diff --git a/notebooks/copasi_process_composer.ipynb b/notebooks/copasi_process_composer.ipynb
index d8a1edec8..de4d9effe 100644
--- a/notebooks/copasi_process_composer.ipynb
+++ b/notebooks/copasi_process_composer.ipynb
@@ -15,11 +15,11 @@
    "execution_count": 1,
    "id": "b43cd4493a594e60",
    "metadata": {
+    "collapsed": false,
     "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:08.935312Z",
-     "start_time": "2024-03-04T16:42:08.931881Z"
-    },
-    "collapsed": false
+     "end_time": "2024-03-04T17:15:40.864594Z",
+     "start_time": "2024-03-04T17:15:40.858286Z"
+    }
    },
    "outputs": [],
    "source": [
@@ -30,15 +30,6 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
-   "id": "65385e04f4f5dd1a",
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:10.809815Z",
-     "start_time": "2024-03-04T16:42:09.047667Z"
-    },
-    "collapsed": false
-   },
    "outputs": [
     {
      "name": "stdout",
@@ -52,12 +43,20 @@
     }
    ],
    "source": [
-    "from builder import Builder, Process\n",
+    "import os \n",
     "from process_bigraph import pp, pf \n",
-    "from biosimulator_processes import CORE\n",
     "from biosimulator_processes.data_model import *\n",
     "from biosimulator_processes.biosimulator_builder import BiosimulatorBuilder"
-   ]
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-03-04T17:15:43.439817Z",
+     "start_time": "2024-03-04T17:15:41.375489Z"
+    }
+   },
+   "id": "65385e04f4f5dd1a",
+   "execution_count": 2
   },
   {
    "cell_type": "markdown",
@@ -74,11 +73,11 @@
    "execution_count": 3,
    "id": "cc709690e20090cf",
    "metadata": {
+    "collapsed": false,
     "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:10.810196Z",
-     "start_time": "2024-03-04T16:42:10.808054Z"
-    },
-    "collapsed": false
+     "end_time": "2024-03-04T17:15:46.687418Z",
+     "start_time": "2024-03-04T17:15:46.682546Z"
+    }
    },
    "outputs": [],
    "source": [
@@ -90,23 +89,16 @@
    "execution_count": 4,
    "id": "41034be54d9cf16",
    "metadata": {
+    "collapsed": false,
     "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:10.813366Z",
-     "start_time": "2024-03-04T16:42:10.811517Z"
-    },
-    "collapsed": false
+     "end_time": "2024-03-04T17:15:46.959980Z",
+     "start_time": "2024-03-04T17:15:46.955838Z"
+    }
    },
    "outputs": [
     {
      "data": {
-      "text/plain": [
-       "['CobraProcess',\n",
-       " 'CopasiProcess',\n",
-       " 'console-emitter',\n",
-       " 'SmoldynProcess',\n",
-       " 'TelluriumProcess',\n",
-       " 'ram-emitter']"
-      ]
+      "text/plain": "['CopasiProcess',\n 'ram-emitter',\n 'console-emitter',\n 'CobraProcess',\n 'SmoldynProcess',\n 'TelluriumProcess']"
      },
      "execution_count": 4,
      "metadata": {},
@@ -129,20 +121,6 @@
     "Let's load a BIOMODEL from `basico` and inspect the parameters we can adjust:"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "id": "f1e5eedb251a22c3",
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:10.828221Z",
-     "start_time": "2024-03-04T16:42:10.813820Z"
-    },
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "markdown",
    "id": "eea00feb4c2651d6",
@@ -165,31 +143,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "edf123175ec3408c",
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:12.560995Z",
-     "start_time": "2024-03-04T16:42:12.555910Z"
-    },
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "True"
-      ]
-     },
-     "execution_count": 5,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
-    "from basico import * \n",
-    "\n",
-    "\n",
     "model_filepath = '../biosimulator_processes/model_files/BIOMD0000000061_url.xml'\n",
     "\n",
     "os.path.exists(model_filepath)"
@@ -197,652 +157,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "40ab6f70ac3f4996",
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:13.555997Z",
-     "start_time": "2024-03-04T16:42:13.490510Z"
-    },
     "collapsed": false
    },
-   "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",
-       "    </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",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>Extracellular glucose</th>\n",
-       "      <td>extracellular</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>6.700000</td>\n",
-       "      <td>4.034834e+21</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>6.700000</td>\n",
-       "      <td>4.034834e+21</td>\n",
-       "      <td>-1.139132e+00</td>\n",
-       "      <td>-6.860013e+20</td>\n",
-       "      <td>Metabolite_0</td>\n",
-       "      <td>GlcX</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Cytosolic glucose</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>0.573074</td>\n",
-       "      <td>3.451132e+20</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.573074</td>\n",
-       "      <td>3.451132e+20</td>\n",
-       "      <td>6.820866e+01</td>\n",
-       "      <td>4.107622e+22</td>\n",
-       "      <td>Metabolite_1</td>\n",
-       "      <td>Glc</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>ATP</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>2.100000</td>\n",
-       "      <td>1.264650e+21</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>2.100000</td>\n",
-       "      <td>1.264650e+21</td>\n",
-       "      <td>-5.374740e-04</td>\n",
-       "      <td>-3.236744e+17</td>\n",
-       "      <td>Metabolite_2</td>\n",
-       "      <td>ATP</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Glucose-6-Phosphate</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>4.200000</td>\n",
-       "      <td>2.529299e+21</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>4.200000</td>\n",
-       "      <td>2.529299e+21</td>\n",
-       "      <td>2.292073e-05</td>\n",
-       "      <td>1.380319e+16</td>\n",
-       "      <td>Metabolite_3</td>\n",
-       "      <td>G6P</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>ADP</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>1.500000</td>\n",
-       "      <td>9.033211e+20</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>1.500000</td>\n",
-       "      <td>9.033211e+20</td>\n",
-       "      <td>9.874740e-04</td>\n",
-       "      <td>5.946708e+17</td>\n",
-       "      <td>Metabolite_4</td>\n",
-       "      <td>ADP</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Fructose-6-Phosphate</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>0.490000</td>\n",
-       "      <td>2.950849e+20</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.490000</td>\n",
-       "      <td>2.950849e+20</td>\n",
-       "      <td>-2.357096e-05</td>\n",
-       "      <td>-1.419477e+16</td>\n",
-       "      <td>Metabolite_5</td>\n",
-       "      <td>F6P</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Fructose 1,6-bisphosphate</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>4.640000</td>\n",
-       "      <td>2.794273e+21</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>4.640000</td>\n",
-       "      <td>2.794273e+21</td>\n",
-       "      <td>3.000184e-05</td>\n",
-       "      <td>1.806753e+16</td>\n",
-       "      <td>Metabolite_6</td>\n",
-       "      <td>FBP</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Glyceraldehyde 3-phosphate</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>0.115000</td>\n",
-       "      <td>6.925462e+19</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.115000</td>\n",
-       "      <td>6.925462e+19</td>\n",
-       "      <td>-1.056219e-04</td>\n",
-       "      <td>-6.360699e+16</td>\n",
-       "      <td>Metabolite_7</td>\n",
-       "      <td>GAP</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Dihydroxyacetone phosphate</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>2.950000</td>\n",
-       "      <td>1.776532e+21</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>2.950000</td>\n",
-       "      <td>1.776532e+21</td>\n",
-       "      <td>8.613930e-05</td>\n",
-       "      <td>5.187430e+16</td>\n",
-       "      <td>Metabolite_8</td>\n",
-       "      <td>DHAP</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>NAD</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>0.650000</td>\n",
-       "      <td>3.914391e+20</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.650000</td>\n",
-       "      <td>3.914391e+20</td>\n",
-       "      <td>-5.799246e-05</td>\n",
-       "      <td>-3.492388e+16</td>\n",
-       "      <td>Metabolite_9</td>\n",
-       "      <td>NAD</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>1,3-Bisphosphoglycerate</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>0.000270</td>\n",
-       "      <td>1.625978e+17</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000270</td>\n",
-       "      <td>1.625978e+17</td>\n",
-       "      <td>5.878219e-05</td>\n",
-       "      <td>3.539946e+16</td>\n",
-       "      <td>Metabolite_10</td>\n",
-       "      <td>BPG</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>NADH</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>0.330000</td>\n",
-       "      <td>1.987306e+20</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.330000</td>\n",
-       "      <td>1.987306e+20</td>\n",
-       "      <td>5.799246e-05</td>\n",
-       "      <td>3.492388e+16</td>\n",
-       "      <td>Metabolite_11</td>\n",
-       "      <td>NADH</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Phosphoenolpyruvate</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>0.040000</td>\n",
-       "      <td>2.408856e+19</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.040000</td>\n",
