Biomass data - soy.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from cobra import io\n",
    "from cobra.core import Metabolite\n",
    "from cobra import flux_analysis\n",
    "from Functions import *\n",
    "from IPython import display\n",
    "import logging\n",
    "logging.basicConfig()\n",
    "logger = logging.getLogger('logger')\n",
    "\n",
    "#import sbml file\n",
    "fname = \"/home/sanu/Documents/Scripts/git/plantcoremetabolism-model/PlantCoreMetabolism_v1_3_0.xml\"\n",
    "model = io.sbml.read_sbml_model(fname)\n",
    "display.clear_output()\n",
    "\n",
    "from sweetlovegroup.transform import fixModelCompatibilityIssueCobra015\n",
    "model = fixModelCompatibilityIssueCobra015(model,fname)\n",
    "\n",
    "\n",
    "#change Biomass_tx to Protein_biomass\n",
    "rxn = model.reactions.get_by_id(\"Biomass_tx\")\n",
    "rxn.id = \"Protein_biomass_tx\"\n",
    "for met in [\"K_b\",\"Ca_b\",\"Mg_b\"]:\n",
    "    met  = model.metabolites.get_by_id(met)\n",
    "    coeff = rxn.metabolites.get(met)\n",
    "    rxn.add_metabolites({met:-1*coeff})\n",
    "met = Metabolite(\"Protein_b\",name=\"Protein_biomass\")\n",
    "formula_dict = rxn.check_mass_balance()\n",
    "met.formula = \"\".join([atom+str(formula_dict[atom]*-1) for atom in formula_dict.keys() if atom != \"charge\"])\n",
    "met.charge = formula_dict[\"charge\"]*-1\n",
    "rxn.add_metabolites({met:1})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "biomass = pd.DataFrame(data={\"\":[\"sSUCROSE_b\",\"GLC_c\",\"FRU_c\",\"Starch_b\",\"Cellulose_b\",\"Xylan_b\",\n",
    "                                 \"L_PHOSPHATIDATE_p\",\"PHOSPHATIDYL_CHOLINE_r\",\n",
    "                                 \"L_1_PHOSPHATIDYL_ETHANOLAMINE_r\",\"DIACYLGLYCEROL_p\",\n",
    "                                 \"Galactosyl_galactosyl_diacyl_glycerols_p\",\n",
    "                                 \"D_Galactosyl_12_diacyl_glycerols_p\",\"2_Lysophosphatidylcholines_r\",\n",
    "                                 \"Lysophosphatidylglycerols_r\",\"Triacylglycerols_p\",\n",
    "                                 \"L_1_PHOSPHATIDYL_GLYCEROL_p\",\"L_1_phosphatidyl_inositols_r\",\n",
    "                                 \"SULFOQUINOVOSYLDIACYLGLYCEROL_p\",\"Protein_b\",\n",
    "                                 \"sMAL_b\",\"sCIT_b\",\"sFUM_b\",\"ARG_c\",\"HIS_c\",\"LYS_c\",\"sASP_b\",\n",
    "                                 \"sGLU_b\",\"sSER_b\",\"THR_c\",\"ASN_c\",\"sGLN_b\",\"CYS_c\",\n",
    "                                 \"GLY_c\",\"PRO_c\",\"sALA_b\",\"VAL_c\",\"ILE_c\",\"LEU_c\",\n",
    "                                 \"MET_c\",\"PHE_c\",\"TYR_c\",\"TRP_c\",\"sGABA_b\",\"PALMITATE_p\",\n",
    "                                 \"CPD_9245_p\",\"CPD_17412_p\",\"CPD_17291\",\"STEARIC_ACID_p\",\n",
    "                                 \"OLEATE_CPD_p\",\"Octadecadienoate_p\",\"LINOLENIC_ACID_p\",\n",
    "                                 \"ARACHIDIC_ACID_p\",\"CPD_16709\",\"DOCOSANOATE_p\"],\n",
    "                             \"leaf\":[0.0]*54,\"stem\":[0.0]*54,\"root\":[0.0]*54,\"seed\":[0.0]*54,},dtype=\"float64\")\n",
    "biomass = biomass.set_index(\"\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "cobra/core/metabolite.py:104 \u001b[1;31mUserWarning\u001b[0m: 17.2020450391 is not an integer (in formula C17.2020450391H25.9492553613O5.7497158698N4.9536245179S0.1420323181)\n",
      "cobra/core/metabolite.py:104 \u001b[1;31mUserWarning\u001b[0m: 25.9492553613 is not an integer (in formula C17.2020450391H25.9492553613O5.7497158698N4.9536245179S0.1420323181)\n",
      "cobra/core/metabolite.py:104 \u001b[1;31mUserWarning\u001b[0m: 5.7497158698 is not an integer (in formula C17.2020450391H25.9492553613O5.7497158698N4.9536245179S0.1420323181)\n",
      "cobra/core/metabolite.py:104 \u001b[1;31mUserWarning\u001b[0m: 4.9536245179 is not an integer (in formula C17.2020450391H25.9492553613O5.7497158698N4.9536245179S0.1420323181)\n",
      "cobra/core/metabolite.py:104 \u001b[1;31mUserWarning\u001b[0m: 0.1420323181 is not an integer (in formula C17.2020450391H25.9492553613O5.7497158698N4.9536245179S0.1420323181)\n"
     ]
    }
   ],
   "source": [
    "proteinMW = model.metabolites.get_by_id(\"Protein_b\").formula_weight"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Mature leaf"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Extract CO2 assimilation rate for PPFD = 600 umol/m2/s between 11:00 and 13:00h from Liu et al 2004, Figure 3\n",
    "\n",
    "<img src=\"references/Screenshot_20190717_132513.png\" height=50% width=50%>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>DAA</th>\n",
       "      <th>Photosynthesis (umol/m2/s)</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>-10.963829</td>\n",
       "      <td>18.421053</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>-9.928693</td>\n",
       "      <td>18.239564</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>-9.025998</td>\n",
       "      <td>14.646098</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>-7.992005</td>\n",
       "      <td>15.989111</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>-6.986978</td>\n",
       "      <td>15.952813</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>-4.054328</td>\n",
       "      <td>25.753176</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>-3.051180</td>\n",
       "      <td>28.221416</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>-2.044328</td>\n",
       "      <td>25.753176</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>-1.020354</td>\n",
       "      <td>20.453721</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>2.906652</td>\n",
       "      <td>24.446461</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>3.945653</td>\n",
       "      <td>19.110708</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>5.866279</td>\n",
       "      <td>18.275862</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>6.865835</td>\n",
       "      <td>25.535390</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>9.802323</td>\n",
       "      <td>30.217786</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          DAA  Photosynthesis (umol/m2/s)\n",
       "0  -10.963829                   18.421053\n",
       "1   -9.928693                   18.239564\n",
       "2   -9.025998                   14.646098\n",
       "3   -7.992005                   15.989111\n",
       "4   -6.986978                   15.952813\n",
       "5   -4.054328                   25.753176\n",
       "6   -3.051180                   28.221416\n",
       "7   -2.044328                   25.753176\n",
       "8   -1.020354                   20.453721\n",
       "9    2.906652                   24.446461\n",
       "10   3.945653                   19.110708\n",
       "11   5.866279                   18.275862\n",
       "12   6.865835                   25.535390\n",
       "13   9.802323                   30.217786"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_matureleaf_data1 = pd.DataFrame(data={\"DAA\":[-10.9638294010889,-9.92869328493648,\n",
    "                                               -9.02599818511797,-7.9920054446461,\n",
    "                                               -6.98697822141561,-4.05432849364791,\n",
    "                                               -3.05117967332123,-2.04432849364791,\n",
    "                                               -1.02035390199637,2.90665154264973,\n",
    "                                               3.94565335753176,5.86627949183303,\n",
    "                                               6.86583484573503,9.80232304900181],\n",
    "                                        \"Photosynthesis (umol/m2/s)\":[18.4210526315789,18.2395644283121,\n",
    "                                                                      14.6460980036298,15.989110707804,\n",
    "                                                                      15.9528130671506,25.7531760435572,\n",
    "                                                                      28.2214156079855,25.7531760435572,\n",
    "                                                                      20.4537205081669,24.4464609800363,\n",
    "                                                                      19.1107078039927,18.2758620689655,\n",
    "                                                                      25.535390199637,30.2177858439201]})\n",
    "df_matureleaf_data1"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Extract CO2 assimilation rate for PPFD = 1000 µmol m−2 s−1 from Figure 1 of Weston et al 2011\n",
    "\n",
    "<img src=\"references/Screenshot_20190924_144100.png\" height=50% width=50%>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Leaf temperature (C)</th>\n",
       "      <th>Photosynthesis (umol/m2/s)</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>24.963235</td>\n",
       "      <td>18.910515</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>28.088235</td>\n",
       "      <td>22.845700</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>30.036765</td>\n",
       "      <td>23.573145</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>32.169118</td>\n",
       "      <td>25.347142</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>35.294118</td>\n",
       "      <td>25.948994</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>38.272059</td>\n",
       "      <td>24.262623</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>40.036765</td>\n",
       "      <td>21.525215</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>41.985294</td>\n",
       "      <td>17.546777</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   Leaf temperature (C)  Photosynthesis (umol/m2/s)\n",
       "0             24.963235                   18.910515\n",
       "1             28.088235                   22.845700\n",
       "2             30.036765                   23.573145\n",
       "3             32.169118                   25.347142\n",
       "4             35.294118                   25.948994\n",
       "5             38.272059                   24.262623\n",
       "6             40.036765                   21.525215\n",
       "7             41.985294                   17.546777"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_matureleaf_data2 = pd.DataFrame(data={\"Leaf temperature (C)\":[24.9632352941176,28.0882352941176,\n",
    "                                                                 30.0367647058823,32.1691176470588,\n",
    "                                                                 35.2941176470588,38.2720588235294,\n",
    "                                                                 40.0367647058824,41.9852941176471],\n",
    "                                        \"Photosynthesis (umol/m2/s)\":[18.9105151864667,22.8457003716519,\n",
    "                                                                      23.5731449442522,25.3471421248238,\n",
    "                                                                      25.9489939766756,24.2626233499936,\n",
    "                                                                      21.5252146610278,17.5467768806869]})\n",
    "df_matureleaf_data2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Dark respiration (umol/m2/s)</th>\n",
       "      <th>Leaf temperature (C)</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0.662433</td>\n",
       "      <td>20.110294</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0.965304</td>\n",
       "      <td>24.926471</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1.580246</td>\n",
       "      <td>30.183824</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>2.506589</td>\n",
       "      <td>35.110294</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>2.757194</td>\n",
       "      <td>39.558824</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   Dark respiration (umol/m2/s)  Leaf temperature (C)\n",
       "0                      0.662433             20.110294\n",
       "1                      0.965304             24.926471\n",
       "2                      1.580246             30.183824\n",
       "3                      2.506589             35.110294\n",
       "4                      2.757194             39.558824"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_matureleaf_data3 = pd.DataFrame(data={\"Leaf temperature (C)\":[20.1102941176471,24.9264705882353,\n",
    "                                                                 30.1838235294118,35.1102941176471,\n",
