Datasets
Models
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Working with SBML models using basico"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"c:\\Users\\Wehling\\code\\AIAgents-Hackathon\\.venv\\Lib\\site-packages\\tqdm\\auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
" from .autonotebook import tqdm as notebook_tqdm\n"
]
}
],
"source": [
"import basico"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"# load SBML model\n",
"model = basico.load_model(\"./Dwivedi_Model537_annotated.xml\")"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>compartment</th>\n",
" <th>type</th>\n",
" <th>unit</th>\n",
" <th>initial_concentration</th>\n",
" <th>initial_particle_number</th>\n",
" <th>initial_expression</th>\n",
" <th>expression</th>\n",
" <th>concentration</th>\n",
" <th>particle_number</th>\n",
" <th>rate</th>\n",
" <th>particle_number_rate</th>\n",
" <th>key</th>\n",
" <th>sbml_id</th>\n",
" <th>transition_time</th>\n",
" <th>display_name</th>\n",
" </tr>\n",
" <tr>\n",
" <th>name</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>IL6</th>\n",
" <td>serum</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>4.356289e-04</td>\n",
" <td>2.623419e+11</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>4.356289e-04</td>\n",
" <td>2.623419e+11</td>\n",
" <td>-1.565877e-17</td>\n",
" <td>-9.429932e-03</td>\n",
" <td>Metabolite_88</td>\n",
" <td>mwf626e95e_543f_41e4_aad4_c6bf60ab345b</td>\n",
" <td>0.028719</td>\n",
" <td>IL6{serum}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>sgp130</th>\n",
" <td>serum</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>3.900000e+00</td>\n",
" <td>2.348635e+15</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>3.900000e+00</td>\n",
" <td>2.348635e+15</td>\n",
" <td>0.000000e+00</td>\n",
" <td>0.000000e+00</td>\n",
" <td>Metabolite_89</td>\n",
" <td>mwbbbce920_e8dd_4320_9386_fc94bfb2fc99</td>\n",
" <td>0.997567</td>\n",
" <td>sgp130{serum}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>sR_IL6_sgp130</th>\n",
" <td>serum</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>8.740607e-02</td>\n",
" <td>5.263716e+13</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>8.740607e-02</td>\n",
" <td>5.263716e+13</td>\n",
" <td>-2.367565e-16</td>\n",
" <td>-1.425781e-01</td>\n",
" <td>Metabolite_90</td>\n",
" <td>mw810ff751_fa4e_4143_bd50_169b3e325e1e</td>\n",
" <td>9.190533</td>\n",
" <td>sR_IL6_sgp130{serum}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CRP</th>\n",
" <td>serum</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>2.210637e+02</td>\n",
" <td>1.331277e+17</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>2.210637e+02</td>\n",
" <td>1.331277e+17</td>\n",
" <td>6.243627e-13</td>\n",
" <td>3.760000e+02</td>\n",
" <td>Metabolite_91</td>\n",
" <td>mw114aa90f_5f5b_4fe8_9406_361c8489b6a1</td>\n",
" <td>2.777778</td>\n",
" <td>CRP{serum}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>sR</th>\n",
" <td>serum</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>4.253507e+00</td>\n",
" <td>2.561522e+15</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>4.253507e+00</td>\n",
" <td>2.561522e+15</td>\n",
" <td>1.307675e-14</td>\n",
" <td>7.875000e+00</td>\n",
" <td>Metabolite_92</td>\n",
" <td>mw30ae63db_6cd3_4b6f_93ad_3350cd360bcc</td>\n",
" <td>3.283772</td>\n",
" <td>sR{serum}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>sR_IL6</th>\n",
" <td>serum</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>1.094243e-03</td>\n",
" <td>6.589683e+11</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>1.094243e-03</td>\n",
" <td>6.589683e+11</td>\n",
" <td>5.032090e-17</td>\n",
" <td>3.030396e-02</td>\n",
" <td>Metabolite_93</td>\n",
" <td>mw03db56ac_8dc6_4931_ae82_fef706d2ee3d</td>\n",
" <td>0.518949</td>\n",
" <td>sR_IL6{serum}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Ab</th>\n",
" <td>serum</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>2.381820e-29</td>\n",
" <td>1.434365e-14</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>2.381820e-29</td>\n",
" <td>1.434365e-14</td>\n",
" <td>5.129906e-26</td>\n",
" <td>3.089302e-11</td>\n",
" <td>Metabolite_94</td>\n",
" <td>mwf345ed7a_0622_403c_b816_c8749a2c9ded</td>\n",
" <td>0.000464</td>\n",
" <td>Ab{serum}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Ab_sR</th>\n",