-       "      <td>2.408856e+19</td>\n",
-       "      <td>-2.664671e-05</td>\n",
-       "      <td>-1.604702e+16</td>\n",
-       "      <td>Metabolite_12</td>\n",
-       "      <td>PEP</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Pyruvate</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>8.700000</td>\n",
-       "      <td>5.239262e+21</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>8.700000</td>\n",
-       "      <td>5.239262e+21</td>\n",
-       "      <td>-3.001996e-05</td>\n",
-       "      <td>-1.807844e+16</td>\n",
-       "      <td>Metabolite_13</td>\n",
-       "      <td>Pyr</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Acetaldehyde</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>1.481530</td>\n",
-       "      <td>8.921982e+20</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>1.481530</td>\n",
-       "      <td>8.921982e+20</td>\n",
-       "      <td>5.754463e-05</td>\n",
-       "      <td>3.465418e+16</td>\n",
-       "      <td>Metabolite_14</td>\n",
-       "      <td>ACA</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>EtOH</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>19.237900</td>\n",
-       "      <td>1.158533e+22</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>19.237900</td>\n",
-       "      <td>1.158533e+22</td>\n",
-       "      <td>7.012204e-05</td>\n",
-       "      <td>4.222848e+16</td>\n",
-       "      <td>Metabolite_15</td>\n",
-       "      <td>EtOH</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Extracellular ethanol</th>\n",
-       "      <td>extracellular</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>16.451400</td>\n",
-       "      <td>9.907265e+21</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>16.451400</td>\n",
-       "      <td>9.907265e+21</td>\n",
-       "      <td>-1.437288e-06</td>\n",
-       "      <td>-8.655551e+14</td>\n",
-       "      <td>Metabolite_16</td>\n",
-       "      <td>EtOHX</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Glycerol</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>4.196000</td>\n",
-       "      <td>2.526890e+21</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>4.196000</td>\n",
-       "      <td>2.526890e+21</td>\n",
-       "      <td>-1.733231e-05</td>\n",
-       "      <td>-1.043776e+16</td>\n",
-       "      <td>Metabolite_17</td>\n",
-       "      <td>Glyc</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Extracellular glycerol</th>\n",
-       "      <td>extracellular</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>1.684780</td>\n",
-       "      <td>1.014598e+21</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>1.684780</td>\n",
-       "      <td>1.014598e+21</td>\n",
-       "      <td>3.566102e-07</td>\n",
-       "      <td>2.147557e+14</td>\n",
-       "      <td>Metabolite_18</td>\n",
-       "      <td>GlycX</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Extracellular acetaldehyde</th>\n",
-       "      <td>extracellular</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>1.288360</td>\n",
-       "      <td>7.758685e+20</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>1.288360</td>\n",
-       "      <td>7.758685e+20</td>\n",
-       "      <td>1.261075e-07</td>\n",
-       "      <td>7.594373e+13</td>\n",
-       "      <td>Metabolite_19</td>\n",
-       "      <td>ACAX</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Extracellular cyanide</th>\n",
-       "      <td>extracellular</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>5.203580</td>\n",
-       "      <td>3.133669e+21</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>5.203580</td>\n",
-       "      <td>3.133669e+21</td>\n",
-       "      <td>9.153125e-08</td>\n",
-       "      <td>5.512141e+13</td>\n",
-       "      <td>Metabolite_20</td>\n",
-       "      <td>CNX</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>AMP</th>\n",
-       "      <td>cytosol</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>0.330000</td>\n",
-       "      <td>1.987306e+20</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.330000</td>\n",
-       "      <td>1.987306e+20</td>\n",
-       "      <td>-4.500000e-04</td>\n",
-       "      <td>-2.709963e+17</td>\n",
-       "      <td>Metabolite_21</td>\n",
-       "      <td>AMP</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>P</th>\n",
-       "      <td>extracellular</td>\n",
-       "      <td>fixed</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_22</td>\n",
-       "      <td>P</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Mixed flow cyanide</th>\n",
-       "      <td>extracellular</td>\n",
-       "      <td>fixed</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>5.600000</td>\n",
-       "      <td>3.372399e+21</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>5.600000</td>\n",
-       "      <td>3.372399e+21</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_23</td>\n",
-       "      <td>CNX0</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Mixed flow glucose</th>\n",
-       "      <td>extracellular</td>\n",
-       "      <td>fixed</td>\n",
-       "      <td>mmol/l</td>\n",
-       "      <td>24.000000</td>\n",
-       "      <td>1.445314e+22</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>24.000000</td>\n",
-       "      <td>1.445314e+22</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_24</td>\n",
-       "      <td>GlcX0</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "                              compartment       type    unit  \\\n",
-       "name                                                           \n",
-       "Extracellular glucose       extracellular  reactions  mmol/l   \n",
-       "Cytosolic glucose                 cytosol  reactions  mmol/l   \n",
-       "ATP                               cytosol  reactions  mmol/l   \n",
-       "Glucose-6-Phosphate               cytosol  reactions  mmol/l   \n",
-       "ADP                               cytosol  reactions  mmol/l   \n",
-       "Fructose-6-Phosphate              cytosol  reactions  mmol/l   \n",
-       "Fructose 1,6-bisphosphate         cytosol  reactions  mmol/l   \n",
-       "Glyceraldehyde 3-phosphate        cytosol  reactions  mmol/l   \n",
-       "Dihydroxyacetone phosphate        cytosol  reactions  mmol/l   \n",
-       "NAD                               cytosol  reactions  mmol/l   \n",
-       "1,3-Bisphosphoglycerate           cytosol  reactions  mmol/l   \n",
-       "NADH                              cytosol  reactions  mmol/l   \n",
-       "Phosphoenolpyruvate               cytosol  reactions  mmol/l   \n",
-       "Pyruvate                          cytosol  reactions  mmol/l   \n",
-       "Acetaldehyde                      cytosol  reactions  mmol/l   \n",
-       "EtOH                              cytosol  reactions  mmol/l   \n",
-       "Extracellular ethanol       extracellular  reactions  mmol/l   \n",
-       "Glycerol                          cytosol  reactions  mmol/l   \n",
-       "Extracellular glycerol      extracellular  reactions  mmol/l   \n",
-       "Extracellular acetaldehyde  extracellular  reactions  mmol/l   \n",
-       "Extracellular cyanide       extracellular  reactions  mmol/l   \n",
-       "AMP                               cytosol  reactions  mmol/l   \n",
-       "P                           extracellular      fixed  mmol/l   \n",
-       "Mixed flow cyanide          extracellular      fixed  mmol/l   \n",
-       "Mixed flow glucose          extracellular      fixed  mmol/l   \n",
-       "\n",
-       "                            initial_concentration  initial_particle_number  \\\n",
-       "name                                                                         \n",
-       "Extracellular glucose                    6.700000             4.034834e+21   \n",
-       "Cytosolic glucose                        0.573074             3.451132e+20   \n",
-       "ATP                                      2.100000             1.264650e+21   \n",
-       "Glucose-6-Phosphate                      4.200000             2.529299e+21   \n",
-       "ADP                                      1.500000             9.033211e+20   \n",
-       "Fructose-6-Phosphate                     0.490000             2.950849e+20   \n",
-       "Fructose 1,6-bisphosphate                4.640000             2.794273e+21   \n",
-       "Glyceraldehyde 3-phosphate               0.115000             6.925462e+19   \n",
-       "Dihydroxyacetone phosphate               2.950000             1.776532e+21   \n",
-       "NAD                                      0.650000             3.914391e+20   \n",
-       "1,3-Bisphosphoglycerate                  0.000270             1.625978e+17   \n",
-       "NADH                                     0.330000             1.987306e+20   \n",
-       "Phosphoenolpyruvate                      0.040000             2.408856e+19   \n",
-       "Pyruvate                                 8.700000             5.239262e+21   \n",
-       "Acetaldehyde                             1.481530             8.921982e+20   \n",
-       "EtOH                                    19.237900             1.158533e+22   \n",
-       "Extracellular ethanol                   16.451400             9.907265e+21   \n",
-       "Glycerol                                 4.196000             2.526890e+21   \n",
-       "Extracellular glycerol                   1.684780             1.014598e+21   \n",
-       "Extracellular acetaldehyde               1.288360             7.758685e+20   \n",
-       "Extracellular cyanide                    5.203580             3.133669e+21   \n",