    "                                                                 39.5588235294118],\n",
    "                                        \"Dark respiration (umol/m2/s)\":[0.662433155080194,0.965304303539575,\n",
    "                                                                      1.58024573465748,2.50658899923604,\n",
    "                                                                      2.75719378660553]})\n",
    "df_matureleaf_data3"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Extract diurnal starch, sucrose, hemicellulose and simple sugar content from Clements 1930, Figure 6, 9, 13 and 14. Based on Figure 1 and 2, dawn = 8am and dusk = 8pm\n",
    "\n",
    "<img src=\"references/Screenshot_20190717_161155.png\" height=50% width=50%>\n",
    "\n",
    "<img src=\"references/Screenshot_20190717_160304.png\" height=50% width=50%>\n",
    "\n",
    "<img src=\"references/Screenshot_20190717_161259.png\" height=50% width=50%>\n",
    "\n",
    "<img src=\"references/Screenshot_20190717_160242.png\" height=50% width=50%>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>hemicellulose_dawn (g/100gFW)</th>\n",
       "      <th>hemicellulose_dusk (g/100gFW)</th>\n",
       "      <th>simple sugars_dawn (g/100gFW)</th>\n",
       "      <th>simple sugars_dusk (g/100gFW)</th>\n",
       "      <th>starch_dawn (g/100gFW)</th>\n",
       "      <th>starch_dusk (g/100gFW)</th>\n",
       "      <th>sucrose_dawn (g/100gFW)</th>\n",
       "      <th>sucrose_dusk (g/100gFW)</th>\n",
       "      <th>Δstarch</th>\n",
       "      <th>Δhemicellulose</th>\n",
       "      <th>Δsimple sugars</th>\n",
       "      <th>Δsucrose</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Series</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>1</th>\n",
       "      <td>1.089463</td>\n",
       "      <td>1.089463</td>\n",
       "      <td>0.271941</td>\n",
       "      <td>0.032023</td>\n",
       "      <td>0.424568</td>\n",
       "      <td>1.328468</td>\n",
       "      <td>0.271941</td>\n",
       "      <td>0.460078</td>\n",
       "      <td>0.903900</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>-0.239919</td>\n",
       "      <td>0.188136</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1.892274</td>\n",
       "      <td>0.663310</td>\n",
       "      <td>0.650125</td>\n",
       "      <td>0.353374</td>\n",
       "      <td>0.497429</td>\n",
       "      <td>1.600012</td>\n",
       "      <td>0.454127</td>\n",
       "      <td>0.187004</td>\n",
       "      <td>1.102582</td>\n",
       "      <td>-1.228963</td>\n",
       "      <td>-0.296751</td>\n",
       "      <td>-0.267123</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.861645</td>\n",
       "      <td>0.951069</td>\n",
       "      <td>0.568619</td>\n",
       "      <td>0.413878</td>\n",
       "      <td>0.889538</td>\n",
       "      <td>2.625428</td>\n",
       "      <td>0.097705</td>\n",
       "      <td>0.396437</td>\n",
       "      <td>1.735890</td>\n",
       "      <td>0.089424</td>\n",
       "      <td>-0.154741</td>\n",
       "      <td>0.298732</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1.122133</td>\n",
       "      <td>1.072162</td>\n",
       "      <td>0.553381</td>\n",
       "      <td>0.389194</td>\n",
       "      <td>1.252666</td>\n",
       "      <td>1.097803</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.142069</td>\n",
       "      <td>-0.154863</td>\n",
       "      <td>-0.049971</td>\n",
       "      <td>-0.164187</td>\n",
       "      <td>0.142069</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        hemicellulose_dawn (g/100gFW)  hemicellulose_dusk (g/100gFW)  \\\n",
       "Series                                                                 \n",
       "1                            1.089463                       1.089463   \n",
       "2                            1.892274                       0.663310   \n",
       "3                            0.861645                       0.951069   \n",
       "4                            1.122133                       1.072162   \n",
       "\n",
       "        simple sugars_dawn (g/100gFW)  simple sugars_dusk (g/100gFW)  \\\n",
       "Series                                                                 \n",
       "1                            0.271941                       0.032023   \n",
       "2                            0.650125                       0.353374   \n",
       "3                            0.568619                       0.413878   \n",
       "4                            0.553381                       0.389194   \n",
       "\n",
       "        starch_dawn (g/100gFW)  starch_dusk (g/100gFW)  \\\n",
       "Series                                                   \n",
       "1                     0.424568                1.328468   \n",
       "2                     0.497429                1.600012   \n",
       "3                     0.889538                2.625428   \n",
       "4                     1.252666                1.097803   \n",
       "\n",
       "        sucrose_dawn (g/100gFW)  sucrose_dusk (g/100gFW)   Δstarch  \\\n",
       "Series                                                               \n",
       "1                      0.271941                 0.460078  0.903900   \n",
       "2                      0.454127                 0.187004  1.102582   \n",
       "3                      0.097705                 0.396437  1.735890   \n",
       "4                      0.000000                 0.142069 -0.154863   \n",
       "\n",
       "        Δhemicellulose  Δsimple sugars  Δsucrose  \n",
       "Series                                            \n",
       "1             0.000000       -0.239919  0.188136  \n",
       "2            -1.228963       -0.296751 -0.267123  \n",
       "3             0.089424       -0.154741  0.298732  \n",
       "4            -0.049971       -0.164187  0.142069  "
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_matureleaf_content_1 = pd.DataFrame(data={\"Series\":[1,2,3,4],\n",
    "                                           \"starch_dawn (g/100gFW)\":[0.4245676464308603,0.4974291547005305,\n",
    "                                                                     0.8895379007845832,1.2526663271935523],\n",
    "                                           \"hemicellulose_dawn (g/100gFW)\":[1.089463383389083,\n",
    "                                                                            1.8922736237500428,\n",
    "                                                                            0.8616451473404596,\n",
    "                                                                            1.1221330617548415],\n",
    "                                           \"simple sugars_dawn (g/100gFW)\":[0.2719414988257076,\n",
    "                                                                            0.6501251398452184,\n",
    "                                                                            0.5686189976083096,\n",
    "                                                                            0.5533809766290336],\n",
    "                                           \"sucrose_dawn (g/100gFW)\":[0.2719414988257076,0.454127308166961,\n",
    "                                                                      0.09770538968660913,0],\n",
    "                                           \"starch_dusk (g/100gFW)\":[1.3284677247171013,1.600011533626287,\n",
    "                                                                     2.6254282537133005,1.0978029358571406],\n",
    "                                           \"hemicellulose_dusk (g/100gFW)\":[1.089463383389083,\n",
    "                                                                            0.6633103814170216,\n",
    "                                                                            0.9510687588805857,\n",
    "                                                                            1.0721624730031074],\n",
    "                                           \"simple sugars_dusk (g/100gFW)\":[0.03202263184115184,\n",
    "                                                                            0.35337416237039254,\n",
    "                                                                            0.4138784209550903,\n",
    "                                                                            0.3891937806184267],\n",
    "                                           \"sucrose_dusk (g/100gFW)\":[0.46007757454985465,0.18700390989930638,\n",
    "                                                                      0.3964371762172485,0.14206905936682546]})\n",
    "df_matureleaf_content_1.set_index(\"Series\",drop=True,inplace=True)\n",
    "df_matureleaf_content_1[\"Δstarch\"] = df_matureleaf_content_1[\"starch_dusk (g/100gFW)\"]- \\\n",
    "                                                        df_matureleaf_content_1[\"starch_dawn (g/100gFW)\"]\n",
    "df_matureleaf_content_1[\"Δhemicellulose\"] = df_matureleaf_content_1[\"hemicellulose_dusk (g/100gFW)\"]- \\\n",
    "                                                        df_matureleaf_content_1[\"hemicellulose_dawn (g/100gFW)\"]\n",
    "df_matureleaf_content_1[\"Δsimple sugars\"] = df_matureleaf_content_1[\"simple sugars_dusk (g/100gFW)\"]- \\\n",
    "                                                        df_matureleaf_content_1[\"simple sugars_dawn (g/100gFW)\"]\n",
    "df_matureleaf_content_1[\"Δsucrose\"] = df_matureleaf_content_1[\"sucrose_dusk (g/100gFW)\"]- \\\n",
    "                                                        df_matureleaf_content_1[\"sucrose_dawn (g/100gFW)\"]\n",
    "df_matureleaf_content_1"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Series 3 ignored because of diurnal fluctuations in metabolite levels were not observed, calculate average from remaining data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>avg. Δsimple sugars (g/100gFW)</th>\n",
       "      <th>avg. Δstarch (%)</th>\n",
       "      <th>avg. Δstarch (g/100gFW)</th>\n",
       "      <th>avg. Δsucrose (%)</th>\n",
       "      <th>avg. Δsucrose (g/100gFW)</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>-0.213899</td>\n",
       "      <td>47.240852</td>\n",
       "      <td>0.896877</td>\n",
       "      <td>18.350658</td>\n",
       "      <td>0.090453</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   avg. Δsimple sugars (g/100gFW)  avg. Δstarch (%)  avg. Δstarch (g/100gFW)  \\\n",
       "0                       -0.213899         47.240852                 0.896877   \n",
       "\n",
       "   avg. Δsucrose (%)  avg. Δsucrose (g/100gFW)  \n",
       "0          18.350658                  0.090453  "
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_matureleaf_content_1_std = pd.DataFrame(data={\"avg. Δstarch (g/100gFW)\":\n",
    "                                                 [find_average(df_matureleaf_content_1[\"Δstarch\"])],\n",
    "                                                 \"avg. Δstarch (%)\":\n",
    "                                                 [100*find_average(df_matureleaf_content_1[\"Δstarch\"]/ \\\n",
    "                                                               df_matureleaf_content_1[\"starch_dusk (g/100gFW)\"])],\n",
    "                                                 \"avg. Δsimple sugars (g/100gFW)\":\n",
    "                                                 [find_average(df_matureleaf_content_1[\"Δsimple sugars\"])],\n",
    "                                                 \"avg. Δsucrose (g/100gFW)\":\n",
    "                                                 [find_average(df_matureleaf_content_1[\"Δsucrose\"])],\n",
    "                                                 \"avg. Δsucrose (%)\":\n",
    "                                                  [100*find_average(df_matureleaf_content_1[\"Δsucrose\"]/ \\\n",
    "                                                                df_matureleaf_content_1[\"sucrose_dusk (g/100gFW)\"])]})\n",
    "df_matureleaf_content_1_std"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Starch to sucrose ratio = 9.9153546986\n"
     ]
    }
   ],
   "source": [
    "print(\"Starch to sucrose ratio = \"+str(float(df_matureleaf_content_1_std[\"avg. Δstarch (g/100gFW)\"]/ \\\n",
    "                                      df_matureleaf_content_1_std[\"avg. Δsucrose (g/100gFW)\"])))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Leaf"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Extract sucrose,hexose and starch content from Liu et al 2004, Figure 4 (PPFD = 600 umol/m2/s, photoperiod=12h, sampled between 11:00 and 13:00 h into photoperiod)\n",
