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  1. {
  2. "cells": [
  3. {
  4. "metadata": {
  5. "toc": "true"
  6. },
  7. "cell_type": "markdown",
  8. "source": "# Table of Contents\n <p><div class=\"lev1 toc-item\"><a href=\"#Develop-Thermodynamic-kinetic-Maximum-Entropy-Model\" data-toc-modified-id=\"Develop-Thermodynamic-kinetic-Maximum-Entropy-Model-1\"><span class=\"toc-item-num\">1&nbsp;&nbsp;</span>Develop Thermodynamic-kinetic Maximum Entropy Model</a></div><div class=\"lev2 toc-item\"><a href=\"#Reactions-File\" data-toc-modified-id=\"Reactions-File-11\"><span class=\"toc-item-num\">1.1&nbsp;&nbsp;</span>Reactions File</a></div><div class=\"lev3 toc-item\"><a href=\"#Read-the-file-into-a-dataframe-and-create-a-stoichiometric-matrix\" data-toc-modified-id=\"Read-the-file-into-a-dataframe-and-create-a-stoichiometric-matrix-111\"><span class=\"toc-item-num\">1.1.1&nbsp;&nbsp;</span>Read the file into a dataframe and create a stoichiometric matrix</a></div><div class=\"lev2 toc-item\"><a href=\"#Calculate-Standard-Free-Energies-of-Reaction\" data-toc-modified-id=\"Calculate-Standard-Free-Energies-of-Reaction-12\"><span class=\"toc-item-num\">1.2&nbsp;&nbsp;</span>Calculate Standard Free Energies of Reaction</a></div><div class=\"lev3 toc-item\"><a href=\"#Determine-Pyruvate-transport-reaction-manually\" data-toc-modified-id=\"Determine-Pyruvate-transport-reaction-manually-121\"><span class=\"toc-item-num\">1.2.1&nbsp;&nbsp;</span>Determine Pyruvate transport reaction manually</a></div><div class=\"lev3 toc-item\"><a href=\"#Output-the-Standard-Reaction-Free-Energies-for-use-in-a-Boltzmann-Simulation\" data-toc-modified-id=\"Output-the-Standard-Reaction-Free-Energies-for-use-in-a-Boltzmann-Simulation-122\"><span class=\"toc-item-num\">1.2.2&nbsp;&nbsp;</span>Output the Standard Reaction Free Energies for use in a Boltzmann Simulation</a></div><div class=\"lev2 toc-item\"><a href=\"#Set-Fixed-Concentrations/Boundary-Conditions\" data-toc-modified-id=\"Set-Fixed-Concentrations/Boundary-Conditions-13\"><span class=\"toc-item-num\">1.3&nbsp;&nbsp;</span>Set Fixed Concentrations/Boundary Conditions</a></div><div class=\"lev2 toc-item\"><a href=\"#Prepare-model-for-optimization\" data-toc-modified-id=\"Prepare-model-for-optimization-14\"><span class=\"toc-item-num\">1.4&nbsp;&nbsp;</span>Prepare model for optimization</a></div><div class=\"lev1 toc-item\"><a href=\"#Nonlinear-Least-Squares-Optimization-of-Concentrations\" data-toc-modified-id=\"Nonlinear-Least-Squares-Optimization-of-Concentrations-2\"><span class=\"toc-item-num\">2&nbsp;&nbsp;</span>Nonlinear Least Squares Optimization of Concentrations</a></div><div class=\"lev2 toc-item\"><a href=\"#Apply-Regulation-and-Optimize\" data-toc-modified-id=\"Apply-Regulation-and-Optimize-21\"><span class=\"toc-item-num\">2.1&nbsp;&nbsp;</span>Apply Regulation and Optimize</a></div><div class=\"lev1 toc-item\"><a href=\"#ODE-Simulations\" data-toc-modified-id=\"ODE-Simulations-3\"><span class=\"toc-item-num\">3&nbsp;&nbsp;</span>ODE Simulations</a></div><div class=\"lev2 toc-item\"><a href=\"#Calculate-Rate-Constants\" data-toc-modified-id=\"Calculate-Rate-Constants-31\"><span class=\"toc-item-num\">3.1&nbsp;&nbsp;</span>Calculate Rate Constants</a></div><div class=\"lev2 toc-item\"><a href=\"#ODE-Solvers:-Python-interface-using-libroadrunner-to-Sundials/CVODE\" data-toc-modified-id=\"ODE-Solvers:-Python-interface-using-libroadrunner-to-Sundials/CVODE-32\"><span class=\"toc-item-num\">3.2&nbsp;&nbsp;</span>ODE Solvers: Python interface using libroadrunner to Sundials/CVODE</a></div>"
  9. },
  10. {
  11. "metadata": {},
  12. "cell_type": "markdown",
  13. "source": "# Develop Thermodynamic-kinetic Maximum Entropy Model"
  14. },
  15. {
  16. "metadata": {
  17. "trusted": true
  18. },
  19. "cell_type": "code",
  20. "source": "import numpy as np\nimport pandas as pd\nimport matplotlib.pyplot as plt\nimport matplotlib\nimport subprocess\nimport re\nimport os\nimport roadrunner as rr\nfrom IPython.core.display import display\npd.set_option('display.max_columns', None,'display.max_rows', None)\n#from ipynb_latex_setup import *\n%matplotlib inline\nT = 298.15\nR = 8.314e-03\nRT = R*T\nN_avogadro = 6.022140857e+23\nVolCell = 1.0e-15\nConcentration2Count = N_avogadro * VolCell\nconcentration_increment = 1/(N_avogadro*VolCell)",
  21. "execution_count": 1,
  22. "outputs": []
  23. },
  24. {
  25. "metadata": {
  26. "trusted": true
  27. },
  28. "cell_type": "code",
  29. "source": "# Comment/uncomment to change to your directory, if needed:\ncwd = os.getcwd()\nmydir = '/Users/d3k137/docs/projects/boltzmann/code/06212017/run/aerobic_respiration'\nif 'aerobic_respiration' not in cwd: \n os.chdir(mydir)",
  30. "execution_count": 2,
  31. "outputs": []
  32. },
  33. {
  34. "metadata": {},
  35. "cell_type": "markdown",
  36. "source": "## Reactions File"
  37. },
  38. {
  39. "metadata": {
  40. "scrolled": false,
  41. "trusted": true
  42. },
  43. "cell_type": "code",
  44. "source": "cat neurospora_aerobic_respiration3.dat",
  45. "execution_count": 3,
  46. "outputs": [
  47. {
  48. "output_type": "stream",
  49. "text": "REACTION ME1m\r\nLEFT\t(S)-MALATE + NAD+ \r\nRIGHT\tpyruvate + NADH + CO2\r\nLEFT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nRIGHT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nENZYME_LEVEL\t0.0\r\n//\r\nREACTION ME2m\r\nLEFT (S)-MALATE + NADP+\r\nRIGHT PYRUVATE + NADPH + CO2\r\nLEFT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nRIGHT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nENZYME_LEVEL\t0.0\r\n//\r\nREACTION CSm\r\nLEFT\tOXALOACETATE + ACETYL-COA + H2O\r\nRIGHT\tCITRATE + COA\r\nLEFT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nRIGHT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nCOMMENT\tPH = 7.0, IONIC STRENGTH = 0.15 M \r\n//\r\nREACTION ACONTm\r\nLEFT\tCITRATE\r\nRIGHT\tISOCITRATE\r\nLEFT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nRIGHT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nCOMMENT\t PH = 7.0, IONIC STRENGTH = 0.15 M \r\nCOMMENT DOn't split into two reactions if max entropy is being used - only one enzyme needs to be epressed\r\n//\r\nREACTION ICDHxm\r\nLEFT\tISOCITRATE + NAD+\r\nRIGHT\t2-OXOGLUTARATE + NADH + CO2\r\nLEFT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nRIGHT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nCOMMENT\tPH = 7.0, IONIC STRENGTH = 0.15 M\r\n//\r\nREACTION AKGDm\r\nLEFT\t2-OXOGLUTARATE + COA + NAD+\r\nRIGHT\tSUCCINYL-COA + CO2 + NADH\r\nLEFT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nRIGHT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nCOMMENT PH = 7.0, IONIC STRENGTH = 0.15 M\r\n//\r\nREACTION SUCOASm\r\nLEFT \tSUCCINYL-COA + ADP + Orthophosphate\r\nRIGHT\tSUCCINATE + ATP + COA\r\nLEFT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nRIGHT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nCOMMENT\tPH = 7.0, IONIC STRENGTH = 0.15 M\r\n//\r\nREACTION SUCD1m\r\nLEFT\tSUCCINATE:MITOCHONDRIAL_MATRIX + oxygen + NADH\r\nRIGHT\tFUMARATE:MITOCHONDRIAL_MATRIX + 2 H2O + NAD+\r\nLEFT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nRIGHT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nCOMMENT\tPH = 7.0, IONIC STRENGTH = 0.15 M\r\n//\r\nREACTION FUMm\r\nLEFT\tFUMARATE + H2O\r\nRIGHT\t(S)-MALATE \r\nLEFT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nRIGHT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nCOMMENT\tPH = 7.0, IONIC STRENGTH = 0.15 M\r\n//\r\nREACTION MDHm\r\nLEFT\t(S)-MALATE + NAD+\r\nRIGHT\tOXALOACETATE + NADH\r\nLEFT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nRIGHT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nCOMMENT\tPH = 7.0, IONIC STRENGTH = 0.15 M\r\n// \r\nREACTION GAPD \r\nLEFT\tD-GLYCERALDEHYDE-3-PHOSPHATE + ORTHOPHOSPHATE + NAD+\r\nRIGHT\t3-Phospho-D-glyceroyl_phosphate + NADH\r\nENZYME_LEVEL\t1.0\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nPATHWAY GLUCONEOGENESIS, GLYCOLYSIS\r\nCOMMENTS From Dennis\r\n//\r\nREACTION PGK\r\nLEFT\t3-Phospho-D-glyceroyl_phosphate + ADP\r\nRIGHT\t3-PHOSPHO-D-GLYCERATE + ATP\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t1.0\r\nPATHWAY\tGLUCONEOGENESIS, GLYCOLYSIS, CALVIN CYCLE\r\nCOMMENTS From Dennis\r\n//\r\nREACTION TPI\r\nLEFT\tGlycerone_phosphate\r\nRIGHT\tD-GLYCERALDEHYDE-3-PHOSPHATE\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t1.0\r\nCOMMENT From Equilibrator\r\nPATHWAY CALVIN CYCLE, GLYCOLYSIS\r\n//\r\nREACTION MDH\r\nLEFT\t(S)-MALATE + NAD+\r\nRIGHT\tOXALOACETATE + NADH\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t0.0\r\nCOMMENT\tPH = 7.0, IONIC STRENGTH = 0.15 M\r\nCOMMENT\tCytosolic\r\n//\r\nREACTION PEP_Carboxylase\r\nLEFT oxaloacetate + orthophosphate\r\nRIGHT phosphoenolpyruvate + CO2 + H2O\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL 0.0\r\nPATHWAY GLUCONEOGENSESIS\r\nCOMMENTS\r\n//\r\nREACTION PPCK\r\nLEFT\toxaloacetate + ATP \r\nRIGHT\tphosphoenolpyruvate + ADP + CO2\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t0.0\r\nPATHWAY\tGLUCONEOGENSESIS\r\nCOMMENTS \r\n//\r\nREACTION FBA\r\nLEFT\tD-FRUCTOSE_1,6-BISPHOSPHATE\r\nRIGHT\tGlycerone_phosphate + D-GLYCERALDEHYDE-3-PHOSPHATE\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t1.0\r\nPATHWAY\tGLUCONEOGENSESIS, GLYCOLYSIS, CALVIN CYCLE\r\nCOMMENTS From Dennis\r\n//\r\nREACTION FBP\r\nLEFT\tD-FRUCTOSE_6-PHOSPHATE + Orthophosphate\r\nRIGHT\tH2O + D-FRUCTOSE_1,6-BISPHOSPHATE\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t0.0\r\nPATHWAY\tGLUCONEOGENESIS, CALVIN CYCLE\r\nCOMMENTS From Dennis\r\n//\r\nREACTION TKT2\r\nLEFT\tD-FRUCTOSE_6-PHOSPHATE + D-GLYCERALDEHYDE-3-PHOSPHATE\r\nRIGHT\tD-ERYTHROSE-4-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t0.0\r\nPATHWAY\tCALVIN CYCLE, PENTOSE PHOSPHATE PATHWAY, RUBISCO SHUNT\r\nCOMMENT From Equilibrator pH 7.5, IS 0.15\r\n//\r\nREACTION RPE\r\nLEFT\tD-XYLULOSE-5-PHOSPHATE\r\nRIGHT\tD-RIBULOSE-5-PHOSPHATE\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t0.0\r\nPATHWAY\tCALVIN CYCLE, PENTOSE PHOSPHATE PATHWAY, RUBISCO SHUNT\r\nCOMMENT From Dennis\r\n//\r\nREACTION Xylulokinase\r\nLEFT\tD-XYLULOSE + ATP\r\nRIGHT\tD-XYLULOSE-5-PHOSPHATE + ADP \r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t0.0\r\nPATHWAY\tCALVIN CYCLE, PENTOSE PHOSPHATE PATHWAY, RUBISCO SHUNT\r\nCOMMENT \r\n//\r\nREACTION PYK_org\r\nLEFT\tADP + PHOSPHOENOLPYRUVATE\r\nRIGHT\tPYRUVATE + ATP\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t0.0\r\nPATHWAY GLYCOLYSIS, PYRUVATE METABOLISM, RUBISCO SHUNT\r\nCOMMENT From Dennis\r\n//\r\nREACTION PYK\r\nLEFT\tADP + PHOSPHOENOLPYRUVATE\r\nRIGHT\tPYRUVATE + ATP\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t1.0\r\nPATHWAY GLYCOLYSIS, PYRUVATE METABOLISM, RUBISCO SHUNT\r\nCOMMENT From Dennis\r\n//\r\nREACTION RPI\r\nLEFT\tD-RIBOSE-5-PHOSPHATE\r\nRIGHT\tD-RIBULOSE-5-PHOSPHATE\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t0.0\r\nPATHWAY\tCALVIN CYCLE, PENTOSE PHOSPHATE PATHWAY, RUBISCO SHUNT\r\nCOMMENT From Dennis\r\n//\r\nREACTION TKT1\r\nLEFT\tSEDOHEPTULOSE_7-PHOSPHATE + D-GLYCERALDEHYDE-3-PHOSPHATE\r\nRIGHT\tD-RIBOSE-5-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t0.0\r\nPATHWAY\tCALVIN CYCLE, PENTOSE PHOSPHATE PATHWAY, RUBISCO SHUNT\r\nCOMMENT From Equilibrator pH 7.5, IS 0.15\r\n//\r\nREACTION TALA\r\nLEFT\tD-GLYCERALDEHYDE-3-PHOSPHATE + SEDOHEPTULOSE_7-PHOSPHATE\r\nRIGHT\tD-FRUCTOSE_6-PHOSPHATE + D-ERYTHROSE-4-PHOSPHATE\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t0.0\r\nPATHWAY RUBISCO SHUNT, PENTOSE PHOSPHATE PATHWAY\r\nCOMMENT From Equilibrator pH 7.5 IS 0.15\r\n//\r\nREACTION PGM\r\nLEFT\t3-PHOSPHO-D-GLYCERATE\r\nRIGHT\t2-PHOSPHO-D-GLYCERATE\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t1.0\r\nPATHWAY GLUCONEOGENESIS, RUBISCO SHUNT, GLYCOLYSIS I\r\nCOMMENTS From Dennis\r\n//\r\nREACTION ENO\r\nLEFT\t2-PHOSPHO-D-GLYCERATE\r\nRIGHT\tPHOSPHOENOLPYRUVATE + H2O\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t1.0\r\nPATHWAY GLUCONEOGENESIS, RUBISCO SHUNT, GLYCOLYSIS I\r\nCOMMENTS From Dennis\r\n//\r\n# Pentose Phosphate reactions (oxidative branch):\r\nREACTION GND\r\nLEFT NADPH + D-RIBULOSE-5-PHOSPHATE + CO2\r\nRIGHT NADP+ + 6-PHOSPHO-D-GLUCONATE\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nPATHWAY PENTOSE PHOSPHATE PATHWAY\r\nENZYME_LEVEL\t0.0\r\n//\r\nREACTION PGL\r\nLEFT 6-PHOSPHO-D-GLUCONATE\r\nRIGHT D-Glucono-1,5-lactone_6-phosphate + H2O\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nCOMMENT From Dennis\r\nPATHWAY PENTOSE PHOSPHATE PATHWAY\r\nENZYME_LEVEL\t0.0\r\n//\r\nREACTION HEX1\r\nLEFT\tBETA-D-GLUCOSE + ATP\r\nRIGHT\tBETA-D-GLUCOSE-6-PHOSPHATE + ADP\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nNREGULATION ATP 2.80e-03 10\r\nENZYME_LEVEL\t1.0\r\nPATHWAY\tGLUCONEOGENESIS, (GLYCOLYSIS-YEAST), GLYCOLYSIS\r\nCOMMENTS From Dennis\r\n//\r\nREACTION PGI\r\nLEFT\tBETA-D-GLUCOSE-6-PHOSPHATE\r\nRIGHT\tD-FRUCTOSE_6-PHOSPHATE\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t1.0\r\nPATHWAY\tGLUCONEOGENESIS, (GLYCOLYSIS-YEAST), GLYCOLYSIS\r\nCOMMENTS From Dennis\r\n//\r\n# Gluconeogenesis reactions :\r\nREACTION G6PDH2r\r\nLEFT\tBETA-D-GLUCOSE-6-PHOSPHATE + NADP+\r\nRIGHT\tD-Glucono-1,5-lactone_6-phosphate + NADPH\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t0.0\r\nCOMMENT From Dennis\r\nPATHWAY GLUCONEOGENESIS\r\n//\r\n# Glycolysis reactions :\r\nREACTION PFK\r\nLEFT \tD-FRUCTOSE_6-PHOSPHATE + ATP\r\nRIGHT\tADP + D-FRUCTOSE_1,6-BISPHOSPHATE\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nNREGULATION ATP 2.80e-03 10\r\nENZYME_LEVEL\t1.0\r\nPATHWAY GLYCOLYSIS\r\nCOMMENT From Equilibrator\r\n//\r\nREACTION PYRt2m\r\nLEFT\tPYRUVATE\r\nRIGHT\tPYRUVATE\r\nDGZERO\t-5.94\r\nCOMMENT -5.94\r\nDGZERO-UNITS\tKJ/MOL\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nENZYME_LEVEL\t1.0\r\nCOMMENT PYRUVATE TRANSPORT INTO MITOCHONDRIA - Assuming free energy difference = \\Delta -RT \\Delta pH = -RT log 10\r\n//\r\n# Acetyl CoA synthesis\r\nREACTION PDHm\r\nLEFT\tCOA + NAD+ + PYRUVATE\r\nRIGHT\tACETYL-COA + CO2 + NADH\r\nLEFT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nRIGHT_COMPARTMENT MITOCHONDRIAL_MATRIX\r\nENZYME_LEVEL\t1.0\r\nNREGULATION ACETYL-COA 1.00e-03 20\r\nPATHWAY ACETYL COA BIOSYNTHESIS\r\nCOMMENT PYRUVATE DEHYDROGENASE SUMMARY REACTION\r\n//\r\nREACTION ICL\r\nLEFT isocitrate\r\nRIGHT\tglyoxylate + succinate\r\nLEFT_COMPARTMENT GLYOXYSOME\r\nRIGHT_COMPARTMENT GLYOXYSOME\r\nENZYME_LEVEL\t0.0\r\nPATHWAY glyoxylate shunt\r\nCOMMENT \r\n//\r\nREACTION MAS\r\nLEFT acetyl-CoA + glyoxylate + H2O \r\nRIGHT\t(S)-MALATE + COA\r\nLEFT_COMPARTMENT GLYOXYSOME\r\nRIGHT_COMPARTMENT GLYOXYSOME\r\nENZYME_LEVEL\t0.0\r\nPATHWAY glyoxylate shunt\r\nCOMMENT \r\n//\r\nREACTION PYRDC\r\nLEFT pyruvate \r\nRIGHT acetaldehyde + CO2\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t0.0\r\nPATHWAY fermentation\r\nCOMMENT \r\n//\r\nREACTION ALDD2y\r\nLEFT acetaldehyde + NADP+ + H2O\r\nRIGHT acetate + NADPH\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t0.0\r\nPATHWAY fermentation\r\nCOMMENT \r\n//\r\nREACTION ALCD2X_copy1\r\nLEFT acetaldehyde + NADH \r\nRIGHT ethanol + NAD+\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t0.0\r\nPATHWAY fermentation\r\nCOMMENT \r\n//\r\nREACTION LactateDehydrogenase\r\nLEFT pyruvate + NADH\r\nRIGHT lactate + NAD+\r\nLEFT_COMPARTMENT CYTOSOL\r\nRIGHT_COMPARTMENT CYTOSOL\r\nENZYME_LEVEL\t0.0\r\nPATHWAY fermentation\r\nCOMMENT \r\n//\r\nREACTION Mitochondrial complex I/NADH ubiquinone oxidoredectase\r\nLEFT NADH:MITOCHONDRIAL_MATRIX + ubiquinone-6:MITOCHONDRIAL_MEMBRANE \r\nRIGHT NAD+:MITOCHONDRIAL_MATRIX + ubiquinol-6:MITOCHONDRIAL_MEMBRANE \r\nENZYME_LEVEL\t0.0\r\nPATHWAY \r\nCOMMENT transfers protons and electron to ubiqunone\r\n//\r\nREACTION Mitochondrial complex III\r\nLEFT ubiquinol-6 + 2 ferricytochrome_c\r\nRIGHT ubiQUINONE-6 + 2 ferrocytochrome_c\r\nLEFT_COMPARTMENT Mitochondrial_Membrane\r\nRIGHT_COMPARTMENT Mitochondrial_Membrane\r\nENZYME_LEVEL\t0.0\r\nPATHWAY \r\n//\r\nREACTION Mitochondrial complex IV\r\nLEFT 4 ferrocytochrome_c:mitochondrial_membrane + oxygen:mitochondrial_matrix\r\nRIGHT 4 ferricytochrome_c:mitochondrial_membrane + 2 H2O:mitochondrial_matrix\r\nENZYME_LEVEL\t0.0\r\nPATHWAY \r\nCOMMENT transfers protons and electron to ubiqunone\r\n//\r\n",
  50. "name": "stdout"
  51. }
  52. ]
  53. },
  54. {
  55. "metadata": {},
  56. "cell_type": "markdown",
  57. "source": "### Read the file into a dataframe and create a stoichiometric matrix"
  58. },
  59. {
  60. "metadata": {
  61. "scrolled": false,
  62. "trusted": true
  63. },
  64. "cell_type": "code",
  65. "source": "fdat = open('neurospora_aerobic_respiration3.dat', 'r')\nleft ='LEFT'\nright = 'RIGHT'\nleft_compartment = 'LEFT_COMPARTMENT'\nright_compartment = 'RIGHT_COMPARTMENT'\nenzyme_level = 'ENZYME_LEVEL'\ndeltag0 = 'DGZERO'\ndeltag0_sigma = 'DGZERO StdDev'\nsame_compartment = 'Same Compartment?'\nfull_rxn = 'Full Rxn'\n\nreactions = pd.DataFrame(index=[],columns=[left, right, left_compartment, right_compartment, enzyme_level, deltag0, deltag0_sigma, same_compartment,full_rxn])\nreactions.index.name='REACTION'\nS_matrix = pd.DataFrame(index=[],columns=[enzyme_level])\nS_matrix.index.name='REACTION'\n\nfor line in fdat:\n if (line.startswith('REACTION ')):\n rxn_name = line[9:-1].lstrip()\n S_matrix.loc[rxn_name,enzyme_level] = 1.0\n reactions.loc[rxn_name,enzyme_level] = 1.0\n\n if (re.match(\"^LEFT\\s\",line)):\n line = line.upper()\n left_rxn = line[4:-1].lstrip()\n left_rxn = re.sub(r'\\s+$', '', left_rxn) #Remove trailing white space\n reactions.loc[rxn_name,left] = left_rxn\n\n elif (re.match('^RIGHT\\s',line)):\n line = line.upper()\n right_rxn = line[5:-1].lstrip()\n right_rxn = re.sub(r'\\s+$', '', right_rxn) #Remove trailing white space\n reactions.loc[rxn_name,right] = right_rxn\n \n elif (line.startswith(left_compartment)):\n cpt_name = line[16:-1].lstrip()\n reactions.loc[rxn_name,left_compartment] = cpt_name\n reactants = re.split(' \\+ ',left_rxn)\n for idx in reactants:\n values = re.split(' ', idx);\n if len(values) == 2:\n stoichiometry = np.float64(values[0]);\n molecule = values[1];\n if not re.search(':',molecule):\n molecule = molecule + ':' + cpt_name\n else:\n stoichiometry = np.float64(-1.0);\n molecule = values[0]; \n if not re.search(':',molecule):\n molecule = molecule + ':' + cpt_name\n S_matrix.loc[rxn_name,molecule] = stoichiometry;\n\n\n elif (line.startswith(right_compartment)):\n cpt_name = line[17:-1].lstrip()\n reactions.loc[rxn_name,right_compartment] = cpt_name\n products = re.split(' \\+ ',right_rxn)\n for idx in products:\n values = re.split(' ', idx);\n if len(values) == 2:\n stoichiometry = np.float64(values[0]);\n molecule = values[1];\n if not re.search(':',molecule):\n molecule = molecule + ':' + cpt_name\n else:\n stoichiometry = np.float64(1.0);\n molecule = values[0];\n if not re.search(':',molecule):\n molecule = molecule + ':' + cpt_name\n S_matrix.loc[rxn_name,molecule] = stoichiometry;\n\n elif (re.match(\"^ENZYME_LEVEL\\s\", line)):\n level = line[12:-1].lstrip()\n reactions.loc[rxn_name,enzyme_level] = float(level)\n S_matrix.loc[rxn_name,enzyme_level] = float(level)\n \n elif re.match('^COMMENT',line):\n continue\n elif re.match(r'//',line):\n continue\n elif re.match('^#',line):\n continue\n \n# elif (re.match(\"^[N,P]REGULATION\\s\", line)):\n# reg = line\n# reactions.loc[rxn_name,regulation] = reg\nfdat.close()\nS_matrix.fillna(0,inplace=True)\nS_active = S_matrix[S_matrix[enzyme_level] > 0.0]\nactive_reactions = reactions[reactions[enzyme_level] > 0.0]\ndel S_active[enzyme_level]\n# Delete any columns/metabolites that have all zeros in the S matrix:\nS_active = S_active.loc[:, (S_active != 0).any(axis=0)]\nnp.shape(S_active.values)\ndisplay(S_active.shape)\ndisplay(S_active)\nreactions[full_rxn] = reactions[left] + ' = ' + reactions[right]",
  66. "execution_count": 4,
  67. "outputs": [
  68. {
  69. "output_type": "display_data",
  70. "data": {
  71. "text/plain": "(20, 36)"
  72. },
  73. "metadata": {}
  74. },
  75. {
  76. "output_type": "display_data",
  77. "data": {
  78. "text/plain": " (S)-MALATE:MITOCHONDRIAL_MATRIX NAD+:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 -1.0 \nAKGDm 0.0 -1.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 1.0 \nFUMm 1.0 0.0 \nMDHm -1.0 -1.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 -1.0 \n\n PYRUVATE:MITOCHONDRIAL_MATRIX NADH:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 1.0 \nAKGDm 0.0 1.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 -1.0 \nFUMm 0.0 0.0 \nMDHm 0.0 1.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 1.0 0.0 \nPDHm -1.0 1.0 \n\n CO2:MITOCHONDRIAL_MATRIX OXALOACETATE:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 -1.0 \nACONTm 0.0 0.0 \nICDHxm 1.0 0.0 \nAKGDm 1.0 0.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 1.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 1.0 0.0 \n\n ACETYL-COA:MITOCHONDRIAL_MATRIX H2O:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm -1.0 -1.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 2.0 \nFUMm 0.0 -1.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 1.0 0.0 \n\n CITRATE:MITOCHONDRIAL_MATRIX COA:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 1.0 1.0 \nACONTm -1.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 -1.0 \nSUCOASm 0.0 1.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 -1.0 \n\n ISOCITRATE:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 \nACONTm 1.0 \nICDHxm -1.0 \nAKGDm 0.0 \nSUCOASm 0.0 \nSUCD1m 0.0 \nFUMm 0.0 \nMDHm 0.0 \nGAPD 0.0 \nPGK 0.0 \nTPI 0.0 \nFBA 0.0 \nPYK 0.0 \nPGM 0.0 \nENO 0.0 \nHEX1 0.0 \nPGI 0.0 \nPFK 0.0 \nPYRt2m 0.0 \nPDHm 0.0 \n\n 2-OXOGLUTARATE:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 \nACONTm 0.0 \nICDHxm 1.0 \nAKGDm -1.0 \nSUCOASm 0.0 \nSUCD1m 0.0 \nFUMm 0.0 \nMDHm 0.0 \nGAPD 0.0 \nPGK 0.0 \nTPI 0.0 \nFBA 0.0 \nPYK 0.0 \nPGM 0.0 \nENO 0.0 \nHEX1 0.0 \nPGI 0.0 \nPFK 0.0 \nPYRt2m 0.0 \nPDHm 0.0 \n\n SUCCINYL-COA:MITOCHONDRIAL_MATRIX ADP:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 1.0 0.0 \nSUCOASm -1.0 -1.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 0.0 \n\n ORTHOPHOSPHATE:MITOCHONDRIAL_MATRIX SUCCINATE:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm -1.0 1.0 \nSUCD1m 0.0 -1.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 0.0 \n\n ATP:MITOCHONDRIAL_MATRIX OXYGEN:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm 1.0 0.0 \nSUCD1m 0.0 -1.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 0.0 \n\n FUMARATE:MITOCHONDRIAL_MATRIX D-GLYCERALDEHYDE-3-PHOSPHATE:CYTOSOL \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm 0.0 0.0 \nSUCD1m 1.0 0.0 \nFUMm -1.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 -1.0 \nPGK 0.0 0.0 \nTPI 0.0 1.0 \nFBA 0.0 1.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 0.0 \n\n ORTHOPHOSPHATE:CYTOSOL NAD+:CYTOSOL \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD -1.0 -1.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 0.0 \n\n 3-PHOSPHO-D-GLYCEROYL_PHOSPHATE:CYTOSOL NADH:CYTOSOL ADP:CYTOSOL \\\nREACTION \nCSm 0.0 0.0 0.0 \nACONTm 0.0 0.0 0.0 \nICDHxm 0.0 0.0 0.0 \nAKGDm 0.0 0.0 0.0 \nSUCOASm 0.0 0.0 0.0 \nSUCD1m 0.0 0.0 0.0 \nFUMm 0.0 0.0 0.0 \nMDHm 0.0 0.0 0.0 \nGAPD 1.0 1.0 0.0 \nPGK -1.0 0.0 -1.0 \nTPI 0.0 0.0 0.0 \nFBA 0.0 0.0 0.0 \nPYK 0.0 0.0 -1.0 \nPGM 0.0 0.0 0.0 \nENO 0.0 0.0 0.0 \nHEX1 0.0 0.0 1.0 \nPGI 0.0 0.0 0.0 \nPFK 0.0 0.0 1.0 \nPYRt2m 0.0 0.0 0.0 \nPDHm 0.0 0.0 0.0 \n\n 3-PHOSPHO-D-GLYCERATE:CYTOSOL ATP:CYTOSOL \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 1.0 1.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 1.0 \nPGM -1.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 -1.0 \nPGI 0.0 0.0 \nPFK 0.0 -1.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 0.0 \n\n GLYCERONE_PHOSPHATE:CYTOSOL PHOSPHOENOLPYRUVATE:CYTOSOL \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI -1.0 0.0 \nFBA 1.0 0.0 \nPYK 0.0 -1.0 \nPGM 0.0 0.0 \nENO 0.0 1.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 0.0 \n\n H2O:CYTOSOL D-FRUCTOSE_1,6-BISPHOSPHATE:CYTOSOL \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 -1.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 1.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 1.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 0.0 \n\n D-FRUCTOSE_6-PHOSPHATE:CYTOSOL PYRUVATE:CYTOSOL \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 1.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 1.0 0.0 \nPFK -1.0 0.0 \nPYRt2m 0.0 -1.0 \nPDHm 0.0 0.0 \n\n 2-PHOSPHO-D-GLYCERATE:CYTOSOL BETA-D-GLUCOSE:CYTOSOL \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 1.0 0.0 \nENO -1.0 0.0 \nHEX1 0.0 -1.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 0.0 \n\n BETA-D-GLUCOSE-6-PHOSPHATE:CYTOSOL \nREACTION \nCSm 0.0 \nACONTm 0.0 \nICDHxm 0.0 \nAKGDm 0.0 \nSUCOASm 0.0 \nSUCD1m 0.0 \nFUMm 0.0 \nMDHm 0.0 \nGAPD 0.0 \nPGK 0.0 \nTPI 0.0 \nFBA 0.0 \nPYK 0.0 \nPGM 0.0 \nENO 0.0 \nHEX1 1.0 \nPGI -1.0 \nPFK 0.0 \nPYRt2m 0.0 \nPDHm 0.0 ",
  79. "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>(S)-MALATE:MITOCHONDRIAL_MATRIX</th>\n <th>NAD+:MITOCHONDRIAL_MATRIX</th>\n <th>PYRUVATE:MITOCHONDRIAL_MATRIX</th>\n <th>NADH:MITOCHONDRIAL_MATRIX</th>\n <th>CO2:MITOCHONDRIAL_MATRIX</th>\n <th>OXALOACETATE:MITOCHONDRIAL_MATRIX</th>\n <th>ACETYL-COA:MITOCHONDRIAL_MATRIX</th>\n <th>H2O:MITOCHONDRIAL_MATRIX</th>\n <th>CITRATE:MITOCHONDRIAL_MATRIX</th>\n <th>COA:MITOCHONDRIAL_MATRIX</th>\n <th>ISOCITRATE:MITOCHONDRIAL_MATRIX</th>\n <th>2-OXOGLUTARATE:MITOCHONDRIAL_MATRIX</th>\n <th>SUCCINYL-COA:MITOCHONDRIAL_MATRIX</th>\n <th>ADP:MITOCHONDRIAL_MATRIX</th>\n <th>ORTHOPHOSPHATE:MITOCHONDRIAL_MATRIX</th>\n <th>SUCCINATE:MITOCHONDRIAL_MATRIX</th>\n <th>ATP:MITOCHONDRIAL_MATRIX</th>\n <th>OXYGEN:MITOCHONDRIAL_MATRIX</th>\n <th>FUMARATE:MITOCHONDRIAL_MATRIX</th>\n <th>D-GLYCERALDEHYDE-3-PHOSPHATE:CYTOSOL</th>\n <th>ORTHOPHOSPHATE:CYTOSOL</th>\n <th>NAD+:CYTOSOL</th>\n <th>3-PHOSPHO-D-GLYCEROYL_PHOSPHATE:CYTOSOL</th>\n <th>NADH:CYTOSOL</th>\n <th>ADP:CYTOSOL</th>\n <th>3-PHOSPHO-D-GLYCERATE:CYTOSOL</th>\n <th>ATP:CYTOSOL</th>\n <th>GLYCERONE_PHOSPHATE:CYTOSOL</th>\n <th>PHOSPHOENOLPYRUVATE:CYTOSOL</th>\n <th>H2O:CYTOSOL</th>\n <th>D-FRUCTOSE_1,6-BISPHOSPHATE:CYTOSOL</th>\n <th>D-FRUCTOSE_6-PHOSPHATE:CYTOSOL</th>\n <th>PYRUVATE:CYTOSOL</th>\n <th>2-PHOSPHO-D-GLYCERATE:CYTOSOL</th>\n <th>BETA-D-GLUCOSE:CYTOSOL</th>\n <th>BETA-D-GLUCOSE-6-PHOSPHATE:CYTOSOL</th>\n </tr>\n <tr>\n <th>REACTION</th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <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>CSm</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>-1.0</td>\n <td>-1.0</td>\n <td>1.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>ACONTm</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>ICDHxm</th>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>AKGDm</th>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>SUCOASm</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>-1.0</td>\n <td>-1.0</td>\n <td>1.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>SUCD1m</th>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>2.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>FUMm</th>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>MDHm</th>\n <td>-1.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>GAPD</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>-1.0</td>\n <td>-1.0</td>\n <td>1.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>PGK</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>1.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>TPI</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>FBA</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>PYK</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>PGM</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>ENO</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>HEX1</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>1.0</td>\n </tr>\n <tr>\n <th>PGI</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n </tr>\n <tr>\n <th>PFK</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>PYRt2m</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>PDHm</th>\n <td>0.0</td>\n <td>-1.0</td>\n <td>-1.0</td>\n <td>1.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n </tbody>\n</table>\n</div>"
