TumorInvasion_CABEAN.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/markdown": [
       "This notebook has been executed using the docker image `colomoto/colomoto-docker:2020-07-01`"
      ],
      "text/plain": [
       "<IPython.core.display.Markdown object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import cabean\n",
    "import biolqm\n",
    "from colomoto_jupyter import tabulate"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Import the model for the tumour cell invation and migration (Cohen et al. https://doi.org/10.1371/journal.pcbi.1004571)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/markdown": [
       "Downloading http://ginsim.org/sites/default/files/SuppMat_Model_Master_Model.zginml"
      ],
      "text/plain": [
       "<IPython.core.display.Markdown object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "model = biolqm.load(\"http://ginsim.org/sites/default/files/SuppMat_Model_Master_Model.zginml\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Use the decompositon-based attractor detection method to identify all the exact attractors of the network. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 13.5 ms, sys: 6.58 ms, total: 20 ms\n",
      "Wall time: 991 ms\n"
     ]
    },
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>AKT1</th>\n",
       "      <th>AKT2</th>\n",
       "      <th>Apoptosis</th>\n",
       "      <th>CDH1</th>\n",
       "      <th>CDH2</th>\n",
       "      <th>CTNNB1</th>\n",
       "      <th>CellCycleArrest</th>\n",
       "      <th>DKK1</th>\n",
       "      <th>DNAdamage</th>\n",
       "      <th>ECMicroenv</th>\n",
       "      <th>EMT</th>\n",
       "      <th>ERK</th>\n",
       "      <th>GF</th>\n",
       "      <th>Invasion</th>\n",
       "      <th>Metastasis</th>\n",
       "      <th>Migration</th>\n",
       "      <th>NICD</th>\n",
       "      <th>SMAD</th>\n",
       "      <th>SNAI1</th>\n",
       "      <th>SNAI2</th>\n",
       "      <th>TGFbeta</th>\n",
       "      <th>TWIST1</th>\n",
       "      <th>VIM</th>\n",
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      "text/plain": [
       "   AKT1  AKT2  Apoptosis  CDH1  CDH2  CTNNB1  CellCycleArrest  DKK1  \\\n",
       "0     0     0          0     1     0       0                0     0   \n",
       "1     0     0          1     1     0       0                1     0   \n",
       "2     0     0          1     1     0       0                1     0   \n",
       "3     0     0          1     1     0       0                1     0   \n",
       "4     0     0          1     1     0       0                1     0   \n",
       "5     0     1          0     0     1       0                1     0   \n",
       "6     0     1          0     0     1       0                1     0   \n",
       "7     0     1          0     0     1       0                1     1   \n",
       "8     0     1          0     0     1       0                1     1   \n",
       "\n",
       "   DNAdamage  ECMicroenv  EMT  ERK  GF  Invasion  Metastasis  Migration  NICD  \\\n",
       "0          0           0    0    0   0         0           0          0     0   \n",
       "1          1           0    0    0   0         0           0          0     0   \n",
       "2          1           0    0    0   0         0           0          0     0   \n",
       "3          1           1    0    0   0         0           0          0     0   \n",
       "4          1           1    0    0   0         0           0          0     0   \n",
       "5          0           0    1    1   1         0           0          0     0   \n",
       "6          1           0    1    1   1         0           0          0     0   \n",
       "7          0           1    1    1   1         1           1          1     1   \n",
       "8          1           1    1    1   1         1           1          1     1   \n",
       "\n",
       "   SMAD  SNAI1  SNAI2  TGFbeta  TWIST1  VIM  ZEB1  ZEB2  miR200  miR203  \\\n",
       "0     0      0      0        0       0    0     0     0       0       0   \n",
       "1     0      0      0        0       0    0     0     0       1       0   \n",
       "2     0      0      0        0       0    0     0     0       1       1   \n",
       "3     0      0      0        1       0    0     0     0       1       0   \n",
       "4     0      0      0        1       0    0     0     0       1       1   \n",
       "5     0      1      1        0       1    1     1     1       0       0   \n",
       "6     0      1      1        0       1    1     1     1       0       0   \n",
       "7     1      1      1        1       1    1     1     1       0       0   \n",
       "8     1      1      1        1       1    1     1     1       0       0   \n",
       "\n",
       "   miR34  p21  p53  p63  p73  \n",
       "0      0    0    0    0    0  \n",
       "1      0    1    0    1    1  \n",
       "2      0    1    1    0    0  \n",
       "3      0    1    0    1    1  \n",
       "4      0    1    1    0    0  \n",
       "5      0    0    0    0    0  \n",
       "6      0    0    0    0    0  \n",
       "7      0    0    0    0    0  \n",
       "8      0    0    0    0    0  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%time attractors = cabean.attractors(model)\n",
    "tabulate(attractors)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Define the properties of the source and target attractors. Note that source or target may correspond to serveral attractors."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "source = {\"Invasion\":0,\"Migration\":0}\n",
    "target = {\"CellCycleArrest\": 1,\"EMT\":1,\"Invasion\":1,\"Migration\":1,\"Metastasis\":1,\"Apoptosis\":0}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Define a set of nodes that cannot be perturbed. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "exclude = [\"DNAdamage\", \"ECMicroenv\", \"AKT1\", \"AKT2\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Compute the minimal one-step instantaneous control (OI) from the source to the target."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 22.1 ms, sys: 46.9 ms, total: 69.1 ms\n",
      "Wall time: 19.2 s\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "[\n",
       " FromSteadyState('a3', InstantaneousPerturbation(CDH2=1, SNAI1=1, SNAI2=1, TWIST1=1, miR200=0)),\n",
       " \n",
       " FromSteadyState('a4', InstantaneousPerturbation(NICD=1, SNAI2=1, ZEB1=1, miR200=0, miR203=0, p53=0))]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "c1i = cabean.OneStep_Instantaneous(model)\n",
    "%time s1i = c1i.attractor_to_attractor(source, target, exclude=exclude)\n",