    "\n",
    "<img src=\"references/Screenshot_20190717_135552.png\" height=50% width=50%>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>hexose (mg/gDW)</th>\n",
       "      <th>starch (mg/gDW)</th>\n",
       "      <th>sucrose (mg/gDW)</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DAA</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>61.643836</td>\n",
       "      <td>47.422680</td>\n",
       "      <td>6.349206</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>81.369863</td>\n",
       "      <td>47.010309</td>\n",
       "      <td>5.079365</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>82.465753</td>\n",
       "      <td>37.525773</td>\n",
       "      <td>5.079365</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>69.315068</td>\n",
       "      <td>35.257732</td>\n",
       "      <td>4.206349</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>45.570776</td>\n",
       "      <td>64.329897</td>\n",
       "      <td>1.746032</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     hexose (mg/gDW)  starch (mg/gDW)  sucrose (mg/gDW)\n",
       "DAA                                                    \n",
       "0          61.643836        47.422680          6.349206\n",
       "3          81.369863        47.010309          5.079365\n",
       "5          82.465753        37.525773          5.079365\n",
       "7          69.315068        35.257732          4.206349\n",
       "10         45.570776        64.329897          1.746032"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_leaf_content_1 = pd.DataFrame(data={\"DAA\":[0,3,5,7,10],\n",
    "                                       \"sucrose (mg/gDW)\":[6.3492063492063275,5.0793650793650515,\n",
    "                                                           5.0793650793650515,4.20634920634918,\n",
    "                                                           1.746031746031723],\n",
    "                                       \"hexose (mg/gDW)\":[61.64383561643821,81.36986301369862,\n",
    "                                                          82.46575342465738,69.3150684931507,\n",
    "                                                          45.5707762557078],\n",
    "                                       \"starch (mg/gDW)\":[47.42268041237085,47.01030927835024,\n",
    "                                                          37.525773195875956,35.25773195876279,\n",
    "                                                          64.32989690721634]})\n",
    "df_leaf_content_1.set_index(\"DAA\",inplace=True,drop=True)\n",
    "df_leaf_content_1"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Using Clements 1930 data on starch accumulated in 12h to estimate starch, hexose and sucrose content when diel fluctuations are ignored."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>hexose (mg/gDW)</th>\n",
       "      <th>starch (mg/gDW)</th>\n",
       "      <th>sucrose (mg/gDW)</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DAA</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>61.643836</td>\n",
       "      <td>25.019802</td>\n",
       "      <td>5.184085</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>81.369863</td>\n",
       "      <td>24.802239</td>\n",
       "      <td>4.147268</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>82.465753</td>\n",
       "      <td>19.798278</td>\n",
       "      <td>4.147268</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>69.315068</td>\n",
       "      <td>18.601679</td>\n",
       "      <td>3.434456</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>45.570776</td>\n",
       "      <td>33.939906</td>\n",
       "      <td>1.425623</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     hexose (mg/gDW)  starch (mg/gDW)  sucrose (mg/gDW)\n",
       "DAA                                                    \n",
       "0          61.643836        25.019802          5.184085\n",
       "3          81.369863        24.802239          4.147268\n",
       "5          82.465753        19.798278          4.147268\n",
       "7          69.315068        18.601679          3.434456\n",
       "10         45.570776        33.939906          1.425623"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_leaf_content_1_revised = pd.DataFrame(data={\"sucrose (mg/gDW)\":df_leaf_content_1[\"sucrose (mg/gDW)\"]* \\\n",
    "                                                  (100-df_matureleaf_content_1_std[\"avg. Δsucrose (%)\"][0])/100,\n",
    "                                           \"starch (mg/gDW)\":df_leaf_content_1[\"starch (mg/gDW)\"]* \\\n",
    "                                                  (100-df_matureleaf_content_1_std[\"avg. Δstarch (%)\"][0])/100,\n",
    "                                           \"hexose (mg/gDW)\":df_leaf_content_1[\"hexose (mg/gDW)\"]})\n",
    "df_leaf_content_1_revised"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Gather stach, hexose and sucrose content, 8hrs after illumination from Huber 2008, Table 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>hexose (mg/dm2)</th>\n",
       "      <th>starch (mg/dm2)</th>\n",
       "      <th>sucrose (mg/dm2)</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>cultivar</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>Maple Presto</th>\n",
       "      <td>0.0</td>\n",
       "      <td>190</td>\n",
       "      <td>8.7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ransom</th>\n",
       "      <td>1.9</td>\n",
       "      <td>78</td>\n",
       "      <td>4.9</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "              hexose (mg/dm2)  starch (mg/dm2)  sucrose (mg/dm2)\n",
       "cultivar                                                        \n",
       "Maple Presto              0.0              190               8.7\n",
       "Ransom                    1.9               78               4.9"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_leaf_content_2 = pd.DataFrame(data={\"cultivar\":[\"Maple Presto\",\"Ransom\"],\n",
    "                                       \"starch (mg/dm2)\":[190,78],\n",
    "                                       \"hexose (mg/dm2)\":[0,1.9],\n",
    "                                       \"sucrose (mg/dm2)\":[8.7,4.9]})\n",
    "df_leaf_content_2.set_index(\"cultivar\",drop=True,inplace=True)\n",
    "df_leaf_content_2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Extract amino acid content from Chiozza et al 2010, Figure 2\n",
    "\n",
    "<img src=\"references/Screenshot_20190717_143619.png\" height=50% width=50%>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Asn (nmol/50mgFW)</th>\n",
       "      <th>GABA (nmol/50mgFW)</th>\n",
       "      <th>Gln (nmol/50mgFW)</th>\n",
       "      <th>Glt (nmol/50mgFW)</th>\n",
       "      <th>His (nmol/50mgFW)</th>\n",
       "      <th>Pro (nmol/50mgFW)</th>\n",
       "      <th>Ser (nmol/50mgFW)</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Variety</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>aphid resitant</th>\n",
       "      <td>67.260274</td>\n",
       "      <td>0.828767</td>\n",
       "      <td>82.876712</td>\n",
       "      <td>184.589041</td>\n",
       "      <td>11.778523</td>\n",
       "      <td>19.062500</td>\n",
       "      <td>87.282051</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>aphid sensitive</th>\n",
       "      <td>86.164384</td>\n",
       "      <td>1.013699</td>\n",
       "      <td>99.315068</td>\n",
       "      <td>234.931507</td>\n",
       "      <td>13.657718</td>\n",
       "      <td>20.681818</td>\n",
       "      <td>100.410256</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                 Asn (nmol/50mgFW)  GABA (nmol/50mgFW)  Gln (nmol/50mgFW)  \\\n",
       "Variety                                                                     \n",
       "aphid resitant           67.260274            0.828767          82.876712   \n",
       "aphid sensitive          86.164384            1.013699          99.315068   \n",
       "\n",
       "                 Glt (nmol/50mgFW)  His (nmol/50mgFW)  Pro (nmol/50mgFW)  \\\n",
       "Variety                                                                    \n",
       "aphid resitant          184.589041          11.778523          19.062500   \n",
       "aphid sensitive         234.931507          13.657718          20.681818   \n",
       "\n",
       "                 Ser (nmol/50mgFW)  \n",
       "Variety                             \n",
       "aphid resitant           87.282051  \n",
       "aphid sensitive         100.410256  "
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_leaf_content_3 = pd.DataFrame(data={\"Variety\":[\"aphid resitant\",\"aphid sensitive\"],\n",
    "                                       \"GABA (nmol/50mgFW)\":[0.8287671232876719,1.0136986301369868],\n",
    "                                       \"Asn (nmol/50mgFW)\":[67.26027397260277,86.1643835616437],\n",
    "                                       \"Gln (nmol/50mgFW)\":[82.87671232876716,99.31506849315056],\n",
    "                                       \"Glt (nmol/50mgFW)\":[184.58904109589022,234.93150684931462],\n",
    "                                       \"His (nmol/50mgFW)\":[11.778523489932848,13.657718120805297],\n",
    "                                       \"Pro (nmol/50mgFW)\":[19.062499999999943,20.68181818181808],\n",
    "                                       \"Ser (nmol/50mgFW)\":[87.28205128205093,100.4102564102559]})\n",
    "df_leaf_content_3.set_index(\"Variety\",drop=True,inplace=True)\n",
    "df_leaf_content_3"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Use Clements 1930 data to extract baseline sucrose, simple sugars, starch and hemicellulose data from diel metabolite levels"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>baseline hemicellulose (g/100gFW)</th>\n",
       "      <th>baseline simple sugars (g/100gFW)</th>\n",
       "      <th>baseline starch (g/100gFW)</th>\n",
       "      <th>baseline sucrose (g/100gFW)</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Series</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1.089463</td>\n",
       "      <td>0.032023</td>\n",
       "      <td>0.424568</td>\n",
       "      <td>0.271941</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0.663310</td>\n",
       "      <td>0.353374</td>\n",
       "      <td>0.497429</td>\n",
       "      <td>0.187004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.861645</td>\n",
       "      <td>0.413878</td>\n",
       "      <td>0.889538</td>\n",
       "      <td>0.097705</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        baseline hemicellulose (g/100gFW)  baseline simple sugars (g/100gFW)  \\\n",
       "Series                                                                         \n",
       "1                                1.089463                           0.032023   \n",
       "2                                0.663310                           0.353374   \n",
       "3                                0.861645                           0.413878   \n",
       "\n",
       "        baseline starch (g/100gFW)  baseline sucrose (g/100gFW)  \n",
       "Series                                                           \n",
       "1                         0.424568                     0.271941  \n",
       "2                         0.497429                     0.187004  \n",
       "3                         0.889538                     0.097705  "
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "xlist = list()\n",
    "ylist = list()\n",
    "ylist2 = list()\n",
    "ylist3 = list()\n",
    "ylist4 = list()\n",
    "for i in df_matureleaf_content_1.index:\n",
    "    if i == 4:\n",
    "        continue\n",
    "    xlist.append(i)\n",
    "    ylist.append(min(df_matureleaf_content_1[\"simple sugars_dawn (g/100gFW)\"][i],\n",
    "                     df_matureleaf_content_1[\"simple sugars_dusk (g/100gFW)\"][i]))\n",
    "    ylist2.append(min(df_matureleaf_content_1[\"sucrose_dawn (g/100gFW)\"][i],\n",
    "                      df_matureleaf_content_1[\"sucrose_dusk (g/100gFW)\"][i]))\n",
    "    ylist3.append(min(df_matureleaf_content_1[\"hemicellulose_dawn (g/100gFW)\"][i],\n",
    "                      df_matureleaf_content_1[\"hemicellulose_dusk (g/100gFW)\"][i]))\n",
    "    ylist4.append(min(df_matureleaf_content_1[\"starch_dawn (g/100gFW)\"][i],\n",