" <td>serum</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>6.104391e-26</td>\n",
" <td>3.676150e-11</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>6.104391e-26</td>\n",
" <td>3.676150e-11</td>\n",
" <td>-5.097542e-26</td>\n",
" <td>-3.069812e-11</td>\n",
" <td>Metabolite_95</td>\n",
" <td>mw1da111f2_a036_4392_8512_015005bdcbb7</td>\n",
" <td>1.185348</td>\n",
" <td>Ab_sR{serum}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Ab_sR_IL6</th>\n",
" <td>serum</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>-7.413309e-29</td>\n",
" <td>-4.464399e-14</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>-7.413309e-29</td>\n",
" <td>-4.464399e-14</td>\n",
" <td>5.137413e-29</td>\n",
" <td>3.093822e-14</td>\n",
" <td>Metabolite_96</td>\n",
" <td>mw9947742a_0e4b_4636_9a4b_b6eef2a8f6ac</td>\n",
" <td>1.159408</td>\n",
" <td>Ab_sR_IL6{serum}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CRP Suppression (%)</th>\n",
" <td>serum</td>\n",
" <td>assignment</td>\n",
" <td>nmol/l</td>\n",
" <td>-0.000000e+00</td>\n",
" <td>-0.000000e+00</td>\n",
" <td></td>\n",
" <td>( [CRP{serum}] - {Values[Initial for CRP]} ) /...</td>\n",
" <td>-0.000000e+00</td>\n",
" <td>-0.000000e+00</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>Metabolite_97</td>\n",
" <td>CRP_Suppression___</td>\n",
" <td>NaN</td>\n",
" <td>CRP Suppression (%)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CRP (% of baseline)</th>\n",
" <td>serum</td>\n",
" <td>assignment</td>\n",
" <td>nmol/l</td>\n",
" <td>1.000000e+02</td>\n",
" <td>6.022141e+16</td>\n",
" <td></td>\n",
" <td>[CRP{serum}] / {Values[Initial for CRP]} * 100</td>\n",
" <td>1.000000e+02</td>\n",
" <td>6.022141e+16</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>Metabolite_98</td>\n",
" <td>CRP____of_baseline</td>\n",
" <td>NaN</td>\n",
" <td>CRP (% of baseline)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>gp130</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>3.889589e-01</td>\n",
" <td>2.342365e+14</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>3.889589e-01</td>\n",
" <td>2.342365e+14</td>\n",
" <td>6.486481e-17</td>\n",
" <td>3.906250e-02</td>\n",
" <td>Metabolite_99</td>\n",
" <td>mw80848184_e2dd_47ce_86d7_7a21479342bd</td>\n",
" <td>5.678232</td>\n",
" <td>gp130{liver}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>R_IL6_gp130</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>6.599359e-05</td>\n",
" <td>3.974227e+10</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>6.599359e-05</td>\n",
" <td>3.974227e+10</td>\n",
" <td>-5.270266e-18</td>\n",
" <td>-3.173828e-03</td>\n",
" <td>Metabolite_100</td>\n",
" <td>mwd2d9d93a_3bd1_4f17_bac1_baba9ef2d55a</td>\n",
" <td>0.006371</td>\n",
" <td>R_IL6_gp130{liver}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>sR_IL6</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>9.761649e-04</td>\n",
" <td>5.878603e+11</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>9.761649e-04</td>\n",
" <td>5.878603e+11</td>\n",
" <td>-2.918916e-16</td>\n",
" <td>-1.757812e-01</td>\n",
" <td>Metabolite_101</td>\n",
" <td>mw4638f126_8cb8_4021_ab41_6ae195743ba0</td>\n",
" <td>0.123541</td>\n",
" <td>sR_IL6{liver}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>R</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>4.382358e-01</td>\n",
" <td>2.639118e+14</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>4.382358e-01</td>\n",
" <td>2.639118e+14</td>\n",
" <td>-6.486481e-17</td>\n",
" <td>-3.906250e-02</td>\n",
" <td>Metabolite_102</td>\n",
" <td>mw10315fa3_6f13_4618_bda8_a8694bd3c374</td>\n",
" <td>6.397603</td>\n",
" <td>R</td>\n",
" </tr>\n",
" <tr>\n",
" <th>IL6</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>7.256658e-04</td>\n",
" <td>4.370062e+11</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>7.256658e-04</td>\n",
" <td>4.370062e+11</td>\n",
" <td>1.444255e-18</td>\n",
" <td>8.697510e-04</td>\n",
" <td>Metabolite_103</td>\n",
" <td>mw0adf3eb4_a196_4c48_b10d_4e9e9faaf9e1</td>\n",
" <td>4.075710</td>\n",
" <td>IL6{liver}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>R_IL6</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>1.600365e-05</td>\n",
" <td>9.637625e+09</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>1.600365e-05</td>\n",
" <td>9.637625e+09</td>\n",