-       "AMP                                      0.330000             1.987306e+20   \n",
-       "P                                        0.000000             0.000000e+00   \n",
-       "Mixed flow cyanide                       5.600000             3.372399e+21   \n",
-       "Mixed flow glucose                      24.000000             1.445314e+22   \n",
-       "\n",
-       "                           initial_expression expression  concentration  \\\n",
-       "name                                                                      \n",
-       "Extracellular glucose                                          6.700000   \n",
-       "Cytosolic glucose                                              0.573074   \n",
-       "ATP                                                            2.100000   \n",
-       "Glucose-6-Phosphate                                            4.200000   \n",
-       "ADP                                                            1.500000   \n",
-       "Fructose-6-Phosphate                                           0.490000   \n",
-       "Fructose 1,6-bisphosphate                                      4.640000   \n",
-       "Glyceraldehyde 3-phosphate                                     0.115000   \n",
-       "Dihydroxyacetone phosphate                                     2.950000   \n",
-       "NAD                                                            0.650000   \n",
-       "1,3-Bisphosphoglycerate                                        0.000270   \n",
-       "NADH                                                           0.330000   \n",
-       "Phosphoenolpyruvate                                            0.040000   \n",
-       "Pyruvate                                                       8.700000   \n",
-       "Acetaldehyde                                                   1.481530   \n",
-       "EtOH                                                          19.237900   \n",
-       "Extracellular ethanol                                         16.451400   \n",
-       "Glycerol                                                       4.196000   \n",
-       "Extracellular glycerol                                         1.684780   \n",
-       "Extracellular acetaldehyde                                     1.288360   \n",
-       "Extracellular cyanide                                          5.203580   \n",
-       "AMP                                                            0.330000   \n",
-       "P                                                              0.000000   \n",
-       "Mixed flow cyanide                                             5.600000   \n",
-       "Mixed flow glucose                                            24.000000   \n",
-       "\n",
-       "                            particle_number          rate  \\\n",
-       "name                                                        \n",
-       "Extracellular glucose          4.034834e+21 -1.139132e+00   \n",
-       "Cytosolic glucose              3.451132e+20  6.820866e+01   \n",
-       "ATP                            1.264650e+21 -5.374740e-04   \n",
-       "Glucose-6-Phosphate            2.529299e+21  2.292073e-05   \n",
-       "ADP                            9.033211e+20  9.874740e-04   \n",
-       "Fructose-6-Phosphate           2.950849e+20 -2.357096e-05   \n",
-       "Fructose 1,6-bisphosphate      2.794273e+21  3.000184e-05   \n",
-       "Glyceraldehyde 3-phosphate     6.925462e+19 -1.056219e-04   \n",
-       "Dihydroxyacetone phosphate     1.776532e+21  8.613930e-05   \n",
-       "NAD                            3.914391e+20 -5.799246e-05   \n",
-       "1,3-Bisphosphoglycerate        1.625978e+17  5.878219e-05   \n",
-       "NADH                           1.987306e+20  5.799246e-05   \n",
-       "Phosphoenolpyruvate            2.408856e+19 -2.664671e-05   \n",
-       "Pyruvate                       5.239262e+21 -3.001996e-05   \n",
-       "Acetaldehyde                   8.921982e+20  5.754463e-05   \n",
-       "EtOH                           1.158533e+22  7.012204e-05   \n",
-       "Extracellular ethanol          9.907265e+21 -1.437288e-06   \n",
-       "Glycerol                       2.526890e+21 -1.733231e-05   \n",
-       "Extracellular glycerol         1.014598e+21  3.566102e-07   \n",
-       "Extracellular acetaldehyde     7.758685e+20  1.261075e-07   \n",
-       "Extracellular cyanide          3.133669e+21  9.153125e-08   \n",
-       "AMP                            1.987306e+20 -4.500000e-04   \n",
-       "P                              0.000000e+00  0.000000e+00   \n",
-       "Mixed flow cyanide             3.372399e+21  0.000000e+00   \n",
-       "Mixed flow glucose             1.445314e+22  0.000000e+00   \n",
-       "\n",
-       "                            particle_number_rate            key sbml_id  \n",
-       "name                                                                     \n",
-       "Extracellular glucose              -6.860013e+20   Metabolite_0    GlcX  \n",
-       "Cytosolic glucose                   4.107622e+22   Metabolite_1     Glc  \n",
-       "ATP                                -3.236744e+17   Metabolite_2     ATP  \n",
-       "Glucose-6-Phosphate                 1.380319e+16   Metabolite_3     G6P  \n",
-       "ADP                                 5.946708e+17   Metabolite_4     ADP  \n",
-       "Fructose-6-Phosphate               -1.419477e+16   Metabolite_5     F6P  \n",
-       "Fructose 1,6-bisphosphate           1.806753e+16   Metabolite_6     FBP  \n",
-       "Glyceraldehyde 3-phosphate         -6.360699e+16   Metabolite_7     GAP  \n",
-       "Dihydroxyacetone phosphate          5.187430e+16   Metabolite_8    DHAP  \n",
-       "NAD                                -3.492388e+16   Metabolite_9     NAD  \n",
-       "1,3-Bisphosphoglycerate             3.539946e+16  Metabolite_10     BPG  \n",
-       "NADH                                3.492388e+16  Metabolite_11    NADH  \n",
-       "Phosphoenolpyruvate                -1.604702e+16  Metabolite_12     PEP  \n",
-       "Pyruvate                           -1.807844e+16  Metabolite_13     Pyr  \n",
-       "Acetaldehyde                        3.465418e+16  Metabolite_14     ACA  \n",
-       "EtOH                                4.222848e+16  Metabolite_15    EtOH  \n",
-       "Extracellular ethanol              -8.655551e+14  Metabolite_16   EtOHX  \n",
-       "Glycerol                           -1.043776e+16  Metabolite_17    Glyc  \n",
-       "Extracellular glycerol              2.147557e+14  Metabolite_18   GlycX  \n",
-       "Extracellular acetaldehyde          7.594373e+13  Metabolite_19    ACAX  \n",
-       "Extracellular cyanide               5.512141e+13  Metabolite_20     CNX  \n",
-       "AMP                                -2.709963e+17  Metabolite_21     AMP  \n",
-       "P                                   0.000000e+00  Metabolite_22       P  \n",
-       "Mixed flow cyanide                  0.000000e+00  Metabolite_23    CNX0  \n",
-       "Mixed flow glucose                  0.000000e+00  Metabolite_24   GlcX0  "
-      ]
-     },
-     "execution_count": 6,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
-    "model_from_file = load_model(model_filepath)\n",
-    "get_species(model=model_from_file)"
+    "# Uncomment if you wish to inspect the species referenced below\n",
+    "# model_from_file = load_model(model_filepath)\n",
+    "# get_species(model=model_from_file)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "id": "d02a547b85138f96",
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:14.251034Z",
-     "start_time": "2024-03-04T16:42:14.219527Z"
-    },
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "{ 'global_parameter_changes': [],\n",
-      "  'reaction_changes': [],\n",
-      "  'species_changes': [ { 'expression': '',\n",
-      "                         'initial_concentration': 9.261000000000001,\n",
-      "                         'initial_expression': '',\n",
-      "                         'initial_particle_number': None,\n",
-      "                         'name': 'ADP',\n",
-      "                         'unit': ''}]}\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# 1. specify model changes\n",
     "process_model_changes = ModelChanges(\n",
@@ -855,36 +189,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "id": "1b6c269646357d7d",
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:14.814108Z",
-     "start_time": "2024-03-04T16:42:14.810827Z"
-    },
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "{ 'model_changes': { 'global_parameter_changes': [],\n",
-      "                     'reaction_changes': [],\n",
-      "                     'species_changes': [ { 'expression': '',\n",
-      "                                            'initial_concentration': 9.261000000000001,\n",
-      "                                            'initial_expression': '',\n",
-      "                                            'initial_particle_number': None,\n",
-      "                                            'name': 'ADP',\n",
-      "                                            'unit': ''}]},\n",
-      "  'model_id': 'copasi_process_from_file',\n",
-      "  'model_language': 'sbml',\n",
-      "  'model_name': 'Simple Composite Process from File',\n",
-      "  'model_source': { 'value': '../biosimulator_processes/model_files/BIOMD0000000061_url.xml'},\n",
-      "  'model_units': None}\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# 2. define the model schema to be used by the composite process (one of the copasiprocess config parameters)\n",
     "\n",