    "                      df_matureleaf_content_1[\"starch_dusk (g/100gFW)\"][i]))\n",
    "df_leaf_content_4 = pd.DataFrame(data={\"Series\":xlist,\n",
    "                                       \"baseline starch (g/100gFW)\":ylist4,\n",
    "                                       \"baseline hemicellulose (g/100gFW)\":ylist3,\n",
    "                                       \"baseline sucrose (g/100gFW)\":ylist2,\n",
    "                                       \"baseline simple sugars (g/100gFW)\":ylist})\n",
    "df_leaf_content_4.set_index(\"Series\",drop=True,inplace=True)\n",
    "df_leaf_content_4"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Summary\n",
    "\n",
    "- Since amino acid content was only available in g/gFW and FW/DW data was not available, diel starch and sucrose levels (in g/gFW) were used to predict baseline starch and sucrose levels in leaf\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "        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>Asn (nmol/50mgFW)</th>\n",
       "      <th>GABA (nmol/50mgFW)</th>\n",
       "      <th>Gln (nmol/50mgFW)</th>\n",
       "      <th>Glt (nmol/50mgFW)</th>\n",
       "      <th>His (nmol/50mgFW)</th>\n",
       "      <th>Pro (nmol/50mgFW)</th>\n",
       "      <th>Ser (nmol/50mgFW)</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Variety</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>aphid resitant</th>\n",
       "      <td>67.260274</td>\n",
       "      <td>0.828767</td>\n",
       "      <td>82.876712</td>\n",
       "      <td>184.589041</td>\n",
       "      <td>11.778523</td>\n",
       "      <td>19.062500</td>\n",
       "      <td>87.282051</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>aphid sensitive</th>\n",
       "      <td>86.164384</td>\n",
       "      <td>1.013699</td>\n",
       "      <td>99.315068</td>\n",
       "      <td>234.931507</td>\n",
       "      <td>13.657718</td>\n",
       "      <td>20.681818</td>\n",
       "      <td>100.410256</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                 Asn (nmol/50mgFW)  GABA (nmol/50mgFW)  Gln (nmol/50mgFW)  \\\n",
       "Variety                                                                     \n",
       "aphid resitant           67.260274            0.828767          82.876712   \n",
       "aphid sensitive          86.164384            1.013699          99.315068   \n",
       "\n",
       "                 Glt (nmol/50mgFW)  His (nmol/50mgFW)  Pro (nmol/50mgFW)  \\\n",
       "Variety                                                                    \n",
       "aphid resitant          184.589041          11.778523          19.062500   \n",
       "aphid sensitive         234.931507          13.657718          20.681818   \n",
       "\n",
       "                 Ser (nmol/50mgFW)  \n",
       "Variety                             \n",
       "aphid resitant           87.282051  \n",
       "aphid sensitive         100.410256  "
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_leaf_content_3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "biomass.at[\"sSUCROSE_b\",\"leaf\"]=1000*find_average(df_leaf_content_4[\"baseline sucrose (g/100gFW)\"])/ \\\n",
    "                                                model.metabolites.get_by_id(\"SUCROSE_c\").formula_weight\n",
    "biomass.at[\"Starch_b\",\"leaf\"]=1000*find_average(df_leaf_content_4[\"baseline starch (g/100gFW)\"])/ \\\n",
    "                                                model.metabolites.get_by_id(\"SUCROSE_c\").formula_weight\n",
    "biomass.at[\"GLC_c\",\"leaf\"]=1000*find_average(df_leaf_content_4[\"baseline simple sugars (g/100gFW)\"])/ \\\n",
    "                                                model.metabolites.get_by_id(\"SUCROSE_c\").formula_weight\n",
    "\n",
    "biomass.at[\"ASN_c\",\"leaf\"]= 100*0.001*find_average(df_leaf_content_3[\"Asn (nmol/50mgFW)\"])/50\n",
    "biomass.at[\"sGABA_b\",\"leaf\"]= 100*0.001*find_average(df_leaf_content_3[\"GABA (nmol/50mgFW)\"])/50\n",
    "biomass.at[\"sGLN_b\",\"leaf\"]= 100*0.001*find_average(df_leaf_content_3[\"Gln (nmol/50mgFW)\"])/50\n",
    "biomass.at[\"sGLU_b\",\"leaf\"]= 100*0.001*find_average(df_leaf_content_3[\"Glt (nmol/50mgFW)\"])/50\n",
    "biomass.at[\"HIS_c\",\"leaf\"]= 100*0.001*find_average(df_leaf_content_3[\"His (nmol/50mgFW)\"])/50\n",
    "biomass.at[\"PRO_c\",\"leaf\"]= 100*0.001*find_average(df_leaf_content_3[\"Pro (nmol/50mgFW)\"])/50\n",
    "biomass.at[\"sSER_b\",\"leaf\"]= 100*0.001*find_average(df_leaf_content_3[\"Ser (nmol/50mgFW)\"])/50"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>leaf</th>\n",
       "      <th>root</th>\n",
       "      <th>seed</th>\n",
       "      <th>stem</th>\n",
       "    </tr>\n",
       "    <tr>\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>sSUCROSE_b</th>\n",
       "      <td>0.542075</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GLC_c</th>\n",
       "      <td>0.778346</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>FRU_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Starch_b</th>\n",
       "      <td>1.764099</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Cellulose_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Xylan_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L_PHOSPHATIDATE_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PHOSPHATIDYL_CHOLINE_r</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L_1_PHOSPHATIDYL_ETHANOLAMINE_r</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DIACYLGLYCEROL_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Galactosyl_galactosyl_diacyl_glycerols_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>D_Galactosyl_12_diacyl_glycerols_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2_Lysophosphatidylcholines_r</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Lysophosphatidylglycerols_r</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Triacylglycerols_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L_1_PHOSPHATIDYL_GLYCEROL_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L_1_phosphatidyl_inositols_r</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SULFOQUINOVOSYLDIACYLGLYCEROL_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Protein_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sMAL_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sCIT_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sFUM_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ARG_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>HIS_c</th>\n",
       "      <td>0.025436</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LYS_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sASP_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sGLU_b</th>\n",
       "      <td>0.419521</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sSER_b</th>\n",
       "      <td>0.187692</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>THR_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ASN_c</th>\n",
       "      <td>0.153425</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sGLN_b</th>\n",
       "      <td>0.182192</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CYS_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GLY_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PRO_c</th>\n",
       "      <td>0.039744</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sALA_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>VAL_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ILE_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LEU_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MET_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PHE_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TYR_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TRP_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sGABA_b</th>\n",
       "      <td>0.001842</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PALMITATE_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CPD_9245_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CPD_17412_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CPD_17291</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>STEARIC_ACID_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>OLEATE_CPD_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Octadecadienoate_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LINOLENIC_ACID_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ARACHIDIC_ACID_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CPD_16709</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DOCOSANOATE_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                              leaf  root  seed  stem\n",
       "                                                                    \n",
       "sSUCROSE_b                                0.542075   0.0   0.0   0.0\n",
       "GLC_c                                     0.778346   0.0   0.0   0.0\n",
       "FRU_c                                     0.000000   0.0   0.0   0.0\n",
       "Starch_b                                  1.764099   0.0   0.0   0.0\n",
       "Cellulose_b                               0.000000   0.0   0.0   0.0\n",
       "Xylan_b                                   0.000000   0.0   0.0   0.0\n",
       "L_PHOSPHATIDATE_p                         0.000000   0.0   0.0   0.0\n",
       "PHOSPHATIDYL_CHOLINE_r                    0.000000   0.0   0.0   0.0\n",
       "L_1_PHOSPHATIDYL_ETHANOLAMINE_r           0.000000   0.0   0.0   0.0\n",
       "DIACYLGLYCEROL_p                          0.000000   0.0   0.0   0.0\n",
       "Galactosyl_galactosyl_diacyl_glycerols_p  0.000000   0.0   0.0   0.0\n",
       "D_Galactosyl_12_diacyl_glycerols_p        0.000000   0.0   0.0   0.0\n",
       "2_Lysophosphatidylcholines_r              0.000000   0.0   0.0   0.0\n",
       "Lysophosphatidylglycerols_r               0.000000   0.0   0.0   0.0\n",
       "Triacylglycerols_p                        0.000000   0.0   0.0   0.0\n",
       "L_1_PHOSPHATIDYL_GLYCEROL_p               0.000000   0.0   0.0   0.0\n",
       "L_1_phosphatidyl_inositols_r              0.000000   0.0   0.0   0.0\n",
       "SULFOQUINOVOSYLDIACYLGLYCEROL_p           0.000000   0.0   0.0   0.0\n",
       "Protein_b                                 0.000000   0.0   0.0   0.0\n",
       "sMAL_b                                    0.000000   0.0   0.0   0.0\n",
       "sCIT_b                                    0.000000   0.0   0.0   0.0\n",
       "sFUM_b                                    0.000000   0.0   0.0   0.0\n",
       "ARG_c                                     0.000000   0.0   0.0   0.0\n",
       "HIS_c                                     0.025436   0.0   0.0   0.0\n",
       "LYS_c                                     0.000000   0.0   0.0   0.0\n",
       "sASP_b                                    0.000000   0.0   0.0   0.0\n",
       "sGLU_b                                    0.419521   0.0   0.0   0.0\n",
       "sSER_b                                    0.187692   0.0   0.0   0.0\n",
       "THR_c                                     0.000000   0.0   0.0   0.0\n",
       "ASN_c                                     0.153425   0.0   0.0   0.0\n",
       "sGLN_b                                    0.182192   0.0   0.0   0.0\n",
       "CYS_c                                     0.000000   0.0   0.0   0.0\n",
       "GLY_c                                     0.000000   0.0   0.0   0.0\n",
       "PRO_c                                     0.039744   0.0   0.0   0.0\n",
       "sALA_b                                    0.000000   0.0   0.0   0.0\n",
       "VAL_c                                     0.000000   0.0   0.0   0.0\n",
       "ILE_c                                     0.000000   0.0   0.0   0.0\n",
       "LEU_c                                     0.000000   0.0   0.0   0.0\n",
       "MET_c                                     0.000000   0.0   0.0   0.0\n",
       "PHE_c                                     0.000000   0.0   0.0   0.0\n",
       "TYR_c                                     0.000000   0.0   0.0   0.0\n",
       "TRP_c                                     0.000000   0.0   0.0   0.0\n",
       "sGABA_b                                   0.001842   0.0   0.0   0.0\n",
       "PALMITATE_p                               0.000000   0.0   0.0   0.0\n",
       "CPD_9245_p                                0.000000   0.0   0.0   0.0\n",
       "CPD_17412_p                               0.000000   0.0   0.0   0.0\n",