    "s1i"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
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       "             background-color:  lime;\n",
       "        }</style><table id=\"T_01f9013e_bc3b_11ea_acd2_0242ac110002\" ><thead>    <tr>        <th class=\"blank level0\" ></th>        <th class=\"col_heading level0 col0\" >CDH2</th>        <th class=\"col_heading level0 col1\" >NICD</th>        <th class=\"col_heading level0 col2\" >SNAI1</th>        <th class=\"col_heading level0 col3\" >SNAI2</th>        <th class=\"col_heading level0 col4\" >TWIST1</th>        <th class=\"col_heading level0 col5\" >ZEB1</th>        <th class=\"col_heading level0 col6\" >miR200</th>        <th class=\"col_heading level0 col7\" >miR203</th>        <th class=\"col_heading level0 col8\" >p53</th>    </tr></thead><tbody>\n",
       "                <tr>\n",
       "                        <th id=\"T_01f9013e_bc3b_11ea_acd2_0242ac110002level0_row0\" class=\"row_heading level0 row0\" >0</th>\n",
       "                        <td id=\"T_01f9013e_bc3b_11ea_acd2_0242ac110002row0_col0\" class=\"data row0 col0\" ></td>\n",
       "                        <td id=\"T_01f9013e_bc3b_11ea_acd2_0242ac110002row0_col1\" class=\"data row0 col1\" >1</td>\n",
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       "                        <td id=\"T_01f9013e_bc3b_11ea_acd2_0242ac110002row0_col4\" class=\"data row0 col4\" ></td>\n",
       "                        <td id=\"T_01f9013e_bc3b_11ea_acd2_0242ac110002row0_col5\" class=\"data row0 col5\" >1</td>\n",
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       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_01f9013e_bc3b_11ea_acd2_0242ac110002level0_row1\" class=\"row_heading level0 row1\" >1</th>\n",
       "                        <td id=\"T_01f9013e_bc3b_11ea_acd2_0242ac110002row1_col0\" class=\"data row1 col0\" >1</td>\n",
       "                        <td id=\"T_01f9013e_bc3b_11ea_acd2_0242ac110002row1_col1\" class=\"data row1 col1\" ></td>\n",
       "                        <td id=\"T_01f9013e_bc3b_11ea_acd2_0242ac110002row1_col2\" class=\"data row1 col2\" >1</td>\n",
       "                        <td id=\"T_01f9013e_bc3b_11ea_acd2_0242ac110002row1_col3\" class=\"data row1 col3\" >1</td>\n",
       "                        <td id=\"T_01f9013e_bc3b_11ea_acd2_0242ac110002row1_col4\" class=\"data row1 col4\" >1</td>\n",
       "                        <td id=\"T_01f9013e_bc3b_11ea_acd2_0242ac110002row1_col5\" class=\"data row1 col5\" ></td>\n",
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     "execution_count": 7,
     "metadata": {},
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   ],
   "source": [
    "s1i.as_table()"
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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Compute the attractor-based sequential instantaneous control (ASI) from the source to the target."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 25.4 ms, sys: 50.6 ms, total: 76 ms\n",
      "Wall time: 19.1 s\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "[\n",
       " FromSteadyState('a3', InstantaneousPerturbation(CDH2=1, SNAI1=1, SNAI2=1, TWIST1=1, miR200=0)),\n",
       " \n",
       " FromSteadyState('a4', InstantaneousPerturbation(NICD=1, SNAI2=1, ZEB1=1, miR200=0, miR203=0, p53=0))]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ci = cabean.AttractorSequential_Instantaneous(model)\n",
    "%time si = ci.attractor_to_attractor(source, target, exclude=exclude)\n",
    "si"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
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     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "si.as_graph()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
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     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "si.as_table()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Compute the minimal one-step temporary control (OT) from the source to the target."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 23.9 ms, sys: 54.7 ms, total: 78.6 ms\n",
      "Wall time: 24 s\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "[FromSteadyState('a3', TemporaryPerturbation(SNAI2=1, p63=0)),\n",
       " FromSteadyState('a3', TemporaryPerturbation(SNAI1=1, SNAI2=1)),\n",
       " FromSteadyState('a3', TemporaryPerturbation(SNAI2=1, TWIST1=1)),\n",
       " FromSteadyState('a3', TemporaryPerturbation(NICD=1, SNAI2=1)),\n",
       " FromSteadyState('a3', TemporaryPerturbation(CTNNB1=1, SNAI2=1)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(SNAI1=1, p73=1)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(SNAI1=1, p53=0)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(SNAI1=1, SNAI2=1)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(TWIST1=1, p73=1)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(TWIST1=1, p53=0)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(SNAI2=1, TWIST1=1)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(NICD=1, p73=1)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(NICD=1, p53=0)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(NICD=1, SNAI2=1)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(CTNNB1=1, p53=0)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(CTNNB1=1, SNAI2=1))]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "r1t = cabean.OneStep_Temporary(model)\n",
    "%time s1t = r1t.attractor_to_attractor(source, target, exclude=exclude)\n",
    "s1t"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
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       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row0_col7 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row1_col4 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row1_col5 {\n",
       "            color:  black;\n",
       "             background-color:  lime;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row2_col3 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row2_col6 {\n",
       "            color:  black;\n",
       "             background-color:  lime;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row3_col3 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row3_col4 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row4_col2 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row4_col7 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row5_col2 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row5_col5 {\n",
       "            color:  black;\n",
