + + + +e_55_center + + + + +h_e->e_55_center + + + + +e_62_center + + + + +h_e->e_62_center + + + + +e_77_center + + + + +h_e->e_77_center + + + + +e_83_center + + + + +h_e->e_83_center + + + + +e_86_center + + + + +h_e->e_86_center + + + + +e_87_center + + + + +h_e->e_87_center + + + + +h_e->e_91_center + + + + +e_5_center->h_c + + + + + +e_5_center->ac_c + + + + + +amp_c + +amp_c + + + +amp_c->e_6_center + + + + +e_6_center->adp_c + + + + + +akg_c + +akg_c + + + +akg_c->e_7_center + + + + +akg_c->e_54_center + + + + +co2_c + +co2_c + + + +co2_c->e_78_center + + + + +succoa_c + +succoa_c + + + +e_7_center->nadh_c + + + + + +e_7_center->co2_c + + + + + +e_7_center->succoa_c + + + + + +akg_e + +akg_e + + + +akg_e->e_8_center + + + + +e_21_target + + + + +akg_e->e_21_target + + + + + +e_8_center->h_c + + + + + +e_8_center->akg_c + + + + + +etoh_c + +etoh_c + + + +etoh_c->e_9_center + + + + +e_9_center->acald_c + + + + + +e_9_center->h_c + + + + + +e_9_center->nadh_c + + + + + +pi_c + +pi_c + + + +pi_c->e_11_center + + + + +pi_c->e_48_center + + + + +pi_c->e_81_center + + + + +e_10_center->h_c + + + + + +e_10_center->adp_c + + + + + +e_10_center->pi_c + + + + + +e_11_center->h_c + + + + + +e_11_center->atp_c + + + + + +e_11_center->h2o_c + + + + + +r5p_c + +r5p_c + + + +r5p_c->e_12_center + + + + +ru5p__D_c + +ru5p__D_c + + + +r5p_c->ru5p__D_c + + + + + +e_92_center + + + + +r5p_c->e_92_center + + + + +nadph_c + +nadph_c + + + +nadph_c->e_12_center + + + + +nadph_c->e_54_center + + + + +nadph_c->e_67_center + + + + +oaa_c + +oaa_c + + + +oaa_c->e_12_center + + + + +oaa_c->e_14_center + + + + +oaa_c->e_79_center + + + + +glu__L_c + +glu__L_c + + + +glu__L_c->e_12_center + + + + +glu__L_c->e_50_center + + + + +glu__L_c->e_52_center + + + + +g3p_c + +g3p_c + + + +g3p_c->e_12_center + + + + +g3p_c->e_48_center + + + + +e_90_center + + + + +g3p_c->e_90_center + + + + +3pg_c + +3pg_c + + + +3pg_c->e_12_center + + + + +3pg_c->e_74_center + + + + +pyr_c + +pyr_c + + + +pyr_c->e_12_center + + + + +pyr_c->e_70_center + + + + +pyr_c->e_72_center + + + + +pyr_c->e_80_center + + + + +pep_c + +pep_c + + + +pep_c->e_12_center + + + + +e_44_center + + + + +pep_c->e_44_center + + + + +e_49_center + + + + +pep_c->e_49_center + + + + +pep_c->e_78_center + + + + +pep_c->e_82_center + + + + +f6p_c + +f6p_c + + + +f6p_c->e_12_center + + + + +f6p_c->e_71_center + + + + +g6p_c + +g6p_c + + + +g6p_c->f6p_c + + + + + +g6p_c->e_12_center + + + + +e_47_center + + + + +g6p_c->e_47_center + + + + +e4p_c + +e4p_c + + + +e4p_c->e_12_center + + + + +e_93_center + + + + +e4p_c->e_93_center + + + + +gln__L_c + +gln__L_c + + + +gln__L_c->e_12_center + + + + +gln__L_c->e_53_center + + + + +gln__L_c->e_54_center + + + + +nadp_c + +nadp_c + + + +nadp_c->e_47_center + + + + +nadp_c->e_52_center + + + + +e_56_center + + + + +nadp_c->e_56_center + + + + +nadp_c->e_58_center + + + + +e_65_center + + + + +nadp_c->e_65_center + + + + +nadp_c->e_91_center + + + + +e_12_center->coa_c + + + + + +e_12_center->h_c + + + + + +e_12_center->nadh_c + + + + + +e_12_center->adp_c + + + + + +e_12_center->akg_c + + + + + +e_12_center->pi_c + + + + + +e_12_center->nadp_c + + + + + +co2_e + +co2_e + + + +co2_e->co2_c + + + + + +e_22_target + + + + +co2_e->e_22_target + + + + + +e_14_center->coa_c + + + + + +e_14_center->h_c + + + + + +e_14_center->cit_c + + + + + +o2_c + +o2_c + + + +o2_c->e_15_center + + + + +q8h2_c + +q8h2_c + + + +q8h2_c->e_15_center + + + + +e_43_center + + + + +q8h2_c->e_43_center + + + + +q8_c + +q8_c + + + +q8_c->e_66_center + + + + +e_88_center + + + + +q8_c->e_88_center + + + + +e_15_center->h2o_c + + + + + +e_15_center->h_e + + + + + +e_15_center->q8_c + + + + + +lac__D_e + +lac__D_e + + + +lac__D_e->e_16_center + + + + +e_32_target + + + + +lac__D_e->e_32_target + + + + + +lac__D_c + +lac__D_c + + + +lac__D_c->e_60_center + + + + +e_16_center->h_c + + + + + +e_16_center->lac__D_c + + + + + +2pg_c + +2pg_c + + + +2pg_c->3pg_c + + + + + +e_17_center + + + + +2pg_c->e_17_center + + + + +e_17_center->h2o_c + + + + + +e_17_center->pep_c + + + + + +etoh_e + +etoh_e + + + +etoh_e->e_18_center + + + + +e_23_target + + + + +etoh_e->e_23_target + + + + + +e_18_center->h_c + + + + + +e_18_center->etoh_c + + + + + +e_24_target + + + + +for_e + +for_e + + + +for_e->e_24_target + + + + + +for_e->e_41_center + + + + +e_25_target + + + + +fru_e + +fru_e + + + +fru_e->e_25_target + + + + + +fru_e->e_44_center + + + + +e_26_target + + + + +fum_e + +fum_e + + + +fum_e->e_26_target + + + + + +fum_e->e_46_center + + + + +e_27_target + + + + +glc__D_e + +glc__D_e + + + +glc__D_e->e_27_target + + + + + +glc__D_e->e_49_center + + + + +e_28_target + + + + +gln__L_e + +gln__L_e + + + +gln__L_e->e_28_target + + + + + +gln__L_e->e_51_center + + + + +e_29_target + + + + +glu__L_e + +glu__L_e + + + +glu__L_e->e_29_target + + + + + +glu__L_e->e_55_center + + + + +e_31_target + + + + +h2o_e + +h2o_e + + + +h2o_e->h2o_c + + + + + +h2o_e->e_31_target + + + + + +e_33_target + + + + +mal__L_e + +mal__L_e + + + +mal__L_e->e_33_target + + + + + +mal__L_e->e_62_center + + + + +e_34_target + + + + +nh4_e + +nh4_e + + + +nh4_e->e_34_target + + + + + +nh4_c + +nh4_c + + + +nh4_e->nh4_c + + + + + +e_35_target + + + + +o2_e + +o2_e + + + +o2_e->o2_c + + + + + +o2_e->e_35_target + + + + + +e_36_target + + + + +pi_e + +pi_e + + + +pi_e->e_36_target + + + + + +pi_e->e_77_center + + + + +e_37_target + + + + +pyr_e + +pyr_e + + + +pyr_e->e_37_target + + + + + +pyr_e->e_83_center + + + + +e_38_target + + + + +succ_e + +succ_e + + + +succ_e->e_38_target + + + + + +succ_e->e_86_center + + + + +fdp_c + +fdp_c + + + +e_39_center + + + + +fdp_c->e_39_center + + + + +fdp_c->e_40_center + + + + +dhap_c + +dhap_c + + + +dhap_c->g3p_c + + + + + +e_39_center->g3p_c + + + + + +e_39_center->dhap_c + + + + + +e_40_center->pi_c + + + + + +e_40_center->f6p_c + + + + + +for_c + +for_c + + + +for_c->for_e + + + + + +e_41_center->h_c + + + + + +e_41_center->for_c + + + + + +fum_c + +fum_c + + + +fum_c->e_43_center + + + + +fum_c->e_45_center + + + + +succ_c + +succ_c + + + +succ_c->e_87_center + + + + +succ_c->e_88_center + + + + +succ_c->e_89_center + + + + +e_43_center->q8_c + + + + + +e_43_center->succ_c + + + + + +e_44_center->pyr_c + + + + + +e_44_center->f6p_c + + + + + +mal__L_c + +mal__L_c + + + +mal__L_c->e_63_center + + + + +mal__L_c->e_64_center + + + + +mal__L_c->e_65_center + + + + +e_45_center->mal__L_c + + + + + +e_46_center->h_c + + + + + +e_46_center->fum_c + + + + + +6pgl_c + +6pgl_c + + + +6pgl_c->e_75_center + + + + +e_47_center->h_c + + + + + +e_47_center->nadph_c + + + + + +e_47_center->6pgl_c + + + + + +13dpg_c + +13dpg_c + + + +e_48_center->h_c + + + + + +e_48_center->nadh_c + + + + + +e_48_center->13dpg_c + + + + + +e_49_center->pyr_c + + + + + +e_49_center->g6p_c + + + + + +nh4_c->e_50_center + + + + +e_50_center->h_c + + + + + +e_50_center->adp_c + + + + + +e_50_center->pi_c + + + + + +e_50_center->gln__L_c + + + + + +e_51_center->h_c + + + + + +e_51_center->adp_c + + + + + +e_51_center->pi_c + + + + + +e_51_center->gln__L_c + + + + + +e_52_center->h_c + + + + + +e_52_center->akg_c + + + + + +e_52_center->nadph_c + + + + + +e_52_center->nh4_c + + + + + +e_53_center->glu__L_c + + + + + +e_53_center->nh4_c + + + + + +e_54_center->glu__L_c + + + + + +e_54_center->nadp_c + + + + + +e_55_center->h_c + + + + + +e_55_center->glu__L_c + + + + + +6pgc_c + +6pgc_c + + + +6pgc_c->e_56_center + + + + +xu5p__D_c + +xu5p__D_c + + + +ru5p__D_c->xu5p__D_c + + + + + +e_56_center->co2_c + + + + + +e_56_center->nadph_c + + + + + +e_56_center->ru5p__D_c + + + + + +e_58_center->akg_c + + + + + +e_58_center->co2_c + + + + + +e_58_center->nadph_c + + + + + +glx_c + +glx_c + + + +glx_c->e_61_center + + + + +e_59_center->succ_c + + + + + +e_59_center->glx_c + + + + + +e_60_center->h_c + + + + + +e_60_center->nadh_c + + + + + +e_60_center->pyr_c + + + + + +e_61_center->coa_c + + + + + +e_61_center->h_c + + + + + +e_61_center->mal__L_c + + + + + +e_62_center->h_c + + + + + +e_62_center->mal__L_c + + + + + +e_63_center->h_c + + + + + +e_63_center->nadh_c + + + + + +e_63_center->oaa_c + + + + + +e_64_center->nadh_c + + + + + +e_64_center->co2_c + + + + + +e_64_center->pyr_c + + + + + +e_65_center->co2_c + + + + + +e_65_center->nadph_c + + + + + +e_65_center->pyr_c + + + + + +e_66_center->nad_c + + + + + +e_66_center->h_e + + + + + +e_66_center->q8h2_c + + + + + +e_67_center->nadh_c + + + + + +e_67_center->nadp_c + + + + + +e_70_center->accoa_c + + + + + +e_70_center->nadh_c + + + + + +e_70_center->co2_c + + + + + +e_71_center->h_c + + + + + +e_71_center->adp_c + + + + + +e_71_center->fdp_c + + + + + +e_72_center->accoa_c + + + + + +e_72_center->for_c + + + + + +e_74_center->adp_c + + + + + +e_74_center->13dpg_c + + + + + +e_75_center->h_c + + + + + +e_75_center->6pgc_c + + + + + +e_77_center->h_c + + + + + +e_77_center->pi_c + + + + + +e_78_center->h_c + + + + + +e_78_center->pi_c + + + + + +e_78_center->oaa_c + + + + + +e_79_center->adp_c + + + + + +e_79_center->co2_c + + + + + +e_79_center->pep_c + + + + + +e_80_center->h_c + + + + + +e_80_center->amp_c + + + + + +e_80_center->pi_c + + + + + +e_80_center->pep_c + + + + + +e_81_center->coa_c + + + + + +e_81_center->actp_c + + + + + +e_82_center->atp_c + + + + + +e_82_center->pyr_c + + + + + +e_83_center->h_c + + + + + +e_83_center->pyr_c + + + + + +xu5p__D_c->e_92_center + + + + +xu5p__D_c->e_93_center + + + + +e_86_center->h_c + + + + + +e_86_center->succ_c + + + + + +e_87_center->h_c + + + + + +e_87_center->succ_e + + + + + +e_88_center->q8h2_c + + + + + +e_88_center->fum_c + + + + + +e_89_center->adp_c + + + + + +e_89_center->succoa_c + + + + + +e_89_center->pi_c + + + + + +s7p_c + +s7p_c + + + +s7p_c->e_90_center + + + + +e_90_center->f6p_c + + + + + +e_90_center->e4p_c + + + + + +e_91_center->nad_c + + + + + +e_91_center->h_c + + + + + +e_91_center->nadph_c + + + + + +e_92_center->g3p_c + + + + + +e_92_center->s7p_c + + + + + +e_93_center->g3p_c + + + + + +e_93_center->f6p_c + + + + + \ No newline at end of file diff --git a/main/_images/2c64097f5da14ea3c688e1a93dc4dc0c510c4e41d0fe34fa9dfae3bc662b2bb2.svg b/main/_images/2c64097f5da14ea3c688e1a93dc4dc0c510c4e41d0fe34fa9dfae3bc662b2bb2.svg new file mode 100644 index 00000000..f48a01f9 --- /dev/null +++ b/main/_images/2c64097f5da14ea3c688e1a93dc4dc0c510c4e41d0fe34fa9dfae3bc662b2bb2.svg @@ -0,0 +1,131 @@ + + + + + + +%3 + + + +A + +A + + + +e_0_center + + + + +A->e_0_center + + + + +B + +B + + + +B->e_0_center + + + + +C + +C + + + +e_4_target + + + + +C->e_4_target + + + + + +D + +D + + + +e_1_center + + + + +D->e_1_center + + + + +e_0_center->C + + + + + +e_0_center->D + + + + + +F + +F + + + +E + +E + + + +e_1_center->F + + + + + +e_1_center->E + + + + + +e_2_source + + + + +e_2_source->A + + + + + +e_3_source + + + + +e_3_source->B + + + + + \ No newline at end of file diff --git a/main/_images/443cf7bd4db35676d58fdb902fcfd857934e3a7c2731577a6acf2f279d44b8b3.svg b/main/_images/443cf7bd4db35676d58fdb902fcfd857934e3a7c2731577a6acf2f279d44b8b3.svg new file mode 100644 index 00000000..1319a462 --- /dev/null +++ b/main/_images/443cf7bd4db35676d58fdb902fcfd857934e3a7c2731577a6acf2f279d44b8b3.svg @@ -0,0 +1,170 @@ + + + + + + +%3 + + + +I1 + +I1 + + + +N1 + +N1 + + + +I1->N1 + + + + + +M1 + +M1 + + + +N1->M1 + + + + + +M2 + +M2 + + + +N1->M2 + + + + + +_meas_c0 + +_meas_c0 + + + +M1->_meas_c0 + + + + + +M2->_meas_c0 + + + + + +I2 + +I2 + + + +N2 + +N2 + + + +I2->N2 + + + + + + +N2->M1 + + + + + + +N2->M2 + + + + + + +_s + +_s + + + +_pert_c0 + +_pert_c0 + + + +_s->_pert_c0 + + + + + +_pert_c0->I1 + + + + + +_pert_c0->I2 + + + + + +_t + +_t + + + +_meas_c0->_t + + + + + +e_13_target + + + + +_t->e_13_target + + + + + +e_12_source + + + + +e_12_source->_s + + + + + \ No newline at end of file diff --git a/main/_images/5b572f011bdaf826106697ae16ecadb3e0ff5a4bd81ae225a115f4bf9e56ae53.svg b/main/_images/5b572f011bdaf826106697ae16ecadb3e0ff5a4bd81ae225a115f4bf9e56ae53.svg new file mode 100644 index 00000000..e2fdfd18 --- /dev/null +++ b/main/_images/5b572f011bdaf826106697ae16ecadb3e0ff5a4bd81ae225a115f4bf9e56ae53.svg @@ -0,0 +1,210 @@ + + + + + + +%3 + + + +M1 + +M1 + + + +e_0_center + + + + +M1->e_0_center + + + + +M4 + +M4 + + + +M1->M4 + + + + + +M2 + +M2 + + + +M2->e_0_center + + + + +M5 + +M5 + + + +e_7_target + + + + +M5->e_7_target + + + + + +M6 + +M6 + + + +M9 + +M9 + + + +M6->M9 + + + + + +e_0_center->M5 + + + + + +e_0_center->M6 + + + + + +e_2_center + + + + +M4->e_2_center + + + + +M3 + +M3 + + + +M3->e_2_center + + + + +M8 + +M8 + + + +e_9_target + + + + +M8->e_9_target + + + + + +M7 + +M7 + + + +e_8_target + + + + +M7->e_8_target + + + + + +e_2_center->M8 + + + + + +e_2_center->M7 + + + + + +e_10_target + + + + +M9->e_10_target + + + + + +e_4_source + + + + +e_4_source->M1 + + + + + +e_5_source + + + + +e_5_source->M2 + + + + + +e_6_source + + + + +e_6_source->M3 + + + + + \ No newline at end of file diff --git a/main/_images/7d51afb160f63cb72df323a55c7f6b4d57dbccbd0120e59abc2f30407c7dfed9.svg b/main/_images/7d51afb160f63cb72df323a55c7f6b4d57dbccbd0120e59abc2f30407c7dfed9.svg new file mode 100644 index 00000000..b7c17409 --- /dev/null +++ b/main/_images/7d51afb160f63cb72df323a55c7f6b4d57dbccbd0120e59abc2f30407c7dfed9.svg @@ -0,0 +1,210 @@ + + + + + + +%3 + + + +M1 + +M1 + + + +e_0_center + + + + +M1->e_0_center + + + + +M4 + +M4 + + + +M1->M4 + + + + + +M2 + +M2 + + + +M2->e_0_center + + + + +M5 + +M5 + + + +e_7_target + + + + +M5->e_7_target + + + + + +M6 + +M6 + + + +M9 + +M9 + + + +M6->M9 + + + + + +e_0_center->M5 + + + + + +e_0_center->M6 + + + + + +e_2_center + + + + +M4->e_2_center + + + + +M3 + +M3 + + + +M3->e_2_center + + + + +M8 + +M8 + + + +e_9_target + + + + +M8->e_9_target + + + + + +M7 + +M7 + + + +e_8_target + + + + +M7->e_8_target + + + + + +e_2_center->M8 + + + + + +e_2_center->M7 + + + + + +e_10_target + + + + +M9->e_10_target + + + + + +e_4_source + + + + +e_4_source->M1 + + + + + +e_5_source + + + + +e_5_source->M2 + + + + + +e_6_source + + + + +e_6_source->M3 + + + + + \ No newline at end of file diff --git a/main/_images/868a4c4ff4d416d677b3e548cce59f6202431263bc98d2b38ab5d3e0881995b8.svg b/main/_images/868a4c4ff4d416d677b3e548cce59f6202431263bc98d2b38ab5d3e0881995b8.svg new file mode 100644 index 00000000..08ee5d59 --- /dev/null +++ b/main/_images/868a4c4ff4d416d677b3e548cce59f6202431263bc98d2b38ab5d3e0881995b8.svg @@ -0,0 +1,2802 @@ + + + + + + +%3 + + + +nad_c + +nad_c + + + +e_0_center + + + + +nad_c->e_0_center + + + + +e_7_center + + + + +nad_c->e_7_center + + + + +e_9_center + + + + +nad_c->e_9_center + + + + +e_12_center + + + + +nad_c->e_12_center + + + + +e_48_center + + + + +nad_c->e_48_center + + + + +e_60_center + + + + +nad_c->e_60_center + + + + +e_63_center + + + + +nad_c->e_63_center + + + + +e_64_center + + + + +nad_c->e_64_center + + + + +e_67_center + + + + +nad_c->e_67_center + + + + +e_70_center + + + + +nad_c->e_70_center + + + + +acald_c + +acald_c + + + +acald_c->e_0_center + + + + +coa_c + +coa_c + + + +coa_c->e_0_center + + + + +coa_c->e_7_center + + + + +coa_c->e_70_center + + + + +e_72_center + + + + +coa_c->e_72_center + + + + +e_89_center + + + + +coa_c->e_89_center + + + + +h_c + +h_c + + + +e_15_center + + + + +h_c->e_15_center + + + + +e_54_center + + + + +h_c->e_54_center + + + + +e_66_center + + + + +h_c->e_66_center + + + + +e_82_center + + + + +h_c->e_82_center + + + + +nadh_c + +nadh_c + + + +nadh_c->e_66_center + + + + +e_91_center + + + + +nadh_c->e_91_center + + + + +accoa_c + +accoa_c + + + +accoa_c->e_12_center + + + + +e_14_center + + + + +accoa_c->e_14_center + + + + +e_61_center + + + + +accoa_c->e_61_center + + + + +e_81_center + + + + +accoa_c->e_81_center + + + + +e_0_center->h_c + + + + + +e_0_center->nadh_c + + + + + +e_0_center->accoa_c + + + + + +acald_e + +acald_e + + + +acald_e->acald_c + + + + + +e_20_target + + + + +acald_e->e_20_target + + + + + +ac_c + +ac_c + + + +e_2_center + + + + +ac_c->e_2_center + + + + +atp_c + +atp_c + + + +atp_c->e_2_center + + + + +e_6_center + + + + +atp_c->e_6_center + + + + +e_10_center + + + + +atp_c->e_10_center + + + + +atp_c->e_12_center + + + + +e_50_center + + + + +atp_c->e_50_center + + + + +e_51_center + + + + +atp_c->e_51_center + + + + +e_71_center + + + + +atp_c->e_71_center + + + + +e_74_center + + + + +atp_c->e_74_center + + + + +e_79_center + + + + +atp_c->e_79_center + + + + +e_80_center + + + + +atp_c->e_80_center + + + + +atp_c->e_89_center + + + + +adp_c + +adp_c + + + +e_11_center + + + + +adp_c->e_11_center + + + + +adp_c->e_82_center + + + + +actp_c + +actp_c + + + +e_2_center->adp_c + + + + + +e_2_center->actp_c + + + + + +cit_c + +cit_c + + + +e_3_center + + + + +cit_c->e_3_center + + + + +h2o_c + +h2o_c + + + +e_4_center + + + + +h2o_c->e_4_center + + + + +h2o_c->e_10_center + + + + +h2o_c->e_12_center + + + + +h2o_c->e_14_center + + + + +e_40_center + + + + +h2o_c->e_40_center + + + + +e_45_center + + + + +h2o_c->e_45_center + + + + +h2o_c->e_51_center + + + + +e_52_center + + + + +h2o_c->e_52_center + + + + +e_53_center + + + + +h2o_c->e_53_center + + + + +h2o_c->e_61_center + + + + +e_75_center + + + + +h2o_c->e_75_center + + + + +e_78_center + + + + +h2o_c->e_78_center + + + + +h2o_c->e_80_center + + + + +acon_C_c + +acon_C_c + + + +acon_C_c->e_4_center + + + + +e_3_center->h2o_c + + + + + +e_3_center->acon_C_c + + + + + +icit_c + +icit_c + + + +e_58_center + + + + +icit_c->e_58_center + + + + +e_59_center + + + + +icit_c->e_59_center + + + + +e_4_center->icit_c + + + + + +ac_e + +ac_e + + + +e_5_center + + + + +ac_e->e_5_center + + + + +e_19_target + + + + +ac_e->e_19_target + + + + + +h_e + +h_e + + + +h_e->e_5_center + + + + +e_8_center + + + + +h_e->e_8_center + + + + +h_e->e_11_center + + + + +e_16_center + + + + +h_e->e_16_center + + + + +e_18_center + + + + +h_e->e_18_center + + + + +e_30_target + + + + +h_e->e_30_target + + + + + +e_41_center + + + + +h_e->e_41_center + + + + +e_46_center + + + + +h_e->e_46_center + + + + +e_55_center + + + + +h_e->e_55_center + + + + +e_62_center + + + + +h_e->e_62_center + + + + +e_77_center + + + + +h_e->e_77_center + + + + +e_83_center + + + + +h_e->e_83_center + + + + +e_86_center + + + + +h_e->e_86_center + + + + +e_87_center + + + + +h_e->e_87_center + + + + +h_e->e_91_center + + + + +e_5_center->h_c + + + + + +e_5_center->ac_c + + + + + +amp_c + +amp_c + + + +amp_c->e_6_center + + + + +e_6_center->adp_c + + + + + +akg_c + +akg_c + + + +akg_c->e_7_center + + + + +akg_c->e_54_center + + + + +co2_c + +co2_c + + + +co2_c->e_78_center + + + + +succoa_c + +succoa_c + + + +e_7_center->nadh_c + + + + + +e_7_center->co2_c + + + + + +e_7_center->succoa_c + + + + + +akg_e + +akg_e + + + +akg_e->e_8_center + + + + +e_21_target + + + + +akg_e->e_21_target + + + + + +e_8_center->h_c + + + + + +e_8_center->akg_c + + + + + +etoh_c + +etoh_c + + + +etoh_c->e_9_center + + + + +e_9_center->acald_c + + + + + +e_9_center->h_c + + + + + +e_9_center->nadh_c + + + + + +pi_c + +pi_c + + + +pi_c->e_11_center + + + + +pi_c->e_48_center + + + + +pi_c->e_81_center + + + + +e_10_center->h_c + + + + + +e_10_center->adp_c + + + + + +e_10_center->pi_c + + + + + +e_11_center->h_c + + + + + +e_11_center->atp_c + + + + + +e_11_center->h2o_c + + + + + +gln__L_c + +gln__L_c + + + +gln__L_c->e_12_center + + + + +gln__L_c->e_53_center + + + + +gln__L_c->e_54_center + + + + +pep_c + +pep_c + + + +pep_c->e_12_center + + + + +e_44_center + + + + +pep_c->e_44_center + + + + +e_49_center + + + + +pep_c->e_49_center + + + + +pep_c->e_78_center + + + + +pep_c->e_82_center + + + + +glu__L_c + +glu__L_c + + + +glu__L_c->e_12_center + + + + +glu__L_c->e_50_center + + + + +glu__L_c->e_52_center + + + + +oaa_c + +oaa_c + + + +oaa_c->e_12_center + + + + +oaa_c->e_14_center + + + + +oaa_c->e_79_center + + + + +nadph_c + +nadph_c + + + +nadph_c->e_12_center + + + + +nadph_c->e_54_center + + + + +nadph_c->e_67_center + + + + +f6p_c + +f6p_c + + + +f6p_c->e_12_center + + + + +f6p_c->e_71_center + + + + +g3p_c + +g3p_c + + + +g3p_c->e_12_center + + + + +g3p_c->e_48_center + + + + +e_90_center + + + + +g3p_c->e_90_center + + + + +pyr_c + +pyr_c + + + +pyr_c->e_12_center + + + + +pyr_c->e_70_center + + + + +pyr_c->e_72_center + + + + +pyr_c->e_80_center + + + + +g6p_c + +g6p_c + + + +g6p_c->f6p_c + + + + + +g6p_c->e_12_center + + + + +e_47_center + + + + +g6p_c->e_47_center + + + + +e4p_c + +e4p_c + + + +e4p_c->e_12_center + + + + +e_93_center + + + + +e4p_c->e_93_center + + + + +3pg_c + +3pg_c + + + +3pg_c->e_12_center + + + + +3pg_c->e_74_center + + + + +r5p_c + +r5p_c + + + +r5p_c->e_12_center + + + + +ru5p__D_c + +ru5p__D_c + + + +r5p_c->ru5p__D_c + + + + + +e_92_center + + + + +r5p_c->e_92_center + + + + +nadp_c + +nadp_c + + + +nadp_c->e_47_center + + + + +nadp_c->e_52_center + + + + +e_56_center + + + + +nadp_c->e_56_center + + + + +nadp_c->e_58_center + + + + +e_65_center + + + + +nadp_c->e_65_center + + + + +nadp_c->e_91_center + + + + +e_12_center->coa_c + + + + + +e_12_center->h_c + + + + + +e_12_center->nadh_c + + + + + +e_12_center->adp_c + + + + + +e_12_center->akg_c + + + + + +e_12_center->pi_c + + + + + +e_12_center->nadp_c + + + + + +co2_e + +co2_e + + + +co2_e->co2_c + + + + + +e_22_target + + + + +co2_e->e_22_target + + + + + +e_14_center->coa_c + + + + + +e_14_center->h_c + + + + + +e_14_center->cit_c + + + + + +o2_c + +o2_c + + + +o2_c->e_15_center + + + + +q8h2_c + +q8h2_c + + + +q8h2_c->e_15_center + + + + +e_43_center + + + + +q8h2_c->e_43_center + + + + +q8_c + +q8_c + + + +q8_c->e_66_center + + + + +e_88_center + + + + +q8_c->e_88_center + + + + +e_15_center->h2o_c + + + + + +e_15_center->h_e + + + + + +e_15_center->q8_c + + + + + +lac__D_e + +lac__D_e + + + +lac__D_e->e_16_center + + + + +e_32_target + + + + +lac__D_e->e_32_target + + + + + +lac__D_c + +lac__D_c + + + +lac__D_c->e_60_center + + + + +e_16_center->h_c + + + + + +e_16_center->lac__D_c + + + + + +2pg_c + +2pg_c + + + +2pg_c->3pg_c + + + + + +e_17_center + + + + +2pg_c->e_17_center + + + + +e_17_center->h2o_c + + + + + +e_17_center->pep_c + + + + + +etoh_e + +etoh_e + + + +etoh_e->e_18_center + + + + +e_23_target + + + + +etoh_e->e_23_target + + + + + +e_18_center->h_c + + + + + +e_18_center->etoh_c + + + + + +e_24_target + + + + +for_e + +for_e + + + +for_e->e_24_target + + + + + +for_e->e_41_center + + + + +e_25_target + + + + +fru_e + +fru_e + + + +fru_e->e_25_target + + + + + +fru_e->e_44_center + + + + +e_26_target + + + + +fum_e + +fum_e + + + +fum_e->e_26_target + + + + + +fum_e->e_46_center + + + + +e_27_target + + + + +glc__D_e + +glc__D_e + + + +glc__D_e->e_27_target + + + + + +glc__D_e->e_49_center + + + + +e_28_target + + + + +gln__L_e + +gln__L_e + + + +gln__L_e->e_28_target + + + + + +gln__L_e->e_51_center + + + + +e_29_target + + + + +glu__L_e + +glu__L_e + + + +glu__L_e->e_29_target + + + + + +glu__L_e->e_55_center + + + + +e_31_target + + + + +h2o_e + +h2o_e + + + +h2o_e->h2o_c + + + + + +h2o_e->e_31_target + + + + + +e_33_target + + + + +mal__L_e + +mal__L_e + + + +mal__L_e->e_33_target + + + + + +mal__L_e->e_62_center + + + + +e_34_target + + + + +nh4_e + +nh4_e + + + +nh4_e->e_34_target + + + + + +nh4_c + +nh4_c + + + +nh4_e->nh4_c + + + + + +e_35_target + + + + +o2_e + +o2_e + + + +o2_e->o2_c + + + + + +o2_e->e_35_target + + + + + +e_36_target + + + + +pi_e + +pi_e + + + +pi_e->e_36_target + + + + + +pi_e->e_77_center + + + + +e_37_target + + + + +pyr_e + +pyr_e + + + +pyr_e->e_37_target + + + + + +pyr_e->e_83_center + + + + +e_38_target + + + + +succ_e + +succ_e + + + +succ_e->e_38_target + + + + + +succ_e->e_86_center + + + + +fdp_c + +fdp_c + + + +e_39_center + + + + +fdp_c->e_39_center + + + + +fdp_c->e_40_center + + + + +dhap_c + +dhap_c + + + +dhap_c->g3p_c + + + + + +e_39_center->g3p_c + + + + + +e_39_center->dhap_c + + + + + +e_40_center->pi_c + + + + + +e_40_center->f6p_c + + + + + +for_c + +for_c + + + +for_c->for_e + + + + + +e_41_center->h_c + + + + + +e_41_center->for_c + + + + + +fum_c + +fum_c + + + +fum_c->e_43_center + + + + +fum_c->e_45_center + + + + +succ_c + +succ_c + + + +succ_c->e_87_center + + + + +succ_c->e_88_center + + + + +succ_c->e_89_center + + + + +e_43_center->q8_c + + + + + +e_43_center->succ_c + + + + + +e_44_center->f6p_c + + + + + +e_44_center->pyr_c + + + + + +mal__L_c + +mal__L_c + + + +mal__L_c->e_63_center + + + + +mal__L_c->e_64_center + + + + +mal__L_c->e_65_center + + + + +e_45_center->mal__L_c + + + + + +e_46_center->h_c + + + + + +e_46_center->fum_c + + + + + +6pgl_c + +6pgl_c + + + +6pgl_c->e_75_center + + + + +e_47_center->h_c + + + + + +e_47_center->nadph_c + + + + + +e_47_center->6pgl_c + + + + + +13dpg_c + +13dpg_c + + + +e_48_center->h_c + + + + + +e_48_center->nadh_c + + + + + +e_48_center->13dpg_c + + + + + +e_49_center->pyr_c + + + + + +e_49_center->g6p_c + + + + + +nh4_c->e_50_center + + + + +e_50_center->h_c + + + + + +e_50_center->adp_c + + + + + +e_50_center->pi_c + + + + + +e_50_center->gln__L_c + + + + + +e_51_center->h_c + + + + + +e_51_center->adp_c + + + + + +e_51_center->pi_c + + + + + +e_51_center->gln__L_c + + + + + +e_52_center->h_c + + + + + +e_52_center->akg_c + + + + + +e_52_center->nadph_c + + + + + +e_52_center->nh4_c + + + + + +e_53_center->glu__L_c + + + + + +e_53_center->nh4_c + + + + + +e_54_center->glu__L_c + + + + + +e_54_center->nadp_c + + + + + +e_55_center->h_c + + + + + +e_55_center->glu__L_c + + + + + +6pgc_c + +6pgc_c + + + +6pgc_c->e_56_center + + + + +xu5p__D_c + +xu5p__D_c + + + +ru5p__D_c->xu5p__D_c + + + + + +e_56_center->co2_c + + + + + +e_56_center->nadph_c + + + + + +e_56_center->ru5p__D_c + + + + + +e_58_center->akg_c + + + + + +e_58_center->co2_c + + + + + +e_58_center->nadph_c + + + + + +glx_c + +glx_c + + + +glx_c->e_61_center + + + + +e_59_center->succ_c + + + + + +e_59_center->glx_c + + + + + +e_60_center->h_c + + + + + +e_60_center->nadh_c + + + + + +e_60_center->pyr_c + + + + + +e_61_center->coa_c + + + + + +e_61_center->h_c + + + + + +e_61_center->mal__L_c + + + + + +e_62_center->h_c + + + + + +e_62_center->mal__L_c + + + + + +e_63_center->h_c + + + + + +e_63_center->nadh_c + + + + + +e_63_center->oaa_c + + + + + +e_64_center->nadh_c + + + + + +e_64_center->co2_c + + + + + +e_64_center->pyr_c + + + + + +e_65_center->co2_c + + + + + +e_65_center->nadph_c + + + + + +e_65_center->pyr_c + + + + + +e_66_center->nad_c + + + + + +e_66_center->h_e + + + + + +e_66_center->q8h2_c + + + + + +e_67_center->nadh_c + + + + + +e_67_center->nadp_c + + + + + +e_70_center->nadh_c + + + + + +e_70_center->accoa_c + + + + + +e_70_center->co2_c + + + + + +e_71_center->h_c + + + + + +e_71_center->adp_c + + + + + +e_71_center->fdp_c + + + + + +e_72_center->accoa_c + + + + + +e_72_center->for_c + + + + + +e_74_center->adp_c + + + + + +e_74_center->13dpg_c + + + + + +e_75_center->h_c + + + + + +e_75_center->6pgc_c + + + + + +e_77_center->h_c + + + + + +e_77_center->pi_c + + + + + +e_78_center->h_c + + + + + +e_78_center->pi_c + + + + + +e_78_center->oaa_c + + + + + +e_79_center->adp_c + + + + + +e_79_center->co2_c + + + + + +e_79_center->pep_c + + + + + +e_80_center->h_c + + + + + +e_80_center->amp_c + + + + + +e_80_center->pi_c + + + + + +e_80_center->pep_c + + + + + +e_81_center->coa_c + + + + + +e_81_center->actp_c + + + + + +e_82_center->atp_c + + + + + +e_82_center->pyr_c + + + + + +e_83_center->h_c + + + + + +e_83_center->pyr_c + + + + + +xu5p__D_c->e_92_center + + + + +xu5p__D_c->e_93_center + + + + +e_86_center->h_c + + + + + +e_86_center->succ_c + + + + + +e_87_center->h_c + + + + + +e_87_center->succ_e + + + + + +e_88_center->q8h2_c + + + + + +e_88_center->fum_c + + + + + +e_89_center->adp_c + + + + + +e_89_center->succoa_c + + + + + +e_89_center->pi_c + + + + + +s7p_c + +s7p_c + + + +s7p_c->e_90_center + + + + +e_90_center->f6p_c + + + + + +e_90_center->e4p_c + + + + + +e_91_center->nad_c + + + + + +e_91_center->h_c + + + + + +e_91_center->nadph_c + + + + + +e_92_center->g3p_c + + + + + +e_92_center->s7p_c + + + + + +e_93_center->f6p_c + + + + + +e_93_center->g3p_c + + + + + \ No newline at end of file diff --git a/main/_images/a18af31210c20b9afdc10fc3443dfc3ddab9d41d7f88310804f0f80d84116ddc.svg b/main/_images/a18af31210c20b9afdc10fc3443dfc3ddab9d41d7f88310804f0f80d84116ddc.svg new file mode 100644 index 00000000..abb919aa --- /dev/null +++ b/main/_images/a18af31210c20b9afdc10fc3443dfc3ddab9d41d7f88310804f0f80d84116ddc.svg @@ -0,0 +1,58 @@ + + + + + + +%3 + + + +I2 + +I2 + + + +N2 + +N2 + + + +I2->N2 + + + + + + +M2 + +M2 + + + +N2->M2 + + + + + + +M1 + +M1 + + + +N2->M1 + + + + + + \ No newline at end of file diff --git a/main/_images/a611717058041567090a4563f14a2f8125974cc83a7f80508687554b10f489ef.svg b/main/_images/a611717058041567090a4563f14a2f8125974cc83a7f80508687554b10f489ef.svg new file mode 100644 index 00000000..06648725 --- /dev/null +++ b/main/_images/a611717058041567090a4563f14a2f8125974cc83a7f80508687554b10f489ef.svg @@ -0,0 +1,339 @@ + + + + + + +%3 + + + +EGFR + +EGFR + + + +STAT1 + +STAT1 + + + +EGFR->STAT1 + + + + + +ERBB2 + +ERBB2 + + + +EGFR->ERBB2 + + + + + +MAP2K1 + +MAP2K1 + + + +EGFR->MAP2K1 + + + + + +PIK3R1 + +PIK3R1 + + + +EGFR->PIK3R1 + + + + + +CRK + +CRK + + + +EGFR->CRK + + + + + + +PTPN1 + +PTPN1 + + + +EGFR->PTPN1 + + + + + +CREBBP + +CREBBP + + + +STAT1->CREBBP + + + + + + +MAPK8 + +MAPK8 + + + +SIRT1 + +SIRT1 + + + +MAPK8->SIRT1 + + + + + +NFATC4 + +NFATC4 + + + +MAPK8->NFATC4 + + + + + + +CDK1 + +CDK1 + + + +ERBB2->CDK1 + + + + + + +MAPK1 + +MAPK1 + + + +MAP2K1->MAPK1 + + + + + +MAPK3 + +MAPK3 + + + +MAP2K1->MAPK3 + + + + + +ELK1 + +ELK1 + + + +MAPK1->ELK1 + + + + + +AEBP1 + +AEBP1 + + + +MAPK1->AEBP1 + + + + + +TP53 + +TP53 + + + +CREBBP->TP53 + + + + + +CSNK2A1 + +CSNK2A1 + + + +HOXB7 + +HOXB7 + + + +CSNK2A1->HOXB7 + + + + + + +ABL1 + +ABL1 + + + +HIPK2 + +HIPK2 + + + +ABL1->HIPK2 + + + + + +ZBTB4 + +ZBTB4 + + + +HIPK2->ZBTB4 + + + + + + +RAC1 + +RAC1 + + + +PIK3R1->RAC1 + + + + + +MAP3K10 + +MAP3K10 + + + +RAC1->MAP3K10 + + + + + +RUNX2 + +RUNX2 + + + +MAPK3->RUNX2 + + + + + +CRK->MAPK8 + + + + + +PTPN1->ABL1 + + + + + + +NFYB + +NFYB + + + +TP53->NFYB + + + + + + +CDK1->CSNK2A1 + + + + + +NEUROD1 + +NEUROD1 + + + +MAP3K10->NEUROD1 + + + + + \ No newline at end of file diff --git a/main/_images/aa13e66ecb35e387e408e46e79325f80b19a3d0487cc439bf3c02c3ed740686c.svg b/main/_images/aa13e66ecb35e387e408e46e79325f80b19a3d0487cc439bf3c02c3ed740686c.svg new file mode 100644 index 00000000..f8836717 --- /dev/null +++ b/main/_images/aa13e66ecb35e387e408e46e79325f80b19a3d0487cc439bf3c02c3ed740686c.svg @@ -0,0 +1,2802 @@ + + + + + + +%3 + + + +acald_c + +acald_c + + + +e_0_center + + + + +acald_c->e_0_center + + + + +nad_c + +nad_c + + + +nad_c->e_0_center + + + + +e_7_center + + + + +nad_c->e_7_center + + + + +e_9_center + + + + +nad_c->e_9_center + + + + +e_12_center + + + + +nad_c->e_12_center + + + + +e_48_center + + + + +nad_c->e_48_center + + + + +e_60_center + + + + +nad_c->e_60_center + + + + +e_63_center + + + + +nad_c->e_63_center + + + + +e_64_center + + + + +nad_c->e_64_center + + + + +e_67_center + + + + +nad_c->e_67_center + + + + +e_70_center + + + + +nad_c->e_70_center + + + + +coa_c + +coa_c + + + +coa_c->e_0_center + + + + +coa_c->e_7_center + + + + +coa_c->e_70_center + + + + +e_72_center + + + + +coa_c->e_72_center + + + + +e_89_center + + + + +coa_c->e_89_center + + + + +accoa_c + +accoa_c + + + +accoa_c->e_12_center + + + + +e_14_center + + + + +accoa_c->e_14_center + + + + +e_61_center + + + + +accoa_c->e_61_center + + + + +e_81_center + + + + +accoa_c->e_81_center + + + + +h_c + +h_c + + + +e_15_center + + + + +h_c->e_15_center + + + + +e_54_center + + + + +h_c->e_54_center + + + + +e_66_center + + + + +h_c->e_66_center + + + + +e_82_center + + + + +h_c->e_82_center + + + + +nadh_c + +nadh_c + + + +nadh_c->e_66_center + + + + +e_91_center + + + + +nadh_c->e_91_center + + + + +e_0_center->accoa_c + + + + + +e_0_center->h_c + + + + + +e_0_center->nadh_c + + + + + +acald_e + +acald_e + + + +acald_e->acald_c + + + + + +e_20_target + + + + +acald_e->e_20_target + + + + + +atp_c + +atp_c + + + +e_2_center + + + + +atp_c->e_2_center + + + + +e_6_center + + + + +atp_c->e_6_center + + + + +e_10_center + + + + +atp_c->e_10_center + + + + +atp_c->e_12_center + + + + +e_50_center + + + + +atp_c->e_50_center + + + + +e_51_center + + + + +atp_c->e_51_center + + + + +e_71_center + + + + +atp_c->e_71_center + + + + +e_74_center + + + + +atp_c->e_74_center + + + + +e_79_center + + + + +atp_c->e_79_center + + + + +e_80_center + + + + +atp_c->e_80_center + + + + +atp_c->e_89_center + + + + +ac_c + +ac_c + + + +ac_c->e_2_center + + + + +actp_c + +actp_c + + + +adp_c + +adp_c + + + +e_11_center + + + + +adp_c->e_11_center + + + + +adp_c->e_82_center + + + + +e_2_center->actp_c + + + + + +e_2_center->adp_c + + + + + +cit_c + +cit_c + + + +e_3_center + + + + +cit_c->e_3_center + + + + +acon_C_c + +acon_C_c + + + +e_4_center + + + + +acon_C_c->e_4_center + + + + +h2o_c + +h2o_c + + + +h2o_c->e_4_center + + + + +h2o_c->e_10_center + + + + +h2o_c->e_12_center + + + + +h2o_c->e_14_center + + + + +e_40_center + + + + +h2o_c->e_40_center + + + + +e_45_center + + + + +h2o_c->e_45_center + + + + +h2o_c->e_51_center + + + + +e_52_center + + + + +h2o_c->e_52_center + + + + +e_53_center + + + + +h2o_c->e_53_center + + + + +h2o_c->e_61_center + + + + +e_75_center + + + + +h2o_c->e_75_center + + + + +e_78_center + + + + +h2o_c->e_78_center + + + + +h2o_c->e_80_center + + + + +e_3_center->acon_C_c + + + + + +e_3_center->h2o_c + + + + + +icit_c + +icit_c + + + +e_58_center + + + + +icit_c->e_58_center + + + + +e_59_center + + + + +icit_c->e_59_center + + + + +e_4_center->icit_c + + + + + +ac_e + +ac_e + + + +e_5_center + + + + +ac_e->e_5_center + + + + +e_19_target + + + + +ac_e->e_19_target + + + + + +h_e + +h_e + + + +h_e->e_5_center + + + + +e_8_center + + + + +h_e->e_8_center + + + + +h_e->e_11_center + + + + +e_16_center + + + + +h_e->e_16_center + + + + +e_18_center + + + + +h_e->e_18_center + + + + +e_30_target + + + + +h_e->e_30_target + + + + + +e_41_center + + + + +h_e->e_41_center + + + + +e_46_center + + + + +h_e->e_46_center + + + + +e_55_center + + + + +h_e->e_55_center + + + + +e_62_center + + + + +h_e->e_62_center + + + + +e_77_center + + + + +h_e->e_77_center + + + + +e_83_center + + + + +h_e->e_83_center + + + + +e_86_center + + + + +h_e->e_86_center + + + + +e_87_center + + + + +h_e->e_87_center + + + + +h_e->e_91_center + + + + +e_5_center->h_c + + + + + +e_5_center->ac_c + + + + + +amp_c + +amp_c + + + +amp_c->e_6_center + + + + +e_6_center->adp_c + + + + + +akg_c + +akg_c + + + +akg_c->e_7_center + + + + +akg_c->e_54_center + + + + +co2_c + +co2_c + + + +co2_c->e_78_center + + + + +succoa_c + +succoa_c + + + +e_7_center->nadh_c + + + + + +e_7_center->co2_c + + + + + +e_7_center->succoa_c + + + + + +akg_e + +akg_e + + + +akg_e->e_8_center + + + + +e_21_target + + + + +akg_e->e_21_target + + + + + +e_8_center->h_c + + + + + +e_8_center->akg_c + + + + + +etoh_c + +etoh_c + + + +etoh_c->e_9_center + + + + +e_9_center->acald_c + + + + + +e_9_center->h_c + + + + + +e_9_center->nadh_c + + + + + +pi_c + +pi_c + + + +pi_c->e_11_center + + + + +pi_c->e_48_center + + + + +pi_c->e_81_center + + + + +e_10_center->h_c + + + + + +e_10_center->adp_c + + + + + +e_10_center->pi_c + + + + + +e_11_center->h_c + + + + + +e_11_center->atp_c + + + + + +e_11_center->h2o_c + + + + + +r5p_c + +r5p_c + + + +r5p_c->e_12_center + + + + +ru5p__D_c + +ru5p__D_c + + + +r5p_c->ru5p__D_c + + + + + +e_92_center + + + + +r5p_c->e_92_center + + + + +nadph_c + +nadph_c + + + +nadph_c->e_12_center + + + + +nadph_c->e_54_center + + + + +nadph_c->e_67_center + + + + +oaa_c + +oaa_c + + + +oaa_c->e_12_center + + + + +oaa_c->e_14_center + + + + +oaa_c->e_79_center + + + + +glu__L_c + +glu__L_c + + + +glu__L_c->e_12_center + + + + +glu__L_c->e_50_center + + + + +glu__L_c->e_52_center + + + + +g3p_c + +g3p_c + + + +g3p_c->e_12_center + + + + +g3p_c->e_48_center + + + + +e_90_center + + + + +g3p_c->e_90_center + + + + +3pg_c + +3pg_c + + + +3pg_c->e_12_center + + + + +3pg_c->e_74_center + + + + +pyr_c + +pyr_c + + + +pyr_c->e_12_center + + + + +pyr_c->e_70_center + + + + +pyr_c->e_72_center + + + + +pyr_c->e_80_center + + + + +pep_c + +pep_c + + + +pep_c->e_12_center + + + + +e_44_center + + + + +pep_c->e_44_center + + + + +e_49_center + + + + +pep_c->e_49_center + + + + +pep_c->e_78_center + + + + +pep_c->e_82_center + + + + +f6p_c + +f6p_c + + + +f6p_c->e_12_center + + + + +f6p_c->e_71_center + + + + +g6p_c + +g6p_c + + + +g6p_c->f6p_c + + + + + +g6p_c->e_12_center + + + + +e_47_center + + + + +g6p_c->e_47_center + + + + +e4p_c + +e4p_c + + + +e4p_c->e_12_center + + + + +e_93_center + + + + +e4p_c->e_93_center + + + + +gln__L_c + +gln__L_c + + + +gln__L_c->e_12_center + + + + +gln__L_c->e_53_center + + + + +gln__L_c->e_54_center + + + + +nadp_c + +nadp_c + + + +nadp_c->e_47_center + + + + +nadp_c->e_52_center + + + + +e_56_center + + + + +nadp_c->e_56_center + + + + +nadp_c->e_58_center + + + + +e_65_center + + + + +nadp_c->e_65_center + + + + +nadp_c->e_91_center + + + + +e_12_center->coa_c + + + + + +e_12_center->h_c + + + + + +e_12_center->nadh_c + + + + + +e_12_center->adp_c + + + + + +e_12_center->akg_c + + + + + +e_12_center->pi_c + + + + + +e_12_center->nadp_c + + + + + +co2_e + +co2_e + + + +co2_e->co2_c + + + + + +e_22_target + + + + +co2_e->e_22_target + + + + + +e_14_center->coa_c + + + + + +e_14_center->h_c + + + + + +e_14_center->cit_c + + + + + +o2_c + +o2_c + + + +o2_c->e_15_center + + + + +q8h2_c + +q8h2_c + + + +q8h2_c->e_15_center + + + + +e_43_center + + + + +q8h2_c->e_43_center + + + + +q8_c + +q8_c + + + +q8_c->e_66_center + + + + +e_88_center + + + + +q8_c->e_88_center + + + + +e_15_center->h2o_c + + + + + +e_15_center->h_e + + + + + +e_15_center->q8_c + + + + + +lac__D_e + +lac__D_e + + + +lac__D_e->e_16_center + + + + +e_32_target + + + + +lac__D_e->e_32_target + + + + + +lac__D_c + +lac__D_c + + + +lac__D_c->e_60_center + + + + +e_16_center->h_c + + + + + +e_16_center->lac__D_c + + + + + +2pg_c + +2pg_c + + + +2pg_c->3pg_c + + + + + +e_17_center + + + + +2pg_c->e_17_center + + + + +e_17_center->h2o_c + + + + + +e_17_center->pep_c + + + + + +etoh_e + +etoh_e + + + +etoh_e->e_18_center + + + + +e_23_target + + + + +etoh_e->e_23_target + + + + + +e_18_center->h_c + + + + + +e_18_center->etoh_c + + + + + +e_24_target + + + + +for_e + +for_e + + + +for_e->e_24_target + + + + + +for_e->e_41_center + + + + +e_25_target + + + + +fru_e + +fru_e + + + +fru_e->e_25_target + + + + + +fru_e->e_44_center + + + + +e_26_target + + + + +fum_e + +fum_e + + + +fum_e->e_26_target + + + + + +fum_e->e_46_center + + + + +e_27_target + + + + +glc__D_e + +glc__D_e + + + +glc__D_e->e_27_target + + + + + +glc__D_e->e_49_center + + + + +e_28_target + + + + +gln__L_e + +gln__L_e + + + +gln__L_e->e_28_target + + + + + +gln__L_e->e_51_center + + + + +e_29_target + + + + +glu__L_e + +glu__L_e + + + +glu__L_e->e_29_target + + + + + +glu__L_e->e_55_center + + + + +e_31_target + + + + +h2o_e + +h2o_e + + + +h2o_e->h2o_c + + + + + +h2o_e->e_31_target + + + + + +e_33_target + + + + +mal__L_e + +mal__L_e + + + +mal__L_e->e_33_target + + + + + +mal__L_e->e_62_center + + + + +e_34_target + + + + +nh4_e + +nh4_e + + + +nh4_e->e_34_target + + + + + +nh4_c + +nh4_c + + + +nh4_e->nh4_c + + + + + +e_35_target + + + + +o2_e + +o2_e + + + +o2_e->o2_c + + + + + +o2_e->e_35_target + + + + + +e_36_target + + + + +pi_e + +pi_e + + + +pi_e->e_36_target + + + + + +pi_e->e_77_center + + + + +e_37_target + + + + +pyr_e + +pyr_e + + + +pyr_e->e_37_target + + + + + +pyr_e->e_83_center + + + + +e_38_target + + + + +succ_e + +succ_e + + + +succ_e->e_38_target + + + + + +succ_e->e_86_center + + + + +fdp_c + +fdp_c + + + +e_39_center + + + + +fdp_c->e_39_center + + + + +fdp_c->e_40_center + + + + +dhap_c + +dhap_c + + + +dhap_c->g3p_c + + + + + +e_39_center->g3p_c + + + + + +e_39_center->dhap_c + + + + + +e_40_center->pi_c + + + + + +e_40_center->f6p_c + + + + + +for_c + +for_c + + + +for_c->for_e + + + + + +e_41_center->h_c + + + + + +e_41_center->for_c + + + + + +fum_c + +fum_c + + + +fum_c->e_43_center + + + + +fum_c->e_45_center + + + + +succ_c + +succ_c + + + +succ_c->e_87_center + + + + +succ_c->e_88_center + + + + +succ_c->e_89_center + + + + +e_43_center->q8_c + + + + + +e_43_center->succ_c + + + + + +e_44_center->pyr_c + + + + + +e_44_center->f6p_c + + + + + +mal__L_c + +mal__L_c + + + +mal__L_c->e_63_center + + + + +mal__L_c->e_64_center + + + + +mal__L_c->e_65_center + + + + +e_45_center->mal__L_c + + + + + +e_46_center->h_c + + + + + +e_46_center->fum_c + + + + + +6pgl_c + +6pgl_c + + + +6pgl_c->e_75_center + + + + +e_47_center->h_c + + + + + +e_47_center->nadph_c + + + + + +e_47_center->6pgl_c + + + + + +13dpg_c + +13dpg_c + + + +e_48_center->h_c + + + + + +e_48_center->nadh_c + + + + + +e_48_center->13dpg_c + + + + + +e_49_center->pyr_c + + + + + +e_49_center->g6p_c + + + + + +nh4_c->e_50_center + + + + +e_50_center->h_c + + + + + +e_50_center->adp_c + + + + + +e_50_center->pi_c + + + + + +e_50_center->gln__L_c + + + + + +e_51_center->h_c + + + + + +e_51_center->adp_c + + + + + +e_51_center->pi_c + + + + + +e_51_center->gln__L_c + + + + + +e_52_center->h_c + + + + + +e_52_center->akg_c + + + + + +e_52_center->nadph_c + + + + + +e_52_center->nh4_c + + + + + +e_53_center->glu__L_c + + + + + +e_53_center->nh4_c + + + + + +e_54_center->glu__L_c + + + + + +e_54_center->nadp_c + + + + + +e_55_center->h_c + + + + + +e_55_center->glu__L_c + + + + + +6pgc_c + +6pgc_c + + + +6pgc_c->e_56_center + + + + +xu5p__D_c + +xu5p__D_c + + + +ru5p__D_c->xu5p__D_c + + + + + +e_56_center->co2_c + + + + + +e_56_center->nadph_c + + + + + +e_56_center->ru5p__D_c + + + + + +e_58_center->akg_c + + + + + +e_58_center->co2_c + + + + + +e_58_center->nadph_c + + + + + +glx_c + +glx_c + + + +glx_c->e_61_center + + + + +e_59_center->succ_c + + + + + +e_59_center->glx_c + + + + + +e_60_center->h_c + + + + + +e_60_center->nadh_c + + + + + +e_60_center->pyr_c + + + + + +e_61_center->coa_c + + + + + +e_61_center->h_c + + + + + +e_61_center->mal__L_c + + + + + +e_62_center->h_c + + + + + +e_62_center->mal__L_c + + + + + +e_63_center->h_c + + + + + +e_63_center->nadh_c + + + + + +e_63_center->oaa_c + + + + + +e_64_center->nadh_c + + + + + +e_64_center->co2_c + + + + + +e_64_center->pyr_c + + + + + +e_65_center->co2_c + + + + + +e_65_center->nadph_c + + + + + +e_65_center->pyr_c + + + + + +e_66_center->nad_c + + + + + +e_66_center->h_e + + + + + +e_66_center->q8h2_c + + + + + +e_67_center->nadh_c + + + + + +e_67_center->nadp_c + + + + + +e_70_center->accoa_c + + + + + +e_70_center->nadh_c + + + + + +e_70_center->co2_c + + + + + +e_71_center->h_c + + + + + +e_71_center->adp_c + + + + + +e_71_center->fdp_c + + + + + +e_72_center->accoa_c + + + + + +e_72_center->for_c + + + + + +e_74_center->adp_c + + + + + +e_74_center->13dpg_c + + + + + +e_75_center->h_c + + + + + +e_75_center->6pgc_c + + + + + +e_77_center->h_c + + + + + +e_77_center->pi_c + + + + + +e_78_center->h_c + + + + + +e_78_center->pi_c + + + + + +e_78_center->oaa_c + + + + + +e_79_center->adp_c + + + + + +e_79_center->co2_c + + + + + +e_79_center->pep_c + + + + + +e_80_center->h_c + + + + + +e_80_center->amp_c + + + + + +e_80_center->pi_c + + + + + +e_80_center->pep_c + + + + + +e_81_center->coa_c + + + + + +e_81_center->actp_c + + + + + +e_82_center->atp_c + + + + + +e_82_center->pyr_c + + + + + +e_83_center->h_c + + + + + +e_83_center->pyr_c + + + + + +xu5p__D_c->e_92_center + + + + +xu5p__D_c->e_93_center + + + + +e_86_center->h_c + + + + + +e_86_center->succ_c + + + + + +e_87_center->h_c + + + + + +e_87_center->succ_e + + + + + +e_88_center->q8h2_c + + + + + +e_88_center->fum_c + + + + + +e_89_center->adp_c + + + + + +e_89_center->succoa_c + + + + + +e_89_center->pi_c + + + + + +s7p_c + +s7p_c + + + +s7p_c->e_90_center + + + + +e_90_center->f6p_c + + + + + +e_90_center->e4p_c + + + + + +e_91_center->nad_c + + + + + +e_91_center->h_c + + + + + +e_91_center->nadph_c + + + + + +e_92_center->g3p_c + + + + + +e_92_center->s7p_c + + + + + +e_93_center->g3p_c + + + + + +e_93_center->f6p_c + + + + + \ No newline at end of file diff --git