       "CPD_17291                                 0.000000   0.0   0.0   0.0\n",
       "STEARIC_ACID_p                            0.000000   0.0   0.0   0.0\n",
       "OLEATE_CPD_p                              0.000000   0.0   0.0   0.0\n",
       "Octadecadienoate_p                        0.000000   0.0   0.0   0.0\n",
       "LINOLENIC_ACID_p                          0.000000   0.0   0.0   0.0\n",
       "ARACHIDIC_ACID_p                          0.000000   0.0   0.0   0.0\n",
       "CPD_16709                                 0.000000   0.0   0.0   0.0\n",
       "DOCOSANOATE_p                             0.000000   0.0   0.0   0.0"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "biomass"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Stem\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Extract diurnal starch, sucrose, hemicellulose and simple sugar content from Clements 1930, Figure 6, 9, 13 and 14. Based on Figure 1 and 2, dawn = 8am and dusk = 8pm\n",
    "\n",
    "<img src=\"references/Screenshot_20190717_161155.png\" height=50% width=50%>\n",
    "\n",
    "<img src=\"references/Screenshot_20190717_160304.png\" height=50% width=50%>\n",
    "\n",
    "<img src=\"references/Screenshot_20190717_161259.png\" height=50% width=50%>\n",
    "\n",
    "<img src=\"references/Screenshot_20190717_160242.png\" height=50% width=50%>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\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>baseline simple sugars (g/100gFW)</th>\n",
       "      <th>baseline sucrose (g/100gFW)</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Series</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0.089283</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0.993034</td>\n",
       "      <td>0.086064</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.229412</td>\n",
       "      <td>0.141176</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0.755800</td>\n",
       "      <td>0.255357</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        baseline simple sugars (g/100gFW)  baseline sucrose (g/100gFW)\n",
       "Series                                                                \n",
       "1                                0.089283                     0.000000\n",
       "2                                0.993034                     0.086064\n",
       "3                                0.229412                     0.141176\n",
       "4                                0.755800                     0.255357"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_stem_content = pd.DataFrame(data={\"Series\":[1,2,3,4],\n",
    "                                     \"simple sugars_dawn (g/100gFW)\":[0.08928305478569998,1.0069230769230781,\n",
    "                                                                      0.22941176470588265,0.755800478743633],\n",
    "                                     \"sucrose_dawn (g/100gFW)\":[0.24999412110523256,0.10918376068376556,\n",
    "                                                                0.14117647058823524,0.36680114242250283],\n",
    "                                     \"simple sugars_dusk (g/100gFW)\":[0.27423868312757205,0.9930341880341897,\n",
    "                                                                      0.23368616214394122,0.8292719666520014],\n",
    "                                     \"sucrose_dusk (g/100gFW)\":[0,0.08606410256411046,\n",
    "                                                                0.1748626327321765,0.2553567833200341]})\n",
    "df_stem_content.set_index(\"Series\",drop=True,inplace=True)\n",
    "df_stem_content[\"avg. Δsimple sugars (g/100gFW)\"] = df_stem_content[\"simple sugars_dusk (g/100gFW)\"]- \\\n",
    "                                                        df_stem_content[\"simple sugars_dawn (g/100gFW)\"]\n",
    "df_stem_content[\"avg. Δsucrose (g/100gFW)\"] = df_stem_content[\"sucrose_dusk (g/100gFW)\"]- \\\n",
    "                                                        df_stem_content[\"sucrose_dawn (g/100gFW)\"]\n",
    "\n",
    "xlist = list()\n",
    "ylist = list()\n",
    "ylist2 = list()\n",
    "for i in df_matureleaf_content_1.index:\n",
    "    xlist.append(i)\n",
    "    ylist.append(min(df_stem_content[\"simple sugars_dawn (g/100gFW)\"][i],\n",
    "                     df_stem_content[\"simple sugars_dusk (g/100gFW)\"][i]))\n",
    "    ylist2.append(min(df_stem_content[\"sucrose_dawn (g/100gFW)\"][i],\n",
    "                      df_stem_content[\"sucrose_dusk (g/100gFW)\"][i]))\n",
    "df_stem_content_std = pd.DataFrame(data={\"Series\":xlist,\n",
    "                                       \"baseline sucrose (g/100gFW)\":ylist2,\n",
    "                                       \"baseline simple sugars (g/100gFW)\":ylist})\n",
    "df_stem_content_std.set_index(\"Series\",drop=True,inplace=True)\n",
    "df_stem_content_std"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Summary\n",
    "\n",
    "- Sucrose, hexose content data is per FW and conversion to DW is not available\n",
    "\n",
    "Assumptions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "biomass.at[\"sSUCROSE_b\",\"stem\"] = 1000*find_average(df_stem_content_std[\"baseline sucrose (g/100gFW)\"])/ \\\n",
    "                                        model.metabolites.get_by_id(\"SUCROSE_c\").formula_weight\n",
    "biomass.at[\"GLC_c\",\"stem\"]= 1000*find_average(df_stem_content_std[\"baseline simple sugars (g/100gFW)\"])/ \\\n",
    "                                        model.metabolites.get_by_id(\"GLC_c\").formula_weight"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Root"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Gather root exudate content from Canarini et al 2016, Figure 2\n",
    "\n",
    "<img src=\"references/Screenshot_20190718_145459.png\" height=50% width=50%>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "amount of C exudate =8.68995633188 ug/gDWroot/2h\n",
      "amount of N exudate =1.31578947368 ug/gDWroot/2h\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "    }\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>Amino acids</th>\n",
       "      <th>Inorganic ions</th>\n",
       "      <th>Organic acids</th>\n",
       "      <th>Sugars</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>%C or %N</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>%C</th>\n",
       "      <td>10.736842</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>4.421053</td>\n",
       "      <td>14.947368</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>%N</th>\n",
       "      <td>42.105263</td>\n",
       "      <td>42.105263</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          Amino acids  Inorganic ions  Organic acids     Sugars\n",
       "%C or %N                                                       \n",
       "%C          10.736842        0.000000       4.421053  14.947368\n",
       "%N          42.105263       42.105263       0.000000   0.000000"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "print(\"amount of C exudate =\"+str(8.689956331877875)+\" ug/gDWroot/2h\")\n",
    "print(\"amount of N exudate =\"+str(1.315789473684226)+\" ug/gDWroot/2h\")\n",
    "\n",
    "df_root_exudate_1 = pd.DataFrame(data={\"%C or %N\":[\"%C\",\"%N\"],\"Sugars\":[14.947368421052634,0],\n",
    "                                       \"Amino acids\":[25.684210526315788 - 14.947368421052634,\n",
    "                                                      67.89473684210535 - 25.789473684210833],\n",
    "                                       \"Organic acids\":[30.105263157894733 - 25.684210526315788,0],\n",
    "                                       \"Inorganic ions\":[0,67.89473684210535 - 25.789473684210833]})\n",
    "df_root_exudate_1.set_index(\"%C or %N\",inplace=True,drop=True)\n",
    "df_root_exudate_1"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Gathering fatty-acid content from Thomas et al 2007 Table I"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Fatty acid 16:0</th>\n",
       "      <th>Fatty acid 16:1</th>\n",
       "      <th>Fatty acid 18:0</th>\n",
       "      <th>Fatty acid 18:1</th>\n",
       "      <th>Fatty acid 20:0</th>\n",
       "      <th>Fatty acid 22:0</th>\n",
       "      <th>Total (ug/cm2)</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tissue type</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>Conrad - Epidermis</th>\n",
       "      <td>0.39</td>\n",
       "      <td>0.21</td>\n",
       "      <td>0.32</td>\n",
       "      <td>0.71</td>\n",
       "      <td>0.05</td>\n",
       "      <td>0.09</td>\n",
       "      <td>1.77</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>OX760-6 - Epidermis</th>\n",
       "      <td>0.25</td>\n",
       "      <td>0.05</td>\n",
       "      <td>0.04</td>\n",
       "      <td>0.18</td>\n",
       "      <td>0.03</td>\n",
       "      <td>0.04</td>\n",
       "      <td>0.59</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Conrad - Endodermis</th>\n",
       "      <td>1.50</td>\n",
       "      <td>0.82</td>\n",
       "      <td>0.83</td>\n",
       "      <td>7.46</td>\n",
       "      <td>0.28</td>\n",
       "      <td>0.31</td>\n",
       "      <td>11.20</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>OX760-6 - Endodermis</th>\n",
       "      <td>0.72</td>\n",
       "      <td>0.39</td>\n",
       "      <td>0.30</td>\n",
       "      <td>1.46</td>\n",
       "      <td>0.49</td>\n",
       "      <td>0.31</td>\n",
       "      <td>3.67</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                      Fatty acid 16:0  Fatty acid 16:1  Fatty acid 18:0  \\\n",
       "Tissue type                                                               \n",
       "Conrad - Epidermis               0.39             0.21             0.32   \n",
       "OX760-6 - Epidermis              0.25             0.05             0.04   \n",
       "Conrad - Endodermis              1.50             0.82             0.83   \n",
       "OX760-6 - Endodermis             0.72             0.39             0.30   \n",
       "\n",
       "                      Fatty acid 18:1  Fatty acid 20:0  Fatty acid 22:0  \\\n",
       "Tissue type                                                               \n",
       "Conrad - Epidermis               0.71             0.05             0.09   \n",
       "OX760-6 - Epidermis              0.18             0.03             0.04   \n",
       "Conrad - Endodermis              7.46             0.28             0.31   \n",
       "OX760-6 - Endodermis             1.46             0.49             0.31   \n",
       "\n",
       "                      Total (ug/cm2)  \n",
       "Tissue type                           \n",
       "Conrad - Epidermis              1.77  \n",
       "OX760-6 - Epidermis             0.59  \n",
       "Conrad - Endodermis            11.20  \n",
       "OX760-6 - Endodermis            3.67  "
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_root_content_1 = pd.DataFrame(data={\"Tissue type\":[\"Conrad - Epidermis\",\"OX760-6 - Epidermis\",\n",
    "                                                      \"Conrad - Endodermis\",\"OX760-6 - Endodermis\"],\n",
    "                                       \"Fatty acid 16:1\":[0.21,0.05,0.82,0.39],\n",
    "                                       \"Fatty acid 16:0\":[0.39,0.25,1.50,0.72],\n",
    "                                       \"Fatty acid 18:1\":[0.71,0.18,7.46,1.46],\n",
    "                                       \"Fatty acid 18:0\":[0.32,0.04,0.83,0.30],\n",
    "                                       \"Fatty acid 20:0\":[0.05,0.03,0.28,0.49],\n",
    "                                       \"Fatty acid 22:0\":[0.09,0.04,0.31,0.31],\n",
    "                                       \"Total (ug/cm2)\":[1.77,0.59,11.20,3.67]})\n",
    "df_root_content_1.set_index(\"Tissue type\",inplace=True,drop=True)\n",
    "df_root_content_1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "biomass.at[\"PALMITATE_c\",\"root\"] = find_average(df_root_content_1[\"Fatty acid 16:0\"])\n",
    "biomass.at[\"CPD_9245_p\",\"root\"] = find_average(df_root_content_1[\"Fatty acid 16:1\"])\n",
    "biomass.at[\"STEARIC_ACID_p\",\"root\"] = find_average(df_root_content_1[\"Fatty acid 18:0\"])\n",
    "biomass.at[\"OLEATE_CPD_p\",\"root\"] = find_average(df_root_content_1[\"Fatty acid 18:1\"])\n",
    "biomass.at[\"ARACHIDIC_ACID_p\",\"root\"] = find_average(df_root_content_1[\"Fatty acid 20:0\"])\n",