" <td>-6.334454e-21</td>\n",
" <td>-3.814697e-06</td>\n",
" <td>Metabolite_104</td>\n",
" <td>mw7d86cc23_a1af_44c3_bdb9_71e9b1bb2a83</td>\n",
" <td>0.175114</td>\n",
" <td>R_IL6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Ractive</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>7.654165e-01</td>\n",
" <td>4.609446e+14</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>7.654165e-01</td>\n",
" <td>4.609446e+14</td>\n",
" <td>2.432430e-18</td>\n",
" <td>1.464844e-03</td>\n",
" <td>Metabolite_105</td>\n",
" <td>mw0eb6c959_d408_45a0_a450_928b8c5876bb</td>\n",
" <td>74.828042</td>\n",
" <td>Ractive{liver}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>STAT3</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>7.775373e-01</td>\n",
" <td>4.682439e+14</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>7.775373e-01</td>\n",
" <td>4.682439e+14</td>\n",
" <td>1.556755e-16</td>\n",
" <td>9.375000e-02</td>\n",
" <td>Metabolite_106</td>\n",
" <td>mw42054cd7_17af_46da_970c_7f99151906ad</td>\n",
" <td>1.980238</td>\n",
" <td>STAT3{liver}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>pSTAT3</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>9.222463e+00</td>\n",
" <td>5.553897e+15</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>9.222463e+00</td>\n",
" <td>5.553897e+15</td>\n",
" <td>-1.556755e-16</td>\n",
" <td>-9.375000e-02</td>\n",
" <td>Metabolite_107</td>\n",
" <td>mw39c2e431_fdc3_4964_be29_6ca856620b1b</td>\n",
" <td>23.487843</td>\n",
" <td>pSTAT3{liver}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CRP</th>\n",
" <td>liver</td>\n",
" <td>assignment</td>\n",
" <td>nmol/l</td>\n",
" <td>1.583258e+02</td>\n",
" <td>9.534605e+16</td>\n",
" <td></td>\n",
" <td>Values[VmProtSynth] * [pSTAT3{liver}] / ( Valu...</td>\n",
" <td>1.583258e+02</td>\n",
" <td>9.534605e+16</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>Metabolite_108</td>\n",
" <td>mwd5313618_89eb_4c8c_bc82_66f10f966349</td>\n",
" <td>NaN</td>\n",
" <td>CRP{liver}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>sR</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>6.087047e+00</td>\n",
" <td>3.665705e+15</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>6.087047e+00</td>\n",
" <td>3.665705e+15</td>\n",
" <td>-7.654706e-15</td>\n",
" <td>-4.609772e+00</td>\n",
" <td>Metabolite_109</td>\n",
" <td>mw2e464cf3_a09c_4b7c_9f3c_06720016a48e</td>\n",
" <td>34187.965404</td>\n",
" <td>sR{liver}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>CRPExtracellular</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>4.097753e+02</td>\n",
" <td>2.467725e+17</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>4.097753e+02</td>\n",
" <td>2.467725e+17</td>\n",
" <td>-5.048039e-13</td>\n",
" <td>-3.040000e+02</td>\n",
" <td>Metabolite_110</td>\n",
" <td>mw36ea78c1_ed71_4def_96d3_857a442d7195</td>\n",
" <td>5.176354</td>\n",
" <td>CRPExtracellular</td>\n",
" </tr>\n",
" <tr>\n",
" <th>sgp130</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>5.589699e+00</td>\n",
" <td>3.366195e+15</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>5.589699e+00</td>\n",
" <td>3.366195e+15</td>\n",
" <td>3.468646e-15</td>\n",
" <td>2.088867e+00</td>\n",
" <td>Metabolite_111</td>\n",
" <td>mw147d30ec_478e_4090_b496_128a131d29eb</td>\n",
" <td>755.173729</td>\n",
" <td>sgp130{liver}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>sR_IL6_sgp130</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>1.163437e-01</td>\n",
" <td>7.006379e+13</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>1.163437e-01</td>\n",
" <td>7.006379e+13</td>\n",
" <td>5.416211e-16</td>\n",
" <td>3.261719e-01</td>\n",
" <td>Metabolite_112</td>\n",
" <td>mwab41493c_6349_45f1_a226_3030cfed0e06</td>\n",
" <td>15.718141</td>\n",
" <td>sR_IL6_sgp130{liver}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Ab_sR</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>8.616193e-26</td>\n",
" <td>5.188793e-11</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>8.616193e-26</td>\n",
" <td>5.188793e-11</td>\n",
" <td>-8.215556e-26</td>\n",
" <td>-4.947523e-11</td>\n",
" <td>Metabolite_113</td>\n",
" <td>mwf405687b_7401_44ec_a0d6_4a2b35c13e8a</td>\n",
" <td>1.048766</td>\n",
" <td>Ab_sR{liver}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Ab</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>2.200207e-29</td>\n",
