diff --git a/docs/source/examples/JN_02_analysis.ipynb b/docs/source/examples/JN_02_analysis.ipynb
index 70a3a23..dc15f26 100644
--- a/docs/source/examples/JN_02_analysis.ipynb
+++ b/docs/source/examples/JN_02_analysis.ipynb
@@ -24,9 +24,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Set parameter Username\n",
+      "Academic license - for non-commercial use only - expires 2022-07-13\n"
+     ]
+    }
+   ],
    "source": [
     "import cobra\n",
     "import straindesign as sd\n",
@@ -126,14 +135,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "The sum of fluxes of the regular FBA: 2508.293334194643is usually higher than of the parsimoniuos FBA: 518.4220855176071\n"
+      "The sum of fluxes of the regular FBA: 2508.293334194643 is usually higher than of the parsimoniuos FBA: 518.4220855176071\n"
      ]
     }
    ],
@@ -153,7 +162,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -182,7 +191,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -191,7 +200,7 @@
        "{'cplex', 'glpk', 'gurobi', 'scip'}"
       ]
      },
-     "execution_count": 17,
+     "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -209,7 +218,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -235,14 +244,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "When the model's solver is '<optlang.gurobi_interface.Configuration object at 0x000001C9B8A5A970>', StrainDesign selects gurobi.\n"
+      "When the model's solver is '<optlang.gurobi_interface.Configuration object at 0x0000027BA3654160>', StrainDesign selects gurobi.\n"
      ]
     }
    ],
@@ -259,7 +268,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
@@ -290,7 +299,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
@@ -328,7 +337,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
@@ -373,15 +382,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 68,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Minimum yield (FBA): 0.031965425062067315.\n",
-      "Minimum yield (yOpt): 0.03629426243040193.\n"
+     "ename": "AttributeError",
+     "evalue": "'DataFrame' object has no attribute 'fluxes'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[1;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
+      "\u001b[1;32mc:\\Users\\Philipp\\Documents\\Python\\straindesign\\docs\\source\\examples\\JN_02_analysis.ipynb Cell 29'\u001b[0m in \u001b[0;36m<cell line: 6>\u001b[1;34m()\u001b[0m\n\u001b[0;32m      <a href='vscode-notebook-cell:/c%3A/Users/Philipp/Documents/Python/straindesign/docs/source/examples/JN_02_analysis.ipynb#ch0000028?line=2'>3</a>\u001b[0m constraint \u001b[39m=\u001b[39m \u001b[39m'\u001b[39m\u001b[39m-EX_o2_e <= 3\u001b[39m\u001b[39m'\u001b[39m\n\u001b[0;32m      <a href='vscode-notebook-cell:/c%3A/Users/Philipp/Documents/Python/straindesign/docs/source/examples/JN_02_analysis.ipynb#ch0000028?line=4'>5</a>\u001b[0m sol_fba \u001b[39m=\u001b[39m sd\u001b[39m.\u001b[39mfba(model,obj\u001b[39m=\u001b[39m\u001b[39m'\u001b[39m\u001b[39mBIOMASS_Ecoli_core_w_GAM\u001b[39m\u001b[39m'\u001b[39m,obj_sense\u001b[39m=\u001b[39m\u001b[39m'\u001b[39m\u001b[39mmaximize\u001b[39m\u001b[39m'\u001b[39m,constraints\u001b[39m=\u001b[39mconstraint)\n\u001b[1;32m----> <a href='vscode-notebook-cell:/c%3A/Users/Philipp/Documents/Python/straindesign/docs/source/examples/JN_02_analysis.ipynb#ch0000028?line=5'>6</a>\u001b[0m fba_yield \u001b[39m=\u001b[39m solution\u001b[39m.\u001b[39;49mfluxes[numerator] \u001b[39m/\u001b[39m \u001b[39m-\u001b[39msolution\u001b[39m.