    "biomass.at[\"DOCOSANOATE_p\",\"root\"] = find_average(df_root_content_1[\"Fatty acid 22:0\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Summary\n",
    "\n",
    "- sugars, amino acids and organic acids as %C and %N data could not be used directly.\n",
    "- lipid composition in ug/cm2 cannot be translated to mg/gDW"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Seed\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Gather non-reducing sugars, reducing sugars, starch, proteins, phospholipids, glycolipids, sterols and free fatty acid content from Guleria et al 2008, Table 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "scrolled": true
   },
   "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>16:0 (mg/gDW)</th>\n",
       "      <th>18:0 (mg/gDW)</th>\n",
       "      <th>18:1 (mg/gDW)</th>\n",
       "      <th>18:2 (mg/gDW)</th>\n",
       "      <th>18:3 (mg/gDW)</th>\n",
       "      <th>glycolipids (mg/gDW)</th>\n",
       "      <th>non-reducing sugars (mg/gDW)</th>\n",
       "      <th>phospholipids (mg/gDW)</th>\n",
       "      <th>proteins (mg/gDW)</th>\n",
       "      <th>reducing sugars (mg/gDW)</th>\n",
       "      <th>starch (mg/gDW)</th>\n",
       "      <th>sterols (mg/gDW)</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>seed type</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>large</th>\n",
       "      <td>3181.2</td>\n",
       "      <td>698.9</td>\n",
       "      <td>6482.9</td>\n",
       "      <td>12363.3</td>\n",
       "      <td>1349.6</td>\n",
       "      <td>2554.6</td>\n",
       "      <td>100.1</td>\n",
       "      <td>13761.1</td>\n",
       "      <td>377</td>\n",
       "      <td>24.9</td>\n",
       "      <td>49.7</td>\n",
       "      <td>6458.8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>small</th>\n",
       "      <td>2732.8</td>\n",
       "      <td>851.2</td>\n",
       "      <td>5488.0</td>\n",
       "      <td>11603.2</td>\n",
       "      <td>1702.4</td>\n",
       "      <td>2307.2</td>\n",
       "      <td>73.3</td>\n",
       "      <td>13148.8</td>\n",
       "      <td>264</td>\n",
       "      <td>27.7</td>\n",
       "      <td>42.3</td>\n",
       "      <td>5913.6</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "           16:0 (mg/gDW)  18:0 (mg/gDW)  18:1 (mg/gDW)  18:2 (mg/gDW)  \\\n",
       "seed type                                                               \n",
       "large             3181.2          698.9         6482.9        12363.3   \n",
       "small             2732.8          851.2         5488.0        11603.2   \n",
       "\n",
       "           18:3 (mg/gDW)  glycolipids (mg/gDW)  non-reducing sugars (mg/gDW)  \\\n",
       "seed type                                                                      \n",
       "large             1349.6                2554.6                         100.1   \n",
       "small             1702.4                2307.2                          73.3   \n",
       "\n",
       "           phospholipids (mg/gDW)  proteins (mg/gDW)  \\\n",
       "seed type                                              \n",
       "large                     13761.1                377   \n",
       "small                     13148.8                264   \n",
       "\n",
       "           reducing sugars (mg/gDW)  starch (mg/gDW)  sterols (mg/gDW)  \n",
       "seed type                                                               \n",
       "large                          24.9             49.7            6458.8  \n",
       "small                          27.7             42.3            5913.6  "
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_seed_content = pd.DataFrame(data={\"seed type\":[\"large\",\"small\"],\n",
    "                               \"starch (mg/gDW)\":[49.7,42.3],\n",
    "                               \"reducing sugars (mg/gDW)\":[24.9,27.7],\n",
    "                               \"total soluble sugars (mg/gDW)\":[125,101],\n",
    "                               \"proteins (mg/gDW)\":[377,264],\n",
    "                               \"lipid content (mg/gDW)\":[241,224],\n",
    "                               \"phospholipids (mg/gDW lipid)\":[57.1,58.7],\n",
    "                               \"glycolipids (mg/gDW lipid)\":[10.6,10.3],\n",
    "                               \"sterols (mg/gDW lipid)\":[26.8,26.4],\n",
    "                               \"free fatty acids (mg/gDW lipid)\":[0.1,0.1],\n",
    "                               \"16:0 (mg/gDW fatty acds)\":[132,122],\n",
    "                               \"18:0 (mg/gDW fatty acds)\":[29,38],\n",
    "                               \"18:1 (mg/gDW fatty acds)\":[269,245],\n",
    "                               \"18:2 (mg/gDW fatty acds)\":[513,518],\n",
    "                               \"18:3 (mg/gDW fatty acds)\":[56,76]})\n",
    "df_seed_content_std = pd.DataFrame(data={\"seed type\":[\"large\",\"small\"],\n",
    "                               \"starch (mg/gDW)\":[49.7,42.3],\n",
    "                               \"reducing sugars (mg/gDW)\":[24.9,27.7],\n",
    "                               \"non-reducing sugars (mg/gDW)\":df_seed_content[\"total soluble sugars (mg/gDW)\"]-\\\n",
    "                                         df_seed_content[\"reducing sugars (mg/gDW)\"],\n",
    "                               \"proteins (mg/gDW)\":[377,264],\n",
    "                               \"phospholipids (mg/gDW)\":df_seed_content[\"phospholipids (mg/gDW lipid)\"]* \\\n",
    "                                   df_seed_content[\"lipid content (mg/gDW)\"],\n",
    "                               \"glycolipids (mg/gDW)\":df_seed_content[\"glycolipids (mg/gDW lipid)\"]* \\\n",
    "                                   df_seed_content[\"lipid content (mg/gDW)\"],\n",
    "                               \"sterols (mg/gDW)\":df_seed_content[\"sterols (mg/gDW lipid)\"]* \\\n",
    "                                   df_seed_content[\"lipid content (mg/gDW)\"],\n",
    "                               \"16:0 (mg/gDW)\":df_seed_content[\"16:0 (mg/gDW fatty acds)\"]* \\\n",
    "                                         df_seed_content[\"free fatty acids (mg/gDW lipid)\"]* \\\n",
    "                                         df_seed_content[\"lipid content (mg/gDW)\"],\n",
    "                               \"18:0 (mg/gDW)\":df_seed_content[\"18:0 (mg/gDW fatty acds)\"]* \\\n",
    "                                         df_seed_content[\"free fatty acids (mg/gDW lipid)\"]* \\\n",
    "                                         df_seed_content[\"lipid content (mg/gDW)\"],\n",
    "                               \"18:1 (mg/gDW)\":df_seed_content[\"18:1 (mg/gDW fatty acds)\"]* \\\n",
    "                                         df_seed_content[\"free fatty acids (mg/gDW lipid)\"]* \\\n",
    "                                         df_seed_content[\"lipid content (mg/gDW)\"],\n",
    "                               \"18:2 (mg/gDW)\":df_seed_content[\"18:2 (mg/gDW fatty acds)\"]* \\\n",
    "                                         df_seed_content[\"free fatty acids (mg/gDW lipid)\"]* \\\n",
    "                                         df_seed_content[\"lipid content (mg/gDW)\"],\n",
    "                               \"18:3 (mg/gDW)\":df_seed_content[\"18:3 (mg/gDW fatty acds)\"]* \\\n",
    "                                         df_seed_content[\"free fatty acids (mg/gDW lipid)\"]* \\\n",
    "                                         df_seed_content[\"lipid content (mg/gDW)\"]})\n",
    "df_seed_content_std.set_index(\"seed type\",inplace=True,drop=True)\n",
    "df_seed_content_std"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Extract FW/DW, lipid, protein, starch, soluble sugar and reducing sugar content from Sharma et al 2013, Figure 1 and 2\n",
    "\n",
    "\n",
    "<img src=\"references/Screenshot_20190719_101524.png\" height=25% width=25%>\n",
    "\n",
    "<img src=\"references/Screenshot_20190719_101729.png\" height=25% width=25%>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\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>DW/FW</th>\n",
       "      <th>lipid content (mg/gDW)</th>\n",
       "      <th>proteins (mg/gDW)</th>\n",
       "      <th>reducing sugars (mg/gDW)</th>\n",
       "      <th>starch (mg/gDW)</th>\n",
       "      <th>total soluble sugars (mg/gDW)</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>node position</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>4</th>\n",
       "      <td>0.928873</td>\n",
       "      <td>242.223687</td>\n",
       "      <td>251.291825</td>\n",
       "      <td>112.999279</td>\n",
       "      <td>42.513115</td>\n",
       "      <td>90.688797</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>0.927787</td>\n",
       "      <td>264.320110</td>\n",
       "      <td>241.120373</td>\n",
       "      <td>151.966724</td>\n",
       "      <td>40.219935</td>\n",
       "      <td>88.851614</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>0.934611</td>\n",
       "      <td>255.514790</td>\n",
       "      <td>245.770052</td>\n",
       "      <td>122.654640</td>\n",
       "      <td>48.283394</td>\n",
       "      <td>88.465794</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>0.938873</td>\n",
       "      <td>247.835932</td>\n",
       "      <td>222.503856</td>\n",
       "      <td>137.206647</td>\n",
       "      <td>37.240214</td>\n",
       "      <td>105.697140</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>0.937322</td>\n",
       "      <td>237.345219</td>\n",
       "      <td>236.746559</td>\n",
       "      <td>155.484034</td>\n",
       "      <td>41.197034</td>\n",
       "      <td>81.271626</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>0.918329</td>\n",
       "      <td>237.531529</td>\n",
       "      <td>239.656502</td>\n",
       "      <td>157.207037</td>\n",
       "      <td>45.332425</td>\n",
       "      <td>91.663593</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>0.955151</td>\n",
       "      <td>235.470649</td>\n",
       "      <td>269.587981</td>\n",
       "      <td>115.897056</td>\n",
       "      <td>42.681598</td>\n",
       "      <td>98.739498</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>0.944300</td>\n",
       "      <td>225.550332</td>\n",
       "      <td>271.621381</td>\n",
       "      <td>65.482281</td>\n",
       "      <td>40.389427</td>\n",
       "      <td>91.722725</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>0.945539</td>\n",
       "      <td>212.250631</td>\n",
       "      <td>278.882890</td>\n",
       "      <td>49.414171</td>\n",
       "      <td>39.703390</td>\n",
       "      <td>86.777905</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>0.948407</td>\n",
       "      <td>211.313346</td>\n",
       "      <td>334.986058</td>\n",
       "      <td>53.618812</td>\n",
       "      <td>49.195420</td>\n",
       "      <td>86.807178</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>0.948250</td>\n",
       "      <td>207.564205</td>\n",
       "      <td>327.426436</td>\n",
       "      <td>58.654562</td>\n",
       "      <td>40.473668</td>\n",
       "      <td>97.198560</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>0.948560</td>\n",
       "      <td>207.750516</td>\n",
       "      <td>323.350736</td>\n",
       "      <td>78.173352</td>\n",
       "      <td>42.823345</td>\n",
       "      <td>90.596879</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>0.956779</td>\n",
       "      <td>216.922724</td>\n",
       "      <td>316.663206</td>\n",
       "      <td>46.792262</td>\n",
       "      <td>39.815375</td>\n",
       "      <td>81.506982</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>0.958484</td>\n",
       "      <td>221.603417</td>\n",
       "      <td>321.312886</td>\n",
       "      <td>52.240644</td>\n",
       "      <td>35.557910</td>\n",
       "      <td>90.654840</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                  DW/FW  lipid content (mg/gDW)  proteins (mg/gDW)  \\\n",
       "node position                                                        \n",
       "4              0.928873              242.223687         251.291825   \n",
       "5              0.927787              264.320110         241.120373   \n",
       "6              0.934611              255.514790         245.770052   \n",
       "7              0.938873              247.835932         222.503856   \n",
       "8              0.937322              237.345219         236.746559   \n",