  80. },
  81. "metadata": {}
  82. }
  83. ]
  84. },
  85. {
  86. "metadata": {
  87. "scrolled": false,
  88. "trusted": true
  89. },
  90. "cell_type": "code",
  91. "source": "if (1): \n for idx in reactions.index:\n #print(idx,flush=True)\n boltzmann_rxn_str = reactions.loc[idx,'Full Rxn']\n if re.search(':',boltzmann_rxn_str):\n all_cmprts = re.findall(':\\S+', boltzmann_rxn_str)\n [s.replace(':', '') for s in all_cmprts] # remove all the ':'s \n different_compartments = 0\n for cmpt in all_cmprts:\n if not re.match(all_cmprts[0],cmpt):\n different_compartments = 1\n if ((not different_compartments) and (reactions[left_compartment].isnull or reactions[right_compartment].isnull)):\n reactions.loc[idx,left_compartment] = cmpt\n reactions.loc[idx,right_compartment] = cmpt\n reactions.loc[idx,same_compartment] = True\n if different_compartments:\n reactions.loc[idx,same_compartment] = False\n else:\n if (reactions.loc[idx,left_compartment] == reactions.loc[idx,right_compartment]):\n reactions.loc[idx,same_compartment] = True\n else:\n reactions.loc[idx,same_compartment] = False\ndisplay(reactions) \n ",
  92. "execution_count": 5,
  93. "outputs": [
  94. {
  95. "output_type": "display_data",
  96. "data": {
  97. "text/plain": " LEFT \\\nREACTION \nME1m (S)-MALATE + NAD+ \nME2m (S)-MALATE + NADP+ \nCSm OXALOACETATE + ACETYL-COA + H2O \nACONTm CITRATE \nICDHxm ISOCITRATE + NAD+ \nAKGDm 2-OXOGLUTARATE + COA + NAD+ \nSUCOASm SUCCINYL-COA + ADP + ORTHOPHOSPHATE \nSUCD1m SUCCINATE:MITOCHONDRIAL_MATRIX + OXYGEN + NADH \nFUMm FUMARATE + H2O \nMDHm (S)-MALATE + NAD+ \nGAPD D-GLYCERALDEHYDE-3-PHOSPHATE + ORTHOPHOSPHATE ... \nPGK 3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + ADP \nTPI GLYCERONE_PHOSPHATE \nMDH (S)-MALATE + NAD+ \nPEP_Carboxylase OXALOACETATE + ORTHOPHOSPHATE \nPPCK OXALOACETATE + ATP \nFBA D-FRUCTOSE_1,6-BISPHOSPHATE \nFBP D-FRUCTOSE_6-PHOSPHATE + ORTHOPHOSPHATE \nTKT2 D-FRUCTOSE_6-PHOSPHATE + D-GLYCERALDEHYDE-3-PH... \nRPE D-XYLULOSE-5-PHOSPHATE \nXylulokinase D-XYLULOSE + ATP \nPYK_org ADP + PHOSPHOENOLPYRUVATE \nPYK ADP + PHOSPHOENOLPYRUVATE \nRPI D-RIBOSE-5-PHOSPHATE \nTKT1 SEDOHEPTULOSE_7-PHOSPHATE + D-GLYCERALDEHYDE-3... \nTALA D-GLYCERALDEHYDE-3-PHOSPHATE + SEDOHEPTULOSE_7... \nPGM 3-PHOSPHO-D-GLYCERATE \nENO 2-PHOSPHO-D-GLYCERATE \nGND NADPH + D-RIBULOSE-5-PHOSPHATE + CO2 \nPGL 6-PHOSPHO-D-GLUCONATE \nHEX1 BETA-D-GLUCOSE + ATP \nPGI BETA-D-GLUCOSE-6-PHOSPHATE \nG6PDH2r BETA-D-GLUCOSE-6-PHOSPHATE + NADP+ \nPFK D-FRUCTOSE_6-PHOSPHATE + ATP \nPYRt2m PYRUVATE \nPDHm COA + NAD+ + PYRUVATE \nICL ISOCITRATE \nMAS ACETYL-COA + GLYOXYLATE + H2O \nPYRDC PYRUVATE \nALDD2y ACETALDEHYDE + NADP+ + H2O \nALCD2X_copy1 ACETALDEHYDE + NADH \nLactateDehydrogenase PYRUVATE + NADH \nMitochondrial complex I/NADH ubiquinone oxidore... NADH:MITOCHONDRIAL_MATRIX + UBIQUINONE-6:MITOC... \nMitochondrial complex III UBIQUINOL-6 + 2 FERRICYTOCHROME_C \nMitochondrial complex IV 4 FERROCYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + O... \n\n RIGHT \\\nREACTION \nME1m PYRUVATE + NADH + CO2 \nME2m PYRUVATE + NADPH + CO2 \nCSm CITRATE + COA \nACONTm ISOCITRATE \nICDHxm 2-OXOGLUTARATE + NADH + CO2 \nAKGDm SUCCINYL-COA + CO2 + NADH \nSUCOASm SUCCINATE + ATP + COA \nSUCD1m FUMARATE:MITOCHONDRIAL_MATRIX + 2 H2O + NAD+ \nFUMm (S)-MALATE \nMDHm OXALOACETATE + NADH \nGAPD 3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + NADH \nPGK 3-PHOSPHO-D-GLYCERATE + ATP \nTPI D-GLYCERALDEHYDE-3-PHOSPHATE \nMDH OXALOACETATE + NADH \nPEP_Carboxylase PHOSPHOENOLPYRUVATE + CO2 + H2O \nPPCK PHOSPHOENOLPYRUVATE + ADP + CO2 \nFBA GLYCERONE_PHOSPHATE + D-GLYCERALDEHYDE-3-PHOSP... \nFBP H2O + D-FRUCTOSE_1,6-BISPHOSPHATE \nTKT2 D-ERYTHROSE-4-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE \nRPE D-RIBULOSE-5-PHOSPHATE \nXylulokinase D-XYLULOSE-5-PHOSPHATE + ADP \nPYK_org PYRUVATE + ATP \nPYK PYRUVATE + ATP \nRPI D-RIBULOSE-5-PHOSPHATE \nTKT1 D-RIBOSE-5-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE \nTALA D-FRUCTOSE_6-PHOSPHATE + D-ERYTHROSE-4-PHOSPHATE \nPGM 2-PHOSPHO-D-GLYCERATE \nENO PHOSPHOENOLPYRUVATE + H2O \nGND NADP+ + 6-PHOSPHO-D-GLUCONATE \nPGL D-GLUCONO-1,5-LACTONE_6-PHOSPHATE + H2O \nHEX1 BETA-D-GLUCOSE-6-PHOSPHATE + ADP \nPGI D-FRUCTOSE_6-PHOSPHATE \nG6PDH2r D-GLUCONO-1,5-LACTONE_6-PHOSPHATE + NADPH \nPFK ADP + D-FRUCTOSE_1,6-BISPHOSPHATE \nPYRt2m PYRUVATE \nPDHm ACETYL-COA + CO2 + NADH \nICL GLYOXYLATE + SUCCINATE \nMAS (S)-MALATE + COA \nPYRDC ACETALDEHYDE + CO2 \nALDD2y ACETATE + NADPH \nALCD2X_copy1 ETHANOL + NAD+ \nLactateDehydrogenase LACTATE + NAD+ \nMitochondrial complex I/NADH ubiquinone oxidore... NAD+:MITOCHONDRIAL_MATRIX + UBIQUINOL-6:MITOCH... \nMitochondrial complex III UBIQUINONE-6 + 2 FERROCYTOCHROME_C \nMitochondrial complex IV 4 FERRICYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + 2... \n\n LEFT_COMPARTMENT \\\nREACTION \nME1m MITOCHONDRIAL_MATRIX \nME2m MITOCHONDRIAL_MATRIX \nCSm MITOCHONDRIAL_MATRIX \nACONTm MITOCHONDRIAL_MATRIX \nICDHxm MITOCHONDRIAL_MATRIX \nAKGDm MITOCHONDRIAL_MATRIX \nSUCOASm MITOCHONDRIAL_MATRIX \nSUCD1m :MITOCHONDRIAL_MATRIX \nFUMm MITOCHONDRIAL_MATRIX \nMDHm MITOCHONDRIAL_MATRIX \nGAPD CYTOSOL \nPGK CYTOSOL \nTPI CYTOSOL \nMDH CYTOSOL \nPEP_Carboxylase CYTOSOL \nPPCK CYTOSOL \nFBA CYTOSOL \nFBP CYTOSOL \nTKT2 CYTOSOL \nRPE CYTOSOL \nXylulokinase CYTOSOL \nPYK_org CYTOSOL \nPYK CYTOSOL \nRPI CYTOSOL \nTKT1 CYTOSOL \nTALA CYTOSOL \nPGM CYTOSOL \nENO CYTOSOL \nGND CYTOSOL \nPGL CYTOSOL \nHEX1 CYTOSOL \nPGI CYTOSOL \nG6PDH2r CYTOSOL \nPFK CYTOSOL \nPYRt2m CYTOSOL \nPDHm MITOCHONDRIAL_MATRIX \nICL GLYOXYSOME \nMAS GLYOXYSOME \nPYRDC CYTOSOL \nALDD2y CYTOSOL \nALCD2X_copy1 CYTOSOL \nLactateDehydrogenase CYTOSOL \nMitochondrial complex I/NADH ubiquinone oxidore... NaN \nMitochondrial complex III Mitochondrial_Membrane \nMitochondrial complex IV NaN \n\n RIGHT_COMPARTMENT \\\nREACTION \nME1m MITOCHONDRIAL_MATRIX \nME2m MITOCHONDRIAL_MATRIX \nCSm MITOCHONDRIAL_MATRIX \nACONTm MITOCHONDRIAL_MATRIX \nICDHxm MITOCHONDRIAL_MATRIX \nAKGDm MITOCHONDRIAL_MATRIX \nSUCOASm MITOCHONDRIAL_MATRIX \nSUCD1m :MITOCHONDRIAL_MATRIX \nFUMm MITOCHONDRIAL_MATRIX \nMDHm MITOCHONDRIAL_MATRIX \nGAPD CYTOSOL \nPGK CYTOSOL \nTPI CYTOSOL \nMDH CYTOSOL \nPEP_Carboxylase CYTOSOL \nPPCK CYTOSOL \nFBA CYTOSOL \nFBP CYTOSOL \nTKT2 CYTOSOL \nRPE CYTOSOL \nXylulokinase CYTOSOL \nPYK_org CYTOSOL \nPYK CYTOSOL \nRPI CYTOSOL \nTKT1 CYTOSOL \nTALA CYTOSOL \nPGM CYTOSOL \nENO CYTOSOL \nGND CYTOSOL \nPGL CYTOSOL \nHEX1 CYTOSOL \nPGI CYTOSOL \nG6PDH2r CYTOSOL \nPFK CYTOSOL \nPYRt2m MITOCHONDRIAL_MATRIX \nPDHm MITOCHONDRIAL_MATRIX \nICL GLYOXYSOME \nMAS GLYOXYSOME \nPYRDC CYTOSOL \nALDD2y CYTOSOL \nALCD2X_copy1 CYTOSOL \nLactateDehydrogenase CYTOSOL \nMitochondrial complex I/NADH ubiquinone oxidore... NaN \nMitochondrial complex III Mitochondrial_Membrane \nMitochondrial complex IV NaN \n\n ENZYME_LEVEL DGZERO \\\nREACTION \nME1m 0 NaN \nME2m 0 NaN \nCSm 1 NaN \nACONTm 1 NaN \nICDHxm 1 NaN \nAKGDm 1 NaN \nSUCOASm 1 NaN \nSUCD1m 1 NaN \nFUMm 1 NaN \nMDHm 1 NaN \nGAPD 1 NaN \nPGK 1 NaN \nTPI 1 NaN \nMDH 0 NaN \nPEP_Carboxylase 0 NaN \nPPCK 0 NaN \nFBA 1 NaN \nFBP 0 NaN \nTKT2 0 NaN \nRPE 0 NaN \nXylulokinase 0 NaN \nPYK_org 0 NaN \nPYK 1 NaN \nRPI 0 NaN \nTKT1 0 NaN \nTALA 0 NaN \nPGM 1 NaN \nENO 1 NaN \nGND 0 NaN \nPGL 0 NaN \nHEX1 1 NaN \nPGI 1 NaN \nG6PDH2r 0 NaN \nPFK 1 NaN \nPYRt2m 1 NaN \nPDHm 1 NaN \nICL 0 NaN \nMAS 0 NaN \nPYRDC 0 NaN \nALDD2y 0 NaN \nALCD2X_copy1 0 NaN \nLactateDehydrogenase 0 NaN \nMitochondrial complex I/NADH ubiquinone oxidore... 0 NaN \nMitochondrial complex III 0 NaN \nMitochondrial complex IV 0 NaN \n\n DGZERO StdDev \\\nREACTION \nME1m NaN \nME2m NaN \nCSm NaN \nACONTm NaN \nICDHxm NaN \nAKGDm NaN \nSUCOASm NaN \nSUCD1m NaN \nFUMm NaN \nMDHm NaN \nGAPD NaN \nPGK NaN \nTPI NaN \nMDH NaN \nPEP_Carboxylase NaN \nPPCK NaN \nFBA NaN \nFBP NaN \nTKT2 NaN \nRPE NaN \nXylulokinase NaN \nPYK_org NaN \nPYK NaN \nRPI NaN \nTKT1 NaN \nTALA NaN \nPGM NaN \nENO NaN \nGND NaN \nPGL NaN \nHEX1 NaN \nPGI NaN \nG6PDH2r NaN \nPFK NaN \nPYRt2m NaN \nPDHm NaN \nICL NaN \nMAS NaN \nPYRDC NaN \nALDD2y NaN \nALCD2X_copy1 NaN \nLactateDehydrogenase NaN \nMitochondrial complex I/NADH ubiquinone oxidore... NaN \nMitochondrial complex III NaN \nMitochondrial complex IV NaN \n\n Same Compartment? \\\nREACTION \nME1m True \nME2m True \nCSm True \nACONTm True \nICDHxm True \nAKGDm True \nSUCOASm True \nSUCD1m True \nFUMm True \nMDHm True \nGAPD True \nPGK True \nTPI True \nMDH True \nPEP_Carboxylase True \nPPCK True \nFBA True \nFBP True \nTKT2 True \nRPE True \nXylulokinase True \nPYK_org True \nPYK True \nRPI True \nTKT1 True \nTALA True \nPGM True \nENO True \nGND True \nPGL True \nHEX1 True \nPGI True \nG6PDH2r True \nPFK True \nPYRt2m False \nPDHm True \nICL True \nMAS True \nPYRDC True \nALDD2y True \nALCD2X_copy1 True \nLactateDehydrogenase True \nMitochondrial complex I/NADH ubiquinone oxidore... False \nMitochondrial complex III True \nMitochondrial complex IV False \n\n Full Rxn \nREACTION \nME1m (S)-MALATE + NAD+ = PYRUVATE + NADH + CO2 \nME2m (S)-MALATE + NADP+ = PYRUVATE + NADPH + CO2 \nCSm OXALOACETATE + ACETYL-COA + H2O = CITRATE + COA \nACONTm CITRATE = ISOCITRATE \nICDHxm ISOCITRATE + NAD+ = 2-OXOGLUTARATE + NADH + CO2 \nAKGDm 2-OXOGLUTARATE + COA + NAD+ = SUCCINYL-COA + C... \nSUCOASm SUCCINYL-COA + ADP + ORTHOPHOSPHATE = SUCCINAT... \nSUCD1m SUCCINATE:MITOCHONDRIAL_MATRIX + OXYGEN + NADH... \nFUMm FUMARATE + H2O = (S)-MALATE \nMDHm (S)-MALATE + NAD+ = OXALOACETATE + NADH \nGAPD D-GLYCERALDEHYDE-3-PHOSPHATE + ORTHOPHOSPHATE ... \nPGK 3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + ADP = 3-PHOS... \nTPI GLYCERONE_PHOSPHATE = D-GLYCERALDEHYDE-3-PHOSP... \nMDH (S)-MALATE + NAD+ = OXALOACETATE + NADH \nPEP_Carboxylase OXALOACETATE + ORTHOPHOSPHATE = PHOSPHOENOLPYR... \nPPCK OXALOACETATE + ATP = PHOSPHOENOLPYRUVATE + ADP... \nFBA D-FRUCTOSE_1,6-BISPHOSPHATE = GLYCERONE_PHOSPH... \nFBP D-FRUCTOSE_6-PHOSPHATE + ORTHOPHOSPHATE = H2O ... \nTKT2 D-FRUCTOSE_6-PHOSPHATE + D-GLYCERALDEHYDE-3-PH... \nRPE D-XYLULOSE-5-PHOSPHATE = D-RIBULOSE-5-PHOSPHATE \nXylulokinase D-XYLULOSE + ATP = D-XYLULOSE-5-PHOSPHATE + ADP \nPYK_org ADP + PHOSPHOENOLPYRUVATE = PYRUVATE + ATP \nPYK ADP + PHOSPHOENOLPYRUVATE = PYRUVATE + ATP \nRPI D-RIBOSE-5-PHOSPHATE = D-RIBULOSE-5-PHOSPHATE \nTKT1 SEDOHEPTULOSE_7-PHOSPHATE + D-GLYCERALDEHYDE-3... \nTALA D-GLYCERALDEHYDE-3-PHOSPHATE + SEDOHEPTULOSE_7... \nPGM 3-PHOSPHO-D-GLYCERATE = 2-PHOSPHO-D-GLYCERATE \nENO 2-PHOSPHO-D-GLYCERATE = PHOSPHOENOLPYRUVATE + H2O \nGND NADPH + D-RIBULOSE-5-PHOSPHATE + CO2 = NADP+ +... \nPGL 6-PHOSPHO-D-GLUCONATE = D-GLUCONO-1,5-LACTONE_... \nHEX1 BETA-D-GLUCOSE + ATP = BETA-D-GLUCOSE-6-PHOSPH... \nPGI BETA-D-GLUCOSE-6-PHOSPHATE = D-FRUCTOSE_6-PHOS... \nG6PDH2r BETA-D-GLUCOSE-6-PHOSPHATE + NADP+ = D-GLUCONO... \nPFK D-FRUCTOSE_6-PHOSPHATE + ATP = ADP + D-FRUCTOS... \nPYRt2m PYRUVATE = PYRUVATE \nPDHm COA + NAD+ + PYRUVATE = ACETYL-COA + CO2 + NADH \nICL ISOCITRATE = GLYOXYLATE + SUCCINATE \nMAS ACETYL-COA + GLYOXYLATE + H2O = (S)-MALATE + COA \nPYRDC PYRUVATE = ACETALDEHYDE + CO2 \nALDD2y ACETALDEHYDE + NADP+ + H2O = ACETATE + NADPH \nALCD2X_copy1 ACETALDEHYDE + NADH = ETHANOL + NAD+ \nLactateDehydrogenase PYRUVATE + NADH = LACTATE + NAD+ \nMitochondrial complex I/NADH ubiquinone oxidore... NADH:MITOCHONDRIAL_MATRIX + UBIQUINONE-6:MITOC... \nMitochondrial complex III UBIQUINOL-6 + 2 FERRICYTOCHROME_C = UBIQUINONE... \nMitochondrial complex IV 4 FERROCYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + O... ",