@@ -901,38 +211,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "id": "5d434956e65b1a42",
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:15.337152Z",
-     "start_time": "2024-03-04T16:42:15.334361Z"
-    },
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "{ 'method': 'stochastic',\n",
-      "  'model': { 'model_changes': { 'global_parameter_changes': [],\n",
-      "                                'reaction_changes': [],\n",
-      "                                'species_changes': [ { 'expression': '',\n",
-      "                                                       'initial_concentration': 9.261000000000001,\n",
-      "                                                       'initial_expression': '',\n",
-      "                                                       'initial_particle_number': None,\n",
-      "                                                       'name': 'ADP',\n",
-      "                                                       'unit': ''}]},\n",
-      "             'model_id': 'copasi_process_from_file',\n",
-      "             'model_language': 'sbml',\n",
-      "             'model_name': 'Simple Composite Process from File',\n",
-      "             'model_source': { 'value': '../biosimulator_processes/model_files/BIOMD0000000061_url.xml'},\n",
-      "             'model_units': None},\n",
-      "  'process_name': 'simple_copasi_from_file'}\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# 3. Define config schema to be used as 'config' parameter of Process constructor\n",
     "process_config_from_file = CopasiProcessConfigSchema(\n",
@@ -947,52 +231,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "id": "de88e95d8f616779",
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:16.043432Z",
-     "start_time": "2024-03-04T16:42:16.040674Z"
-    },
     "collapsed": false
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "{'model_id': 'copasi_process_from_file',\n",
-       " 'model_source': {'value': '../biosimulator_processes/model_files/BIOMD0000000061_url.xml'},\n",
-       " 'model_language': 'sbml',\n",
-       " 'model_name': 'Simple Composite Process from File',\n",
-       " 'model_changes': {'species_changes': [{'name': 'ADP',\n",
-       "    'unit': '',\n",
-       "    'initial_concentration': 9.261000000000001,\n",
-       "    'initial_particle_number': None,\n",
-       "    'initial_expression': '',\n",
-       "    'expression': ''}],\n",
-       "  'global_parameter_changes': [],\n",
-       "  'reaction_changes': []},\n",
-       " 'model_units': None}"
-      ]
-     },
-     "execution_count": 10,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "process_config_from_file.model"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
    "id": "52d81ea2ea688d47",
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:16.698339Z",
-     "start_time": "2024-03-04T16:42:16.522040Z"
-    },
     "collapsed": false
    },
    "outputs": [],
@@ -1009,1188 +262,52 @@
   },
   {
    "cell_type": "markdown",
-   "id": "bfd4af678329923a",
+   "source": [
+    "Let's now add a biomodel with adjusted params (we know ahead of time)"
+   ],
    "metadata": {
     "collapsed": false
    },
-   "source": [
-    "Let's load a BIOMODEL from `basico` and inspect the parameters we can adjust, and then add it to the composite process:"
-   ]
+   "id": "80fd1a5aca61b442"
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": null,
    "id": "f499f96a817d9faf",
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:28.725829Z",
-     "start_time": "2024-03-04T16:42:26.443059Z"
-    },
     "collapsed": false
    },
-   "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",
-       "    </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",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>EpoRJAK2</th>\n",
-       "      <td>cyt</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>3.976220e+00</td>\n",
-       "      <td>9.578143e+14</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>3.976220e+00</td>\n",
-       "      <td>9.578143e+14</td>\n",
-       "      <td>-0.314737</td>\n",
-       "      <td>-7.581552e+13</td>\n",
-       "      <td>Metabolite_50</td>\n",
-       "      <td>EpoRJAK2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>EpoRpJAK2</th>\n",
-       "      <td>cyt</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.314737</td>\n",
-       "      <td>7.581552e+13</td>\n",
-       "      <td>Metabolite_51</td>\n",
-       "      <td>EpoRpJAK2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>p1EpoRpJAK2</th>\n",
-       "      <td>cyt</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_52</td>\n",
-       "      <td>p1EpoRpJAK2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>p2EpoRpJAK2</th>\n",
-       "      <td>cyt</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_53</td>\n",
-       "      <td>p2EpoRpJAK2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>p12EpoRpJAK2</th>\n",
-       "      <td>cyt</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_54</td>\n",
-       "      <td>p12EpoRpJAK2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>EpoRJAK2_CIS</th>\n",
-       "      <td>cyt</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_55</td>\n",
-       "      <td>EpoRJAK2_CIS</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>SHP1</th>\n",
-       "      <td>cyt</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>2.672510e+01</td>\n",
-       "      <td>6.437693e+15</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>2.672510e+01</td>\n",
-       "      <td>6.437693e+15</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_56</td>\n",
-       "      <td>SHP1</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>SHP1Act</th>\n",
-       "      <td>cyt</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_57</td>\n",
-       "      <td>SHP1Act</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>STAT5</th>\n",
-       "      <td>cyt</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>7.975350e+01</td>\n",
-       "      <td>1.921147e+16</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>7.975350e+01</td>\n",
-       "      <td>1.921147e+16</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_58</td>\n",
-       "      <td>STAT5</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>pSTAT5</th>\n",
-       "      <td>cyt</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_59</td>\n",
-       "      <td>pSTAT5</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>npSTAT5</th>\n",
-       "      <td>nuc</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_60</td>\n",
-       "      <td>npSTAT5</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>CISnRNA1</th>\n",
-       "      <td>nuc</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_61</td>\n",
-       "      <td>CISnRNA1</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>CISnRNA2</th>\n",
-       "      <td>nuc</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_62</td>\n",
-       "      <td>CISnRNA2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>CISnRNA3</th>\n",
-       "      <td>nuc</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_63</td>\n",
-       "      <td>CISnRNA3</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>CISnRNA4</th>\n",
-       "      <td>nuc</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_64</td>\n",
-       "      <td>CISnRNA4</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>CISnRNA5</th>\n",
-       "      <td>nuc</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_65</td>\n",
-       "      <td>CISnRNA5</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>CISRNA</th>\n",
-       "      <td>cyt</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_66</td>\n",
-       "      <td>CISRNA</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>CIS</th>\n",
-       "      <td>cyt</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_67</td>\n",
-       "      <td>CIS</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>SOCS3nRNA1</th>\n",
-       "      <td>nuc</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_68</td>\n",
-       "      <td>SOCS3nRNA1</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>SOCS3nRNA2</th>\n",
-       "      <td>nuc</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_69</td>\n",
-       "      <td>SOCS3nRNA2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>SOCS3nRNA3</th>\n",
-       "      <td>nuc</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_70</td>\n",
-       "      <td>SOCS3nRNA3</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>SOCS3nRNA4</th>\n",
-       "      <td>nuc</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_71</td>\n",
-       "      <td>SOCS3nRNA4</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>SOCS3nRNA5</th>\n",
-       "      <td>nuc</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_72</td>\n",
-       "      <td>SOCS3nRNA5</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>SOCS3RNA</th>\n",
-       "      <td>cyt</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_73</td>\n",
-       "      <td>SOCS3RNA</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>SOCS3</th>\n",
-       "      <td>cyt</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_74</td>\n",
-       "      <td>SOCS3</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>Epo</th>\n",
-       "      <td>cyt</td>\n",
-       "      <td>reactions</td>\n",
-       "      <td>nmol/l</td>\n",
-       "      <td>1.249970e-07</td>\n",
-       "      <td>3.010998e+07</td>\n",
-       "      <td></td>\n",
-       "      <td></td>\n",
-       "      <td>1.249970e-07</td>\n",