" <td>1.324996e-14</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>2.200207e-29</td>\n",
" <td>1.324996e-14</td>\n",
" <td>7.691938e-26</td>\n",
" <td>4.632193e-11</td>\n",
" <td>Metabolite_114</td>\n",
" <td>mw3667a5e1_02c9_44a0_acb4_b0431faa822d</td>\n",
" <td>0.000270</td>\n",
" <td>Ab{liver}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Ab_R</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>2.033720e-27</td>\n",
" <td>1.224735e-12</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>2.033720e-27</td>\n",
" <td>1.224735e-12</td>\n",
" <td>4.554136e-27</td>\n",
" <td>2.742565e-12</td>\n",
" <td>Metabolite_115</td>\n",
" <td>mw772cbf20_3fc1_4800_ae59_77884f1ae333</td>\n",
" <td>0.446207</td>\n",
" <td>Ab_R</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Ab_sR_IL6</th>\n",
" <td>liver</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>-3.077935e-29</td>\n",
" <td>-1.853576e-14</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>-3.077935e-29</td>\n",
" <td>-1.853576e-14</td>\n",
" <td>-6.375163e-29</td>\n",
" <td>-3.839213e-14</td>\n",
" <td>Metabolite_116</td>\n",
" <td>mw2ba2b802_9f07_4f4d_94c6_24c8de1a95cf</td>\n",
" <td>0.482382</td>\n",
" <td>Ab_sR_IL6{liver}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>sR_IL6</th>\n",
" <td>gut</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>1.306824e-03</td>\n",
" <td>7.869877e+11</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>1.306824e-03</td>\n",
" <td>7.869877e+11</td>\n",
" <td>1.281080e-16</td>\n",
" <td>7.714844e-02</td>\n",
" <td>Metabolite_117</td>\n",
" <td>mw7becb5fe_8da8_4285_a821_0d77ad811b62</td>\n",
" <td>0.067090</td>\n",
" <td>sR_IL6{gut}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>gp130</th>\n",
" <td>gut</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>3.749627e-01</td>\n",
" <td>2.258078e+14</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>3.749627e-01</td>\n",
" <td>2.258078e+14</td>\n",
" <td>6.486481e-17</td>\n",
" <td>3.906250e-02</td>\n",
" <td>Metabolite_118</td>\n",
" <td>mw8c9107e6_f51d_442d_b2dc_2bfdbb8482ca</td>\n",
" <td>5.473908</td>\n",
" <td>gp130{gut}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>R_IL6_gp130</th>\n",
" <td>gut</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>8.448905e-05</td>\n",
" <td>5.088050e+10</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>8.448905e-05</td>\n",
" <td>5.088050e+10</td>\n",
" <td>-2.997464e-17</td>\n",
" <td>-1.805115e-02</td>\n",
" <td>Metabolite_119</td>\n",
" <td>mw824bc3d4_1ac3_4912_9b51_8f14ff1c96b9</td>\n",
" <td>0.006371</td>\n",
" <td>R_IL6_gp130{gut}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Ractive</th>\n",
" <td>gut</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>9.802725e-01</td>\n",
" <td>5.903339e+14</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>9.802725e-01</td>\n",
" <td>5.903339e+14</td>\n",
" <td>1.135134e-17</td>\n",
" <td>6.835938e-03</td>\n",
" <td>Metabolite_120</td>\n",
" <td>mw6cce2109_0e32_4dd9_98ec_41173e8ef07d</td>\n",
" <td>74.853946</td>\n",
" <td>Ractive{gut}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>STAT3</th>\n",
" <td>gut</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>6.106360e-01</td>\n",
" <td>3.677336e+14</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>6.106360e-01</td>\n",
" <td>3.677336e+14</td>\n",
" <td>-1.037837e-16</td>\n",
" <td>-6.250000e-02</td>\n",
" <td>Metabolite_121</td>\n",
" <td>mw2b255f94_8018_4b99_bde8_918eeac45446</td>\n",
" <td>1.545036</td>\n",
" <td>STAT3{gut}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>pSTAT3</th>\n",
" <td>gut</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>9.389364e+00</td>\n",
" <td>5.654407e+15</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>9.389364e+00</td>\n",
" <td>5.654407e+15</td>\n",
" <td>1.037837e-16</td>\n",
" <td>6.250000e-02</td>\n",
" <td>Metabolite_122</td>\n",
" <td>mw48867e93_f170_44e8_ac7a_185b23e1bf3b</td>\n",
" <td>23.757039</td>\n",
" <td>pSTAT3{gut}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>geneProduct</th>\n",
" <td>gut</td>\n",
" <td>assignment</td>\n",
" <td>nmol/l</td>\n",
" <td>1.598036e+02</td>\n",
" <td>9.623598e+16</td>\n",
" <td></td>\n",
" <td>Values[VmProtSynth] * [pSTAT3{gut}] / ( Values...</td>\n",
" <td>1.598036e+02</td>\n",