  98. "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>LEFT</th>\n <th>RIGHT</th>\n <th>LEFT_COMPARTMENT</th>\n <th>RIGHT_COMPARTMENT</th>\n <th>ENZYME_LEVEL</th>\n <th>DGZERO</th>\n <th>DGZERO StdDev</th>\n <th>Same Compartment?</th>\n <th>Full Rxn</th>\n </tr>\n <tr>\n <th>REACTION</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>ME1m</th>\n <td>(S)-MALATE + NAD+</td>\n <td>PYRUVATE + NADH + CO2</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>(S)-MALATE + NAD+ = PYRUVATE + NADH + CO2</td>\n </tr>\n <tr>\n <th>ME2m</th>\n <td>(S)-MALATE + NADP+</td>\n <td>PYRUVATE + NADPH + CO2</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>(S)-MALATE + NADP+ = PYRUVATE + NADPH + CO2</td>\n </tr>\n <tr>\n <th>CSm</th>\n <td>OXALOACETATE + ACETYL-COA + H2O</td>\n <td>CITRATE + COA</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>OXALOACETATE + ACETYL-COA + H2O = CITRATE + COA</td>\n </tr>\n <tr>\n <th>ACONTm</th>\n <td>CITRATE</td>\n <td>ISOCITRATE</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>CITRATE = ISOCITRATE</td>\n </tr>\n <tr>\n <th>ICDHxm</th>\n <td>ISOCITRATE + NAD+</td>\n <td>2-OXOGLUTARATE + NADH + CO2</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>ISOCITRATE + NAD+ = 2-OXOGLUTARATE + NADH + CO2</td>\n </tr>\n <tr>\n <th>AKGDm</th>\n <td>2-OXOGLUTARATE + COA + NAD+</td>\n <td>SUCCINYL-COA + CO2 + NADH</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>2-OXOGLUTARATE + COA + NAD+ = SUCCINYL-COA + C...</td>\n </tr>\n <tr>\n <th>SUCOASm</th>\n <td>SUCCINYL-COA + ADP + ORTHOPHOSPHATE</td>\n <td>SUCCINATE + ATP + COA</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>SUCCINYL-COA + ADP + ORTHOPHOSPHATE = SUCCINAT...</td>\n </tr>\n <tr>\n <th>SUCD1m</th>\n <td>SUCCINATE:MITOCHONDRIAL_MATRIX + OXYGEN + NADH</td>\n <td>FUMARATE:MITOCHONDRIAL_MATRIX + 2 H2O + NAD+</td>\n <td>:MITOCHONDRIAL_MATRIX</td>\n <td>:MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>SUCCINATE:MITOCHONDRIAL_MATRIX + OXYGEN + NADH...</td>\n </tr>\n <tr>\n <th>FUMm</th>\n <td>FUMARATE + H2O</td>\n <td>(S)-MALATE</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>FUMARATE + H2O = (S)-MALATE</td>\n </tr>\n <tr>\n <th>MDHm</th>\n <td>(S)-MALATE + NAD+</td>\n <td>OXALOACETATE + NADH</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>(S)-MALATE + NAD+ = OXALOACETATE + NADH</td>\n </tr>\n <tr>\n <th>GAPD</th>\n <td>D-GLYCERALDEHYDE-3-PHOSPHATE + ORTHOPHOSPHATE ...</td>\n <td>3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + NADH</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>D-GLYCERALDEHYDE-3-PHOSPHATE + ORTHOPHOSPHATE ...</td>\n </tr>\n <tr>\n <th>PGK</th>\n <td>3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + ADP</td>\n <td>3-PHOSPHO-D-GLYCERATE + ATP</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + ADP = 3-PHOS...</td>\n </tr>\n <tr>\n <th>TPI</th>\n <td>GLYCERONE_PHOSPHATE</td>\n <td>D-GLYCERALDEHYDE-3-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>GLYCERONE_PHOSPHATE = D-GLYCERALDEHYDE-3-PHOSP...</td>\n </tr>\n <tr>\n <th>MDH</th>\n <td>(S)-MALATE + NAD+</td>\n <td>OXALOACETATE + NADH</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>(S)-MALATE + NAD+ = OXALOACETATE + NADH</td>\n </tr>\n <tr>\n <th>PEP_Carboxylase</th>\n <td>OXALOACETATE + ORTHOPHOSPHATE</td>\n <td>PHOSPHOENOLPYRUVATE + CO2 + H2O</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>OXALOACETATE + ORTHOPHOSPHATE = PHOSPHOENOLPYR...</td>\n </tr>\n <tr>\n <th>PPCK</th>\n <td>OXALOACETATE + ATP</td>\n <td>PHOSPHOENOLPYRUVATE + ADP + CO2</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>OXALOACETATE + ATP = PHOSPHOENOLPYRUVATE + ADP...</td>\n </tr>\n <tr>\n <th>FBA</th>\n <td>D-FRUCTOSE_1,6-BISPHOSPHATE</td>\n <td>GLYCERONE_PHOSPHATE + D-GLYCERALDEHYDE-3-PHOSP...</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>D-FRUCTOSE_1,6-BISPHOSPHATE = GLYCERONE_PHOSPH...</td>\n </tr>\n <tr>\n <th>FBP</th>\n <td>D-FRUCTOSE_6-PHOSPHATE + ORTHOPHOSPHATE</td>\n <td>H2O + D-FRUCTOSE_1,6-BISPHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>D-FRUCTOSE_6-PHOSPHATE + ORTHOPHOSPHATE = H2O ...</td>\n </tr>\n <tr>\n <th>TKT2</th>\n <td>D-FRUCTOSE_6-PHOSPHATE + D-GLYCERALDEHYDE-3-PH...</td>\n <td>D-ERYTHROSE-4-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>D-FRUCTOSE_6-PHOSPHATE + D-GLYCERALDEHYDE-3-PH...</td>\n </tr>\n <tr>\n <th>RPE</th>\n <td>D-XYLULOSE-5-PHOSPHATE</td>\n <td>D-RIBULOSE-5-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>D-XYLULOSE-5-PHOSPHATE = D-RIBULOSE-5-PHOSPHATE</td>\n </tr>\n <tr>\n <th>Xylulokinase</th>\n <td>D-XYLULOSE + ATP</td>\n <td>D-XYLULOSE-5-PHOSPHATE + ADP</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>D-XYLULOSE + ATP = D-XYLULOSE-5-PHOSPHATE + ADP</td>\n </tr>\n <tr>\n <th>PYK_org</th>\n <td>ADP + PHOSPHOENOLPYRUVATE</td>\n <td>PYRUVATE + ATP</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>ADP + PHOSPHOENOLPYRUVATE = PYRUVATE + ATP</td>\n </tr>\n <tr>\n <th>PYK</th>\n <td>ADP + PHOSPHOENOLPYRUVATE</td>\n <td>PYRUVATE + ATP</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>ADP + PHOSPHOENOLPYRUVATE = PYRUVATE + ATP</td>\n </tr>\n <tr>\n <th>RPI</th>\n <td>D-RIBOSE-5-PHOSPHATE</td>\n <td>D-RIBULOSE-5-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>D-RIBOSE-5-PHOSPHATE = D-RIBULOSE-5-PHOSPHATE</td>\n </tr>\n <tr>\n <th>TKT1</th>\n <td>SEDOHEPTULOSE_7-PHOSPHATE + D-GLYCERALDEHYDE-3...</td>\n <td>D-RIBOSE-5-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>SEDOHEPTULOSE_7-PHOSPHATE + D-GLYCERALDEHYDE-3...</td>\n </tr>\n <tr>\n <th>TALA</th>\n <td>D-GLYCERALDEHYDE-3-PHOSPHATE + SEDOHEPTULOSE_7...</td>\n <td>D-FRUCTOSE_6-PHOSPHATE + D-ERYTHROSE-4-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>D-GLYCERALDEHYDE-3-PHOSPHATE + SEDOHEPTULOSE_7...</td>\n </tr>\n <tr>\n <th>PGM</th>\n <td>3-PHOSPHO-D-GLYCERATE</td>\n <td>2-PHOSPHO-D-GLYCERATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>3-PHOSPHO-D-GLYCERATE = 2-PHOSPHO-D-GLYCERATE</td>\n </tr>\n <tr>\n <th>ENO</th>\n <td>2-PHOSPHO-D-GLYCERATE</td>\n <td>PHOSPHOENOLPYRUVATE + H2O</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>2-PHOSPHO-D-GLYCERATE = PHOSPHOENOLPYRUVATE + H2O</td>\n </tr>\n <tr>\n <th>GND</th>\n <td>NADPH + D-RIBULOSE-5-PHOSPHATE + CO2</td>\n <td>NADP+ + 6-PHOSPHO-D-GLUCONATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>NADPH + D-RIBULOSE-5-PHOSPHATE + CO2 = NADP+ +...</td>\n </tr>\n <tr>\n <th>PGL</th>\n <td>6-PHOSPHO-D-GLUCONATE</td>\n <td>D-GLUCONO-1,5-LACTONE_6-PHOSPHATE + H2O</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>6-PHOSPHO-D-GLUCONATE = D-GLUCONO-1,5-LACTONE_...</td>\n </tr>\n <tr>\n <th>HEX1</th>\n <td>BETA-D-GLUCOSE + ATP</td>\n <td>BETA-D-GLUCOSE-6-PHOSPHATE + ADP</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>BETA-D-GLUCOSE + ATP = BETA-D-GLUCOSE-6-PHOSPH...</td>\n </tr>\n <tr>\n <th>PGI</th>\n <td>BETA-D-GLUCOSE-6-PHOSPHATE</td>\n <td>D-FRUCTOSE_6-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>BETA-D-GLUCOSE-6-PHOSPHATE = D-FRUCTOSE_6-PHOS...</td>\n </tr>\n <tr>\n <th>G6PDH2r</th>\n <td>BETA-D-GLUCOSE-6-PHOSPHATE + NADP+</td>\n <td>D-GLUCONO-1,5-LACTONE_6-PHOSPHATE + NADPH</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>BETA-D-GLUCOSE-6-PHOSPHATE + NADP+ = D-GLUCONO...</td>\n </tr>\n <tr>\n <th>PFK</th>\n <td>D-FRUCTOSE_6-PHOSPHATE + ATP</td>\n <td>ADP + D-FRUCTOSE_1,6-BISPHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>D-FRUCTOSE_6-PHOSPHATE + ATP = ADP + D-FRUCTOS...</td>\n </tr>\n <tr>\n <th>PYRt2m</th>\n <td>PYRUVATE</td>\n <td>PYRUVATE</td>\n <td>CYTOSOL</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>False</td>\n <td>PYRUVATE = PYRUVATE</td>\n </tr>\n <tr>\n <th>PDHm</th>\n <td>COA + NAD+ + PYRUVATE</td>\n <td>ACETYL-COA + CO2 + NADH</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>COA + NAD+ + PYRUVATE = ACETYL-COA + CO2 + NADH</td>\n </tr>\n <tr>\n <th>ICL</th>\n <td>ISOCITRATE</td>\n <td>GLYOXYLATE + SUCCINATE</td>\n <td>GLYOXYSOME</td>\n <td>GLYOXYSOME</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>ISOCITRATE = GLYOXYLATE + SUCCINATE</td>\n </tr>\n <tr>\n <th>MAS</th>\n <td>ACETYL-COA + GLYOXYLATE + H2O</td>\n <td>(S)-MALATE + COA</td>\n <td>GLYOXYSOME</td>\n <td>GLYOXYSOME</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>ACETYL-COA + GLYOXYLATE + H2O = (S)-MALATE + COA</td>\n </tr>\n <tr>\n <th>PYRDC</th>\n <td>PYRUVATE</td>\n <td>ACETALDEHYDE + CO2</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>PYRUVATE = ACETALDEHYDE + CO2</td>\n </tr>\n <tr>\n <th>ALDD2y</th>\n <td>ACETALDEHYDE + NADP+ + H2O</td>\n <td>ACETATE + NADPH</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>ACETALDEHYDE + NADP+ + H2O = ACETATE + NADPH</td>\n </tr>\n <tr>\n <th>ALCD2X_copy1</th>\n <td>ACETALDEHYDE + NADH</td>\n <td>ETHANOL + NAD+</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>ACETALDEHYDE + NADH = ETHANOL + NAD+</td>\n </tr>\n <tr>\n <th>LactateDehydrogenase</th>\n <td>PYRUVATE + NADH</td>\n <td>LACTATE + NAD+</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>PYRUVATE + NADH = LACTATE + NAD+</td>\n </tr>\n <tr>\n <th>Mitochondrial complex I/NADH ubiquinone oxidoredectase</th>\n <td>NADH:MITOCHONDRIAL_MATRIX + UBIQUINONE-6:MITOC...</td>\n <td>NAD+:MITOCHONDRIAL_MATRIX + UBIQUINOL-6:MITOCH...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>False</td>\n <td>NADH:MITOCHONDRIAL_MATRIX + UBIQUINONE-6:MITOC...</td>\n </tr>\n <tr>\n <th>Mitochondrial complex III</th>\n <td>UBIQUINOL-6 + 2 FERRICYTOCHROME_C</td>\n <td>UBIQUINONE-6 + 2 FERROCYTOCHROME_C</td>\n <td>Mitochondrial_Membrane</td>\n <td>Mitochondrial_Membrane</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>True</td>\n <td>UBIQUINOL-6 + 2 FERRICYTOCHROME_C = UBIQUINONE...</td>\n </tr>\n <tr>\n <th>Mitochondrial complex IV</th>\n <td>4 FERROCYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + O...</td>\n <td>4 FERRICYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + 2...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>0</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>False</td>\n <td>4 FERROCYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + O...</td>\n </tr>\n </tbody>\n</table>\n</div>"
  99. },
  100. "metadata": {}
  101. }
  102. ]
  103. },
  104. {
  105. "metadata": {},
  106. "cell_type": "markdown",
  107. "source": "## Calculate Standard Free Energies of Reaction "
  108. },
  109. {
  110. "metadata": {
  111. "scrolled": false,
  112. "trusted": true
  113. },
  114. "cell_type": "code",
  115. "source": "import sys\n#sys.path.append('/Users/d3k137/docs/projects/equilibrator/equilibrator-api/')\n#from equilibrator_api import ComponentContribution, Reaction, ReactionMatcher\nfrom equilibrator_api import *\n#import inspect\nfrom equilibrator_api.reaction_matcher import ReactionMatcher\nreaction_matcher = ReactionMatcher()\n\nif (0):\n eq_api = ComponentContribution(pH=7.0, ionic_strength=0.15) # loads data\n boltzmann_rxn_str = reactions.loc['CTP','Full Rxn']\n full_rxn_str_no_cmprt = re.sub(':\\S+','', boltzmann_rxn_str)\n full_rxn_str_no_cmprt = re.sub('BETA-D-GLUCOSE','D-GLUCOSE',full_rxn_str_no_cmprt )\n print(full_rxn_str_no_cmprt)\n rxn = reaction_matcher.match(full_rxn_str_no_cmprt)\n dG0_prime, dG0_uncertainty = eq_api.dG0_prime(rxn)\n display(dG0_prime, dG0_uncertainty)\n\nif (1):\n eq_api = ComponentContribution(pH=7.0, ionic_strength=0.15) # loads data\n for idx in reactions.index:\n print(idx, flush=True)\n boltzmann_rxn_str = reactions.loc[idx,'Full Rxn']\n full_rxn_str_no_cmprt = re.sub(':\\S+','', boltzmann_rxn_str)\n print(full_rxn_str_no_cmprt)\n full_rxn_str_no_cmprt = re.sub('BETA-D-GLUCOSE','D-GLUCOSE',full_rxn_str_no_cmprt )\n rxn = reaction_matcher.match(full_rxn_str_no_cmprt)\n if not rxn.check_full_reaction_balancing():\n print('Reaction %s is not balanced:\\n %s\\n' % (idx, full_rxn_str_no_cmprt), flush=True)\n dG0_prime, dG0_uncertainty = eq_api.dG0_prime(rxn)\n display(dG0_prime, dG0_uncertainty)\n reactions.loc[idx,deltag0] = dG0_prime\n reactions.loc[idx,deltag0_sigma] = dG0_uncertainty\nif (0):\n eq_api = ComponentContribution(pH=7.0, ionic_strength=0.15) # loads data\n rxn_list = []\n for idx in reactions.index:\n print(idx,flush=True)\n boltzmann_rxn_str = reactions.loc[idx,'Full Rxn']\n full_rxn_str_no_cmprt = re.sub(':\\S+','', boltzmann_rxn_str)\n full_rxn_str_no_cmprt = re.sub('BETA-D-GLUCOSE','D-GLUCOSE',full_rxn_str_no_cmprt )\n print(full_rxn_str_no_cmprt)\n rxn = reaction_matcher.match(full_rxn_str_no_cmprt)\n if not rxn.check_full_reaction_balancing():\n print('Reaction %s is not balanced:\\n %s\\n' % (idx, full_rxn_str_no_cmprt), flush=True)\n rxn_list.append(rxn)\n dG0_prime, dG0_uncertainty = eq_api.dG0_prime_multi(rxn_list)\n display(dG0_prime)\n\nreactions.loc['PYRt2m',deltag0] = -RT*np.log(10)\ndisplay(reactions)\n\n# From Elad Noor regarding pyruvate => pyruvate reaction:\n# Sorry for the delayed response. For formation energies you should use the function Compound.dG0_prime(). Here is some example code:\n# cm = CompoundMatcher()\n# df = cm.match('ATP')\n# c = Compound(Reaction.COMPOUND_DICT[df['CID'].iloc[0]])\n# print('Formation energy of ATP: %.2f' % c.dG0_prime(pH=7, pMg=0, I=0.1))\n#The fact that reaction strings like 'ATP = ATP' worked was actually a bug and has just been fixed. If you parse the same string now, you will get an empty reaction.\n#Regarding the compartments, the uncertainty does not depend on the aqueous conditions, and neither does the covariance between the uncertainty. Therefore, you can calculate all compartments at once or separately, it should not make a difference.\n\n",
  116. "execution_count": 6,
  117. "outputs": [
  118. {
  119. "output_type": "stream",
  120. "text": "ME1m\n(S)-MALATE + NAD+ = PYRUVATE + NADH + CO2\n",
  121. "name": "stdout"
  122. },
  123. {