       "             background-color:  lime;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row6_col2 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row6_col3 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row7_col1 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row7_col7 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row8_col1 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row8_col5 {\n",
       "            color:  black;\n",
       "             background-color:  lime;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row9_col1 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row9_col3 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row10_col0 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row10_col5 {\n",
       "            color:  black;\n",
       "             background-color:  lime;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row11_col0 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row11_col3 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }</style><table id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002\" ><thead>    <tr>        <th class=\"blank level0\" ></th>        <th class=\"col_heading level0 col0\" >CTNNB1</th>        <th class=\"col_heading level0 col1\" >NICD</th>        <th class=\"col_heading level0 col2\" >SNAI1</th>        <th class=\"col_heading level0 col3\" >SNAI2</th>        <th class=\"col_heading level0 col4\" >TWIST1</th>        <th class=\"col_heading level0 col5\" >p53</th>        <th class=\"col_heading level0 col6\" >p63</th>        <th class=\"col_heading level0 col7\" >p73</th>    </tr></thead><tbody>\n",
       "                <tr>\n",
       "                        <th id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002level0_row0\" class=\"row_heading level0 row0\" >0</th>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row0_col0\" class=\"data row0 col0\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row0_col1\" class=\"data row0 col1\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row0_col2\" class=\"data row0 col2\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row0_col3\" class=\"data row0 col3\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row0_col4\" class=\"data row0 col4\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row0_col5\" class=\"data row0 col5\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row0_col6\" class=\"data row0 col6\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row0_col7\" class=\"data row0 col7\" >1</td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002level0_row1\" class=\"row_heading level0 row1\" >1</th>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row1_col0\" class=\"data row1 col0\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row1_col1\" class=\"data row1 col1\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row1_col2\" class=\"data row1 col2\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row1_col3\" class=\"data row1 col3\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row1_col4\" class=\"data row1 col4\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row1_col5\" class=\"data row1 col5\" >0</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row1_col6\" class=\"data row1 col6\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row1_col7\" class=\"data row1 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002level0_row2\" class=\"row_heading level0 row2\" >2</th>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row2_col0\" class=\"data row2 col0\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row2_col1\" class=\"data row2 col1\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row2_col2\" class=\"data row2 col2\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row2_col3\" class=\"data row2 col3\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row2_col4\" class=\"data row2 col4\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row2_col5\" class=\"data row2 col5\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row2_col6\" class=\"data row2 col6\" >0</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row2_col7\" class=\"data row2 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002level0_row3\" class=\"row_heading level0 row3\" >3</th>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row3_col0\" class=\"data row3 col0\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row3_col1\" class=\"data row3 col1\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row3_col2\" class=\"data row3 col2\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row3_col3\" class=\"data row3 col3\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row3_col4\" class=\"data row3 col4\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row3_col5\" class=\"data row3 col5\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row3_col6\" class=\"data row3 col6\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row3_col7\" class=\"data row3 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002level0_row4\" class=\"row_heading level0 row4\" >4</th>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row4_col0\" class=\"data row4 col0\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row4_col1\" class=\"data row4 col1\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row4_col2\" class=\"data row4 col2\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row4_col3\" class=\"data row4 col3\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row4_col4\" class=\"data row4 col4\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row4_col5\" class=\"data row4 col5\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row4_col6\" class=\"data row4 col6\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row4_col7\" class=\"data row4 col7\" >1</td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002level0_row5\" class=\"row_heading level0 row5\" >5</th>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row5_col0\" class=\"data row5 col0\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row5_col1\" class=\"data row5 col1\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row5_col2\" class=\"data row5 col2\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row5_col3\" class=\"data row5 col3\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row5_col4\" class=\"data row5 col4\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row5_col5\" class=\"data row5 col5\" >0</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row5_col6\" class=\"data row5 col6\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row5_col7\" class=\"data row5 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002level0_row6\" class=\"row_heading level0 