" <td>9.623598e+16</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>Metabolite_123</td>\n",
" <td>mw0083d743_836f_4238_a17f_4602193d5bc0</td>\n",
" <td>NaN</td>\n",
" <td>geneProduct</td>\n",
" </tr>\n",
" <tr>\n",
" <th>sR</th>\n",
" <td>gut</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>6.064107e+00</td>\n",
" <td>3.651890e+15</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>6.064107e+00</td>\n",
" <td>3.651890e+15</td>\n",
" <td>-5.510265e-15</td>\n",
" <td>-3.318359e+00</td>\n",
" <td>Metabolite_124</td>\n",
" <td>mwd31f52cc_04e7_40e0_885f_c7b2d9e62215</td>\n",
" <td>314.866866</td>\n",
" <td>sR{gut}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>IL6</th>\n",
" <td>gut</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>9.348199e-03</td>\n",
" <td>5.629617e+12</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>9.348199e-03</td>\n",
" <td>5.629617e+12</td>\n",
" <td>0.000000e+00</td>\n",
" <td>0.000000e+00</td>\n",
" <td>Metabolite_125</td>\n",
" <td>mw2c9b0499_3325_4394_8af3_bbf653a944a0</td>\n",
" <td>0.259672</td>\n",
" <td>IL6{gut}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>sgp130</th>\n",
" <td>gut</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>5.569739e+00</td>\n",
" <td>3.354175e+15</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>5.569739e+00</td>\n",
" <td>3.354175e+15</td>\n",
" <td>-3.747564e-15</td>\n",
" <td>-2.256836e+00</td>\n",
" <td>Metabolite_126</td>\n",
" <td>mwd65b5b39_dc1b_4e77_a999_67277a880e5e</td>\n",
" <td>585.644296</td>\n",
" <td>sgp130{gut}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>sR_IL6_sgp130</th>\n",
" <td>gut</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>1.363039e-01</td>\n",
" <td>8.208413e+13</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>1.363039e-01</td>\n",
" <td>8.208413e+13</td>\n",
" <td>-1.654053e-16</td>\n",
" <td>-9.960938e-02</td>\n",
" <td>Metabolite_127</td>\n",
" <td>mw6335d5d7_c7b0_4bc0_b883_f7ee4915c2c3</td>\n",
" <td>14.332020</td>\n",
" <td>sR_IL6_sgp130{gut}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Ab</th>\n",
" <td>gut</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>2.158790e-29</td>\n",
" <td>1.300053e-14</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>2.158790e-29</td>\n",
" <td>1.300053e-14</td>\n",
" <td>-6.539663e-26</td>\n",
" <td>-3.938277e-11</td>\n",
" <td>Metabolite_128</td>\n",
" <td>mwf7796221_1fea_4274_a93e_c00adbf5778c</td>\n",
" <td>0.000330</td>\n",
" <td>Ab{gut}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Ab_sR</th>\n",
" <td>gut</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>2.620597e-26</td>\n",
" <td>1.578160e-11</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>2.620597e-26</td>\n",
" <td>1.578160e-11</td>\n",
" <td>6.543913e-26</td>\n",
" <td>3.940837e-11</td>\n",
" <td>Metabolite_129</td>\n",
" <td>mw5d764bb8_5693_4ac8_9557_f65992cc5eb0</td>\n",
" <td>0.400175</td>\n",
" <td>Ab_sR{gut}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Ab_sR_IL6</th>\n",
" <td>gut</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>-1.209167e-28</td>\n",
" <td>-7.281774e-14</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>-1.209167e-28</td>\n",
" <td>-7.281774e-14</td>\n",
" <td>1.278399e-29</td>\n",
" <td>7.698701e-15</td>\n",
" <td>Metabolite_130</td>\n",
" <td>mwedc1bc00_adf7_4144_a1c2_7dc1a9565dc2</td>\n",
" <td>9.458444</td>\n",
" <td>Ab_sR_IL6{gut}</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Ab</th>\n",
" <td>peripheral</td>\n",
" <td>reactions</td>\n",
" <td>nmol/l</td>\n",
" <td>1.679209e-29</td>\n",
" <td>1.011244e-14</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>1.679209e-29</td>\n",
" <td>1.011244e-14</td>\n",
" <td>-2.088274e-32</td>\n",
" <td>-1.257588e-17</td>\n",
" <td>Metabolite_131</td>\n",
" <td>mwbc2f5464_81e5_43fd_8b39_f5a2756af72f</td>\n",
" <td>804.113764</td>\n",
" <td>Ab{peripheral}</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" compartment type unit initial_concentration \\\n",
"name \n",
"IL6 serum reactions nmol/l 4.356289e-04 \n",
"sgp130 serum reactions nmol/l 3.900000e+00 \n",
"sR_IL6_sgp130 serum reactions nmol/l 8.740607e-02 \n",
"CRP serum reactions nmol/l 2.210637e+02 \n",
"sR serum reactions nmol/l 4.253507e+00 \n",
"sR_IL6 serum reactions nmol/l 1.094243e-03 \n",