\u001b[39mfluxes[\u001b[39m'\u001b[39m\u001b[39mEX_glc__D_e\u001b[39m\u001b[39m'\u001b[39m] \n\u001b[0;32m      <a href='vscode-notebook-cell:/c%3A/Users/Philipp/Documents/Python/straindesign/docs/source/examples/JN_02_analysis.ipynb#ch0000028?line=7'>8</a>\u001b[0m sol_yopt \u001b[39m=\u001b[39m sd\u001b[39m.\u001b[39myopt(model,obj_num\u001b[39m=\u001b[39mnumerator,obj_den\u001b[39m=\u001b[39mdenominator,obj_sense\u001b[39m=\u001b[39m\u001b[39m'\u001b[39m\u001b[39mmaximize\u001b[39m\u001b[39m'\u001b[39m,constraints\u001b[39m=\u001b[39mconstraint)\n\u001b[0;32m      <a href='vscode-notebook-cell:/c%3A/Users/Philipp/Documents/Python/straindesign/docs/source/examples/JN_02_analysis.ipynb#ch0000028?line=8'>9</a>\u001b[0m yopt_yield \u001b[39m=\u001b[39m sol_yopt\u001b[39m.\u001b[39mobjective_value\n",
+      "File \u001b[1;32mc:\\Users\\Philipp\\anaconda3\\envs\\cnapy-dev\\lib\\site-packages\\pandas\\core\\generic.py:5575\u001b[0m, in \u001b[0;36mNDFrame.__getattr__\u001b[1;34m(self, name)\u001b[0m\n\u001b[0;32m   <a href='file:///c%3A/Users/Philipp/anaconda3/envs/cnapy-dev/lib/site-packages/pandas/core/generic.py?line=5567'>5568</a>\u001b[0m \u001b[39mif\u001b[39;00m (\n\u001b[0;32m   <a href='file:///c%3A/Users/Philipp/anaconda3/envs/cnapy-dev/lib/site-packages/pandas/core/generic.py?line=5568'>5569</a>\u001b[0m     name \u001b[39mnot\u001b[39;00m \u001b[39min\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_internal_names_set\n\u001b[0;32m   <a href='file:///c%3A/Users/Philipp/anaconda3/envs/cnapy-dev/lib/site-packages/pandas/core/generic.py?line=5569'>5570</a>\u001b[0m     \u001b[39mand\u001b[39;00m name \u001b[39mnot\u001b[39;00m \u001b[39min\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_metadata\n\u001b[0;32m   <a href='file:///c%3A/Users/Philipp/anaconda3/envs/cnapy-dev/lib/site-packages/pandas/core/generic.py?line=5570'>5571</a>\u001b[0m     \u001b[39mand\u001b[39;00m name \u001b[39mnot\u001b[39;00m \u001b[39min\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_accessors\n\u001b[0;32m   <a href='file:///c%3A/Users/Philipp/anaconda3/envs/cnapy-dev/lib/site-packages/pandas/core/generic.py?line=5571'>5572</a>\u001b[0m     \u001b[39mand\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_info_axis\u001b[39m.\u001b[39m_can_hold_identifiers_and_holds_name(name)\n\u001b[0;32m   <a href='file:///c%3A/Users/Philipp/anaconda3/envs/cnapy-dev/lib/site-packages/pandas/core/generic.py?line=5572'>5573</a>\u001b[0m ):\n\u001b[0;32m   <a href='file:///c%3A/Users/Philipp/anaconda3/envs/cnapy-dev/lib/site-packages/pandas/core/generic.py?line=5573'>5574</a>\u001b[0m     \u001b[39mreturn\u001b[39;00m \u001b[39mself\u001b[39m[name]\n\u001b[1;32m-> <a href='file:///c%3A/Users/Philipp/anaconda3/envs/cnapy-dev/lib/site-packages/pandas/core/generic.py?line=5574'>5575</a>\u001b[0m \u001b[39mreturn\u001b[39;00m \u001b[39mobject\u001b[39;49m\u001b[39m.\u001b[39;49m\u001b[39m__getattribute__\u001b[39;49m(\u001b[39mself\u001b[39;49m, name)\n",
+      "\u001b[1;31mAttributeError\u001b[0m: 'DataFrame' object has no attribute 'fluxes'"
      ]
     }
    ],
@@ -434,11 +447,11 @@
     "\\begin{array}{l c}\n",
     "\t\\text{maximize} \\; & y  \\\\\\\\\n",
     "\t\\text{subject to} &\n",
-    "\t\\begin{bmatrix*}[r]\n",
+    "\t\\begin{bmatrix}\n",
     "\t\t\\mathbf{A~} &  \\mathbf{-b} &  \\mathbf{0} \\\\\n",
     "\t\t\\mathbf{d}^\\intercal &  0 \t\t  &  0 \\\\\n",
     "\t\t\\mathbf{c}^\\intercal &  0  \t\t  &  -1 \\\\\n",
-    "\t\\end{bmatrix*} \n",
+    "\t\\end{bmatrix} \n",
     "\t\\begin{bmatrix}\\mathbf{\\tilde{x}} \\\\ e \\\\ y \\end{bmatrix} \n",
     "\t\\begin{matrix} \\le  \\\\ = \\\\ = \\end{matrix} \n",
     "\t\\begin{bmatrix}\\mathbf{0} \\\\ 1 \\\\ 0 \\end{bmatrix}\\\\\\\\\n",