row6\" >6</th>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row6_col0\" class=\"data row6 col0\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row6_col1\" class=\"data row6 col1\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row6_col2\" class=\"data row6 col2\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row6_col3\" class=\"data row6 col3\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row6_col4\" class=\"data row6 col4\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row6_col5\" class=\"data row6 col5\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row6_col6\" class=\"data row6 col6\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row6_col7\" class=\"data row6 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002level0_row7\" class=\"row_heading level0 row7\" >7</th>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row7_col0\" class=\"data row7 col0\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row7_col1\" class=\"data row7 col1\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row7_col2\" class=\"data row7 col2\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row7_col3\" class=\"data row7 col3\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row7_col4\" class=\"data row7 col4\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row7_col5\" class=\"data row7 col5\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row7_col6\" class=\"data row7 col6\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row7_col7\" class=\"data row7 col7\" >1</td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002level0_row8\" class=\"row_heading level0 row8\" >8</th>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row8_col0\" class=\"data row8 col0\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row8_col1\" class=\"data row8 col1\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row8_col2\" class=\"data row8 col2\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row8_col3\" class=\"data row8 col3\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row8_col4\" class=\"data row8 col4\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row8_col5\" class=\"data row8 col5\" >0</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row8_col6\" class=\"data row8 col6\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row8_col7\" class=\"data row8 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002level0_row9\" class=\"row_heading level0 row9\" >9</th>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row9_col0\" class=\"data row9 col0\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row9_col1\" class=\"data row9 col1\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row9_col2\" class=\"data row9 col2\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row9_col3\" class=\"data row9 col3\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row9_col4\" class=\"data row9 col4\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row9_col5\" class=\"data row9 col5\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row9_col6\" class=\"data row9 col6\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row9_col7\" class=\"data row9 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002level0_row10\" class=\"row_heading level0 row10\" >10</th>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row10_col0\" class=\"data row10 col0\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row10_col1\" class=\"data row10 col1\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row10_col2\" class=\"data row10 col2\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row10_col3\" class=\"data row10 col3\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row10_col4\" class=\"data row10 col4\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row10_col5\" class=\"data row10 col5\" >0</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row10_col6\" class=\"data row10 col6\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row10_col7\" class=\"data row10 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002level0_row11\" class=\"row_heading level0 row11\" >11</th>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row11_col0\" class=\"data row11 col0\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row11_col1\" class=\"data row11 col1\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row11_col2\" class=\"data row11 col2\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row11_col3\" class=\"data row11 col3\" >1</td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row11_col4\" class=\"data row11 col4\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row11_col5\" class=\"data row11 col5\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row11_col6\" class=\"data row11 col6\" ></td>\n",
       "                        <td id=\"T_1caf4a9c_bc3b_11ea_acd2_0242ac110002row11_col7\" class=\"data row11 col7\" ></td>\n",
       "            </tr>\n",
       "    </tbody></table>"
      ],
      "text/plain": [
       "<pandas.io.formats.style.Styler at 0x7f6315cd6650>"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "s1t.as_table()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Compute the attractor-based sequential temporary control (AST) from the source to the target."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 23 ms, sys: 51.8 ms, total: 74.8 ms\n",
      "Wall time: 22.9 s\n"
     ]
    },
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       "[FromSteadyState('a3', TemporaryPerturbation(SNAI2=1, p63=0)),\n",
       " FromSteadyState('a3', TemporaryPerturbation(SNAI1=1, SNAI2=1)),\n",
       " FromSteadyState('a3', TemporaryPerturbation(SNAI2=1, TWIST1=1)),\n",
       " FromSteadyState('a3', TemporaryPerturbation(NICD=1, SNAI2=1)),\n",
       " FromSteadyState('a3', TemporaryPerturbation(CTNNB1=1, SNAI2=1)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(SNAI1=1, p73=1)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(SNAI1=1, p53=0)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(SNAI1=1, SNAI2=1)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(TWIST1=1, p73=1)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(TWIST1=1, p53=0)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(SNAI2=1, TWIST1=1)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(NICD=1, p73=1)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(NICD=1, p53=0)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(NICD=1, SNAI2=1)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(CTNNB1=1, p53=0)),\n",
       " FromSteadyState('a4', TemporaryPerturbation(CTNNB1=1, SNAI2=1))]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ct = cabean.AttractorSequential_Temporary(model)\n",