       "9              0.918329              237.531529         239.656502   \n",
       "10             0.955151              235.470649         269.587981   \n",
       "11             0.944300              225.550332         271.621381   \n",
       "12             0.945539              212.250631         278.882890   \n",
       "13             0.948407              211.313346         334.986058   \n",
       "14             0.948250              207.564205         327.426436   \n",
       "15             0.948560              207.750516         323.350736   \n",
       "16             0.956779              216.922724         316.663206   \n",
       "17             0.958484              221.603417         321.312886   \n",
       "\n",
       "               reducing sugars (mg/gDW)  starch (mg/gDW)  \\\n",
       "node position                                              \n",
       "4                            112.999279        42.513115   \n",
       "5                            151.966724        40.219935   \n",
       "6                            122.654640        48.283394   \n",
       "7                            137.206647        37.240214   \n",
       "8                            155.484034        41.197034   \n",
       "9                            157.207037        45.332425   \n",
       "10                           115.897056        42.681598   \n",
       "11                            65.482281        40.389427   \n",
       "12                            49.414171        39.703390   \n",
       "13                            53.618812        49.195420   \n",
       "14                            58.654562        40.473668   \n",
       "15                            78.173352        42.823345   \n",
       "16                            46.792262        39.815375   \n",
       "17                            52.240644        35.557910   \n",
       "\n",
       "               total soluble sugars (mg/gDW)  \n",
       "node position                                 \n",
       "4                                  90.688797  \n",
       "5                                  88.851614  \n",
       "6                                  88.465794  \n",
       "7                                 105.697140  \n",
       "8                                  81.271626  \n",
       "9                                  91.663593  \n",
       "10                                 98.739498  \n",
       "11                                 91.722725  \n",
       "12                                 86.777905  \n",
       "13                                 86.807178  \n",
       "14                                 97.198560  \n",
       "15                                 90.596879  \n",
       "16                                 81.506982  \n",
       "17                                 90.654840  "
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_seed_content_2 = pd.DataFrame(data={\"node position\":range(4,18),\n",
    "                               \"DW/FW\":[0.928872804935928,0.927787138111058,0.934610821072615,\n",
    "                                        0.938872804935928,0.937322021831989,0.918329378262933,\n",
    "                                        0.95515068818225,0.944299952539155,0.945538680588514,\n",
    "                                        0.948406502135738,0.948249881347888,0.948559563360228,\n",
    "                                        0.956778595158994,0.958483626008543],\n",
    "                               \"lipid content (mg/gDW)\":[242.2236872277,264.320110066498,255.514790185737,\n",
    "                                                         247.835932125659,237.345218986471,237.531529465719,\n",
    "                                                         235.470648933731,225.550332492547,212.250630589314,\n",
    "                                                         211.313345562944,207.564205457464,207.750515936712,\n",
    "                                                         216.922724145838,221.603416647558],\n",
    "                               \"proteins (mg/gDW)\":[251.291824869483,241.120372567632,245.770052206929,\n",
    "                                                    222.503856193641,236.746559088752,239.656502135738,\n",
    "                                                    269.587980541054,271.621381110584,278.882890365449,\n",
    "                                                    334.986058376839,327.426435690555,323.350735643094,\n",
    "                                                    316.663205980066,321.312885619364],\n",
    "                               \"starch (mg/gDW)\":[42.5131154156578,40.2199354317999,48.283393866021,\n",
    "                                                  37.240213882163,41.1970338983051,45.3324253430186,\n",
    "                                                  42.681598062954,40.3894269572236,39.7033898305085,\n",
    "                                                  49.195419693301,40.4736682808717,42.8233454398709,\n",
    "                                                  39.8153753026634,35.5579096045198],\n",
    "                               \"total soluble sugars (mg/gDW)\":[90.6887971663593,88.8516144140979,\n",
    "                                                                88.4657943268639,105.697140013466,\n",
    "                                                                81.2716255378942,91.6635929861538,\n",
    "                                                                98.7394982582477,91.7227247445918,\n",
    "                                                                86.7779046280847,86.8071777758262,\n",
    "                                                                97.1985597611311,90.5968794824508,\n",
    "                                                                81.5069816457364,90.6548403149791],\n",
    "                               \"reducing sugars (mg/gDW)\":[112.999279159929,151.966724463752,\n",
    "                                                           122.654639677375,137.206647314383,\n",
    "                                                           155.484034366537,157.207036957665,\n",
    "                                                           115.897056245007,65.4822809717704,\n",
    "                                                           49.4141713261512,53.6188119776346,\n",
    "                                                           58.6545617487192,78.173352295973,\n",
    "                                                           46.7922616844281,52.2406436907015]})\n",
    "df_seed_content_2.set_index(\"node position\",drop=True,inplace=True)\n",
    "df_seed_content_2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Summary\n",
    "\n",
    "Assumptions\n",
    "\n",
    "- Sharma et al 2013 data has reducing  sugar content higher than total soluble sugar content and so given that the same data was available from Guleria et al 2008, this data was ignored"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>leaf</th>\n",
       "      <th>root</th>\n",
       "      <th>seed</th>\n",
       "      <th>stem</th>\n",
       "    </tr>\n",
       "    <tr>\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>sSUCROSE_b</th>\n",
       "      <td>0.542075</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.253289</td>\n",
       "      <td>0.352470</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GLC_c</th>\n",
       "      <td>0.778346</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.145985</td>\n",
       "      <td>2.869084</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>FRU_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Starch_b</th>\n",
       "      <td>1.764099</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.255334</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Cellulose_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Xylan_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L_PHOSPHATIDATE_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>20.799909</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PHOSPHATIDYL_CHOLINE_r</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L_1_PHOSPHATIDYL_ETHANOLAMINE_r</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DIACYLGLYCEROL_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Galactosyl_galactosyl_diacyl_glycerols_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>D_Galactosyl_12_diacyl_glycerols_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2_Lysophosphatidylcholines_r</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Lysophosphatidylglycerols_r</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Triacylglycerols_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L_1_PHOSPHATIDYL_GLYCEROL_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L_1_phosphatidyl_inositols_r</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SULFOQUINOVOSYLDIACYLGLYCEROL_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Protein_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.802620</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sMAL_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sCIT_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sFUM_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ARG_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>HIS_c</th>\n",
       "      <td>0.025436</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LYS_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sASP_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sGLU_b</th>\n",
       "      <td>0.419521</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sSER_b</th>\n",
       "      <td>0.187692</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>THR_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ASN_c</th>\n",
       "      <td>0.153425</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sGLN_b</th>\n",
       "      <td>0.182192</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CYS_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GLY_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PRO_c</th>\n",
       "      <td>0.039744</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sALA_b</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>VAL_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ILE_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LEU_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MET_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PHE_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TYR_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TRP_c</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sGABA_b</th>\n",
       "      <td>0.001842</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PALMITATE_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CPD_9245_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.3675</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CPD_17412_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CPD_17291</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>STEARIC_ACID_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.3725</td>\n",
       "      <td>3.034460</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>OLEATE_CPD_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>2.4525</td>\n",
       "      <td>23.434110</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Octadecadienoate_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>46.916573</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LINOLENIC_ACID_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>5.974564</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ARACHIDIC_ACID_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.2125</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CPD_16709</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DOCOSANOATE_p</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.1875</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PALMITATE_c</th>\n",
       "      <td>NaN</td>\n",
       "      <td>0.7150</td>\n",
       "      <td>11.577185</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                              leaf    root       seed  \\\n",
       "                                                                        \n",
       "sSUCROSE_b                                0.542075  0.0000   0.253289   \n",
       "GLC_c                                     0.778346  0.0000   0.145985   \n",
       "FRU_c                                     0.000000  0.0000   0.000000   \n",