-       "      <td>3.010998e+07</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Metabolite_75</td>\n",
-       "      <td>Epo</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "             compartment       type    unit  initial_concentration  \\\n",
-       "name                                                                 \n",
-       "EpoRJAK2             cyt  reactions  nmol/l           3.976220e+00   \n",
-       "EpoRpJAK2            cyt  reactions  nmol/l           0.000000e+00   \n",
-       "p1EpoRpJAK2          cyt  reactions  nmol/l           0.000000e+00   \n",
-       "p2EpoRpJAK2          cyt  reactions  nmol/l           0.000000e+00   \n",
-       "p12EpoRpJAK2         cyt  reactions  nmol/l           0.000000e+00   \n",
-       "EpoRJAK2_CIS         cyt  reactions  nmol/l           0.000000e+00   \n",
-       "SHP1                 cyt  reactions  nmol/l           2.672510e+01   \n",
-       "SHP1Act              cyt  reactions  nmol/l           0.000000e+00   \n",
-       "STAT5                cyt  reactions  nmol/l           7.975350e+01   \n",
-       "pSTAT5               cyt  reactions  nmol/l           0.000000e+00   \n",
-       "npSTAT5              nuc  reactions  nmol/l           0.000000e+00   \n",
-       "CISnRNA1             nuc  reactions  nmol/l           0.000000e+00   \n",
-       "CISnRNA2             nuc  reactions  nmol/l           0.000000e+00   \n",
-       "CISnRNA3             nuc  reactions  nmol/l           0.000000e+00   \n",
-       "CISnRNA4             nuc  reactions  nmol/l           0.000000e+00   \n",
-       "CISnRNA5             nuc  reactions  nmol/l           0.000000e+00   \n",
-       "CISRNA               cyt  reactions  nmol/l           0.000000e+00   \n",
-       "CIS                  cyt  reactions  nmol/l           0.000000e+00   \n",
-       "SOCS3nRNA1           nuc  reactions  nmol/l           0.000000e+00   \n",
-       "SOCS3nRNA2           nuc  reactions  nmol/l           0.000000e+00   \n",
-       "SOCS3nRNA3           nuc  reactions  nmol/l           0.000000e+00   \n",
-       "SOCS3nRNA4           nuc  reactions  nmol/l           0.000000e+00   \n",
-       "SOCS3nRNA5           nuc  reactions  nmol/l           0.000000e+00   \n",
-       "SOCS3RNA             cyt  reactions  nmol/l           0.000000e+00   \n",
-       "SOCS3                cyt  reactions  nmol/l           0.000000e+00   \n",
-       "Epo                  cyt  reactions  nmol/l           1.249970e-07   \n",
-       "\n",
-       "              initial_particle_number initial_expression expression  \\\n",
-       "name                                                                  \n",
-       "EpoRJAK2                 9.578143e+14                                 \n",
-       "EpoRpJAK2                0.000000e+00                                 \n",
-       "p1EpoRpJAK2              0.000000e+00                                 \n",
-       "p2EpoRpJAK2              0.000000e+00                                 \n",
-       "p12EpoRpJAK2             0.000000e+00                                 \n",
-       "EpoRJAK2_CIS             0.000000e+00                                 \n",
-       "SHP1                     6.437693e+15                                 \n",
-       "SHP1Act                  0.000000e+00                                 \n",
-       "STAT5                    1.921147e+16                                 \n",
-       "pSTAT5                   0.000000e+00                                 \n",
-       "npSTAT5                  0.000000e+00                                 \n",
-       "CISnRNA1                 0.000000e+00                                 \n",
-       "CISnRNA2                 0.000000e+00                                 \n",
-       "CISnRNA3                 0.000000e+00                                 \n",
-       "CISnRNA4                 0.000000e+00                                 \n",
-       "CISnRNA5                 0.000000e+00                                 \n",
-       "CISRNA                   0.000000e+00                                 \n",
-       "CIS                      0.000000e+00                                 \n",
-       "SOCS3nRNA1               0.000000e+00                                 \n",
-       "SOCS3nRNA2               0.000000e+00                                 \n",
-       "SOCS3nRNA3               0.000000e+00                                 \n",
-       "SOCS3nRNA4               0.000000e+00                                 \n",
-       "SOCS3nRNA5               0.000000e+00                                 \n",
-       "SOCS3RNA                 0.000000e+00                                 \n",
-       "SOCS3                    0.000000e+00                                 \n",
-       "Epo                      3.010998e+07                                 \n",
-       "\n",
-       "              concentration  particle_number      rate  particle_number_rate  \\\n",
-       "name                                                                           \n",
-       "EpoRJAK2       3.976220e+00     9.578143e+14 -0.314737         -7.581552e+13   \n",
-       "EpoRpJAK2      0.000000e+00     0.000000e+00  0.314737          7.581552e+13   \n",
-       "p1EpoRpJAK2    0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "p2EpoRpJAK2    0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "p12EpoRpJAK2   0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "EpoRJAK2_CIS   0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "SHP1           2.672510e+01     6.437693e+15  0.000000          0.000000e+00   \n",
-       "SHP1Act        0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "STAT5          7.975350e+01     1.921147e+16  0.000000          0.000000e+00   \n",
-       "pSTAT5         0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "npSTAT5        0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "CISnRNA1       0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "CISnRNA2       0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "CISnRNA3       0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "CISnRNA4       0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "CISnRNA5       0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "CISRNA         0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "CIS            0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "SOCS3nRNA1     0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "SOCS3nRNA2     0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "SOCS3nRNA3     0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "SOCS3nRNA4     0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "SOCS3nRNA5     0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "SOCS3RNA       0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "SOCS3          0.000000e+00     0.000000e+00  0.000000          0.000000e+00   \n",
-       "Epo            1.249970e-07     3.010998e+07  0.000000          0.000000e+00   \n",
-       "\n",
-       "                        key       sbml_id  \n",
-       "name                                       \n",
-       "EpoRJAK2      Metabolite_50      EpoRJAK2  \n",
-       "EpoRpJAK2     Metabolite_51     EpoRpJAK2  \n",
-       "p1EpoRpJAK2   Metabolite_52   p1EpoRpJAK2  \n",
-       "p2EpoRpJAK2   Metabolite_53   p2EpoRpJAK2  \n",
-       "p12EpoRpJAK2  Metabolite_54  p12EpoRpJAK2  \n",
-       "EpoRJAK2_CIS  Metabolite_55  EpoRJAK2_CIS  \n",
-       "SHP1          Metabolite_56          SHP1  \n",
-       "SHP1Act       Metabolite_57       SHP1Act  \n",
-       "STAT5         Metabolite_58         STAT5  \n",
-       "pSTAT5        Metabolite_59        pSTAT5  \n",
-       "npSTAT5       Metabolite_60       npSTAT5  \n",
-       "CISnRNA1      Metabolite_61      CISnRNA1  \n",
-       "CISnRNA2      Metabolite_62      CISnRNA2  \n",
-       "CISnRNA3      Metabolite_63      CISnRNA3  \n",
-       "CISnRNA4      Metabolite_64      CISnRNA4  \n",
-       "CISnRNA5      Metabolite_65      CISnRNA5  \n",
-       "CISRNA        Metabolite_66        CISRNA  \n",
-       "CIS           Metabolite_67           CIS  \n",
-       "SOCS3nRNA1    Metabolite_68    SOCS3nRNA1  \n",
-       "SOCS3nRNA2    Metabolite_69    SOCS3nRNA2  \n",
-       "SOCS3nRNA3    Metabolite_70    SOCS3nRNA3  \n",
-       "SOCS3nRNA4    Metabolite_71    SOCS3nRNA4  \n",
-       "SOCS3nRNA5    Metabolite_72    SOCS3nRNA5  \n",
-       "SOCS3RNA      Metabolite_73      SOCS3RNA  \n",
-       "SOCS3         Metabolite_74         SOCS3  \n",
-       "Epo           Metabolite_75           Epo  "
-      ]
-     },
-     "execution_count": 12,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
-    "from basico import *\n",
-    "from basico import biomodels\n",
-    "\n",
-    "\n",
-    "biomodel_id = 'BIOMD0000000861'\n",
-    "biomodel = load_biomodel(biomodel_id)\n",
-    "get_species(model=biomodel)"
+    "# Uncomment if you wish to introspect the model referred below\n",
+    "# from basico import *\n",
+    "# from basico import biomodels\n",
+    "# \n",
+    "# \n",
+    "# biomodel_id = 'BIOMD0000000861'\n",
+    "# biomodel = load_biomodel(biomodel_id)\n",
+    "# get_species(model=biomodel)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": null,
    "id": "c24594c6e8229e20",
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:28.737875Z",
-     "start_time": "2024-03-04T16:42:28.733747Z"
-    },
     "collapsed": false
    },
-   "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>scheme</th>\n",
-       "      <th>flux</th>\n",
-       "      <th>particle_flux</th>\n",
-       "      <th>function</th>\n",
-       "      <th>key</th>\n",
-       "      <th>sbml_id</th>\n",