    "%time st = ct.attractor_to_attractor(source, target, exclude=exclude)\n",
    "st"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
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       "        }    #T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row5_col5 {\n",
       "            color:  black;\n",
       "             background-color:  lime;\n",
       "        }    #T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row6_col2 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row6_col3 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row7_col1 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row7_col7 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row8_col1 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row8_col5 {\n",
       "            color:  black;\n",
       "             background-color:  lime;\n",
       "        }    #T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row9_col1 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row9_col3 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row10_col0 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row10_col5 {\n",
       "            color:  black;\n",
       "             background-color:  lime;\n",
       "        }    #T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row11_col0 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row11_col3 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }</style><table id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002\" ><thead>    <tr>        <th class=\"blank level0\" ></th>        <th class=\"col_heading level0 col0\" >CTNNB1</th>        <th class=\"col_heading level0 col1\" >NICD</th>        <th class=\"col_heading level0 col2\" >SNAI1</th>        <th class=\"col_heading level0 col3\" >SNAI2</th>        <th class=\"col_heading level0 col4\" >TWIST1</th>        <th class=\"col_heading level0 col5\" >p53</th>        <th class=\"col_heading level0 col6\" >p63</th>        <th class=\"col_heading level0 col7\" >p73</th>    </tr></thead><tbody>\n",
       "                <tr>\n",
       "                        <th id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002level0_row0\" class=\"row_heading level0 row0\" >0</th>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row0_col0\" class=\"data row0 col0\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row0_col1\" class=\"data row0 col1\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row0_col2\" class=\"data row0 col2\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row0_col3\" class=\"data row0 col3\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row0_col4\" class=\"data row0 col4\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row0_col5\" class=\"data row0 col5\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row0_col6\" class=\"data row0 col6\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row0_col7\" class=\"data row0 col7\" >1</td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002level0_row1\" class=\"row_heading level0 row1\" >1</th>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row1_col0\" class=\"data row1 col0\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row1_col1\" class=\"data row1 col1\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row1_col2\" class=\"data row1 col2\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row1_col3\" class=\"data row1 col3\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row1_col4\" class=\"data row1 col4\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row1_col5\" class=\"data row1 col5\" >0</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row1_col6\" class=\"data row1 col6\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row1_col7\" class=\"data row1 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002level0_row2\" class=\"row_heading level0 row2\" >2</th>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row2_col0\" class=\"data row2 col0\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row2_col1\" class=\"data row2 col1\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row2_col2\" class=\"data row2 col2\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row2_col3\" class=\"data row2 col3\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row2_col4\" class=\"data row2 col4\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row2_col5\" class=\"data row2 col5\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row2_col6\" class=\"data row2 col6\" >0</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row2_col7\" class=\"data row2 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002level0_row3\" class=\"row_heading level0 row3\" >3</th>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row3_col0\" class=\"data row3 col0\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row3_col1\" class=\"data row3 col1\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row3_col2\" class=\"data row3 col2\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row3_col3\" class=\"data row3 col3\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row3_col4\" class=\"data row3 col4\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row3_col5\" class=\"data row3 col5\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row3_col6\" class=\"data row3 col6\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row3_col7\" class=\"data row3 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002level0_row4\" class=\"row_heading level0 row4\" >4</th>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row4_col0\" class=\"data row4 col0\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row4_col1\" class=\"data row4 col1\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row4_col2\" class=\"data row4 col2\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row4_col3\" class=\"data row4 col3\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row4_col4\" class=\"data row4 col4\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row4_col5\" class=\"data row4 col5\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row4_col6\" class=\"data row4 col6\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row4_col7\" class=\"data row4 col7\" >1</td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002level0_row5\" class=\"row_heading level0 row5\" >5</th>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row5_col0\" class=\"data row5 col0\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row5_col1\" class=\"data row5 col1\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row5_col2\" class=\"data row5 col2\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row5_col3\" class=\"data row5 