  124. "output_type": "display_data",
  125. "data": {
  126. "text/plain": "4.563533743842356"
  127. },
  128. "metadata": {}
  129. },
  130. {
  131. "output_type": "display_data",
  132. "data": {
  133. "text/plain": "7.601743679518801"
  134. },
  135. "metadata": {}
  136. },
  137. {
  138. "output_type": "stream",
  139. "text": "ME2m\n(S)-MALATE + NADP+ = PYRUVATE + NADPH + CO2\n",
  140. "name": "stdout"
  141. },
  142. {
  143. "output_type": "display_data",
  144. "data": {
  145. "text/plain": "5.2117362940494445"
  146. },
  147. "metadata": {}
  148. },
  149. {
  150. "output_type": "display_data",
  151. "data": {
  152. "text/plain": "7.61041804639244"
  153. },
  154. "metadata": {}
  155. },
  156. {
  157. "output_type": "stream",
  158. "text": "CSm\nOXALOACETATE + ACETYL-COA + H2O = CITRATE + COA\n",
  159. "name": "stdout"
  160. },
  161. {
  162. "output_type": "display_data",
  163. "data": {
  164. "text/plain": "-35.11660568088746"
  165. },
  166. "metadata": {}
  167. },
  168. {
  169. "output_type": "display_data",
  170. "data": {
  171. "text/plain": "0.9305521760769476"
  172. },
  173. "metadata": {}
  174. },
  175. {
  176. "output_type": "stream",
  177. "text": "ACONTm\nCITRATE = ISOCITRATE\n",
  178. "name": "stdout"
  179. },
  180. {
  181. "output_type": "display_data",
  182. "data": {
  183. "text/plain": "7.629493367233977"
  184. },
  185. "metadata": {}
  186. },
  187. {
  188. "output_type": "display_data",
  189. "data": {
  190. "text/plain": "0.7338467677186133"
  191. },
  192. "metadata": {}
  193. },
  194. {
  195. "output_type": "stream",
  196. "text": "ICDHxm\nISOCITRATE + NAD+ = 2-OXOGLUTARATE + NADH + CO2\n",
  197. "name": "stdout"
  198. },
  199. {
  200. "output_type": "display_data",
  201. "data": {
  202. "text/plain": "-2.8720043783020515"
  203. },
  204. "metadata": {}
  205. },
  206. {
  207. "output_type": "display_data",
  208. "data": {
  209. "text/plain": "7.620950394131831"
  210. },
  211. "metadata": {}
  212. },
  213. {
  214. "output_type": "stream",
  215. "text": "AKGDm\n2-OXOGLUTARATE + COA + NAD+ = SUCCINYL-COA + CO2 + NADH\n",
  216. "name": "stdout"
  217. },
  218. {
  219. "output_type": "display_data",
  220. "data": {
  221. "text/plain": "-36.354933970030515"
  222. },
  223. "metadata": {}
  224. },
  225. {
  226. "output_type": "display_data",
  227. "data": {
  228. "text/plain": "7.971214725204675"
  229. },
  230. "metadata": {}
  231. },
  232. {
  233. "output_type": "stream",
  234. "text": "SUCOASm\nSUCCINYL-COA + ADP + ORTHOPHOSPHATE = SUCCINATE + ATP + COA\n",
  235. "name": "stdout"
  236. },
  237. {
  238. "output_type": "display_data",
  239. "data": {
  240. "text/plain": "1.9244830140419253"
  241. },
  242. "metadata": {}
  243. },
  244. {
  245. "output_type": "display_data",
  246. "data": {
  247. "text/plain": "1.4819742572715635"
  248. },
  249. "metadata": {}
  250. },
  251. {
  252. "output_type": "stream",
  253. "text": "SUCD1m\nSUCCINATE + OXYGEN + NADH = FUMARATE + 2 H2O + NAD+\n",
  254. "name": "stdout"
  255. },
  256. {
  257. "output_type": "display_data",
  258. "data": {
  259. "text/plain": "-380.02338510771915"
  260. },
  261. "metadata": {}
  262. },
  263. {
  264. "output_type": "display_data",
  265. "data": {
  266. "text/plain": "7.80979982346588"
  267. },
  268. "metadata": {}
  269. },
  270. {
  271. "output_type": "stream",
  272. "text": "FUMm\nFUMARATE + H2O = (S)-MALATE\n",
  273. "name": "stdout"
  274. },
  275. {
  276. "output_type": "display_data",
  277. "data": {
  278. "text/plain": "-3.4487297974382045"
  279. },
  280. "metadata": {}
  281. },
  282. {
  283. "output_type": "display_data",
  284. "data": {
  285. "text/plain": "0.6076925254717079"
  286. },
  287. "metadata": {}
  288. },
  289. {
  290. "output_type": "stream",
  291. "text": "MDHm\n(S)-MALATE + NAD+ = OXALOACETATE + NADH\n",
  292. "name": "stdout"
  293. },
  294. {
  295. "output_type": "display_data",
  296. "data": {
  297. "text/plain": "29.99417988444975"
  298. },
  299. "metadata": {}
  300. },
  301. {
  302. "output_type": "display_data",
  303. "data": {
  304. "text/plain": "0.42237575404059413"
  305. },
  306. "metadata": {}
  307. },
  308. {
  309. "output_type": "stream",
  310. "text": "GAPD \nD-GLYCERALDEHYDE-3-PHOSPHATE + ORTHOPHOSPHATE + NAD+ = 3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + NADH\n",
  311. "name": "stdout"
  312. },
  313. {
  314. "output_type": "display_data",
  315. "data": {
  316. "text/plain": "6.6867291290386675"
  317. },
  318. "metadata": {}
  319. },
  320. {
  321. "output_type": "display_data",
  322. "data": {
  323. "text/plain": "0.895659271543223"
  324. },
  325. "metadata": {}
  326. },
  327. {
  328. "output_type": "stream",
  329. "text": "PGK\n3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + ADP = 3-PHOSPHO-D-GLYCERATE + ATP\n",
  330. "name": "stdout"
  331. },
  332. {
  333. "output_type": "display_data",
  334. "data": {
  335. "text/plain": "-18.473297774211005"
  336. },
  337. "metadata": {}
  338. },
  339. {
  340. "output_type": "display_data",
  341. "data": {
  342. "text/plain": "0.8899823716333797"
  343. },
  344. "metadata": {}
  345. },
  346. {
  347. "output_type": "stream",
  348. "text": "TPI\nGLYCERONE_PHOSPHATE = D-GLYCERALDEHYDE-3-PHOSPHATE\n",
  349. "name": "stdout"
  350. },
  351. {
  352. "output_type": "display_data",
  353. "data": {
  354. "text/plain": "5.486424389822787"
  355. },
  356. "metadata": {}
  357. },
  358. {
  359. "output_type": "display_data",
  360. "data": {
  361. "text/plain": "0.7531163572878151"
  362. },
  363. "metadata": {}
  364. },
  365. {
  366. "output_type": "stream",
  367. "text": "MDH\n(S)-MALATE + NAD+ = OXALOACETATE + NADH\n",
  368. "name": "stdout"
  369. },
  370. {
  371. "output_type": "display_data",
  372. "data": {
  373. "text/plain": "29.99417988444975"
  374. },
  375. "metadata": {}
  376. },
  377. {
  378. "output_type": "display_data",
  379. "data": {
  380. "text/plain": "0.42237575404059413"
  381. },
  382. "metadata": {}
  383. },
  384. {
  385. "output_type": "stream",
  386. "text": "PEP_Carboxylase\nOXALOACETATE + ORTHOPHOSPHATE = PHOSPHOENOLPYRUVATE + CO2 + H2O\n",
  387. "name": "stdout"
  388. },
  389. {
  390. "output_type": "display_data",
  391. "data": {
  392. "text/plain": "28.233715229622874"
  393. },
  394. "metadata": {}
  395. },
  396. {
  397. "output_type": "display_data",
  398. "data": {
  399. "text/plain": "7.640872639134253"
  400. },
  401. "metadata": {}
  402. },
  403. {
  404. "output_type": "stream",
  405. "text": "PPCK\nOXALOACETATE + ATP = PHOSPHOENOLPYRUVATE + ADP + CO2\n",
  406. "name": "stdout"
  407. },
  408. {
  409. "output_type": "display_data",
  410. "data": {
  411. "text/plain": "2.105956995405279"
  412. },
  413. "metadata": {}
  414. },
  415. {
  416. "output_type": "display_data",
  417. "data": {
  418. "text/plain": "7.639128086053029"
  419. },
  420. "metadata": {}
  421. },
  422. {
  423. "output_type": "stream",
  424. "text": "FBA\nD-FRUCTOSE_1,6-BISPHOSPHATE = GLYCERONE_PHOSPHATE + D-GLYCERALDEHYDE-3-PHOSPHATE\n",
  425. "name": "stdout"
  426. },
  427. {
  428. "output_type": "display_data",
  429. "data": {
  430. "text/plain": "20.50964300409987"
  431. },
  432. "metadata": {}
  433. },
  434. {
  435. "output_type": "display_data",
  436. "data": {
  437. "text/plain": "0.8722695555013527"
  438. },
  439. "metadata": {}
  440. },
  441. {
  442. "output_type": "stream",
  443. "text": "FBP\nD-FRUCTOSE_6-PHOSPHATE + ORTHOPHOSPHATE = H2O + D-FRUCTOSE_1,6-BISPHOSPHATE\n",
  444. "name": "stdout"
  445. },
  446. {
  447. "output_type": "display_data",
  448. "data": {
  449. "text/plain": "10.672835220250363"
  450. },
  451. "metadata": {}
  452. },
  453. {
  454. "output_type": "display_data",
  455. "data": {
  456. "text/plain": "0.8183864515019575"
  457. },
  458. "metadata": {}
  459. },
  460. {
  461. "output_type": "stream",
  462. "text": "TKT2\nD-FRUCTOSE_6-PHOSPHATE + D-GLYCERALDEHYDE-3-PHOSPHATE = D-ERYTHROSE-4-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE\n",
  463. "name": "stdout"
  464. },
  465. {
  466. "output_type": "display_data",
  467. "data": {
  468. "text/plain": "10.00936030298817"
  469. },
  470. "metadata": {}
  471. },
  472. {
  473. "output_type": "display_data",
  474. "data": {
  475. "text/plain": "2.0868208090573925"
  476. },
  477. "metadata": {}
  478. },
  479. {
  480. "output_type": "stream",
  481. "text": "RPE\nD-XYLULOSE-5-PHOSPHATE = D-RIBULOSE-5-PHOSPHATE\n",
  482. "name": "stdout"
  483. },
  484. {
  485. "output_type": "display_data",
  486. "data": {
  487. "text/plain": "3.370001624099359"
  488. },
  489. "metadata": {}
  490. },
  491. {
  492. "output_type": "display_data",
  493. "data": {
  494. "text/plain": "1.1648469300716529"
  495. },
  496. "metadata": {}
  497. },
  498. {
  499. "output_type": "stream",
  500. "text": "Xylulokinase\nD-XYLULOSE + ATP = D-XYLULOSE-5-PHOSPHATE + ADP\n",
  501. "name": "stdout"
  502. },
  503. {
  504. "output_type": "display_data",
  505. "data": {
  506. "text/plain": "-23.018140689186566"
  507. },
  508. "metadata": {}
  509. },
  510. {
  511. "output_type": "display_data",
  512. "data": {
  513. "text/plain": "2.291584811694708"
  514. },
  515. "metadata": {}
  516. },
  517. {
  518. "output_type": "stream",
  519. "text": "PYK_org\nADP + PHOSPHOENOLPYRUVATE = PYRUVATE + ATP\n",
  520. "name": "stdout"
  521. },
  522. {
  523. "output_type": "display_data",
  524. "data": {
  525. "text/plain": "-27.536603136012673"
  526. },
  527. "metadata": {}
  528. },
  529. {
  530. "output_type": "display_data",
  531. "data": {
  532. "text/plain": "0.939773644474952"
  533. },
  534. "metadata": {}
  535. },
  536. {
  537. "output_type": "stream",
  538. "text": "PYK\nADP + PHOSPHOENOLPYRUVATE = PYRUVATE + ATP\n",
  539. "name": "stdout"
  540. },
  541. {
  542. "output_type": "display_data",
  543. "data": {
  544. "text/plain": "-27.536603136012673"
  545. },
  546. "metadata": {}
  547. },
  548. {
  549. "output_type": "display_data",
  550. "data": {
  551. "text/plain": "0.939773644474952"
  552. },
  553. "metadata": {}
  554. },
  555. {
  556. "output_type": "stream",
  557. "text": "RPI\nD-RIBOSE-5-PHOSPHATE = D-RIBULOSE-5-PHOSPHATE\n",
  558. "name": "stdout"
  559. },
  560. {
  561. "output_type": "display_data",
  562. "data": {
  563. "text/plain": "1.9475935286736785"
  564. },
  565. "metadata": {}
  566. },
  567. {
  568. "output_type": "display_data",
  569. "data": {
  570. "text/plain": "1.163205784951493"
  571. },
  572. "metadata": {}
  573. },
  574. {
  575. "output_type": "stream",
  576. "text": "TKT1\nSEDOHEPTULOSE_7-PHOSPHATE + D-GLYCERALDEHYDE-3-PHOSPHATE = D-RIBOSE-5-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE\n",
  577. "name": "stdout"
  578. },
  579. {
  580. "output_type": "display_data",
  581. "data": {
  582. "text/plain": "3.7925250493419753"
  583. },
  584. "metadata": {}
  585. },
  586. {
  587. "output_type": "display_data",
  588. "data": {
  589. "text/plain": "2.1613266967568294"
  590. },
  591. "metadata": {}
  592. },
  593. {
  594. "output_type": "stream",
  595. "text": "TALA\nD-GLYCERALDEHYDE-3-PHOSPHATE + SEDOHEPTULOSE_7-PHOSPHATE = D-FRUCTOSE_6-PHOSPHATE + D-ERYTHROSE-4-PHOSPHATE\n",
  596. "name": "stdout"
  597. },
  598. {
  599. "output_type": "display_data",
  600. "data": {
  601. "text/plain": "-0.7287669390673273"
  602. },
  603. "metadata": {}
  604. },
  605. {
  606. "output_type": "display_data",
  607. "data": {
  608. "text/plain": "1.6210577467394351"
  609. },
  610. "metadata": {}
  611. },
  612. {
  613. "output_type": "stream",
  614. "text": "PGM\n3-PHOSPHO-D-GLYCERATE = 2-PHOSPHO-D-GLYCERATE\n",
  615. "name": "stdout"
  616. },
  617. {
  618. "output_type": "display_data",
  619. "data": {
  620. "text/plain": "4.199528563935019"
  621. },
  622. "metadata": {}
  623. },
  624. {
  625. "output_type": "display_data",
  626. "data": {
  627. "text/plain": "0.6554195632118891"
  628. },
  629. "metadata": {}
  630. },
  631. {
  632. "output_type": "stream",
  633. "text": "ENO\n2-PHOSPHO-D-GLYCERATE = PHOSPHOENOLPYRUVATE + H2O\n",
  634. "name": "stdout"
  635. },
  636. {
  637. "output_type": "display_data",
  638. "data": {
  639. "text/plain": "-4.082223730437249"
  640. },
  641. "metadata": {}
  642. },
  643. {
  644. "output_type": "display_data",
  645. "data": {
  646. "text/plain": "0.7341928857481885"
  647. },
  648. "metadata": {}
  649. },
  650. {
  651. "output_type": "stream",
  652. "text": "GND\nNADPH + D-RIBULOSE-5-PHOSPHATE + CO2 = NADP+ + 6-PHOSPHO-D-GLUCONATE\n",
  653. "name": "stdout"
  654. },
  655. {
  656. "output_type": "display_data",
  657. "data": {
  658. "text/plain": "-2.55280050266947"
  659. },
  660. "metadata": {}
  661. },
  662. {
  663. "output_type": "display_data",
  664. "data": {
  665. "text/plain": "7.608638991578479"
  666. },
  667. "metadata": {}
  668. },
  669. {
  670. "output_type": "stream",
  671. "text": "PGL\n6-PHOSPHO-D-GLUCONATE = D-GLUCONO-1,5-LACTONE_6-PHOSPHATE + H2O\n",
  672. "name": "stdout"
  673. },
  674. {
  675. "output_type": "display_data",
  676. "data": {
  677. "text/plain": "21.42024108973567"
  678. },
  679. "metadata": {}