       "Starch_b                                  1.764099  0.0000   0.255334   \n",
       "Cellulose_b                               0.000000  0.0000   0.000000   \n",
       "Xylan_b                                   0.000000  0.0000   0.000000   \n",
       "L_PHOSPHATIDATE_p                         0.000000  0.0000  20.799909   \n",
       "PHOSPHATIDYL_CHOLINE_r                    0.000000  0.0000   0.000000   \n",
       "L_1_PHOSPHATIDYL_ETHANOLAMINE_r           0.000000  0.0000   0.000000   \n",
       "DIACYLGLYCEROL_p                          0.000000  0.0000   0.000000   \n",
       "Galactosyl_galactosyl_diacyl_glycerols_p  0.000000  0.0000   0.000000   \n",
       "D_Galactosyl_12_diacyl_glycerols_p        0.000000  0.0000   0.000000   \n",
       "2_Lysophosphatidylcholines_r              0.000000  0.0000   0.000000   \n",
       "Lysophosphatidylglycerols_r               0.000000  0.0000   0.000000   \n",
       "Triacylglycerols_p                        0.000000  0.0000   0.000000   \n",
       "L_1_PHOSPHATIDYL_GLYCEROL_p               0.000000  0.0000   0.000000   \n",
       "L_1_phosphatidyl_inositols_r              0.000000  0.0000   0.000000   \n",
       "SULFOQUINOVOSYLDIACYLGLYCEROL_p           0.000000  0.0000   0.000000   \n",
       "Protein_b                                 0.000000  0.0000   0.802620   \n",
       "sMAL_b                                    0.000000  0.0000   0.000000   \n",
       "sCIT_b                                    0.000000  0.0000   0.000000   \n",
       "sFUM_b                                    0.000000  0.0000   0.000000   \n",
       "ARG_c                                     0.000000  0.0000   0.000000   \n",
       "HIS_c                                     0.025436  0.0000   0.000000   \n",
       "LYS_c                                     0.000000  0.0000   0.000000   \n",
       "sASP_b                                    0.000000  0.0000   0.000000   \n",
       "sGLU_b                                    0.419521  0.0000   0.000000   \n",
       "sSER_b                                    0.187692  0.0000   0.000000   \n",
       "THR_c                                     0.000000  0.0000   0.000000   \n",
       "ASN_c                                     0.153425  0.0000   0.000000   \n",
       "sGLN_b                                    0.182192  0.0000   0.000000   \n",
       "CYS_c                                     0.000000  0.0000   0.000000   \n",
       "GLY_c                                     0.000000  0.0000   0.000000   \n",
       "PRO_c                                     0.039744  0.0000   0.000000   \n",
       "sALA_b                                    0.000000  0.0000   0.000000   \n",
       "VAL_c                                     0.000000  0.0000   0.000000   \n",
       "ILE_c                                     0.000000  0.0000   0.000000   \n",
       "LEU_c                                     0.000000  0.0000   0.000000   \n",
       "MET_c                                     0.000000  0.0000   0.000000   \n",
       "PHE_c                                     0.000000  0.0000   0.000000   \n",
       "TYR_c                                     0.000000  0.0000   0.000000   \n",
       "TRP_c                                     0.000000  0.0000   0.000000   \n",
       "sGABA_b                                   0.001842  0.0000   0.000000   \n",
       "PALMITATE_p                               0.000000  0.0000   0.000000   \n",
       "CPD_9245_p                                0.000000  0.3675   0.000000   \n",
       "CPD_17412_p                               0.000000  0.0000   0.000000   \n",
       "CPD_17291                                 0.000000  0.0000   0.000000   \n",
       "STEARIC_ACID_p                            0.000000  0.3725   3.034460   \n",
       "OLEATE_CPD_p                              0.000000  2.4525  23.434110   \n",
       "Octadecadienoate_p                        0.000000  0.0000  46.916573   \n",
       "LINOLENIC_ACID_p                          0.000000  0.0000   5.974564   \n",
       "ARACHIDIC_ACID_p                          0.000000  0.2125   0.000000   \n",
       "CPD_16709                                 0.000000  0.0000   0.000000   \n",
       "DOCOSANOATE_p                             0.000000  0.1875   0.000000   \n",
       "PALMITATE_c                                    NaN  0.7150  11.577185   \n",
       "\n",
       "                                              stem  \n",
       "                                                    \n",
       "sSUCROSE_b                                0.352470  \n",
       "GLC_c                                     2.869084  \n",
       "FRU_c                                     0.000000  \n",
       "Starch_b                                  0.000000  \n",
       "Cellulose_b                               0.000000  \n",
       "Xylan_b                                   0.000000  \n",
       "L_PHOSPHATIDATE_p                         0.000000  \n",
       "PHOSPHATIDYL_CHOLINE_r                    0.000000  \n",
       "L_1_PHOSPHATIDYL_ETHANOLAMINE_r           0.000000  \n",
       "DIACYLGLYCEROL_p                          0.000000  \n",
       "Galactosyl_galactosyl_diacyl_glycerols_p  0.000000  \n",
       "D_Galactosyl_12_diacyl_glycerols_p        0.000000  \n",
       "2_Lysophosphatidylcholines_r              0.000000  \n",
       "Lysophosphatidylglycerols_r               0.000000  \n",
       "Triacylglycerols_p                        0.000000  \n",
       "L_1_PHOSPHATIDYL_GLYCEROL_p               0.000000  \n",
       "L_1_phosphatidyl_inositols_r              0.000000  \n",
       "SULFOQUINOVOSYLDIACYLGLYCEROL_p           0.000000  \n",
       "Protein_b                                 0.000000  \n",
       "sMAL_b                                    0.000000  \n",
       "sCIT_b                                    0.000000  \n",
       "sFUM_b                                    0.000000  \n",
       "ARG_c                                     0.000000  \n",
       "HIS_c                                     0.000000  \n",
       "LYS_c                                     0.000000  \n",
       "sASP_b                                    0.000000  \n",
       "sGLU_b                                    0.000000  \n",
       "sSER_b                                    0.000000  \n",
       "THR_c                                     0.000000  \n",
       "ASN_c                                     0.000000  \n",
       "sGLN_b                                    0.000000  \n",
       "CYS_c                                     0.000000  \n",
       "GLY_c                                     0.000000  \n",
       "PRO_c                                     0.000000  \n",
       "sALA_b                                    0.000000  \n",
       "VAL_c                                     0.000000  \n",
       "ILE_c                                     0.000000  \n",
       "LEU_c                                     0.000000  \n",
       "MET_c                                     0.000000  \n",
       "PHE_c                                     0.000000  \n",
       "TYR_c                                     0.000000  \n",
       "TRP_c                                     0.000000  \n",
       "sGABA_b                                   0.000000  \n",
       "PALMITATE_p                               0.000000  \n",
       "CPD_9245_p                                0.000000  \n",
       "CPD_17412_p                               0.000000  \n",
       "CPD_17291                                 0.000000  \n",
       "STEARIC_ACID_p                            0.000000  \n",
       "OLEATE_CPD_p                              0.000000  \n",
       "Octadecadienoate_p                        0.000000  \n",
       "LINOLENIC_ACID_p                          0.000000  \n",
       "ARACHIDIC_ACID_p                          0.000000  \n",
       "CPD_16709                                 0.000000  \n",
       "DOCOSANOATE_p                             0.000000  \n",
       "PALMITATE_c                                    NaN  "
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "biomass.at[\"sSUCROSE_b\",\"seed\"] = find_average(df_seed_content_std[\"non-reducing sugars (mg/gDW)\"])/ \\\n",
    "                                        model.metabolites.get_by_id(\"SUCROSE_c\").formula_weight\n",
    "biomass.at[\"GLC_c\",\"seed\"]=find_average(df_seed_content_std[\"reducing sugars (mg/gDW)\"])/ \\\n",
    "                                        model.metabolites.get_by_id(\"GLC_c\").formula_weight\n",
    "biomass.at[\"PALMITATE_c\",\"seed\"]=find_average(df_seed_content_std[\"16:0 (mg/gDW)\"])/ \\\n",
    "                                        model.metabolites.get_by_id(\"PALMITATE_c\").formula_weight\n",
    "biomass.at[\"STEARIC_ACID_p\",\"seed\"]=find_average(df_seed_content_std[\"18:0 (mg/gDW)\"])/ \\\n",
    "                                        model.metabolites.get_by_id(\"PALMITATE_c\").formula_weight\n",
    "biomass.at[\"OLEATE_CPD_p\",\"seed\"]=find_average(df_seed_content_std[\"18:1 (mg/gDW)\"])/ \\\n",
    "                                        model.metabolites.get_by_id(\"PALMITATE_c\").formula_weight\n",
    "biomass.at[\"Octadecadienoate_p\",\"seed\"]=find_average(df_seed_content_std[\"18:2 (mg/gDW)\"])/ \\\n",
    "                                        model.metabolites.get_by_id(\"PALMITATE_c\").formula_weight\n",
    "biomass.at[\"LINOLENIC_ACID_p\",\"seed\"]=find_average(df_seed_content_std[\"18:3 (mg/gDW)\"])/ \\\n",
    "                                        model.metabolites.get_by_id(\"PALMITATE_c\").formula_weight\n",
    "biomass.at[\"L_PHOSPHATIDATE_p\",\"seed\"]=find_average(df_seed_content_std[\"phospholipids (mg/gDW)\"])/ \\\n",
    "                                        model.metabolites.get_by_id(\"L_PHOSPHATIDATE_p\").formula_weight\n",
    "biomass.at[\"Starch_b\",\"seed\"]=find_average(df_seed_content_std[\"starch (mg/gDW)\"])/ \\\n",
    "                                        model.metabolites.get_by_id(\"GLC_c\").formula_weight\n",
    "biomass.at[\"Protein_b\",\"seed\"]=find_average(df_seed_content_std[\"proteins (mg/gDW)\"])/proteinMW\n",
    "biomass.to_csv(\"Data/biomass_soy.csv\")\n",
    "biomass"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### References\n",
    "\n",
    "- Liu, F., Jensen, C.R. and Andersen, M.N. (2004) Drought stress effect on carbohydrate concentration in soybean leaves and pods during early reproductive development: its implication in altering pod set. F. Crop. Res., 86, 1–13. https://doi.org/10.1016/S0378-4290(03)00165-5.\n",
    "- Chiozza, M. V, O’Neal, M.E. and MacIntosh, G.C. (2010) Constitutive and Induced Differential Accumulation of Amino Acid in Leaves of Susceptible and Resistant Soybean Plants in Response to the Soybean Aphid (Hemiptera: Aphididae). Environ. Entomol., 39, 856–864. https://doi.org/10.1603/EN09338.\n",
    "- Huber, S.C. (2008) Biochemical Mechanism for Regulation of Sucrose Accumulation in Leaves during Photosynthesis. PLANT Physiol., 91, 656–662. https://doi.org/10.1104/pp.91.2.656.\n",
    "- White, M.C., Decker, A.M. and Chaney, R.L. (2008) Metal Complexation in Xylem Fluid : I. CHEMICAL COMPOSITION OF TOMATO AND SOYBEAN STEM EXUDATE. PLANT Physiol., 67, 292–300. https://doi.org/10.1104/pp.67.2.292.\n",
    "- Clements, H.F. (1930) Hourly Variations in Carbohydrate Content of Leaves and Petioles. Bot. Gaz., 89, 241–272. https://www.jstor.org/stable/2471041.\n",
    "- Canarini, A., Merchant, A. and Dijkstra, F.A. (2016) Drought effects on Helianthus annuus and Glycine max metabolites: from phloem to root exudates. Rhizosphere, 2, 85–97. https://doi.org/10.1016/j.rhisph.2016.06.003.\n",
    "- Thomas, R., Fang, X., Ranathunge, K., Anderson, T.R., Peterson, C.A. and Bernards, M.A. (2007) Soybean Root Suberin: Anatomical Distribution, Chemical Composition, and Relationship to Partial Resistance to Phytophthora sojae. PLANT Physiol., 144, 299–311. https:doi.org/10.1104/pp.106.091090.\n",
    "- Guleria, S., Sharma, S., Gill, B.S. and Munshi, S.K. (2008) Distribution and biochemical composition of large and small seeds of soybean (Glycine max L.). J. Sci. Food Agric., 88, 269–272. https://doi.org/10.1002/jsfa.2825.\n",
    "- Sharma, S., Kaur, A., Bansal, A. and Gill, B.S. (2013) Positional effects on soybean seed composition during storage. J. Food Sci. Technol., 50, 353–359. https://doi.org/10.1007/s13197-011-0341-0."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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