col3\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row5_col4\" class=\"data row5 col4\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row5_col5\" class=\"data row5 col5\" >0</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row5_col6\" class=\"data row5 col6\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row5_col7\" class=\"data row5 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002level0_row6\" class=\"row_heading level0 row6\" >6</th>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row6_col0\" class=\"data row6 col0\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row6_col1\" class=\"data row6 col1\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row6_col2\" class=\"data row6 col2\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row6_col3\" class=\"data row6 col3\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row6_col4\" class=\"data row6 col4\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row6_col5\" class=\"data row6 col5\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row6_col6\" class=\"data row6 col6\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row6_col7\" class=\"data row6 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002level0_row7\" class=\"row_heading level0 row7\" >7</th>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row7_col0\" class=\"data row7 col0\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row7_col1\" class=\"data row7 col1\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row7_col2\" class=\"data row7 col2\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row7_col3\" class=\"data row7 col3\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row7_col4\" class=\"data row7 col4\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row7_col5\" class=\"data row7 col5\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row7_col6\" class=\"data row7 col6\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row7_col7\" class=\"data row7 col7\" >1</td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002level0_row8\" class=\"row_heading level0 row8\" >8</th>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row8_col0\" class=\"data row8 col0\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row8_col1\" class=\"data row8 col1\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row8_col2\" class=\"data row8 col2\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row8_col3\" class=\"data row8 col3\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row8_col4\" class=\"data row8 col4\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row8_col5\" class=\"data row8 col5\" >0</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row8_col6\" class=\"data row8 col6\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row8_col7\" class=\"data row8 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002level0_row9\" class=\"row_heading level0 row9\" >9</th>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row9_col0\" class=\"data row9 col0\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row9_col1\" class=\"data row9 col1\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row9_col2\" class=\"data row9 col2\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row9_col3\" class=\"data row9 col3\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row9_col4\" class=\"data row9 col4\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row9_col5\" class=\"data row9 col5\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row9_col6\" class=\"data row9 col6\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row9_col7\" class=\"data row9 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002level0_row10\" class=\"row_heading level0 row10\" >10</th>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row10_col0\" class=\"data row10 col0\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row10_col1\" class=\"data row10 col1\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row10_col2\" class=\"data row10 col2\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row10_col3\" class=\"data row10 col3\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row10_col4\" class=\"data row10 col4\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row10_col5\" class=\"data row10 col5\" >0</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row10_col6\" class=\"data row10 col6\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row10_col7\" class=\"data row10 col7\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002level0_row11\" class=\"row_heading level0 row11\" >11</th>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row11_col0\" class=\"data row11 col0\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row11_col1\" class=\"data row11 col1\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row11_col2\" class=\"data row11 col2\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row11_col3\" class=\"data row11 col3\" >1</td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row11_col4\" class=\"data row11 col4\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row11_col5\" class=\"data row11 col5\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row11_col6\" class=\"data row11 col6\" ></td>\n",
       "                        <td id=\"T_2ad52bdc_bc3b_11ea_acd2_0242ac110002row11_col7\" class=\"data row11 col7\" ></td>\n",
       "            </tr>\n",
       "    </tbody></table>"
      ],
      "text/plain": [
       "<pandas.io.formats.style.Styler at 0x7f6315c51750>"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "st.as_table()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Compute the minimal one-step permanent control (OP) from the source to the target."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 27 ms, sys: 53.8 ms, total: 80.9 ms\n",
      "Wall time: 25.2 s\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "[FromSteadyState('a3', PermanentPerturbation(SNAI2=1, p63=0)),\n",
       " FromSteadyState('a3', PermanentPerturbation(SNAI1=1, SNAI2=1)),\n",
       " FromSteadyState('a3', PermanentPerturbation(SNAI2=1, TWIST1=1)),\n",
       " FromSteadyState('a3', PermanentPerturbation(NICD=1, SNAI2=1)),\n",
       " FromSteadyState('a4', PermanentPerturbation(SNAI1=1, p53=0)),\n",
       " FromSteadyState('a4', PermanentPerturbation(SNAI1=1, SNAI2=1)),\n",
       " FromSteadyState('a4', PermanentPerturbation(TWIST1=1, p53=0)),\n",
       " FromSteadyState('a4', PermanentPerturbation(SNAI2=1, TWIST1=1)),\n",
       " FromSteadyState('a4', PermanentPerturbation(NICD=1, SNAI2=1))]"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "c1p = cabean.OneStep_Permanent(model)\n",
    "%time s1p = c1p.attractor_to_attractor(source, target, exclude=exclude)\n",