  680. },
  681. {
  682. "output_type": "display_data",
  683. "data": {
  684. "text/plain": "2.628246334647966"
  685. },
  686. "metadata": {}
  687. },
  688. {
  689. "output_type": "stream",
  690. "text": "HEX1\nBETA-D-GLUCOSE + ATP = BETA-D-GLUCOSE-6-PHOSPHATE + ADP\n",
  691. "name": "stdout"
  692. },
  693. {
  694. "output_type": "display_data",
  695. "data": {
  696. "text/plain": "-17.057763138721384"
  697. },
  698. "metadata": {}
  699. },
  700. {
  701. "output_type": "display_data",
  702. "data": {
  703. "text/plain": "0.7152372520174533"
  704. },
  705. "metadata": {}
  706. },
  707. {
  708. "output_type": "stream",
  709. "text": "PGI\nBETA-D-GLUCOSE-6-PHOSPHATE = D-FRUCTOSE_6-PHOSPHATE\n",
  710. "name": "stdout"
  711. },
  712. {
  713. "output_type": "display_data",
  714. "data": {
  715. "text/plain": "2.524005856552094"
  716. },
  717. "metadata": {}
  718. },
  719. {
  720. "output_type": "display_data",
  721. "data": {
  722. "text/plain": "0.5967754160874962"
  723. },
  724. "metadata": {}
  725. },
  726. {
  727. "output_type": "stream",
  728. "text": "G6PDH2r\nBETA-D-GLUCOSE-6-PHOSPHATE + NADP+ = D-GLUCONO-1,5-LACTONE_6-PHOSPHATE + NADPH\n",
  729. "name": "stdout"
  730. },
  731. {
  732. "output_type": "display_data",
  733. "data": {
  734. "text/plain": "-2.994597289928379"
  735. },
  736. "metadata": {}
  737. },
  738. {
  739. "output_type": "display_data",
  740. "data": {
  741. "text/plain": "2.1185491682097957"
  742. },
  743. "metadata": {}
  744. },
  745. {
  746. "output_type": "stream",
  747. "text": "PFK\nD-FRUCTOSE_6-PHOSPHATE + ATP = ADP + D-FRUCTOSE_1,6-BISPHOSPHATE\n",
  748. "name": "stdout"
  749. },
  750. {
  751. "output_type": "display_data",
  752. "data": {
  753. "text/plain": "-15.45492301396689"
  754. },
  755. "metadata": {}
  756. },
  757. {
  758. "output_type": "display_data",
  759. "data": {
  760. "text/plain": "0.8866293044358426"
  761. },
  762. "metadata": {}
  763. },
  764. {
  765. "output_type": "stream",
  766. "text": "PYRt2m\nPYRUVATE = PYRUVATE\n",
  767. "name": "stdout"
  768. },
  769. {
  770. "output_type": "display_data",
  771. "data": {
  772. "text/plain": "0"
  773. },
  774. "metadata": {}
  775. },
  776. {
  777. "output_type": "display_data",
  778. "data": {
  779. "text/plain": "0.0"
  780. },
  781. "metadata": {}
  782. },
  783. {
  784. "output_type": "stream",
  785. "text": "PDHm\nCOA + NAD+ + PYRUVATE = ACETYL-COA + CO2 + NADH\n",
  786. "name": "stdout"
  787. },
  788. {
  789. "output_type": "display_data",
  790. "data": {
  791. "text/plain": "-43.92192540110432"
  792. },
  793. "metadata": {}
  794. },
  795. {
  796. "output_type": "display_data",
  797. "data": {
  798. "text/plain": "7.664589894955946"
  799. },
  800. "metadata": {}
  801. },
  802. {
  803. "output_type": "stream",
  804. "text": "ICL\nISOCITRATE = GLYOXYLATE + SUCCINATE\n",
  805. "name": "stdout"
  806. },
  807. {
  808. "output_type": "display_data",
  809. "data": {
  810. "text/plain": "8.980599630876213"
  811. },
  812. "metadata": {}
  813. },
  814. {
  815. "output_type": "display_data",
  816. "data": {
  817. "text/plain": "1.66465121824121"
  818. },
  819. "metadata": {}
  820. },
  821. {
  822. "output_type": "stream",
  823. "text": "MAS\nACETYL-COA + GLYOXYLATE + H2O = (S)-MALATE + COA\n",
  824. "name": "stdout"
  825. },
  826. {
  827. "output_type": "display_data",
  828. "data": {
  829. "text/plain": "-33.052421542122374"
  830. },
  831. "metadata": {}
  832. },
  833. {
  834. "output_type": "display_data",
  835. "data": {
  836. "text/plain": "2.3281418635079683"
  837. },
  838. "metadata": {}
  839. },
  840. {
  841. "output_type": "stream",
  842. "text": "PYRDC\nPYRUVATE = ACETALDEHYDE + CO2\n",
  843. "name": "stdout"
  844. },
  845. {
  846. "output_type": "display_data",
  847. "data": {
  848. "text/plain": "-26.584699099532997"
  849. },
  850. "metadata": {}
  851. },
  852. {
  853. "output_type": "display_data",
  854. "data": {
  855. "text/plain": "7.652753180131372"
  856. },
  857. "metadata": {}
  858. },
  859. {
  860. "output_type": "stream",
  861. "text": "ALDD2y\nACETALDEHYDE + NADP+ + H2O = ACETATE + NADPH\n",
  862. "name": "stdout"
  863. },
  864. {
  865. "output_type": "display_data",
  866. "data": {
  867. "text/plain": "-46.84160656344852"
  868. },
  869. "metadata": {}
  870. },
  871. {
  872. "output_type": "display_data",
  873. "data": {
  874. "text/plain": "1.5323381407378422"
  875. },
  876. "metadata": {}
  877. },
  878. {
  879. "output_type": "stream",
  880. "text": "ALCD2X_copy1\nACETALDEHYDE + NADH = ETHANOL + NAD+\n",
  881. "name": "stdout"
  882. },
  883. {
  884. "output_type": "display_data",
  885. "data": {
  886. "text/plain": "-21.343687796639415"
  887. },
  888. "metadata": {}
  889. },
  890. {
  891. "output_type": "display_data",
  892. "data": {
  893. "text/plain": "0.5902455749176418"
  894. },
  895. "metadata": {}
  896. },
  897. {
  898. "output_type": "stream",
  899. "text": "LactateDehydrogenase\nPYRUVATE + NADH = LACTATE + NAD+\n",
  900. "name": "stdout"
  901. },
  902. {
  903. "output_type": "display_data",
  904. "data": {
  905. "text/plain": "-27.134420129702903"
  906. },
  907. "metadata": {}
  908. },
  909. {
  910. "output_type": "display_data",
  911. "data": {
  912. "text/plain": "0.5465754591738695"
  913. },
  914. "metadata": {}
  915. },
  916. {
  917. "output_type": "stream",
  918. "text": "Mitochondrial complex I/NADH ubiquinone oxidoredectase\nNADH + UBIQUINONE-6 = NAD+ + UBIQUINOL-6\n",
  919. "name": "stdout"
  920. },
  921. {
  922. "output_type": "display_data",
  923. "data": {
  924. "text/plain": "-118.69602207031812"
  925. },
  926. "metadata": {}
  927. },
  928. {
  929. "output_type": "display_data",
  930. "data": {
  931. "text/plain": "6.113921364484854"
  932. },
  933. "metadata": {}
  934. },
  935. {
  936. "output_type": "stream",
  937. "text": "Mitochondrial complex III\nUBIQUINOL-6 + 2 FERRICYTOCHROME_C = UBIQUINONE-6 + 2 FERROCYTOCHROME_C\n",
  938. "name": "stdout"
  939. },
  940. {
  941. "output_type": "stream",
  942. "text": "WARNING:root:Cannot obtain the bag of atoms for C00125, as it has an unspecific chemical formula\n",
  943. "name": "stderr"
  944. },
  945. {
  946. "output_type": "stream",
  947. "text": "Reaction Mitochondrial complex III is not balanced:\n UBIQUINOL-6 + 2 FERRICYTOCHROME_C = UBIQUINONE-6 + 2 FERROCYTOCHROME_C\n\n",
  948. "name": "stdout"
  949. },
  950. {
  951. "output_type": "display_data",
  952. "data": {
  953. "text/plain": "54.72910500433363"
  954. },
  955. "metadata": {}
  956. },
  957. {
  958. "output_type": "display_data",
  959. "data": {
  960. "text/plain": "565685.4249814528"
  961. },
  962. "metadata": {}
  963. },
  964. {
  965. "output_type": "stream",
  966. "text": "Mitochondrial complex IV\n4 FERROCYTOCHROME_C + OXYGEN = 4 FERRICYTOCHROME_C + 2 H2O\n",
  967. "name": "stdout"
  968. },
  969. {
  970. "output_type": "stream",
  971. "text": "WARNING:root:Cannot obtain the bag of atoms for C00126, as it has an unspecific chemical formula\n",
  972. "name": "stderr"
  973. },
  974. {
  975. "output_type": "stream",
  976. "text": "Reaction Mitochondrial complex IV is not balanced:\n 4 FERROCYTOCHROME_C + OXYGEN = 4 FERRICYTOCHROME_C + 2 H2O\n\n",
  977. "name": "stdout"
  978. },
  979. {
  980. "output_type": "display_data",
  981. "data": {
  982. "text/plain": "-314.9102374038018"
  983. },
  984. "metadata": {}
  985. },
  986. {
  987. "output_type": "display_data",
  988. "data": {
  989. "text/plain": "1131370.8499264906"
  990. },
  991. "metadata": {}
  992. },
  993. {
  994. "output_type": "display_data",
  995. "data": {
  996. "text/plain": " LEFT \\\nREACTION \nME1m (S)-MALATE + NAD+ \nME2m (S)-MALATE + NADP+ \nCSm OXALOACETATE + ACETYL-COA + H2O \nACONTm CITRATE \nICDHxm ISOCITRATE + NAD+ \nAKGDm 2-OXOGLUTARATE + COA + NAD+ \nSUCOASm SUCCINYL-COA + ADP + ORTHOPHOSPHATE \nSUCD1m SUCCINATE:MITOCHONDRIAL_MATRIX + OXYGEN + NADH \nFUMm FUMARATE + H2O \nMDHm (S)-MALATE + NAD+ \nGAPD D-GLYCERALDEHYDE-3-PHOSPHATE + ORTHOPHOSPHATE ... \nPGK 3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + ADP \nTPI GLYCERONE_PHOSPHATE \nMDH (S)-MALATE + NAD+ \nPEP_Carboxylase OXALOACETATE + ORTHOPHOSPHATE \nPPCK OXALOACETATE + ATP \nFBA D-FRUCTOSE_1,6-BISPHOSPHATE \nFBP D-FRUCTOSE_6-PHOSPHATE + ORTHOPHOSPHATE \nTKT2 D-FRUCTOSE_6-PHOSPHATE + D-GLYCERALDEHYDE-3-PH... \nRPE D-XYLULOSE-5-PHOSPHATE \nXylulokinase D-XYLULOSE + ATP \nPYK_org ADP + PHOSPHOENOLPYRUVATE \nPYK ADP + PHOSPHOENOLPYRUVATE \nRPI D-RIBOSE-5-PHOSPHATE \nTKT1 SEDOHEPTULOSE_7-PHOSPHATE + D-GLYCERALDEHYDE-3... \nTALA D-GLYCERALDEHYDE-3-PHOSPHATE + SEDOHEPTULOSE_7... \nPGM 3-PHOSPHO-D-GLYCERATE \nENO 2-PHOSPHO-D-GLYCERATE \nGND NADPH + D-RIBULOSE-5-PHOSPHATE + CO2 \nPGL 6-PHOSPHO-D-GLUCONATE \nHEX1 BETA-D-GLUCOSE + ATP \nPGI BETA-D-GLUCOSE-6-PHOSPHATE \nG6PDH2r BETA-D-GLUCOSE-6-PHOSPHATE + NADP+ \nPFK D-FRUCTOSE_6-PHOSPHATE + ATP \nPYRt2m PYRUVATE \nPDHm COA + NAD+ + PYRUVATE \nICL ISOCITRATE \nMAS ACETYL-COA + GLYOXYLATE + H2O \nPYRDC PYRUVATE \nALDD2y ACETALDEHYDE + NADP+ + H2O \nALCD2X_copy1 ACETALDEHYDE + NADH \nLactateDehydrogenase PYRUVATE + NADH \nMitochondrial complex I/NADH ubiquinone oxidore... NADH:MITOCHONDRIAL_MATRIX + UBIQUINONE-6:MITOC... \nMitochondrial complex III UBIQUINOL-6 + 2 FERRICYTOCHROME_C \nMitochondrial complex IV 4 FERROCYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + O... \n\n RIGHT \\\nREACTION \nME1m PYRUVATE + NADH + CO2 \nME2m PYRUVATE + NADPH + CO2 \nCSm CITRATE + COA \nACONTm ISOCITRATE \nICDHxm 2-OXOGLUTARATE + NADH + CO2 \nAKGDm SUCCINYL-COA + CO2 + NADH \nSUCOASm SUCCINATE + ATP + COA \nSUCD1m FUMARATE:MITOCHONDRIAL_MATRIX + 2 H2O + NAD+ \nFUMm (S)-MALATE \nMDHm OXALOACETATE + NADH \nGAPD 3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + NADH \nPGK 3-PHOSPHO-D-GLYCERATE + ATP \nTPI D-GLYCERALDEHYDE-3-PHOSPHATE \nMDH OXALOACETATE + NADH \nPEP_Carboxylase PHOSPHOENOLPYRUVATE + CO2 + H2O \nPPCK PHOSPHOENOLPYRUVATE + ADP + CO2 \nFBA GLYCERONE_PHOSPHATE + D-GLYCERALDEHYDE-3-PHOSP... \nFBP H2O + D-FRUCTOSE_1,6-BISPHOSPHATE \nTKT2 D-ERYTHROSE-4-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE \nRPE D-RIBULOSE-5-PHOSPHATE \nXylulokinase D-XYLULOSE-5-PHOSPHATE + ADP \nPYK_org PYRUVATE + ATP \nPYK PYRUVATE + ATP \nRPI D-RIBULOSE-5-PHOSPHATE \nTKT1 D-RIBOSE-5-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE \nTALA D-FRUCTOSE_6-PHOSPHATE + D-ERYTHROSE-4-PHOSPHATE \nPGM 2-PHOSPHO-D-GLYCERATE \nENO PHOSPHOENOLPYRUVATE + H2O \nGND NADP+ + 6-PHOSPHO-D-GLUCONATE \nPGL D-GLUCONO-1,5-LACTONE_6-PHOSPHATE + H2O \nHEX1 BETA-D-GLUCOSE-6-PHOSPHATE + ADP \nPGI D-FRUCTOSE_6-PHOSPHATE \nG6PDH2r D-GLUCONO-1,5-LACTONE_6-PHOSPHATE + NADPH \nPFK ADP + D-FRUCTOSE_1,6-BISPHOSPHATE \nPYRt2m PYRUVATE \nPDHm ACETYL-COA + CO2 + NADH \nICL GLYOXYLATE + SUCCINATE \nMAS (S)-MALATE + COA \nPYRDC ACETALDEHYDE + CO2 \nALDD2y ACETATE + NADPH \nALCD2X_copy1 ETHANOL + NAD+ \nLactateDehydrogenase LACTATE + NAD+ \nMitochondrial complex I/NADH ubiquinone oxidore... NAD+:MITOCHONDRIAL_MATRIX + UBIQUINOL-6:MITOCH... \nMitochondrial complex III UBIQUINONE-6 + 2 FERROCYTOCHROME_C \nMitochondrial complex IV 4 FERRICYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + 2... \n\n LEFT_COMPARTMENT \\\nREACTION \nME1m MITOCHONDRIAL_MATRIX \nME2m MITOCHONDRIAL_MATRIX \nCSm MITOCHONDRIAL_MATRIX \nACONTm MITOCHONDRIAL_MATRIX \nICDHxm MITOCHONDRIAL_MATRIX \nAKGDm MITOCHONDRIAL_MATRIX \nSUCOASm MITOCHONDRIAL_MATRIX \nSUCD1m :MITOCHONDRIAL_MATRIX \nFUMm MITOCHONDRIAL_MATRIX \nMDHm MITOCHONDRIAL_MATRIX \nGAPD CYTOSOL \nPGK CYTOSOL \nTPI CYTOSOL \nMDH CYTOSOL \nPEP_Carboxylase CYTOSOL \nPPCK CYTOSOL \nFBA CYTOSOL \nFBP CYTOSOL \nTKT2 CYTOSOL \nRPE CYTOSOL \nXylulokinase CYTOSOL \nPYK_org CYTOSOL \nPYK CYTOSOL \nRPI CYTOSOL \nTKT1 CYTOSOL \nTALA CYTOSOL \nPGM CYTOSOL \nENO CYTOSOL \nGND CYTOSOL \nPGL CYTOSOL \nHEX1 CYTOSOL \nPGI CYTOSOL \nG6PDH2r CYTOSOL \nPFK CYTOSOL \nPYRt2m CYTOSOL \nPDHm MITOCHONDRIAL_MATRIX \nICL GLYOXYSOME \nMAS GLYOXYSOME \nPYRDC CYTOSOL \nALDD2y CYTOSOL \nALCD2X_copy1 CYTOSOL \nLactateDehydrogenase CYTOSOL \nMitochondrial complex I/NADH ubiquinone oxidore... NaN \nMitochondrial complex III Mitochondrial_Membrane \nMitochondrial complex IV NaN \n\n RIGHT_COMPARTMENT \\\nREACTION \nME1m MITOCHONDRIAL_MATRIX \nME2m MITOCHONDRIAL_MATRIX \nCSm MITOCHONDRIAL_MATRIX \nACONTm MITOCHONDRIAL_MATRIX \nICDHxm MITOCHONDRIAL_MATRIX \nAKGDm MITOCHONDRIAL_MATRIX \nSUCOASm MITOCHONDRIAL_MATRIX \nSUCD1m :MITOCHONDRIAL_MATRIX \nFUMm MITOCHONDRIAL_MATRIX \nMDHm MITOCHONDRIAL_MATRIX \nGAPD CYTOSOL \nPGK CYTOSOL \nTPI CYTOSOL \nMDH CYTOSOL \nPEP_Carboxylase CYTOSOL \nPPCK CYTOSOL \nFBA CYTOSOL \nFBP CYTOSOL \nTKT2 CYTOSOL \nRPE CYTOSOL \nXylulokinase CYTOSOL \nPYK_org CYTOSOL \nPYK CYTOSOL \nRPI CYTOSOL \nTKT1 CYTOSOL \nTALA CYTOSOL \nPGM CYTOSOL \nENO CYTOSOL \nGND CYTOSOL \nPGL CYTOSOL \nHEX1 CYTOSOL \nPGI CYTOSOL \nG6PDH2r CYTOSOL \nPFK CYTOSOL \nPYRt2m MITOCHONDRIAL_MATRIX \nPDHm MITOCHONDRIAL_MATRIX \nICL GLYOXYSOME \nMAS GLYOXYSOME \nPYRDC CYTOSOL \nALDD2y CYTOSOL \nALCD2X_copy1 CYTOSOL \nLactateDehydrogenase CYTOSOL \nMitochondrial complex I/NADH ubiquinone oxidore... NaN \nMitochondrial complex III Mitochondrial_Membrane \nMitochondrial complex IV NaN \n\n ENZYME_LEVEL DGZERO \\\nREACTION \nME1m 0 4.56353 \nME2m 0 5.21174 \nCSm 1 -35.1166 \nACONTm 1 7.62949 \nICDHxm 1 -2.872 \nAKGDm 1 -36.3549 \nSUCOASm 1 1.92448 \nSUCD1m 1 -380.023 \nFUMm 1 -3.44873 \nMDHm 1 29.9942 \nGAPD 1 6.68673 \nPGK 1 -18.4733 \nTPI 1 5.48642 \nMDH 0 29.9942 \nPEP_Carboxylase 0 28.2337 \nPPCK 0 2.10596 \nFBA 1 20.5096 \nFBP 0 10.6728 \nTKT2 0 10.0094 \nRPE 0 3.37 \nXylulokinase 0 -23.0181 \nPYK_org 0 -27.5366 \nPYK 1 -27.5366 \nRPI 0 1.94759 \nTKT1 0 3.79253 \nTALA 0 -0.728767 \nPGM 1 4.19953 \nENO 1 -4.08222 \nGND 0 -2.5528 \nPGL 0 21.4202 \nHEX1 1 -17.0578 \nPGI 1 2.52401 \nG6PDH2r 0 -2.9946 \nPFK 1 -15.4549 \nPYRt2m 1 -5.70769 \nPDHm 1 -43.9219 \nICL 0 8.9806 \nMAS 0 -33.0524 \nPYRDC 0 -26.5847 \nALDD2y 0 -46.8416 \nALCD2X_copy1 0 -21.3437 \nLactateDehydrogenase 0 -27.1344 \nMitochondrial complex I/NADH ubiquinone oxidore... 