-       "      <th>mapping</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",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>reaction_1</th>\n",
-       "      <td>EpoRJAK2 -&gt; EpoRpJAK2;  Epo SOCS3</td>\n",
-       "      <td>0.125895</td>\n",
-       "      <td>7.581552e+13</td>\n",
-       "      <td>Function for reaction_1</td>\n",
-       "      <td>Reaction_48</td>\n",
-       "      <td>reaction_1</td>\n",
-       "      <td>{'Epo': 'Epo', 'EpoRJAK2': 'EpoRJAK2', 'JAK2Ac...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_2</th>\n",
-       "      <td>EpoRpJAK2 -&gt; EpoRJAK2;  SHP1Act</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_2</td>\n",
-       "      <td>Reaction_49</td>\n",
-       "      <td>reaction_2</td>\n",
-       "      <td>{'EpoRpJAK2': 'EpoRpJAK2', 'JAK2EpoRDeaSHP1': ...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_3</th>\n",
-       "      <td>EpoRpJAK2 -&gt; p1EpoRpJAK2;  SOCS3</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_3</td>\n",
-       "      <td>Reaction_50</td>\n",
-       "      <td>reaction_3</td>\n",
-       "      <td>{'EpoRActJAK2': 'EpoRActJAK2', 'EpoRpJAK2': 'E...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_4</th>\n",
-       "      <td>EpoRpJAK2 -&gt; p2EpoRpJAK2;  EpoRJAK2_CIS SOCS3</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_4</td>\n",
-       "      <td>Reaction_51</td>\n",
-       "      <td>reaction_4</td>\n",
-       "      <td>{'EpoRActJAK2': 'EpoRActJAK2', 'EpoRCISInh': '...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_5</th>\n",
-       "      <td>p1EpoRpJAK2 -&gt; p12EpoRpJAK2;  EpoRJAK2_CIS SOCS3</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_5</td>\n",
-       "      <td>Reaction_52</td>\n",
-       "      <td>reaction_5</td>\n",
-       "      <td>{'EpoRActJAK2': 'EpoRActJAK2', 'EpoRCISInh': '...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_6</th>\n",
-       "      <td>p2EpoRpJAK2 -&gt; p12EpoRpJAK2;  SOCS3</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_6</td>\n",
-       "      <td>Reaction_53</td>\n",
-       "      <td>reaction_6</td>\n",
-       "      <td>{'EpoRActJAK2': 'EpoRActJAK2', 'SOCS3': 'SOCS3...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_7</th>\n",
-       "      <td>p1EpoRpJAK2 -&gt; EpoRJAK2;  SHP1Act</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_7</td>\n",
-       "      <td>Reaction_54</td>\n",
-       "      <td>reaction_7</td>\n",
-       "      <td>{'JAK2EpoRDeaSHP1': 'JAK2EpoRDeaSHP1', 'SHP1Ac...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_8</th>\n",
-       "      <td>p2EpoRpJAK2 -&gt; EpoRJAK2;  SHP1Act</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_8</td>\n",
-       "      <td>Reaction_55</td>\n",
-       "      <td>reaction_8</td>\n",
-       "      <td>{'JAK2EpoRDeaSHP1': 'JAK2EpoRDeaSHP1', 'SHP1Ac...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_9</th>\n",
-       "      <td>p12EpoRpJAK2 -&gt; EpoRJAK2;  SHP1Act</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_9</td>\n",
-       "      <td>Reaction_56</td>\n",
-       "      <td>reaction_9</td>\n",
-       "      <td>{'JAK2EpoRDeaSHP1': 'JAK2EpoRDeaSHP1', 'SHP1Ac...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_10</th>\n",
-       "      <td>EpoRJAK2_CIS -&gt; ;  p12EpoRpJAK2 p1EpoRpJAK2</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_10</td>\n",
-       "      <td>Reaction_57</td>\n",
-       "      <td>reaction_10</td>\n",
-       "      <td>{'EpoRCISRemove': 'EpoRCISRemove', 'EpoRJAK2_C...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_11</th>\n",
-       "      <td>SHP1 -&gt; SHP1Act;  EpoRpJAK2 p12EpoRpJAK2 p1Epo...</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_11</td>\n",
-       "      <td>Reaction_58</td>\n",
-       "      <td>reaction_11</td>\n",
-       "      <td>{'EpoRpJAK2': 'EpoRpJAK2', 'SHP1': 'SHP1', 'SH...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_12</th>\n",
-       "      <td>SHP1Act -&gt; SHP1</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Mass action (irreversible)</td>\n",
-       "      <td>Reaction_59</td>\n",
-       "      <td>reaction_12</td>\n",
-       "      <td>{'k1': 'SHP1Dea', 'substrate': 'SHP1Act'}</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_13</th>\n",
-       "      <td>STAT5 -&gt; pSTAT5;  EpoRpJAK2 SOCS3 p12EpoRpJAK2...</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_13</td>\n",
-       "      <td>Reaction_60</td>\n",
-       "      <td>reaction_13</td>\n",
-       "      <td>{'EpoRpJAK2': 'EpoRpJAK2', 'SOCS3': 'SOCS3', '...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_14</th>\n",
-       "      <td>STAT5 -&gt; pSTAT5;  CIS SOCS3 p12EpoRpJAK2 p1Epo...</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_14</td>\n",
-       "      <td>Reaction_61</td>\n",
-       "      <td>reaction_14</td>\n",
-       "      <td>{'CIS': 'CIS', 'CISEqc': 'CISEqc', 'CISInh': '...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_15</th>\n",
-       "      <td>pSTAT5 -&gt; npSTAT5</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_15</td>\n",
-       "      <td>Reaction_62</td>\n",
-       "      <td>reaction_15</td>\n",
-       "      <td>{'STAT5Imp': 'STAT5Imp', 'cyt': 'cyt', 'pSTAT5...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_16</th>\n",
-       "      <td>npSTAT5 -&gt; STAT5</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_16</td>\n",
-       "      <td>Reaction_63</td>\n",
-       "      <td>reaction_16</td>\n",
-       "      <td>{'STAT5Exp': 'STAT5Exp', 'npSTAT5': 'npSTAT5',...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_17</th>\n",
-       "      <td>= CISnRNA1;  npSTAT5</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_17</td>\n",
-       "      <td>Reaction_64</td>\n",
-       "      <td>reaction_17</td>\n",
-       "      <td>{'ActD': 'ActD', 'CISRNAEqc': 'CISRNAEqc', 'CI...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_18</th>\n",
-       "      <td>CISnRNA1 -&gt; CISnRNA2</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Mass action (irreversible)</td>\n",
-       "      <td>Reaction_65</td>\n",
-       "      <td>reaction_18</td>\n",
-       "      <td>{'k1': 'CISRNADelay', 'substrate': 'CISnRNA1'}</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_19</th>\n",
-       "      <td>CISnRNA2 -&gt; CISnRNA3</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Mass action (irreversible)</td>\n",
-       "      <td>Reaction_66</td>\n",
-       "      <td>reaction_19</td>\n",
-       "      <td>{'k1': 'CISRNADelay', 'substrate': 'CISnRNA2'}</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_20</th>\n",
-       "      <td>CISnRNA3 -&gt; CISnRNA4</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Mass action (irreversible)</td>\n",
-       "      <td>Reaction_67</td>\n",
-       "      <td>reaction_20</td>\n",
-       "      <td>{'k1': 'CISRNADelay', 'substrate': 'CISnRNA3'}</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_21</th>\n",
-       "      <td>CISnRNA4 -&gt; CISnRNA5</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Mass action (irreversible)</td>\n",
-       "      <td>Reaction_68</td>\n",
-       "      <td>reaction_21</td>\n",
-       "      <td>{'k1': 'CISRNADelay', 'substrate': 'CISnRNA4'}</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_22</th>\n",
-       "      <td>CISnRNA5 -&gt; CISRNA</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_22</td>\n",
-       "      <td>Reaction_69</td>\n",
-       "      <td>reaction_22</td>\n",
-       "      <td>{'CISRNADelay': 'CISRNADelay', 'CISnRNA5': 'CI...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_23</th>\n",
-       "      <td>CISRNA -&gt;</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Mass action (irreversible)</td>\n",
-       "      <td>Reaction_70</td>\n",
-       "      <td>reaction_23</td>\n",
-       "      <td>{'k1': 'CISRNATurn', 'substrate': 'CISRNA'}</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_24</th>\n",
-       "      <td>-&gt; CIS;  CISRNA</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_24</td>\n",
-       "      <td>Reaction_71</td>\n",
-       "      <td>reaction_24</td>\n",
-       "      <td>{'CISEqc': 'CISEqc', 'CISRNA': 'CISRNA', 'CISR...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_25</th>\n",
-       "      <td>CIS -&gt;</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Mass action (irreversible)</td>\n",
-       "      <td>Reaction_72</td>\n",
-       "      <td>reaction_25</td>\n",
-       "      <td>{'k1': 'CISTurn', 'substrate': 'CIS'}</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_26</th>\n",
-       "      <td>-&gt; CIS</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_26</td>\n",
-       "      <td>Reaction_73</td>\n",
-       "      <td>reaction_26</td>\n",
-       "      <td>{'CISEqc': 'CISEqc', 'CISEqcOE': 'CISEqcOE', '...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_27</th>\n",
-       "      <td>= SOCS3nRNA1;  npSTAT5</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_27</td>\n",
-       "      <td>Reaction_74</td>\n",
-       "      <td>reaction_27</td>\n",
-       "      <td>{'ActD': 'ActD', 'SOCS3RNAEqc': 'SOCS3RNAEqc',...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_28</th>\n",
-       "      <td>SOCS3nRNA1 -&gt; SOCS3nRNA2</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Mass action (irreversible)</td>\n",
-       "      <td>Reaction_75</td>\n",
-       "      <td>reaction_28</td>\n",
-       "      <td>{'k1': 'SOCS3RNADelay', 'substrate': 'SOCS3nRN...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_29</th>\n",