    "s1p"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    #T_3a56ff54_bc3b_11ea_acd2_0242ac110002 th {\n",
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       "          border-right: 1px solid black;\n",
       "          min-width: 2em;\n",
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       "            color:  black;\n",
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       "            color:  black;\n",
       "             background-color:  red;\n",
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       "            color:  black;\n",
       "             background-color:  red;\n",
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       "            color:  black;\n",
       "             background-color:  red;\n",
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       "            color:  black;\n",
       "             background-color:  lime;\n",
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       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_3a56ff54_bc3b_11ea_acd2_0242ac110002row4_col2 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_3a56ff54_bc3b_11ea_acd2_0242ac110002row5_col0 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }    #T_3a56ff54_bc3b_11ea_acd2_0242ac110002row5_col2 {\n",
       "            color:  black;\n",
       "             background-color:  red;\n",
       "        }</style><table id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002\" ><thead>    <tr>        <th class=\"blank level0\" ></th>        <th class=\"col_heading level0 col0\" >NICD</th>        <th class=\"col_heading level0 col1\" >SNAI1</th>        <th class=\"col_heading level0 col2\" >SNAI2</th>        <th class=\"col_heading level0 col3\" >TWIST1</th>        <th class=\"col_heading level0 col4\" >p53</th>        <th class=\"col_heading level0 col5\" >p63</th>    </tr></thead><tbody>\n",
       "                <tr>\n",
       "                        <th id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002level0_row0\" class=\"row_heading level0 row0\" >0</th>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row0_col0\" class=\"data row0 col0\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row0_col1\" class=\"data row0 col1\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row0_col2\" class=\"data row0 col2\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row0_col3\" class=\"data row0 col3\" >1</td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row0_col4\" class=\"data row0 col4\" >0</td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row0_col5\" class=\"data row0 col5\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002level0_row1\" class=\"row_heading level0 row1\" >1</th>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row1_col0\" class=\"data row1 col0\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row1_col1\" class=\"data row1 col1\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row1_col2\" class=\"data row1 col2\" >1</td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row1_col3\" class=\"data row1 col3\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row1_col4\" class=\"data row1 col4\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row1_col5\" class=\"data row1 col5\" >0</td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002level0_row2\" class=\"row_heading level0 row2\" >2</th>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row2_col0\" class=\"data row2 col0\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row2_col1\" class=\"data row2 col1\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row2_col2\" class=\"data row2 col2\" >1</td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row2_col3\" class=\"data row2 col3\" >1</td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row2_col4\" class=\"data row2 col4\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row2_col5\" class=\"data row2 col5\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002level0_row3\" class=\"row_heading level0 row3\" >3</th>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row3_col0\" class=\"data row3 col0\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row3_col1\" class=\"data row3 col1\" >1</td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row3_col2\" class=\"data row3 col2\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row3_col3\" class=\"data row3 col3\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row3_col4\" class=\"data row3 col4\" >0</td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row3_col5\" class=\"data row3 col5\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002level0_row4\" class=\"row_heading level0 row4\" >4</th>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row4_col0\" class=\"data row4 col0\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row4_col1\" class=\"data row4 col1\" >1</td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row4_col2\" class=\"data row4 col2\" >1</td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row4_col3\" class=\"data row4 col3\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row4_col4\" class=\"data row4 col4\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row4_col5\" class=\"data row4 col5\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002level0_row5\" class=\"row_heading level0 row5\" >5</th>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row5_col0\" class=\"data row5 col0\" >1</td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row5_col1\" class=\"data row5 col1\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row5_col2\" class=\"data row5 col2\" >1</td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row5_col3\" class=\"data row5 col3\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row5_col4\" class=\"data row5 col4\" ></td>\n",
       "                        <td id=\"T_3a56ff54_bc3b_11ea_acd2_0242ac110002row5_col5\" class=\"data row5 col5\" ></td>\n",
       "            </tr>\n",
       "    </tbody></table>"
      ],
      "text/plain": [
       "<pandas.io.formats.style.Styler at 0x7f6315be14d0>"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "s1p.as_table()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Compute the attractor-based sequential permanent control (ASP) from the source to the target."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 22.7 ms, sys: 56 ms, total: 78.7 ms\n",
      "Wall time: 25.7 s\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "[FromSteadyState('a3', PermanentPerturbation(SNAI2=1, p63=0)),\n",
       " FromSteadyState('a3', PermanentPerturbation(SNAI1=1, SNAI2=1)),\n",