"Ab serum reactions nmol/l 2.381820e-29 \n",
"Ab_sR serum reactions nmol/l 6.104391e-26 \n",
"Ab_sR_IL6 serum reactions nmol/l -7.413309e-29 \n",
"CRP Suppression (%) serum assignment nmol/l -0.000000e+00 \n",
"CRP (% of baseline) serum assignment nmol/l 1.000000e+02 \n",
"gp130 liver reactions nmol/l 3.889589e-01 \n",
"R_IL6_gp130 liver reactions nmol/l 6.599359e-05 \n",
"sR_IL6 liver reactions nmol/l 9.761649e-04 \n",
"R liver reactions nmol/l 4.382358e-01 \n",
"IL6 liver reactions nmol/l 7.256658e-04 \n",
"R_IL6 liver reactions nmol/l 1.600365e-05 \n",
"Ractive liver reactions nmol/l 7.654165e-01 \n",
"STAT3 liver reactions nmol/l 7.775373e-01 \n",
"pSTAT3 liver reactions nmol/l 9.222463e+00 \n",
"CRP liver assignment nmol/l 1.583258e+02 \n",
"sR liver reactions nmol/l 6.087047e+00 \n",
"CRPExtracellular liver reactions nmol/l 4.097753e+02 \n",
"sgp130 liver reactions nmol/l 5.589699e+00 \n",
"sR_IL6_sgp130 liver reactions nmol/l 1.163437e-01 \n",
"Ab_sR liver reactions nmol/l 8.616193e-26 \n",
"Ab liver reactions nmol/l 2.200207e-29 \n",
"Ab_R liver reactions nmol/l 2.033720e-27 \n",
"Ab_sR_IL6 liver reactions nmol/l -3.077935e-29 \n",
"sR_IL6 gut reactions nmol/l 1.306824e-03 \n",
"gp130 gut reactions nmol/l 3.749627e-01 \n",
"R_IL6_gp130 gut reactions nmol/l 8.448905e-05 \n",
"Ractive gut reactions nmol/l 9.802725e-01 \n",
"STAT3 gut reactions nmol/l 6.106360e-01 \n",
"pSTAT3 gut reactions nmol/l 9.389364e+00 \n",
"geneProduct gut assignment nmol/l 1.598036e+02 \n",
"sR gut reactions nmol/l 6.064107e+00 \n",
"IL6 gut reactions nmol/l 9.348199e-03 \n",
"sgp130 gut reactions nmol/l 5.569739e+00 \n",
"sR_IL6_sgp130 gut reactions nmol/l 1.363039e-01 \n",
"Ab gut reactions nmol/l 2.158790e-29 \n",
"Ab_sR gut reactions nmol/l 2.620597e-26 \n",
"Ab_sR_IL6 gut reactions nmol/l -1.209167e-28 \n",
"Ab peripheral reactions nmol/l 1.679209e-29 \n",
"\n",
" initial_particle_number initial_expression \\\n",
"name \n",
"IL6 2.623419e+11 \n",
"sgp130 2.348635e+15 \n",
"sR_IL6_sgp130 5.263716e+13 \n",
"CRP 1.331277e+17 \n",
"sR 2.561522e+15 \n",
"sR_IL6 6.589683e+11 \n",
"Ab 1.434365e-14 \n",
"Ab_sR 3.676150e-11 \n",
"Ab_sR_IL6 -4.464399e-14 \n",
"CRP Suppression (%) -0.000000e+00 \n",
"CRP (% of baseline) 6.022141e+16 \n",
"gp130 2.342365e+14 \n",
"R_IL6_gp130 3.974227e+10 \n",
"sR_IL6 5.878603e+11 \n",
"R 2.639118e+14 \n",
"IL6 4.370062e+11 \n",
"R_IL6 9.637625e+09 \n",
"Ractive 4.609446e+14 \n",
"STAT3 4.682439e+14 \n",
"pSTAT3 5.553897e+15 \n",
"CRP 9.534605e+16 \n",
"sR 3.665705e+15 \n",
"CRPExtracellular 2.467725e+17 \n",
"sgp130 3.366195e+15 \n",
"sR_IL6_sgp130 7.006379e+13 \n",
"Ab_sR 5.188793e-11 \n",
"Ab 1.324996e-14 \n",
"Ab_R 1.224735e-12 \n",
"Ab_sR_IL6 -1.853576e-14 \n",
"sR_IL6 7.869877e+11 \n",
"gp130 2.258078e+14 \n",
"R_IL6_gp130 5.088050e+10 \n",
"Ractive 5.903339e+14 \n",
"STAT3 3.677336e+14 \n",
"pSTAT3 5.654407e+15 \n",
"geneProduct 9.623598e+16 \n",
"sR 3.651890e+15 \n",
"IL6 5.629617e+12 \n",
"sgp130 3.354175e+15 \n",
"sR_IL6_sgp130 8.208413e+13 \n",
"Ab 1.300053e-14 \n",
"Ab_sR 1.578160e-11 \n",
"Ab_sR_IL6 -7.281774e-14 \n",
"Ab 1.011244e-14 \n",
"\n",
" expression \\\n",
"name \n",
"IL6 \n",
"sgp130 \n",
"sR_IL6_sgp130 \n",
"CRP \n",
"sR \n",
"sR_IL6 \n",
"Ab \n",
"Ab_sR \n",
"Ab_sR_IL6 \n",
"CRP Suppression (%) ( [CRP{serum}] - {Values[Initial for CRP]} ) /... \n",
"CRP (% of baseline) [CRP{serum}] / {Values[Initial for CRP]} * 100 \n",
"gp130 \n",
"R_IL6_gp130 \n",
"sR_IL6 \n",
"R \n",
"IL6 \n",
"R_IL6 \n",
"Ractive \n",
"STAT3 \n",
"pSTAT3 \n",
"CRP Values[VmProtSynth] * [pSTAT3{liver}] / ( Valu... \n",
"sR \n",
"CRPExtracellular \n",
"sgp130 \n",
"sR_IL6_sgp130 \n",
"Ab_sR \n",
"Ab \n",
"Ab_R \n",
"Ab_sR_IL6 \n",
"sR_IL6 \n",
"gp130 \n",
"R_IL6_gp130 \n",
"Ractive \n",
"STAT3 \n",
"pSTAT3 \n",
"geneProduct Values[VmProtSynth] * [pSTAT3{gut}] / ( Values... \n",
"sR \n",
"IL6 \n",
"sgp130 \n",
"sR_IL6_sgp130 \n",
"Ab \n",
"Ab_sR \n",
"Ab_sR_IL6 \n",
"Ab \n",
"\n",
" concentration particle_number rate \\\n",
"name \n",
"IL6 4.356289e-04 2.623419e+11 -1.565877e-17 \n",
"sgp130 3.900000e+00 2.348635e+15 0.000000e+00 \n",
"sR_IL6_sgp130 8.740607e-02 5.263716e+13 -2.367565e-16 \n",
"CRP 2.210637e+02 1.331277e+17 6.243627e-13 \n",
"sR 4.253507e+00 2.561522e+15 1.307675e-14 \n",
"sR_IL6 1.094243e-03 6.589683e+11 5.032090e-17 \n",
"Ab 2.381820e-29 1.434365e-14 5.129906e-26 \n",