-       "      <td>SOCS3nRNA2 -&gt; SOCS3nRNA3</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Mass action (irreversible)</td>\n",
-       "      <td>Reaction_76</td>\n",
-       "      <td>reaction_29</td>\n",
-       "      <td>{'k1': 'SOCS3RNADelay', 'substrate': 'SOCS3nRN...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_30</th>\n",
-       "      <td>SOCS3nRNA3 -&gt; SOCS3nRNA4</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Mass action (irreversible)</td>\n",
-       "      <td>Reaction_77</td>\n",
-       "      <td>reaction_30</td>\n",
-       "      <td>{'k1': 'SOCS3RNADelay', 'substrate': 'SOCS3nRN...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_31</th>\n",
-       "      <td>SOCS3nRNA4 -&gt; SOCS3nRNA5</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Mass action (irreversible)</td>\n",
-       "      <td>Reaction_78</td>\n",
-       "      <td>reaction_31</td>\n",
-       "      <td>{'k1': 'SOCS3RNADelay', 'substrate': 'SOCS3nRN...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_32</th>\n",
-       "      <td>SOCS3nRNA5 -&gt; SOCS3RNA</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_32</td>\n",
-       "      <td>Reaction_79</td>\n",
-       "      <td>reaction_32</td>\n",
-       "      <td>{'SOCS3RNADelay': 'SOCS3RNADelay', 'SOCS3nRNA5...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_33</th>\n",
-       "      <td>SOCS3RNA -&gt;</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Mass action (irreversible)</td>\n",
-       "      <td>Reaction_80</td>\n",
-       "      <td>reaction_33</td>\n",
-       "      <td>{'k1': 'SOCS3RNATurn', 'substrate': 'SOCS3RNA'}</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_34</th>\n",
-       "      <td>-&gt; SOCS3;  SOCS3RNA</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_34</td>\n",
-       "      <td>Reaction_81</td>\n",
-       "      <td>reaction_34</td>\n",
-       "      <td>{'SOCS3Eqc': 'SOCS3Eqc', 'SOCS3RNA': 'SOCS3RNA...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_35</th>\n",
-       "      <td>SOCS3 -&gt;</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Mass action (irreversible)</td>\n",
-       "      <td>Reaction_82</td>\n",
-       "      <td>reaction_35</td>\n",
-       "      <td>{'k1': 'SOCS3Turn', 'substrate': 'SOCS3'}</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>reaction_36</th>\n",
-       "      <td>-&gt; SOCS3</td>\n",
-       "      <td>0.000000</td>\n",
-       "      <td>0.000000e+00</td>\n",
-       "      <td>Function for reaction_36</td>\n",
-       "      <td>Reaction_83</td>\n",
-       "      <td>reaction_36</td>\n",
-       "      <td>{'SOCS3Eqc': 'SOCS3Eqc', 'SOCS3EqcOE': 'SOCS3E...</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "                                                        scheme      flux  \\\n",
-       "name                                                                       \n",
-       "reaction_1                   EpoRJAK2 -> EpoRpJAK2;  Epo SOCS3  0.125895   \n",
-       "reaction_2                     EpoRpJAK2 -> EpoRJAK2;  SHP1Act  0.000000   \n",
-       "reaction_3                    EpoRpJAK2 -> p1EpoRpJAK2;  SOCS3  0.000000   \n",
-       "reaction_4       EpoRpJAK2 -> p2EpoRpJAK2;  EpoRJAK2_CIS SOCS3  0.000000   \n",
-       "reaction_5    p1EpoRpJAK2 -> p12EpoRpJAK2;  EpoRJAK2_CIS SOCS3  0.000000   \n",
-       "reaction_6                 p2EpoRpJAK2 -> p12EpoRpJAK2;  SOCS3  0.000000   \n",
-       "reaction_7                   p1EpoRpJAK2 -> EpoRJAK2;  SHP1Act  0.000000   \n",
-       "reaction_8                   p2EpoRpJAK2 -> EpoRJAK2;  SHP1Act  0.000000   \n",
-       "reaction_9                  p12EpoRpJAK2 -> EpoRJAK2;  SHP1Act  0.000000   \n",
-       "reaction_10        EpoRJAK2_CIS -> ;  p12EpoRpJAK2 p1EpoRpJAK2  0.000000   \n",
-       "reaction_11  SHP1 -> SHP1Act;  EpoRpJAK2 p12EpoRpJAK2 p1Epo...  0.000000   \n",
-       "reaction_12                                    SHP1Act -> SHP1  0.000000   \n",
-       "reaction_13  STAT5 -> pSTAT5;  EpoRpJAK2 SOCS3 p12EpoRpJAK2...  0.000000   \n",
-       "reaction_14  STAT5 -> pSTAT5;  CIS SOCS3 p12EpoRpJAK2 p1Epo...  0.000000   \n",
-       "reaction_15                                  pSTAT5 -> npSTAT5  0.000000   \n",
-       "reaction_16                                   npSTAT5 -> STAT5  0.000000   \n",
-       "reaction_17                               = CISnRNA1;  npSTAT5  0.000000   \n",
-       "reaction_18                               CISnRNA1 -> CISnRNA2  0.000000   \n",
-       "reaction_19                               CISnRNA2 -> CISnRNA3  0.000000   \n",
-       "reaction_20                               CISnRNA3 -> CISnRNA4  0.000000   \n",
-       "reaction_21                               CISnRNA4 -> CISnRNA5  0.000000   \n",
-       "reaction_22                                 CISnRNA5 -> CISRNA  0.000000   \n",
-       "reaction_23                                         CISRNA ->   0.000000   \n",
-       "reaction_24                                    -> CIS;  CISRNA  0.000000   \n",
-       "reaction_25                                            CIS ->   0.000000   \n",
-       "reaction_26                                             -> CIS  0.000000   \n",
-       "reaction_27                             = SOCS3nRNA1;  npSTAT5  0.000000   \n",
-       "reaction_28                           SOCS3nRNA1 -> SOCS3nRNA2  0.000000   \n",
-       "reaction_29                           SOCS3nRNA2 -> SOCS3nRNA3  0.000000   \n",
-       "reaction_30                           SOCS3nRNA3 -> SOCS3nRNA4  0.000000   \n",
-       "reaction_31                           SOCS3nRNA4 -> SOCS3nRNA5  0.000000   \n",
-       "reaction_32                             SOCS3nRNA5 -> SOCS3RNA  0.000000   \n",
-       "reaction_33                                       SOCS3RNA ->   0.000000   \n",
-       "reaction_34                                -> SOCS3;  SOCS3RNA  0.000000   \n",
-       "reaction_35                                          SOCS3 ->   0.000000   \n",
-       "reaction_36                                           -> SOCS3  0.000000   \n",
-       "\n",
-       "             particle_flux                    function          key  \\\n",
-       "name                                                                  \n",
-       "reaction_1    7.581552e+13     Function for reaction_1  Reaction_48   \n",
-       "reaction_2    0.000000e+00     Function for reaction_2  Reaction_49   \n",
-       "reaction_3    0.000000e+00     Function for reaction_3  Reaction_50   \n",
-       "reaction_4    0.000000e+00     Function for reaction_4  Reaction_51   \n",
-       "reaction_5    0.000000e+00     Function for reaction_5  Reaction_52   \n",
-       "reaction_6    0.000000e+00     Function for reaction_6  Reaction_53   \n",
-       "reaction_7    0.000000e+00     Function for reaction_7  Reaction_54   \n",
-       "reaction_8    0.000000e+00     Function for reaction_8  Reaction_55   \n",
-       "reaction_9    0.000000e+00     Function for reaction_9  Reaction_56   \n",
-       "reaction_10   0.000000e+00    Function for reaction_10  Reaction_57   \n",
-       "reaction_11   0.000000e+00    Function for reaction_11  Reaction_58   \n",
-       "reaction_12   0.000000e+00  Mass action (irreversible)  Reaction_59   \n",
-       "reaction_13   0.000000e+00    Function for reaction_13  Reaction_60   \n",
-       "reaction_14   0.000000e+00    Function for reaction_14  Reaction_61   \n",
-       "reaction_15   0.000000e+00    Function for reaction_15  Reaction_62   \n",
-       "reaction_16   0.000000e+00    Function for reaction_16  Reaction_63   \n",
-       "reaction_17   0.000000e+00    Function for reaction_17  Reaction_64   \n",
-       "reaction_18   0.000000e+00  Mass action (irreversible)  Reaction_65   \n",
-       "reaction_19   0.000000e+00  Mass action (irreversible)  Reaction_66   \n",
-       "reaction_20   0.000000e+00  Mass action (irreversible)  Reaction_67   \n",
-       "reaction_21   0.000000e+00  Mass action (irreversible)  Reaction_68   \n",
-       "reaction_22   0.000000e+00    Function for reaction_22  Reaction_69   \n",
-       "reaction_23   0.000000e+00  Mass action (irreversible)  Reaction_70   \n",
-       "reaction_24   0.000000e+00    Function for reaction_24  Reaction_71   \n",
-       "reaction_25   0.000000e+00  Mass action (irreversible)  Reaction_72   \n",
-       "reaction_26   0.000000e+00    Function for reaction_26  Reaction_73   \n",
-       "reaction_27   0.000000e+00    Function for reaction_27  Reaction_74   \n",
-       "reaction_28   0.000000e+00  Mass action (irreversible)  Reaction_75   \n",
-       "reaction_29   0.000000e+00  Mass action (irreversible)  Reaction_76   \n",
-       "reaction_30   0.000000e+00  Mass action (irreversible)  Reaction_77   \n",
-       "reaction_31   0.000000e+00  Mass action (irreversible)  Reaction_78   \n",
-       "reaction_32   0.000000e+00    Function for reaction_32  Reaction_79   \n",
-       "reaction_33   0.000000e+00  Mass action (irreversible)  Reaction_80   \n",
-       "reaction_34   0.000000e+00    Function for reaction_34  Reaction_81   \n",
-       "reaction_35   0.000000e+00  Mass action (irreversible)  Reaction_82   \n",
-       "reaction_36   0.000000e+00    Function for reaction_36  Reaction_83   \n",
-       "\n",
-       "                 sbml_id                                            mapping  \n",
-       "name                                                                         \n",
-       "reaction_1    reaction_1  {'Epo': 'Epo', 'EpoRJAK2': 'EpoRJAK2', 'JAK2Ac...  \n",
-       "reaction_2    reaction_2  {'EpoRpJAK2': 'EpoRpJAK2', 'JAK2EpoRDeaSHP1': ...  \n",
-       "reaction_3    reaction_3  {'EpoRActJAK2': 'EpoRActJAK2', 'EpoRpJAK2': 'E...  \n",