0 -118.696 \nMitochondrial complex III 0 54.7291 \nMitochondrial complex IV 0 -314.91 \n\n DGZERO StdDev \\\nREACTION \nME1m 7.60174 \nME2m 7.61042 \nCSm 0.930552 \nACONTm 0.733847 \nICDHxm 7.62095 \nAKGDm 7.97121 \nSUCOASm 1.48197 \nSUCD1m 7.8098 \nFUMm 0.607693 \nMDHm 0.422376 \nGAPD 0.895659 \nPGK 0.889982 \nTPI 0.753116 \nMDH 0.422376 \nPEP_Carboxylase 7.64087 \nPPCK 7.63913 \nFBA 0.87227 \nFBP 0.818386 \nTKT2 2.08682 \nRPE 1.16485 \nXylulokinase 2.29158 \nPYK_org 0.939774 \nPYK 0.939774 \nRPI 1.16321 \nTKT1 2.16133 \nTALA 1.62106 \nPGM 0.65542 \nENO 0.734193 \nGND 7.60864 \nPGL 2.62825 \nHEX1 0.715237 \nPGI 0.596775 \nG6PDH2r 2.11855 \nPFK 0.886629 \nPYRt2m 0 \nPDHm 7.66459 \nICL 1.66465 \nMAS 2.32814 \nPYRDC 7.65275 \nALDD2y 1.53234 \nALCD2X_copy1 0.590246 \nLactateDehydrogenase 0.546575 \nMitochondrial complex I/NADH ubiquinone oxidore... 6.11392 \nMitochondrial complex III 565685 \nMitochondrial complex IV 1.13137e+06 \n\n Same Compartment? \\\nREACTION \nME1m True \nME2m True \nCSm True \nACONTm True \nICDHxm True \nAKGDm True \nSUCOASm True \nSUCD1m True \nFUMm True \nMDHm True \nGAPD True \nPGK True \nTPI True \nMDH True \nPEP_Carboxylase True \nPPCK True \nFBA True \nFBP True \nTKT2 True \nRPE True \nXylulokinase True \nPYK_org True \nPYK True \nRPI True \nTKT1 True \nTALA True \nPGM True \nENO True \nGND True \nPGL True \nHEX1 True \nPGI True \nG6PDH2r True \nPFK True \nPYRt2m False \nPDHm True \nICL True \nMAS True \nPYRDC True \nALDD2y True \nALCD2X_copy1 True \nLactateDehydrogenase True \nMitochondrial complex I/NADH ubiquinone oxidore... False \nMitochondrial complex III True \nMitochondrial complex IV False \n\n Full Rxn \nREACTION \nME1m (S)-MALATE + NAD+ = PYRUVATE + NADH + CO2 \nME2m (S)-MALATE + NADP+ = PYRUVATE + NADPH + CO2 \nCSm OXALOACETATE + ACETYL-COA + H2O = CITRATE + COA \nACONTm CITRATE = ISOCITRATE \nICDHxm ISOCITRATE + NAD+ = 2-OXOGLUTARATE + NADH + CO2 \nAKGDm 2-OXOGLUTARATE + COA + NAD+ = SUCCINYL-COA + C... \nSUCOASm SUCCINYL-COA + ADP + ORTHOPHOSPHATE = SUCCINAT... \nSUCD1m SUCCINATE:MITOCHONDRIAL_MATRIX + OXYGEN + NADH... \nFUMm FUMARATE + H2O = (S)-MALATE \nMDHm (S)-MALATE + NAD+ = OXALOACETATE + NADH \nGAPD D-GLYCERALDEHYDE-3-PHOSPHATE + ORTHOPHOSPHATE ... \nPGK 3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + ADP = 3-PHOS... \nTPI GLYCERONE_PHOSPHATE = D-GLYCERALDEHYDE-3-PHOSP... \nMDH (S)-MALATE + NAD+ = OXALOACETATE + NADH \nPEP_Carboxylase OXALOACETATE + ORTHOPHOSPHATE = PHOSPHOENOLPYR... \nPPCK OXALOACETATE + ATP = PHOSPHOENOLPYRUVATE + ADP... \nFBA D-FRUCTOSE_1,6-BISPHOSPHATE = GLYCERONE_PHOSPH... \nFBP D-FRUCTOSE_6-PHOSPHATE + ORTHOPHOSPHATE = H2O ... \nTKT2 D-FRUCTOSE_6-PHOSPHATE + D-GLYCERALDEHYDE-3-PH... \nRPE D-XYLULOSE-5-PHOSPHATE = D-RIBULOSE-5-PHOSPHATE \nXylulokinase D-XYLULOSE + ATP = D-XYLULOSE-5-PHOSPHATE + ADP \nPYK_org ADP + PHOSPHOENOLPYRUVATE = PYRUVATE + ATP \nPYK ADP + PHOSPHOENOLPYRUVATE = PYRUVATE + ATP \nRPI D-RIBOSE-5-PHOSPHATE = D-RIBULOSE-5-PHOSPHATE \nTKT1 SEDOHEPTULOSE_7-PHOSPHATE + D-GLYCERALDEHYDE-3... \nTALA D-GLYCERALDEHYDE-3-PHOSPHATE + SEDOHEPTULOSE_7... \nPGM 3-PHOSPHO-D-GLYCERATE = 2-PHOSPHO-D-GLYCERATE \nENO 2-PHOSPHO-D-GLYCERATE = PHOSPHOENOLPYRUVATE + H2O \nGND NADPH + D-RIBULOSE-5-PHOSPHATE + CO2 = NADP+ +... \nPGL 6-PHOSPHO-D-GLUCONATE = D-GLUCONO-1,5-LACTONE_... \nHEX1 BETA-D-GLUCOSE + ATP = BETA-D-GLUCOSE-6-PHOSPH... \nPGI BETA-D-GLUCOSE-6-PHOSPHATE = D-FRUCTOSE_6-PHOS... \nG6PDH2r BETA-D-GLUCOSE-6-PHOSPHATE + NADP+ = D-GLUCONO... \nPFK D-FRUCTOSE_6-PHOSPHATE + ATP = ADP + D-FRUCTOS... \nPYRt2m PYRUVATE = PYRUVATE \nPDHm COA + NAD+ + PYRUVATE = ACETYL-COA + CO2 + NADH \nICL ISOCITRATE = GLYOXYLATE + SUCCINATE \nMAS ACETYL-COA + GLYOXYLATE + H2O = (S)-MALATE + COA \nPYRDC PYRUVATE = ACETALDEHYDE + CO2 \nALDD2y ACETALDEHYDE + NADP+ + H2O = ACETATE + NADPH \nALCD2X_copy1 ACETALDEHYDE + NADH = ETHANOL + NAD+ \nLactateDehydrogenase PYRUVATE + NADH = LACTATE + NAD+ \nMitochondrial complex I/NADH ubiquinone oxidore... NADH:MITOCHONDRIAL_MATRIX + UBIQUINONE-6:MITOC... \nMitochondrial complex III UBIQUINOL-6 + 2 FERRICYTOCHROME_C = UBIQUINONE... \nMitochondrial complex IV 4 FERROCYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + O... ",
  997. "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>LEFT</th>\n <th>RIGHT</th>\n <th>LEFT_COMPARTMENT</th>\n <th>RIGHT_COMPARTMENT</th>\n <th>ENZYME_LEVEL</th>\n <th>DGZERO</th>\n <th>DGZERO StdDev</th>\n <th>Same Compartment?</th>\n <th>Full Rxn</th>\n </tr>\n <tr>\n <th>REACTION</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>ME1m</th>\n <td>(S)-MALATE + NAD+</td>\n <td>PYRUVATE + NADH + CO2</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>0</td>\n <td>4.56353</td>\n <td>7.60174</td>\n <td>True</td>\n <td>(S)-MALATE + NAD+ = PYRUVATE + NADH + CO2</td>\n </tr>\n <tr>\n <th>ME2m</th>\n <td>(S)-MALATE + NADP+</td>\n <td>PYRUVATE + NADPH + CO2</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>0</td>\n <td>5.21174</td>\n <td>7.61042</td>\n <td>True</td>\n <td>(S)-MALATE + NADP+ = PYRUVATE + NADPH + CO2</td>\n </tr>\n <tr>\n <th>CSm</th>\n <td>OXALOACETATE + ACETYL-COA + H2O</td>\n <td>CITRATE + COA</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>-35.1166</td>\n <td>0.930552</td>\n <td>True</td>\n <td>OXALOACETATE + ACETYL-COA + H2O = CITRATE + COA</td>\n </tr>\n <tr>\n <th>ACONTm</th>\n <td>CITRATE</td>\n <td>ISOCITRATE</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>7.62949</td>\n <td>0.733847</td>\n <td>True</td>\n <td>CITRATE = ISOCITRATE</td>\n </tr>\n <tr>\n <th>ICDHxm</th>\n <td>ISOCITRATE + NAD+</td>\n <td>2-OXOGLUTARATE + NADH + CO2</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>-2.872</td>\n <td>7.62095</td>\n <td>True</td>\n <td>ISOCITRATE + NAD+ = 2-OXOGLUTARATE + NADH + CO2</td>\n </tr>\n <tr>\n <th>AKGDm</th>\n <td>2-OXOGLUTARATE + COA + NAD+</td>\n <td>SUCCINYL-COA + CO2 + NADH</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>-36.3549</td>\n <td>7.97121</td>\n <td>True</td>\n <td>2-OXOGLUTARATE + COA + NAD+ = SUCCINYL-COA + C...</td>\n </tr>\n <tr>\n <th>SUCOASm</th>\n <td>SUCCINYL-COA + ADP + ORTHOPHOSPHATE</td>\n <td>SUCCINATE + ATP + COA</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>1.92448</td>\n <td>1.48197</td>\n <td>True</td>\n <td>SUCCINYL-COA + ADP + ORTHOPHOSPHATE = SUCCINAT...</td>\n </tr>\n <tr>\n <th>SUCD1m</th>\n <td>SUCCINATE:MITOCHONDRIAL_MATRIX + OXYGEN + NADH</td>\n <td>FUMARATE:MITOCHONDRIAL_MATRIX + 2 H2O + NAD+</td>\n <td>:MITOCHONDRIAL_MATRIX</td>\n <td>:MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>-380.023</td>\n <td>7.8098</td>\n <td>True</td>\n <td>SUCCINATE:MITOCHONDRIAL_MATRIX + OXYGEN + NADH...</td>\n </tr>\n <tr>\n <th>FUMm</th>\n <td>FUMARATE + H2O</td>\n <td>(S)-MALATE</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>-3.44873</td>\n <td>0.607693</td>\n <td>True</td>\n <td>FUMARATE + H2O = (S)-MALATE</td>\n </tr>\n <tr>\n <th>MDHm</th>\n <td>(S)-MALATE + NAD+</td>\n <td>OXALOACETATE + NADH</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>29.9942</td>\n <td>0.422376</td>\n <td>True</td>\n <td>(S)-MALATE + NAD+ = OXALOACETATE + NADH</td>\n </tr>\n <tr>\n <th>GAPD</th>\n <td>D-GLYCERALDEHYDE-3-PHOSPHATE + ORTHOPHOSPHATE ...</td>\n <td>3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + NADH</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>6.68673</td>\n <td>0.895659</td>\n <td>True</td>\n <td>D-GLYCERALDEHYDE-3-PHOSPHATE + ORTHOPHOSPHATE ...</td>\n </tr>\n <tr>\n <th>PGK</th>\n <td>3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + ADP</td>\n <td>3-PHOSPHO-D-GLYCERATE + ATP</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>-18.4733</td>\n <td>0.889982</td>\n <td>True</td>\n <td>3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + ADP = 3-PHOS...</td>\n </tr>\n <tr>\n <th>TPI</th>\n <td>GLYCERONE_PHOSPHATE</td>\n <td>D-GLYCERALDEHYDE-3-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>5.48642</td>\n <td>0.753116</td>\n <td>True</td>\n <td>GLYCERONE_PHOSPHATE = D-GLYCERALDEHYDE-3-PHOSP...</td>\n </tr>\n <tr>\n <th>MDH</th>\n <td>(S)-MALATE + NAD+</td>\n <td>OXALOACETATE + NADH</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>29.9942</td>\n <td>0.422376</td>\n <td>True</td>\n <td>(S)-MALATE + NAD+ = OXALOACETATE + NADH</td>\n </tr>\n <tr>\n <th>PEP_Carboxylase</th>\n <td>OXALOACETATE + ORTHOPHOSPHATE</td>\n <td>PHOSPHOENOLPYRUVATE + CO2 + H2O</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>28.2337</td>\n <td>7.64087</td>\n <td>True</td>\n <td>OXALOACETATE + ORTHOPHOSPHATE = PHOSPHOENOLPYR...</td>\n </tr>\n <tr>\n <th>PPCK</th>\n <td>OXALOACETATE + ATP</td>\n <td>PHOSPHOENOLPYRUVATE + ADP + CO2</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>2.10596</td>\n <td>7.63913</td>\n <td>True</td>\n <td>OXALOACETATE + ATP = PHOSPHOENOLPYRUVATE + ADP...</td>\n </tr>\n <tr>\n <th>FBA</th>\n <td>D-FRUCTOSE_1,6-BISPHOSPHATE</td>\n <td>GLYCERONE_PHOSPHATE + D-GLYCERALDEHYDE-3-PHOSP...</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>20.5096</td>\n <td>0.87227</td>\n <td>True</td>\n <td>D-FRUCTOSE_1,6-BISPHOSPHATE = GLYCERONE_PHOSPH...</td>\n </tr>\n <tr>\n <th>FBP</th>\n <td>D-FRUCTOSE_6-PHOSPHATE + ORTHOPHOSPHATE</td>\n <td>H2O + D-FRUCTOSE_1,6-BISPHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>10.6728</td>\n <td>0.818386</td>\n <td>True</td>\n <td>D-FRUCTOSE_6-PHOSPHATE + ORTHOPHOSPHATE = H2O ...</td>\n </tr>\n <tr>\n <th>TKT2</th>\n <td>D-FRUCTOSE_6-PHOSPHATE + D-GLYCERALDEHYDE-3-PH...</td>\n <td>D-ERYTHROSE-4-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>10.0094</td>\n <td>2.08682</td>\n <td>True</td>\n <td>D-FRUCTOSE_6-PHOSPHATE + D-GLYCERALDEHYDE-3-PH...</td>\n </tr>\n <tr>\n <th>RPE</th>\n <td>D-XYLULOSE-5-PHOSPHATE</td>\n <td>D-RIBULOSE-5-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>3.37</td>\n <td>1.16485</td>\n <td>True</td>\n <td>D-XYLULOSE-5-PHOSPHATE = D-RIBULOSE-5-PHOSPHATE</td>\n </tr>\n <tr>\n <th>Xylulokinase</th>\n <td>D-XYLULOSE + ATP</td>\n <td>D-XYLULOSE-5-PHOSPHATE + ADP</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-23.0181</td>\n <td>2.29158</td>\n <td>True</td>\n <td>D-XYLULOSE + ATP = D-XYLULOSE-5-PHOSPHATE + ADP</td>\n </tr>\n <tr>\n <th>PYK_org</th>\n <td>ADP + PHOSPHOENOLPYRUVATE</td>\n <td>PYRUVATE + ATP</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-27.5366</td>\n <td>0.939774</td>\n <td>True</td>\n <td>ADP + PHOSPHOENOLPYRUVATE = PYRUVATE + ATP</td>\n </tr>\n <tr>\n <th>PYK</th>\n <td>ADP + PHOSPHOENOLPYRUVATE</td>\n <td>PYRUVATE + ATP</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>-27.5366</td>\n <td>0.939774</td>\n <td>True</td>\n <td>ADP + PHOSPHOENOLPYRUVATE = PYRUVATE + ATP</td>\n </tr>\n <tr>\n <th>RPI</th>\n <td>D-RIBOSE-5-PHOSPHATE</td>\n <td>D-RIBULOSE-5-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>1.94759</td>\n <td>1.16321</td>\n <td>True</td>\n <td>D-RIBOSE-5-PHOSPHATE = D-RIBULOSE-5-PHOSPHATE</td>\n </tr>\n <tr>\n <th>TKT1</th>\n <td>SEDOHEPTULOSE_7-PHOSPHATE + D-GLYCERALDEHYDE-3...</td>\n <td>D-RIBOSE-5-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>3.79253</td>\n <td>2.16133</td>\n <td>True</td>\n <td>SEDOHEPTULOSE_7-PHOSPHATE + D-GLYCERALDEHYDE-3...</td>\n </tr>\n <tr>\n <th>TALA</th>\n <td>D-GLYCERALDEHYDE-3-PHOSPHATE + SEDOHEPTULOSE_7...</td>\n <td>D-FRUCTOSE_6-PHOSPHATE + D-ERYTHROSE-4-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-0.728767</td>\n <td>1.62106</td>\n <td>True</td>\n <td>D-GLYCERALDEHYDE-3-PHOSPHATE + SEDOHEPTULOSE_7...</td>\n </tr>\n <tr>\n <th>PGM</th>\n <td>3-PHOSPHO-D-GLYCERATE</td>\n <td>2-PHOSPHO-D-GLYCERATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>4.19953</td>\n <td>0.65542</td>\n <td>True</td>\n <td>3-PHOSPHO-D-GLYCERATE = 2-PHOSPHO-D-GLYCERATE</td>\n </tr>\n <tr>\n <th>ENO</th>\n <td>2-PHOSPHO-D-GLYCERATE</td>\n <td>PHOSPHOENOLPYRUVATE + H2O</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>-4.08222</td>\n <td>0.734193</td>\n <td>True</td>\n <td>2-PHOSPHO-D-GLYCERATE = PHOSPHOENOLPYRUVATE + H2O</td>\n </tr>\n <tr>\n <th>GND</th>\n <td>NADPH + D-RIBULOSE-5-PHOSPHATE + CO2</td>\n <td>NADP+ + 6-PHOSPHO-D-GLUCONATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-2.5528</td>\n <td>7.60864</td>\n <td>True</td>\n <td>NADPH + D-RIBULOSE-5-PHOSPHATE + CO2 = NADP+ +...</td>\n </tr>\n <tr>\n <th>PGL</th>\n <td>6-PHOSPHO-D-GLUCONATE</td>\n <td>D-GLUCONO-1,5-LACTONE_6-PHOSPHATE + H2O</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>21.4202</td>\n <td>2.62825</td>\n <td>True</td>\n <td>6-PHOSPHO-D-GLUCONATE = D-GLUCONO-1,5-LACTONE_...