       " FromSteadyState('a3', PermanentPerturbation(SNAI2=1, TWIST1=1)),\n",
       " FromSteadyState('a3', PermanentPerturbation(NICD=1, SNAI2=1)),\n",
       " FromSteadyState('a4', PermanentPerturbation(SNAI1=1, p53=0)),\n",
       " FromSteadyState('a4', PermanentPerturbation(SNAI1=1, SNAI2=1)),\n",
       " FromSteadyState('a4', PermanentPerturbation(TWIST1=1, p53=0)),\n",
       " FromSteadyState('a4', PermanentPerturbation(SNAI2=1, TWIST1=1)),\n",
       " FromSteadyState('a4', PermanentPerturbation(NICD=1, p53=0)),\n",
       " FromSteadyState('a4', PermanentPerturbation(NICD=1, SNAI2=1))]"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "c1p = cabean.AttractorSequential_Permanent(model)\n",
    "%time s1p = c1p.attractor_to_attractor(source, target, exclude=[x for x in exclude if x != \"AKT1\"])\n",
    "s1p"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "            color:  black;\n",
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       "            color:  black;\n",
       "             background-color:  red;\n",
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       "            color:  black;\n",
       "             background-color:  red;\n",
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       "            color:  black;\n",
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       "            color:  black;\n",
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       "            color:  black;\n",
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       "        }</style><table id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002\" ><thead>    <tr>        <th class=\"blank level0\" ></th>        <th class=\"col_heading level0 col0\" >NICD</th>        <th class=\"col_heading level0 col1\" >SNAI1</th>        <th class=\"col_heading level0 col2\" >SNAI2</th>        <th class=\"col_heading level0 col3\" >TWIST1</th>        <th class=\"col_heading level0 col4\" >p53</th>        <th class=\"col_heading level0 col5\" >p63</th>    </tr></thead><tbody>\n",
       "                <tr>\n",
       "                        <th id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002level0_row0\" class=\"row_heading level0 row0\" >0</th>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row0_col0\" class=\"data row0 col0\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row0_col1\" class=\"data row0 col1\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row0_col2\" class=\"data row0 col2\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row0_col3\" class=\"data row0 col3\" >1</td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row0_col4\" class=\"data row0 col4\" >0</td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row0_col5\" class=\"data row0 col5\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002level0_row1\" class=\"row_heading level0 row1\" >1</th>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row1_col0\" class=\"data row1 col0\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row1_col1\" class=\"data row1 col1\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row1_col2\" class=\"data row1 col2\" >1</td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row1_col3\" class=\"data row1 col3\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row1_col4\" class=\"data row1 col4\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row1_col5\" class=\"data row1 col5\" >0</td>\n",
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       "            <tr>\n",
       "                        <th id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002level0_row2\" class=\"row_heading level0 row2\" >2</th>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row2_col0\" class=\"data row2 col0\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row2_col1\" class=\"data row2 col1\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row2_col2\" class=\"data row2 col2\" >1</td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row2_col3\" class=\"data row2 col3\" >1</td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row2_col4\" class=\"data row2 col4\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row2_col5\" class=\"data row2 col5\" ></td>\n",
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       "            <tr>\n",
       "                        <th id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002level0_row3\" class=\"row_heading level0 row3\" >3</th>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row3_col0\" class=\"data row3 col0\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row3_col1\" class=\"data row3 col1\" >1</td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row3_col2\" class=\"data row3 col2\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row3_col3\" class=\"data row3 col3\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row3_col4\" class=\"data row3 col4\" >0</td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row3_col5\" class=\"data row3 col5\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002level0_row4\" class=\"row_heading level0 row4\" >4</th>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row4_col0\" class=\"data row4 col0\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row4_col1\" class=\"data row4 col1\" >1</td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row4_col2\" class=\"data row4 col2\" >1</td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row4_col3\" class=\"data row4 col3\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row4_col4\" class=\"data row4 col4\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row4_col5\" class=\"data row4 col5\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002level0_row5\" class=\"row_heading level0 row5\" >5</th>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row5_col0\" class=\"data row5 col0\" >1</td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row5_col1\" class=\"data row5 col1\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row5_col2\" class=\"data row5 col2\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row5_col3\" class=\"data row5 col3\" ></td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row5_col4\" class=\"data row5 col4\" >0</td>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row5_col5\" class=\"data row5 col5\" ></td>\n",
       "            </tr>\n",
       "            <tr>\n",
       "                        <th id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002level0_row6\" class=\"row_heading level0 row6\" >6</th>\n",
       "                        <td id=\"T_4a504186_bc3b_11ea_acd2_0242ac110002row6_col0\" class=\"data row6 col0\" >1</td>\n",
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