-       "reaction_4    reaction_4  {'EpoRActJAK2': 'EpoRActJAK2', 'EpoRCISInh': '...  \n",
-       "reaction_5    reaction_5  {'EpoRActJAK2': 'EpoRActJAK2', 'EpoRCISInh': '...  \n",
-       "reaction_6    reaction_6  {'EpoRActJAK2': 'EpoRActJAK2', 'SOCS3': 'SOCS3...  \n",
-       "reaction_7    reaction_7  {'JAK2EpoRDeaSHP1': 'JAK2EpoRDeaSHP1', 'SHP1Ac...  \n",
-       "reaction_8    reaction_8  {'JAK2EpoRDeaSHP1': 'JAK2EpoRDeaSHP1', 'SHP1Ac...  \n",
-       "reaction_9    reaction_9  {'JAK2EpoRDeaSHP1': 'JAK2EpoRDeaSHP1', 'SHP1Ac...  \n",
-       "reaction_10  reaction_10  {'EpoRCISRemove': 'EpoRCISRemove', 'EpoRJAK2_C...  \n",
-       "reaction_11  reaction_11  {'EpoRpJAK2': 'EpoRpJAK2', 'SHP1': 'SHP1', 'SH...  \n",
-       "reaction_12  reaction_12          {'k1': 'SHP1Dea', 'substrate': 'SHP1Act'}  \n",
-       "reaction_13  reaction_13  {'EpoRpJAK2': 'EpoRpJAK2', 'SOCS3': 'SOCS3', '...  \n",
-       "reaction_14  reaction_14  {'CIS': 'CIS', 'CISEqc': 'CISEqc', 'CISInh': '...  \n",
-       "reaction_15  reaction_15  {'STAT5Imp': 'STAT5Imp', 'cyt': 'cyt', 'pSTAT5...  \n",
-       "reaction_16  reaction_16  {'STAT5Exp': 'STAT5Exp', 'npSTAT5': 'npSTAT5',...  \n",
-       "reaction_17  reaction_17  {'ActD': 'ActD', 'CISRNAEqc': 'CISRNAEqc', 'CI...  \n",
-       "reaction_18  reaction_18     {'k1': 'CISRNADelay', 'substrate': 'CISnRNA1'}  \n",
-       "reaction_19  reaction_19     {'k1': 'CISRNADelay', 'substrate': 'CISnRNA2'}  \n",
-       "reaction_20  reaction_20     {'k1': 'CISRNADelay', 'substrate': 'CISnRNA3'}  \n",
-       "reaction_21  reaction_21     {'k1': 'CISRNADelay', 'substrate': 'CISnRNA4'}  \n",
-       "reaction_22  reaction_22  {'CISRNADelay': 'CISRNADelay', 'CISnRNA5': 'CI...  \n",
-       "reaction_23  reaction_23        {'k1': 'CISRNATurn', 'substrate': 'CISRNA'}  \n",
-       "reaction_24  reaction_24  {'CISEqc': 'CISEqc', 'CISRNA': 'CISRNA', 'CISR...  \n",
-       "reaction_25  reaction_25              {'k1': 'CISTurn', 'substrate': 'CIS'}  \n",
-       "reaction_26  reaction_26  {'CISEqc': 'CISEqc', 'CISEqcOE': 'CISEqcOE', '...  \n",
-       "reaction_27  reaction_27  {'ActD': 'ActD', 'SOCS3RNAEqc': 'SOCS3RNAEqc',...  \n",
-       "reaction_28  reaction_28  {'k1': 'SOCS3RNADelay', 'substrate': 'SOCS3nRN...  \n",
-       "reaction_29  reaction_29  {'k1': 'SOCS3RNADelay', 'substrate': 'SOCS3nRN...  \n",
-       "reaction_30  reaction_30  {'k1': 'SOCS3RNADelay', 'substrate': 'SOCS3nRN...  \n",
-       "reaction_31  reaction_31  {'k1': 'SOCS3RNADelay', 'substrate': 'SOCS3nRN...  \n",
-       "reaction_32  reaction_32  {'SOCS3RNADelay': 'SOCS3RNADelay', 'SOCS3nRNA5...  \n",
-       "reaction_33  reaction_33    {'k1': 'SOCS3RNATurn', 'substrate': 'SOCS3RNA'}  \n",
-       "reaction_34  reaction_34  {'SOCS3Eqc': 'SOCS3Eqc', 'SOCS3RNA': 'SOCS3RNA...  \n",
-       "reaction_35  reaction_35          {'k1': 'SOCS3Turn', 'substrate': 'SOCS3'}  \n",
-       "reaction_36  reaction_36  {'SOCS3Eqc': 'SOCS3Eqc', 'SOCS3EqcOE': 'SOCS3E...  "
-      ]
-     },
-     "execution_count": 13,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
-    "reaction_names = get_reactions(model=biomodel)\n",
-    "\n",
-    "reaction_names"
+    "# reaction_names = get_reactions(model=biomodel)\n",
+    "# \n",
+    "# reaction_names"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": null,
    "id": "454db50d61220bc5",
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:28.738709Z",
-     "start_time": "2024-03-04T16:42:28.736620Z"
-    },
     "collapsed": false
    },
    "outputs": [],
@@ -2218,13 +335,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": null,
    "id": "bd6781fe4a749c29",
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:28.742401Z",
-     "start_time": "2024-03-04T16:42:28.739543Z"
-    },
     "collapsed": false
    },
    "outputs": [],
@@ -2236,73 +349,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": null,
    "id": "e414174a2d6d331b",
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:32.179350Z",
-     "start_time": "2024-03-04T16:42:32.175949Z"
-    },
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "{ 'global_parameter_changes': [],\n",
-      "  'reaction_changes': [ { 'parameter_changes': [ { 'parameter_name': 'EpoRpRJAK2',\n",
-      "                                                   'value': 21312.2},\n",
-      "                                                 { 'parameter_name': 'EpoRJAK2',\n",
-      "                                                   'value': 21312.2}],\n",
-      "                          'reaction_name': 'reaction_1',\n",
-      "                          'reaction_scheme': None},\n",
-      "                        { 'parameter_changes': [],\n",
-      "                          'reaction_name': 'reaction_11',\n",
-      "                          'reaction_scheme': 'A + B -> C'}],\n",
-      "  'species_changes': []}\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "pp(biomodel_process_changes.model_dump())"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": null,
    "id": "9de88bc52fb9a164",
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:42:32.876207Z",
-     "start_time": "2024-03-04T16:42:32.872898Z"
-    },
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "{ 'model_changes': { 'global_parameter_changes': [],\n",
-      "                     'reaction_changes': [ { 'parameter_changes': [ { 'parameter_name': 'EpoRpRJAK2',\n",
-      "                                                                      'value': 21312.2},\n",
-      "                                                                    { 'parameter_name': 'EpoRJAK2',\n",
-      "                                                                      'value': 21312.2}],\n",
-      "                                             'reaction_name': 'reaction_1',\n",
-      "                                             'reaction_scheme': None},\n",
-      "                                           { 'parameter_changes': [],\n",
-      "                                             'reaction_name': 'reaction_11',\n",
-      "                                             'reaction_scheme': 'A + B -> C'}],\n",
-      "                     'species_changes': []},\n",
-      "  'model_id': 'BIOMD0000000861',\n",
-      "  'model_language': 'sbml',\n",
-      "  'model_name': 'composite_from_biomodel',\n",
-      "  'model_source': {'value': 'BIOMD0000000861'},\n",
-      "  'model_units': None}\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "biomodel_process_model = Model(\n",
     "    model_id=biomodel_id,\n",
@@ -2316,45 +380,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": null,
    "id": "25ba11c1e1e75f94",
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:43:56.030421Z",
-     "start_time": "2024-03-04T16:43:56.025326Z"
-    },
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "{ 'method': 'directMethod',\n",
-      "  'model': { 'model_changes': { 'global_parameter_changes': [],\n",
-      "                                'reaction_changes': [ { 'parameter_changes': [ { 'parameter_name': 'EpoRpRJAK2',\n",
-      "                                                                                 'value': 21312.2},\n",
-      "                                                                               { 'parameter_name': 'EpoRJAK2',\n",
-      "                                                                                 'value': 21312.2}],\n",
-      "                                                        'reaction_name': 'reaction_1',\n",
-      "                                                        'reaction_scheme': None},\n",
-      "                                                      { 'parameter_changes': [],\n",
-      "                                                        'reaction_name': 'reaction_11',\n",
-      "                                                        'reaction_scheme': 'A '\n",
-      "                                                                           '+ '\n",
-      "                                                                           'B '\n",
-      "                                                                           '-> '\n",
-      "                                                                           'C'}],\n",
-      "                                'species_changes': []},\n",
-      "             'model_id': 'BIOMD0000000861',\n",
-      "             'model_language': 'sbml',\n",
-      "             'model_name': 'composite_from_biomodel',\n",
-      "             'model_source': {'value': 'BIOMD0000000861'},\n",
-      "             'model_units': None},\n",
-      "  'process_name': 'copasi_process_from_biomodel'}\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "biomodel_process_config = CopasiProcessConfigSchema(\n",
     "    process_name='copasi_process_from_biomodel',\n",
@@ -2378,22 +409,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": null,
    "id": "4c3f073b10e2dcc0",
    "metadata": {
-    "ExecuteTime": {
-     "end_time": "2024-03-04T16:47:41.077497Z",
-     "start_time": "2024-03-04T16:47:41.072238Z"
-    },
     "collapsed": false
    },
    "outputs": [],
    "source": [
-    "# b[biomodel_process_config.process_name].add_process(\n",
-    "#     name='CopasiProcess',\n",
-    "#     model=biomodel_process_config.model,\n",
-    "#     method=biomodel_process_config.method\n",
-    "# )"
+    "b[biomodel_process_config.process_name].add_process(\n",
+    "    name='CopasiProcess',\n",
+    "    model=biomodel_process_config.model,\n",
+    "    method=biomodel_process_config.method\n",
+    ")"
    ]
   },
   {