"Ab_sR 6.104391e-26 3.676150e-11 -5.097542e-26 \n",
"Ab_sR_IL6 -7.413309e-29 -4.464399e-14 5.137413e-29 \n",
"CRP Suppression (%) -0.000000e+00 -0.000000e+00 NaN \n",
"CRP (% of baseline) 1.000000e+02 6.022141e+16 NaN \n",
"gp130 3.889589e-01 2.342365e+14 6.486481e-17 \n",
"R_IL6_gp130 6.599359e-05 3.974227e+10 -5.270266e-18 \n",
"sR_IL6 9.761649e-04 5.878603e+11 -2.918916e-16 \n",
"R 4.382358e-01 2.639118e+14 -6.486481e-17 \n",
"IL6 7.256658e-04 4.370062e+11 1.444255e-18 \n",
"R_IL6 1.600365e-05 9.637625e+09 -6.334454e-21 \n",
"Ractive 7.654165e-01 4.609446e+14 2.432430e-18 \n",
"STAT3 7.775373e-01 4.682439e+14 1.556755e-16 \n",
"pSTAT3 9.222463e+00 5.553897e+15 -1.556755e-16 \n",
"CRP 1.583258e+02 9.534605e+16 NaN \n",
"sR 6.087047e+00 3.665705e+15 -7.654706e-15 \n",
"CRPExtracellular 4.097753e+02 2.467725e+17 -5.048039e-13 \n",
"sgp130 5.589699e+00 3.366195e+15 3.468646e-15 \n",
"sR_IL6_sgp130 1.163437e-01 7.006379e+13 5.416211e-16 \n",
"Ab_sR 8.616193e-26 5.188793e-11 -8.215556e-26 \n",
"Ab 2.200207e-29 1.324996e-14 7.691938e-26 \n",
"Ab_R 2.033720e-27 1.224735e-12 4.554136e-27 \n",
"Ab_sR_IL6 -3.077935e-29 -1.853576e-14 -6.375163e-29 \n",
"sR_IL6 1.306824e-03 7.869877e+11 1.281080e-16 \n",
"gp130 3.749627e-01 2.258078e+14 6.486481e-17 \n",
"R_IL6_gp130 8.448905e-05 5.088050e+10 -2.997464e-17 \n",
"Ractive 9.802725e-01 5.903339e+14 1.135134e-17 \n",
"STAT3 6.106360e-01 3.677336e+14 -1.037837e-16 \n",
"pSTAT3 9.389364e+00 5.654407e+15 1.037837e-16 \n",
"geneProduct 1.598036e+02 9.623598e+16 NaN \n",
"sR 6.064107e+00 3.651890e+15 -5.510265e-15 \n",
"IL6 9.348199e-03 5.629617e+12 0.000000e+00 \n",
"sgp130 5.569739e+00 3.354175e+15 -3.747564e-15 \n",
"sR_IL6_sgp130 1.363039e-01 8.208413e+13 -1.654053e-16 \n",
"Ab 2.158790e-29 1.300053e-14 -6.539663e-26 \n",
"Ab_sR 2.620597e-26 1.578160e-11 6.543913e-26 \n",
"Ab_sR_IL6 -1.209167e-28 -7.281774e-14 1.278399e-29 \n",
"Ab 1.679209e-29 1.011244e-14 -2.088274e-32 \n",
"\n",
" particle_number_rate key \\\n",
"name \n",
"IL6 -9.429932e-03 Metabolite_88 \n",
"sgp130 0.000000e+00 Metabolite_89 \n",
"sR_IL6_sgp130 -1.425781e-01 Metabolite_90 \n",
"CRP 3.760000e+02 Metabolite_91 \n",
"sR 7.875000e+00 Metabolite_92 \n",
"sR_IL6 3.030396e-02 Metabolite_93 \n",
"Ab 3.089302e-11 Metabolite_94 \n",
"Ab_sR -3.069812e-11 Metabolite_95 \n",
"Ab_sR_IL6 3.093822e-14 Metabolite_96 \n",
"CRP Suppression (%) NaN Metabolite_97 \n",
"CRP (% of baseline) NaN Metabolite_98 \n",
"gp130 3.906250e-02 Metabolite_99 \n",
"R_IL6_gp130 -3.173828e-03 Metabolite_100 \n",
"sR_IL6 -1.757812e-01 Metabolite_101 \n",
"R -3.906250e-02 Metabolite_102 \n",
"IL6 8.697510e-04 Metabolite_103 \n",
"R_IL6 -3.814697e-06 Metabolite_104 \n",
"Ractive 1.464844e-03 Metabolite_105 \n",
"STAT3 9.375000e-02 Metabolite_106 \n",
"pSTAT3 -9.375000e-02 Metabolite_107 \n",
"CRP NaN Metabolite_108 \n",
"sR -4.609772e+00 Metabolite_109 \n",
"CRPExtracellular -3.040000e+02 Metabolite_110 \n",
"sgp130 2.088867e+00 Metabolite_111 \n",
"sR_IL6_sgp130 3.261719e-01 Metabolite_112 \n",
"Ab_sR -4.947523e-11 Metabolite_113 \n",
"Ab 4.632193e-11 Metabolite_114 \n",
"Ab_R 2.742565e-12 Metabolite_115 \n",
"Ab_sR_IL6 -3.839213e-14 Metabolite_116 \n",
"sR_IL6 7.714844e-02 Metabolite_117 \n",
"gp130 3.906250e-02 Metabolite_118 \n",
"R_IL6_gp130 -1.805115e-02 Metabolite_119 \n",
"Ractive 6.835938e-03 Metabolite_120 \n",
"STAT3 -6.250000e-02 Metabolite_121 \n",
"pSTAT3 6.250000e-02 Metabolite_122 \n",
"geneProduct NaN Metabolite_123 \n",
"sR -3.318359e+00 Metabolite_124 \n",
"IL6 0.000000e+00 Metabolite_125 \n",
"sgp130 -2.256836e+00 Metabolite_126 \n",
"sR_IL6_sgp130 -9.960938e-02 Metabolite_127 \n",
"Ab -3.938277e-11 Metabolite_128 \n",
"Ab_sR 3.940837e-11 Metabolite_129 \n",
"Ab_sR_IL6 7.698701e-15 Metabolite_130 \n",
"Ab -1.257588e-17 Metabolite_131 \n",
"\n",
" sbml_id transition_time \\\n",
"name \n",
"IL6 mwf626e95e_543f_41e4_aad4_c6bf60ab345b 0.028719 \n",
"sgp130 mwbbbce920_e8dd_4320_9386_fc94bfb2fc99 0.997567 \n",
"sR_IL6_sgp130 mw810ff751_fa4e_4143_bd50_169b3e325e1e 9.190533 \n",
"CRP mw114aa90f_5f5b_4fe8_9406_361c8489b6a1 2.777778 \n",
"sR mw30ae63db_6cd3_4b6f_93ad_3350cd360bcc 3.283772 \n",
"sR_IL6 mw03db56ac_8dc6_4931_ae82_fef706d2ee3d 0.518949 \n",
"Ab mwf345ed7a_0622_403c_b816_c8749a2c9ded 0.000464 \n",
"Ab_sR mw1da111f2_a036_4392_8512_015005bdcbb7 1.185348 \n",