a/main/_images/cec93c0a71c17db5062ee6115e31bc12efabe34882770aed1ced1bdbd70dde75.svg b/main/_images/cec93c0a71c17db5062ee6115e31bc12efabe34882770aed1ced1bdbd70dde75.svg new file mode 100644 index 00000000..93548619 --- /dev/null +++ b/main/_images/cec93c0a71c17db5062ee6115e31bc12efabe34882770aed1ced1bdbd70dde75.svg @@ -0,0 +1,2802 @@ + + + + + + +%3 + + + +nad_c + +nad_c + + + +e_0_center + + + + +nad_c->e_0_center + + + + +e_7_center + + + + +nad_c->e_7_center + + + + +e_9_center + + + + +nad_c->e_9_center + + + + +e_12_center + + + + +nad_c->e_12_center + + + + +e_48_center + + + + +nad_c->e_48_center + + + + +e_60_center + + + + +nad_c->e_60_center + + + + +e_63_center + + + + +nad_c->e_63_center + + + + +e_64_center + + + + +nad_c->e_64_center + + + + +e_67_center + + + + +nad_c->e_67_center + + + + +e_70_center + + + + +nad_c->e_70_center + + + + +acald_c + +acald_c + + + +acald_c->e_0_center + + + + +coa_c + +coa_c + + + +coa_c->e_0_center + + + + +coa_c->e_7_center + + + + +coa_c->e_70_center + + + + +e_72_center + + + + +coa_c->e_72_center + + + + +e_89_center + + + + +coa_c->e_89_center + + + + +h_c + +h_c + + + +e_15_center + + + + +h_c->e_15_center + + + + +e_54_center + + + + +h_c->e_54_center + + + + +e_66_center + + + + +h_c->e_66_center + + + + +e_82_center + + + + +h_c->e_82_center + + + + +nadh_c + +nadh_c + + + +nadh_c->e_66_center + + + + +e_91_center + + + + +nadh_c->e_91_center + + + + +accoa_c + +accoa_c + + + +accoa_c->e_12_center + + + + +e_14_center + + + + +accoa_c->e_14_center + + + + +e_61_center + + + + +accoa_c->e_61_center + + + + +e_81_center + + + + +accoa_c->e_81_center + + + + +e_0_center->h_c + + + + + +e_0_center->nadh_c + + + + + +e_0_center->accoa_c + + + + + +acald_e + +acald_e + + + +acald_e->acald_c + + + + + +e_20_target + + + + +acald_e->e_20_target + + + + + +ac_c + +ac_c + + + +e_2_center + + + + +ac_c->e_2_center + + + + +atp_c + +atp_c + + + +atp_c->e_2_center + + + + +e_6_center + + + + +atp_c->e_6_center + + + + +e_10_center + + + + +atp_c->e_10_center + + + + +atp_c->e_12_center + + + + +e_50_center + + + + +atp_c->e_50_center + + + + +e_51_center + + + + +atp_c->e_51_center + + + + +e_71_center + + + + +atp_c->e_71_center + + + + +e_74_center + + + + +atp_c->e_74_center + + + + +e_79_center + + + + +atp_c->e_79_center + + + + +e_80_center + + + + +atp_c->e_80_center + + + + +atp_c->e_89_center + + + + +adp_c + +adp_c + + + +e_11_center + + + + +adp_c->e_11_center + + + + +adp_c->e_82_center + + + + +actp_c + +actp_c + + + +e_2_center->adp_c + + + + + +e_2_center->actp_c + + + + + +cit_c + +cit_c + + + +e_3_center + + + + +cit_c->e_3_center + + + + +h2o_c + +h2o_c + + + +e_4_center + + + + +h2o_c->e_4_center + + + + +h2o_c->e_10_center + + + + +h2o_c->e_12_center + + + + +h2o_c->e_14_center + + + + +e_40_center + + + + +h2o_c->e_40_center + + + + +e_45_center + + + + +h2o_c->e_45_center + + + + +h2o_c->e_51_center + + + + +e_52_center + + + + +h2o_c->e_52_center + + + + +e_53_center + + + + +h2o_c->e_53_center + + + + +h2o_c->e_61_center + + + + +e_75_center + + + + +h2o_c->e_75_center + + + + +e_78_center + + + + +h2o_c->e_78_center + + + + +h2o_c->e_80_center + + + + +acon_C_c + +acon_C_c + + + +acon_C_c->e_4_center + + + + +e_3_center->h2o_c + + + + + +e_3_center->acon_C_c + + + + + +icit_c + +icit_c + + + +e_58_center + + + + +icit_c->e_58_center + + + + +e_59_center + + + + +icit_c->e_59_center + + + + +e_4_center->icit_c + + + + + +ac_e + +ac_e + + + +e_5_center + + + + +ac_e->e_5_center + + + + +e_19_target + + + + +ac_e->e_19_target + + + + + +h_e + +h_e + + + +h_e->e_5_center + + + + +e_8_center + + + + +h_e->e_8_center + + + + +h_e->e_11_center + + + + +e_16_center + + + + +h_e->e_16_center + + + + +e_18_center + + + + +h_e->e_18_center + + + + +e_30_target + + + + +h_e->e_30_target + + + + + +e_41_center + + + + +h_e->e_41_center + + + + +e_46_center + + + + +h_e->e_46_center + + + + +e_55_center + + + + +h_e->e_55_center + + + + +e_62_center + + + + +h_e->e_62_center + + + + +e_77_center + + + + +h_e->e_77_center + + + + +e_83_center + + + + +h_e->e_83_center + + + + +e_86_center + + + + +h_e->e_86_center + + + + +e_87_center + + + + +h_e->e_87_center + + + + +h_e->e_91_center + + + + +e_5_center->h_c + + + + + +e_5_center->ac_c + + + + + +amp_c + +amp_c + + + +amp_c->e_6_center + + + + +e_6_center->adp_c + + + + + +akg_c + +akg_c + + + +akg_c->e_7_center + + + + +akg_c->e_54_center + + + + +co2_c + +co2_c + + + +co2_c->e_78_center + + + + +succoa_c + +succoa_c + + + +e_7_center->nadh_c + + + + + +e_7_center->co2_c + + + + + +e_7_center->succoa_c + + + + + +akg_e + +akg_e + + + +akg_e->e_8_center + + + + +e_21_target + + + + +akg_e->e_21_target + + + + + +e_8_center->h_c + + + + + +e_8_center->akg_c + + + + + +etoh_c + +etoh_c + + + +etoh_c->e_9_center + + + + +e_9_center->acald_c + + + + + +e_9_center->h_c + + + + + +e_9_center->nadh_c + + + + + +pi_c + +pi_c + + + +pi_c->e_11_center + + + + +pi_c->e_48_center + + + + +pi_c->e_81_center + + + + +e_10_center->h_c + + + + + +e_10_center->adp_c + + + + + +e_10_center->pi_c + + + + + +e_11_center->h_c + + + + + +e_11_center->atp_c + + + + + +e_11_center->h2o_c + + + + + +gln__L_c + +gln__L_c + + + +gln__L_c->e_12_center + + + + +gln__L_c->e_53_center + + + + +gln__L_c->e_54_center + + + + +pep_c + +pep_c + + + +pep_c->e_12_center + + + + +e_44_center + + + + +pep_c->e_44_center + + + + +e_49_center + + + + +pep_c->e_49_center + + + + +pep_c->e_78_center + + + + +pep_c->e_82_center + + + + +glu__L_c + +glu__L_c + + + +glu__L_c->e_12_center + + + + +glu__L_c->e_50_center + + + + +glu__L_c->e_52_center + + + + +oaa_c + +oaa_c + + + +oaa_c->e_12_center + + + + +oaa_c->e_14_center + + + + +oaa_c->e_79_center + + + + +nadph_c + +nadph_c + + + +nadph_c->e_12_center + + + + +nadph_c->e_54_center + + + + +nadph_c->e_67_center + + + + +f6p_c + +f6p_c + + + +f6p_c->e_12_center + + + + +f6p_c->e_71_center + + + + +g3p_c + +g3p_c + + + +g3p_c->e_12_center + + + + +g3p_c->e_48_center + + + + +e_90_center + + + + +g3p_c->e_90_center + + + + +pyr_c + +pyr_c + + + +pyr_c->e_12_center + + + + +pyr_c->e_70_center + + + + +pyr_c->e_72_center + + + + +pyr_c->e_80_center + + + + +g6p_c + +g6p_c + + + +g6p_c->f6p_c + + + + + +g6p_c->e_12_center + + + + +e_47_center + + + + +g6p_c->e_47_center + + + + +e4p_c + +e4p_c + + + +e4p_c->e_12_center + + + + +e_93_center + + + + +e4p_c->e_93_center + + + + +3pg_c + +3pg_c + + + +3pg_c->e_12_center + + + + +3pg_c->e_74_center + + + + +r5p_c + +r5p_c + + + +r5p_c->e_12_center + + + + +ru5p__D_c + +ru5p__D_c + + + +r5p_c->ru5p__D_c + + + + + +e_92_center + + + + +r5p_c->e_92_center + + + + +nadp_c + +nadp_c + + + +nadp_c->e_47_center + + + + +nadp_c->e_52_center + + + + +e_56_center + + + + +nadp_c->e_56_center + + + + +nadp_c->e_58_center + + + + +e_65_center + + + + +nadp_c->e_65_center + + + + +nadp_c->e_91_center + + + + +e_12_center->coa_c + + + + + +e_12_center->h_c + + + + + +e_12_center->nadh_c + + + + + +e_12_center->adp_c + + + + + +e_12_center->akg_c + + + + + +e_12_center->pi_c + + + + + +e_12_center->nadp_c + + + + + +co2_e + +co2_e + + + +co2_e->co2_c + + + + + +e_22_target + + + + +co2_e->e_22_target + + + + + +e_14_center->coa_c + + + + + +e_14_center->h_c + + + + + +e_14_center->cit_c + + + + + +o2_c + +o2_c + + + +o2_c->e_15_center + + + + +q8h2_c + +q8h2_c + + + +q8h2_c->e_15_center + + + + +e_43_center + + + + +q8h2_c->e_43_center + + + + +q8_c + +q8_c + + + +q8_c->e_66_center + + + + +e_88_center + + + + +q8_c->e_88_center + + + + +e_15_center->h2o_c + + + + + +e_15_center->h_e + + + + + +e_15_center->q8_c + + + + + +lac__D_e + +lac__D_e + + + +lac__D_e->e_16_center + + + + +e_32_target + + + + +lac__D_e->e_32_target + + + + + +lac__D_c + +lac__D_c + + + +lac__D_c->e_60_center + + + + +e_16_center->h_c + + + + + +e_16_center->lac__D_c + + + + + +2pg_c + +2pg_c + + + +2pg_c->3pg_c + + + + + +e_17_center + + + + +2pg_c->e_17_center + + + + +e_17_center->h2o_c + + + + + +e_17_center->pep_c + + + + + +etoh_e + +etoh_e + + + +etoh_e->e_18_center + + + + +e_23_target + + + + +etoh_e->e_23_target + + + + + +e_18_center->h_c + + + + + +e_18_center->etoh_c + + + + + +e_24_target + + + + +for_e + +for_e + + + +for_e->e_24_target + + + + + +for_e->e_41_center + + + + +e_25_target + + + + +fru_e + +fru_e + + + +fru_e->e_25_target + + + + + +fru_e->e_44_center + + + + +e_26_target + + + + +fum_e + +fum_e + + + +fum_e->e_26_target + + + + + +fum_e->e_46_center + + + + +e_27_target + + + + +glc__D_e + +glc__D_e + + + +glc__D_e->e_27_target + + + + + +glc__D_e->e_49_center + + + + +e_28_target + + + + +gln__L_e + +gln__L_e + + + +gln__L_e->e_28_target + + + + + +gln__L_e->e_51_center + + + + +e_29_target + + + + +glu__L_e + +glu__L_e + + + +glu__L_e->e_29_target + + + + + +glu__L_e->e_55_center + + + + +e_31_target + + + + +h2o_e + +h2o_e + + + +h2o_e->h2o_c + + + + + +h2o_e->e_31_target + + + + + +e_33_target + + + + +mal__L_e + +mal__L_e + + + +mal__L_e->e_33_target + + + + + +mal__L_e->e_62_center + + + + +e_34_target + + + + +nh4_e + +nh4_e + + + +nh4_e->e_34_target + + + + + +nh4_c + +nh4_c + + + +nh4_e->nh4_c + + + + + +e_35_target + + + + +o2_e + +o2_e + + + +o2_e->o2_c + + + + + +o2_e->e_35_target + + + + + +e_36_target + + + + +pi_e + +pi_e + + + +pi_e->e_36_target + + + + + +pi_e->e_77_center + + + + +e_37_target + + + + +pyr_e + +pyr_e + + + +pyr_e->e_37_target + + + + + +pyr_e->e_83_center + + + + +e_38_target + + + + +succ_e + +succ_e + + + +succ_e->e_38_target + + + + + +succ_e->e_86_center + + + + +fdp_c + +fdp_c + + + +e_39_center + + + + +fdp_c->e_39_center + + + + +fdp_c->e_40_center + + + + +dhap_c + +dhap_c + + + +dhap_c->g3p_c + + + + + +e_39_center->g3p_c + + + + + +e_39_center->dhap_c + + + + + +e_40_center->pi_c + + + + + +e_40_center->f6p_c + + + + + +for_c + +for_c + + + +for_c->for_e + + + + + +e_41_center->h_c + + + + + +e_41_center->for_c + + + + + +fum_c + +fum_c + + + +fum_c->e_43_center + + + + +fum_c->e_45_center + + + + +succ_c + +succ_c + + + +succ_c->e_87_center + + + + +succ_c->e_88_center + + + + +succ_c->e_89_center + + + + +e_43_center->q8_c + + + + + +e_43_center->succ_c + + + + + +e_44_center->f6p_c + + + + + +e_44_center->pyr_c + + + + + +mal__L_c + +mal__L_c + + + +mal__L_c->e_63_center + + + + +mal__L_c->e_64_center + + + + +mal__L_c->e_65_center + + + + +e_45_center->mal__L_c + + + + + +e_46_center->h_c + + + + + +e_46_center->fum_c + + + + + +6pgl_c + +6pgl_c + + + +6pgl_c->e_75_center + + + + +e_47_center->h_c + + + + + +e_47_center->nadph_c + + + + + +e_47_center->6pgl_c + + + + + +13dpg_c + +13dpg_c + + + +e_48_center->h_c + + + + + +e_48_center->nadh_c + + + + + +e_48_center->13dpg_c + + + + + +e_49_center->pyr_c + + + + + +e_49_center->g6p_c + + + + + +nh4_c->e_50_center + + + + +e_50_center->h_c + + + + + +e_50_center->adp_c + + + + + +e_50_center->pi_c + + + + + +e_50_center->gln__L_c + + + + + +e_51_center->h_c + + + + + +e_51_center->adp_c + + + + + +e_51_center->pi_c + + + + + +e_51_center->gln__L_c + + + + + +e_52_center->h_c + + + + + +e_52_center->akg_c + + + + + +e_52_center->nadph_c + + + + + +e_52_center->nh4_c + + + + + +e_53_center->glu__L_c + + + + + +e_53_center->nh4_c + + + + + +e_54_center->glu__L_c + + + + + +e_54_center->nadp_c + + + + + +e_55_center->h_c + + + + + +e_55_center->glu__L_c + + + + + +6pgc_c + +6pgc_c + + + +6pgc_c->e_56_center + + + + +xu5p__D_c + +xu5p__D_c + + + +ru5p__D_c->xu5p__D_c + + + + + +e_56_center->co2_c + + + + + +e_56_center->nadph_c + + + + + +e_56_center->ru5p__D_c + + + + + +e_58_center->akg_c + + + + + +e_58_center->co2_c + + + + + +e_58_center->nadph_c + + + + + +glx_c + +glx_c + + + +glx_c->e_61_center + + + + +e_59_center->succ_c + + + + + +e_59_center->glx_c + + + + + +e_60_center->h_c + + + + + +e_60_center->nadh_c + + + + + +e_60_center->pyr_c + + + + + +e_61_center->coa_c + + + + + +e_61_center->h_c + + + + + +e_61_center->mal__L_c + + + + + +e_62_center->h_c + + + + + +e_62_center->mal__L_c + + + + + +e_63_center->h_c + + + + + +e_63_center->nadh_c + + + + + +e_63_center->oaa_c + + + + + +e_64_center->nadh_c + + + + + +e_64_center->co2_c + + + + + +e_64_center->pyr_c + + + + + +e_65_center->co2_c + + + + + +e_65_center->nadph_c + + + + + +e_65_center->pyr_c + + + + + +e_66_center->nad_c + + + + + +e_66_center->h_e + + + + + +e_66_center->q8h2_c + + + + + +e_67_center->nadh_c + + + + + +e_67_center->nadp_c + + + + + +e_70_center->nadh_c + + + + + +e_70_center->accoa_c + + + + + +e_70_center->co2_c + + + + + +e_71_center->h_c + + + + + +e_71_center->adp_c + + + + + +e_71_center->fdp_c + + + + + +e_72_center->accoa_c + + + + + +e_72_center->for_c + + + + + +e_74_center->adp_c + + + + + +e_74_center->13dpg_c + + + + + +e_75_center->h_c + + + + + +e_75_center->6pgc_c + + + + + +e_77_center->h_c + + + + + +e_77_center->pi_c + + + + + +e_78_center->h_c + + + + + +e_78_center->pi_c + + + + + +e_78_center->oaa_c + + + + + +e_79_center->adp_c + + + + + +e_79_center->co2_c + + + + + +e_79_center->pep_c + + + + + +e_80_center->h_c + + + + + +e_80_center->amp_c + + + + + +e_80_center->pi_c + + + + + +e_80_center->pep_c + + + + + +e_81_center->coa_c + + + + + +e_81_center->actp_c + + + + + +e_82_center->atp_c + + + + + +e_82_center->pyr_c + + + + + +e_83_center->h_c + + + + + +e_83_center->pyr_c + + + + + +xu5p__D_c->e_92_center + + + + +xu5p__D_c->e_93_center + + + + +e_86_center->h_c + + + + + +e_86_center->succ_c + + + + + +e_87_center->h_c + + + + + +e_87_center->succ_e + + + + + +e_88_center->q8h2_c + + + + + +e_88_center->fum_c + + + + + +e_89_center->adp_c + + + + + +e_89_center->succoa_c + + + + + +e_89_center->pi_c + + + + + +s7p_c + +s7p_c + + + +s7p_c->e_90_center + + + + +e_90_center->f6p_c + + + + + +e_90_center->e4p_c + + + + + +e_91_center->nad_c + + + + + +e_91_center->h_c + + + + + +e_91_center->nadph_c + + + + + +e_92_center->g3p_c + + + + + +e_92_center->s7p_c + + + + + +e_93_center->f6p_c + + + + + +e_93_center->g3p_c + + + + + \ No newline at end of file diff --git a/main/_images/d2fa409fe9ed28e8a79df8ed63c6e1d4f2ee9377e328cb7bd41292044252c803.svg b/main/_images/d2fa409fe9ed28e8a79df8ed63c6e1d4f2ee9377e328cb7bd41292044252c803.svg new file mode 100644 index 00000000..7466718a --- /dev/null +++ b/main/_images/d2fa409fe9ed28e8a79df8ed63c6e1d4f2ee9377e328cb7bd41292044252c803.svg @@ -0,0 +1,125 @@ + + + + + + +%3 + + + +4554 + +4554 + + + +7 + +7 + + + +4554->7 + + + + + +113 + +113 + + + +7->113 + + + + + +4107 + +4107 + + + +113->4107 + + + + + +1440 + +1440 + + + +4107->1440 + + + + + +e_2_target + + + + +4047 + +4047 + + + +4047->e_2_target + + + + + +3498 + +3498 + + + +1338 + +1338 + + + +3498->1338 + + + + + +1338->4554 + + + + + +1440->4047 + + + + + +e_7_source + + + + +e_7_source->3498 + + + + + \ No newline at end of file