"Ab_sR_IL6 mw9947742a_0e4b_4636_9a4b_b6eef2a8f6ac 1.159408 \n",
"CRP Suppression (%) CRP_Suppression___ NaN \n",
"CRP (% of baseline) CRP____of_baseline NaN \n",
"gp130 mw80848184_e2dd_47ce_86d7_7a21479342bd 5.678232 \n",
"R_IL6_gp130 mwd2d9d93a_3bd1_4f17_bac1_baba9ef2d55a 0.006371 \n",
"sR_IL6 mw4638f126_8cb8_4021_ab41_6ae195743ba0 0.123541 \n",
"R mw10315fa3_6f13_4618_bda8_a8694bd3c374 6.397603 \n",
"IL6 mw0adf3eb4_a196_4c48_b10d_4e9e9faaf9e1 4.075710 \n",
"R_IL6 mw7d86cc23_a1af_44c3_bdb9_71e9b1bb2a83 0.175114 \n",
"Ractive mw0eb6c959_d408_45a0_a450_928b8c5876bb 74.828042 \n",
"STAT3 mw42054cd7_17af_46da_970c_7f99151906ad 1.980238 \n",
"pSTAT3 mw39c2e431_fdc3_4964_be29_6ca856620b1b 23.487843 \n",
"CRP mwd5313618_89eb_4c8c_bc82_66f10f966349 NaN \n",
"sR mw2e464cf3_a09c_4b7c_9f3c_06720016a48e 34187.965404 \n",
"CRPExtracellular mw36ea78c1_ed71_4def_96d3_857a442d7195 5.176354 \n",
"sgp130 mw147d30ec_478e_4090_b496_128a131d29eb 755.173729 \n",
"sR_IL6_sgp130 mwab41493c_6349_45f1_a226_3030cfed0e06 15.718141 \n",
"Ab_sR mwf405687b_7401_44ec_a0d6_4a2b35c13e8a 1.048766 \n",
"Ab mw3667a5e1_02c9_44a0_acb4_b0431faa822d 0.000270 \n",
"Ab_R mw772cbf20_3fc1_4800_ae59_77884f1ae333 0.446207 \n",
"Ab_sR_IL6 mw2ba2b802_9f07_4f4d_94c6_24c8de1a95cf 0.482382 \n",
"sR_IL6 mw7becb5fe_8da8_4285_a821_0d77ad811b62 0.067090 \n",
"gp130 mw8c9107e6_f51d_442d_b2dc_2bfdbb8482ca 5.473908 \n",
"R_IL6_gp130 mw824bc3d4_1ac3_4912_9b51_8f14ff1c96b9 0.006371 \n",
"Ractive mw6cce2109_0e32_4dd9_98ec_41173e8ef07d 74.853946 \n",
"STAT3 mw2b255f94_8018_4b99_bde8_918eeac45446 1.545036 \n",
"pSTAT3 mw48867e93_f170_44e8_ac7a_185b23e1bf3b 23.757039 \n",
"geneProduct mw0083d743_836f_4238_a17f_4602193d5bc0 NaN \n",
"sR mwd31f52cc_04e7_40e0_885f_c7b2d9e62215 314.866866 \n",
"IL6 mw2c9b0499_3325_4394_8af3_bbf653a944a0 0.259672 \n",
"sgp130 mwd65b5b39_dc1b_4e77_a999_67277a880e5e 585.644296 \n",
"sR_IL6_sgp130 mw6335d5d7_c7b0_4bc0_b883_f7ee4915c2c3 14.332020 \n",
"Ab mwf7796221_1fea_4274_a93e_c00adbf5778c 0.000330 \n",
"Ab_sR mw5d764bb8_5693_4ac8_9557_f65992cc5eb0 0.400175 \n",
"Ab_sR_IL6 mwedc1bc00_adf7_4144_a1c2_7dc1a9565dc2 9.458444 \n",
"Ab mwbc2f5464_81e5_43fd_8b39_f5a2756af72f 804.113764 \n",
"\n",
" display_name \n",
"name \n",
"IL6 IL6{serum} \n",
"sgp130 sgp130{serum} \n",
"sR_IL6_sgp130 sR_IL6_sgp130{serum} \n",
"CRP CRP{serum} \n",
"sR sR{serum} \n",
"sR_IL6 sR_IL6{serum} \n",
"Ab Ab{serum} \n",
"Ab_sR Ab_sR{serum} \n",
"Ab_sR_IL6 Ab_sR_IL6{serum} \n",
"CRP Suppression (%) CRP Suppression (%) \n",
"CRP (% of baseline) CRP (% of baseline) \n",
"gp130 gp130{liver} \n",
"R_IL6_gp130 R_IL6_gp130{liver} \n",
"sR_IL6 sR_IL6{liver} \n",
"R R \n",
"IL6 IL6{liver} \n",
"R_IL6 R_IL6 \n",
"Ractive Ractive{liver} \n",
"STAT3 STAT3{liver} \n",
"pSTAT3 pSTAT3{liver} \n",
"CRP CRP{liver} \n",
"sR sR{liver} \n",
"CRPExtracellular CRPExtracellular \n",
"sgp130 sgp130{liver} \n",
"sR_IL6_sgp130 sR_IL6_sgp130{liver} \n",
"Ab_sR Ab_sR{liver} \n",
"Ab Ab{liver} \n",
"Ab_R Ab_R \n",
"Ab_sR_IL6 Ab_sR_IL6{liver} \n",
"sR_IL6 sR_IL6{gut} \n",
"gp130 gp130{gut} \n",
"R_IL6_gp130 R_IL6_gp130{gut} \n",
"Ractive Ractive{gut} \n",
"STAT3 STAT3{gut} \n",
"pSTAT3 pSTAT3{gut} \n",
"geneProduct geneProduct \n",
"sR sR{gut} \n",
"IL6 IL6{gut} \n",
"sgp130 sgp130{gut} \n",
"sR_IL6_sgp130 sR_IL6_sgp130{gut} \n",
"Ab Ab{gut} \n",
"Ab_sR Ab_sR{gut} \n",
"Ab_sR_IL6 Ab_sR_IL6{gut} \n",
"Ab Ab{peripheral} "
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# get model species\n",
"species = basico.get_species()\n",
"species"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'descriptions': [{'id': '3569',\n",
" 'qualifier': 'is version of',\n",
" 'uri': 'http://identifiers.org/ncbigene/3569',\n",
" 'resource': 'NCBI Gene'},\n",
" {'id': 'P05231',\n",
" 'qualifier': 'is version of',\n",
" 'uri': 'http://identifiers.org/uniprot/P05231',\n",
" 'resource': 'UniProt Knowledgebase'},\n",
" {'id': 'BTO:0001239',\n",
" 'qualifier': 'is version of',\n",
" 'uri': 'http://identifiers.org/BTO:0001239',\n",
" 'resource': 'Brenda Tissue Ontology'}]}"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# get annotations\n",
"basico.get_miriam_annotation(name=\"IL6\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": ".venv",
"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": "3.12.0"
}
},
"nbformat": 4,
"nbformat_minor": 2
}