</td>\n </tr>\n <tr>\n <th>HEX1</th>\n <td>BETA-D-GLUCOSE + ATP</td>\n <td>BETA-D-GLUCOSE-6-PHOSPHATE + ADP</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>-17.0578</td>\n <td>0.715237</td>\n <td>True</td>\n <td>BETA-D-GLUCOSE + ATP = BETA-D-GLUCOSE-6-PHOSPH...</td>\n </tr>\n <tr>\n <th>PGI</th>\n <td>BETA-D-GLUCOSE-6-PHOSPHATE</td>\n <td>D-FRUCTOSE_6-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>2.52401</td>\n <td>0.596775</td>\n <td>True</td>\n <td>BETA-D-GLUCOSE-6-PHOSPHATE = D-FRUCTOSE_6-PHOS...</td>\n </tr>\n <tr>\n <th>G6PDH2r</th>\n <td>BETA-D-GLUCOSE-6-PHOSPHATE + NADP+</td>\n <td>D-GLUCONO-1,5-LACTONE_6-PHOSPHATE + NADPH</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-2.9946</td>\n <td>2.11855</td>\n <td>True</td>\n <td>BETA-D-GLUCOSE-6-PHOSPHATE + NADP+ = D-GLUCONO...</td>\n </tr>\n <tr>\n <th>PFK</th>\n <td>D-FRUCTOSE_6-PHOSPHATE + ATP</td>\n <td>ADP + D-FRUCTOSE_1,6-BISPHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>-15.4549</td>\n <td>0.886629</td>\n <td>True</td>\n <td>D-FRUCTOSE_6-PHOSPHATE + ATP = ADP + D-FRUCTOS...</td>\n </tr>\n <tr>\n <th>PYRt2m</th>\n <td>PYRUVATE</td>\n <td>PYRUVATE</td>\n <td>CYTOSOL</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>-5.70769</td>\n <td>0</td>\n <td>False</td>\n <td>PYRUVATE = PYRUVATE</td>\n </tr>\n <tr>\n <th>PDHm</th>\n <td>COA + NAD+ + PYRUVATE</td>\n <td>ACETYL-COA + CO2 + NADH</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>-43.9219</td>\n <td>7.66459</td>\n <td>True</td>\n <td>COA + NAD+ + PYRUVATE = ACETYL-COA + CO2 + NADH</td>\n </tr>\n <tr>\n <th>ICL</th>\n <td>ISOCITRATE</td>\n <td>GLYOXYLATE + SUCCINATE</td>\n <td>GLYOXYSOME</td>\n <td>GLYOXYSOME</td>\n <td>0</td>\n <td>8.9806</td>\n <td>1.66465</td>\n <td>True</td>\n <td>ISOCITRATE = GLYOXYLATE + SUCCINATE</td>\n </tr>\n <tr>\n <th>MAS</th>\n <td>ACETYL-COA + GLYOXYLATE + H2O</td>\n <td>(S)-MALATE + COA</td>\n <td>GLYOXYSOME</td>\n <td>GLYOXYSOME</td>\n <td>0</td>\n <td>-33.0524</td>\n <td>2.32814</td>\n <td>True</td>\n <td>ACETYL-COA + GLYOXYLATE + H2O = (S)-MALATE + COA</td>\n </tr>\n <tr>\n <th>PYRDC</th>\n <td>PYRUVATE</td>\n <td>ACETALDEHYDE + CO2</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-26.5847</td>\n <td>7.65275</td>\n <td>True</td>\n <td>PYRUVATE = ACETALDEHYDE + CO2</td>\n </tr>\n <tr>\n <th>ALDD2y</th>\n <td>ACETALDEHYDE + NADP+ + H2O</td>\n <td>ACETATE + NADPH</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-46.8416</td>\n <td>1.53234</td>\n <td>True</td>\n <td>ACETALDEHYDE + NADP+ + H2O = ACETATE + NADPH</td>\n </tr>\n <tr>\n <th>ALCD2X_copy1</th>\n <td>ACETALDEHYDE + NADH</td>\n <td>ETHANOL + NAD+</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-21.3437</td>\n <td>0.590246</td>\n <td>True</td>\n <td>ACETALDEHYDE + NADH = ETHANOL + NAD+</td>\n </tr>\n <tr>\n <th>LactateDehydrogenase</th>\n <td>PYRUVATE + NADH</td>\n <td>LACTATE + NAD+</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-27.1344</td>\n <td>0.546575</td>\n <td>True</td>\n <td>PYRUVATE + NADH = LACTATE + NAD+</td>\n </tr>\n <tr>\n <th>Mitochondrial complex I/NADH ubiquinone oxidoredectase</th>\n <td>NADH:MITOCHONDRIAL_MATRIX + UBIQUINONE-6:MITOC...</td>\n <td>NAD+:MITOCHONDRIAL_MATRIX + UBIQUINOL-6:MITOCH...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>0</td>\n <td>-118.696</td>\n <td>6.11392</td>\n <td>False</td>\n <td>NADH:MITOCHONDRIAL_MATRIX + UBIQUINONE-6:MITOC...</td>\n </tr>\n <tr>\n <th>Mitochondrial complex III</th>\n <td>UBIQUINOL-6 + 2 FERRICYTOCHROME_C</td>\n <td>UBIQUINONE-6 + 2 FERROCYTOCHROME_C</td>\n <td>Mitochondrial_Membrane</td>\n <td>Mitochondrial_Membrane</td>\n <td>0</td>\n <td>54.7291</td>\n <td>565685</td>\n <td>True</td>\n <td>UBIQUINOL-6 + 2 FERRICYTOCHROME_C = UBIQUINONE...</td>\n </tr>\n <tr>\n <th>Mitochondrial complex IV</th>\n <td>4 FERROCYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + O...</td>\n <td>4 FERRICYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + 2...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>0</td>\n <td>-314.91</td>\n <td>1.13137e+06</td>\n <td>False</td>\n <td>4 FERROCYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + O...</td>\n </tr>\n </tbody>\n</table>\n</div>"
  998. },
  999. "metadata": {}
  1000. }
  1001. ]
  1002. },
  1003. {
  1004. "metadata": {},
  1005. "cell_type": "markdown",
  1006. "source": "### Determine Pyruvate transport reaction manually"
  1007. },
  1008. {
  1009. "metadata": {
  1010. "scrolled": false,
  1011. "trusted": true
  1012. },
  1013. "cell_type": "code",
  1014. "source": "reactions.loc['PYRt2m',deltag0] = -RT*np.log(10)\nreactions.loc['PYRt2m',deltag0_sigma] = 0\n",
  1015. "execution_count": 7,
  1016. "outputs": []
  1017. },
  1018. {
  1019. "metadata": {},
  1020. "cell_type": "markdown",
  1021. "source": "### Output the Standard Reaction Free Energies for use in a Boltzmann Simulation"
  1022. },
  1023. {
  1024. "metadata": {
  1025. "trusted": true
  1026. },
  1027. "cell_type": "code",
  1028. "source": "reaction_file = open('neurospora_aerobic_respiration.keq', 'w')\nfor y in reactions.index:\n print('%s\\t%e' % (y, np.exp(-reactions.loc[y,'DGZERO']/RT)),file=reaction_file)\nreaction_file.close() \n\nreaction_file = open('neurospora_aerobic_respiration.equilibrator.dat', 'w')\nfor y in reactions.index:\n print(\"REACTION\\t\",y,file=reaction_file)\n #print(reaction_df[y])\n for x in reactions.columns:\n if x == \"Full Rxn\":\n continue\n if x == same_compartment:\n continue\n# if ((x == deltag0) and (reactions.loc[y,same_compartment] == False)):\n# continue\n if pd.notnull(reactions.loc[y,x]):\n print(x, reactions.loc[y,x],file=reaction_file)\n print(\"DGZERO-UNITS KJ/MOL\",file=reaction_file)\n print(\"//\",file=reaction_file)\nreaction_file.close() ",
  1029. "execution_count": 8,
  1030. "outputs": []
  1031. },
  1032. {
  1033. "metadata": {},
  1034. "cell_type": "markdown",
  1035. "source": "## Set Fixed Concentrations/Boundary Conditions"
  1036. },
  1037. {
  1038. "metadata": {
  1039. "scrolled": false,
  1040. "trusted": true
  1041. },
  1042. "cell_type": "code",
  1043. "source": "conc = 'Conc'\nvariable = 'Variable'\nmetabolites = pd.DataFrame(index = S_active.columns, columns=[conc,variable])\nmetabolites[conc] = 0.001\nmetabolites[variable] = True\n\n# Set the fixed metabolites:\nmetabolites.loc['ATP:MITOCHONDRIAL_MATRIX',conc] = 9.600000e-03\nmetabolites.loc['ATP:MITOCHONDRIAL_MATRIX',variable] = False\nmetabolites.loc['ADP:MITOCHONDRIAL_MATRIX',conc] = 5.600000e-04\nmetabolites.loc['ADP:MITOCHONDRIAL_MATRIX',variable] = False\nmetabolites.loc['ORTHOPHOSPHATE:MITOCHONDRIAL_MATRIX',conc] = 2.000000e-02\nmetabolites.loc['ORTHOPHOSPHATE:MITOCHONDRIAL_MATRIX',variable] = False\n\nmetabolites.loc['ATP:CYTOSOL',conc] = 9.600000e-03\nmetabolites.loc['ATP:CYTOSOL',variable] = False\nmetabolites.loc['ADP:CYTOSOL',conc] = 5.600000e-04\nmetabolites.loc['ADP:CYTOSOL',variable] = False\nmetabolites.loc['ORTHOPHOSPHATE:CYTOSOL',conc] = 2.000000e-02\nmetabolites.loc['ORTHOPHOSPHATE:CYTOSOL',variable] = False\n\nmetabolites.loc['NADH:MITOCHONDRIAL_MATRIX',conc] = 8.300000e-05\nmetabolites.loc['NADH:MITOCHONDRIAL_MATRIX',variable] = False\nmetabolites.loc['NAD+:MITOCHONDRIAL_MATRIX',conc] = 2.600000e-03\nmetabolites.loc['NAD+:MITOCHONDRIAL_MATRIX',variable] = False\n\nmetabolites.loc['NADH:CYTOSOL',conc] = 8.300000e-05\nmetabolites.loc['NADH:CYTOSOL',variable] = False\nmetabolites.loc['NAD+:CYTOSOL',conc] = 2.600000e-03\nmetabolites.loc['NAD+:CYTOSOL',variable] = False\n\n#metabolites.loc['NADPH:MITOCHONDRIAL_MATRIX',conc] = 0.1\n#metabolites.loc['NADPH:MITOCHONDRIAL_MATRIX',variable] = False\n#metabolites.loc['NAPD+:MITOCHONDRIAL_MATRIX',conc] = 0.1\n#metabolites.loc['NAPD+:MITOCHONDRIAL_MATRIX',variable] = False\n\n#metabolites.loc['NADPH:CYTOSOL',conc] = 0.1\n#metabolites.loc['NADPH:CYTOSOL',variable] = False\n#metabolites.loc['NADP+:CYTOSOL',conc] = 0.1\n#metabolites.loc['NADP+:CYTOSOL',variable] = False\n\nmetabolites.loc['ACETYL-COA:MITOCHONDRIAL_MATRIX',conc] = 0.1\nmetabolites.loc['ACETYL-COA:MITOCHONDRIAL_MATRIX',variable] = True\n#metabolites.loc['ACETYL-COA:CYTOSOL',conc] = 0.1\n#metabolites.loc['ACETYL-COA:CYTOSOL',variable] = False\n\nmetabolites.loc['COA:MITOCHONDRIAL_MATRIX',conc] = 1.400000e-03\nmetabolites.loc['COA:MITOCHONDRIAL_MATRIX',variable] = False\n#metabolites.loc['COA:CYTOSOL',conc] = 0.1\n#metabolites.loc['COA:CYTOSOL',variable] = False\n#metabolites.loc['COA:GLYOXYSOME',conc] = 0.1\n#metabolites.loc['COA:GLYOXYSOME',variable] = False\n\nmetabolites.loc['CO2:MITOCHONDRIAL_MATRIX',conc] = 1.000000e-04\nmetabolites.loc['CO2:MITOCHONDRIAL_MATRIX',variable] = False\n#metabolites.loc['CO2:CYTOSOL',conc] = 0.1\n#metabolites.loc['CO2:CYTOSOL',variable] = False \n\nmetabolites.loc['H2O:MITOCHONDRIAL_MATRIX',conc] = 55.5\nmetabolites.loc['H2O:MITOCHONDRIAL_MATRIX',variable] = False\nmetabolites.loc['H2O:CYTOSOL',conc] = 55.5\nmetabolites.loc['H2O:CYTOSOL',variable] = False \n\n# What should the concentration of oxygen in the mitochondrial be?\n#metabolites.loc['OXYGEN:MITOCHONDRIAL_MATRIX','Conc',] = 1.0e-28\nmetabolites.loc['OXYGEN:MITOCHONDRIAL_MATRIX',conc] = 1.0e-04\nmetabolites.loc['OXYGEN:MITOCHONDRIAL_MATRIX',variable] = False\n#metabolites.loc['OXYGEN:CYTOSOL',conc] = 55.5\n#metabolites.loc['OXYGEN:CYTOSOL',variable] = False \n\nmetabolites.loc['BETA-D-GLUCOSE:CYTOSOL',conc] = 2.0e-03\nmetabolites.loc['BETA-D-GLUCOSE:CYTOSOL',variable] = False \n\nnvariables = metabolites[metabolites[variable]].count()\nnvar = nvariables[variable]\n\nmetabolites.sort_values(by=variable, axis=0,ascending=False, inplace=True,)\ndisplay(metabolites)",
  1044. "execution_count": 9,
  1045. "outputs": [
  1046. {
  1047. "output_type": "display_data",
  1048. "data": {
  1049. "text/plain": " Conc Variable\n(S)-MALATE:MITOCHONDRIAL_MATRIX 0.001000 True\nSUCCINYL-COA:MITOCHONDRIAL_MATRIX 0.001000 True\n2-PHOSPHO-D-GLYCERATE:CYTOSOL 0.001000 True\nPYRUVATE:CYTOSOL 0.001000 True\nD-FRUCTOSE_6-PHOSPHATE:CYTOSOL 0.001000 True\nD-FRUCTOSE_1,6-BISPHOSPHATE:CYTOSOL 0.001000 True\nPHOSPHOENOLPYRUVATE:CYTOSOL 0.001000 True\nGLYCERONE_PHOSPHATE:CYTOSOL 0.001000 True\n3-PHOSPHO-D-GLYCERATE:CYTOSOL 0.001000 True\n3-PHOSPHO-D-GLYCEROYL_PHOSPHATE:CYTOSOL 0.001000 True\nD-GLYCERALDEHYDE-3-PHOSPHATE:CYTOSOL 0.001000 True\nSUCCINATE:MITOCHONDRIAL_MATRIX 0.001000 True\nFUMARATE:MITOCHONDRIAL_MATRIX 0.001000 True\nBETA-D-GLUCOSE-6-PHOSPHATE:CYTOSOL 0.001000 True\n2-OXOGLUTARATE:MITOCHONDRIAL_MATRIX 0.001000 True\nPYRUVATE:MITOCHONDRIAL_MATRIX 0.001000 True\nISOCITRATE:MITOCHONDRIAL_MATRIX 0.001000 True\nOXALOACETATE:MITOCHONDRIAL_MATRIX 0.001000 True\nACETYL-COA:MITOCHONDRIAL_MATRIX 0.100000 True\nCITRATE:MITOCHONDRIAL_MATRIX 0.001000 True\nATP:CYTOSOL 0.009600 False\nBETA-D-GLUCOSE:CYTOSOL 0.002000 False\nNADH:MITOCHONDRIAL_MATRIX 0.000083 False\nCO2:MITOCHONDRIAL_MATRIX 0.000100 False\nH2O:CYTOSOL 55.500000 False\nH2O:MITOCHONDRIAL_MATRIX 55.500000 False\nADP:MITOCHONDRIAL_MATRIX 0.000560 False\nORTHOPHOSPHATE:MITOCHONDRIAL_MATRIX 0.020000 False\nNADH:CYTOSOL 0.000083 False\nCOA:MITOCHONDRIAL_MATRIX 0.001400 False\nNAD+:CYTOSOL 0.002600 False\nORTHOPHOSPHATE:CYTOSOL 0.020000 False\nNAD+:MITOCHONDRIAL_MATRIX 0.002600 False\nOXYGEN:MITOCHONDRIAL_MATRIX 0.000100 False\nATP:MITOCHONDRIAL_MATRIX 0.009600 False\nADP:CYTOSOL 0.000560 False",
  1050. "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>Conc</th>\n <th>Variable</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th>(S)-MALATE:MITOCHONDRIAL_MATRIX</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>SUCCINYL-COA:MITOCHONDRIAL_MATRIX</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>2-PHOSPHO-D-GLYCERATE:CYTOSOL</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>PYRUVATE:CYTOSOL</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>D-FRUCTOSE_6-PHOSPHATE:CYTOSOL</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>D-FRUCTOSE_1,6-BISPHOSPHATE:CYTOSOL</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>PHOSPHOENOLPYRUVATE:CYTOSOL</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>GLYCERONE_PHOSPHATE:CYTOSOL</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>3-PHOSPHO-D-GLYCERATE:CYTOSOL</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>3-PHOSPHO-D-GLYCEROYL_PHOSPHATE:CYTOSOL</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>D-GLYCERALDEHYDE-3-PHOSPHATE:CYTOSOL</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>SUCCINATE:MITOCHONDRIAL_MATRIX</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>FUMARATE:MITOCHONDRIAL_MATRIX</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>BETA-D-GLUCOSE-6-PHOSPHATE:CYTOSOL</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>2-OXOGLUTARATE:MITOCHONDRIAL_MATRIX</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>PYRUVATE:MITOCHONDRIAL_MATRIX</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>ISOCITRATE:MITOCHONDRIAL_MATRIX</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>OXALOACETATE:MITOCHONDRIAL_MATRIX</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>ACETYL-COA:MITOCHONDRIAL_MATRIX</th>\n <td>0.100000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>CITRATE:MITOCHONDRIAL_MATRIX</th>\n <td>0.001000</td>\n <td>True</td>\n </tr>\n <tr>\n <th>ATP:CYTOSOL</th>\n <td>0.009600</td>\n <td>False</td>\n </tr>\n <tr>\n <th>BETA-D-GLUCOSE:CYTOSOL</th>\n <td>0.002000</td>\n <td>False</td>\n </tr>\n <tr>\n <th>NADH:MITOCHONDRIAL_MATRIX</th>\n <td>0.000083</td>\n <td>False</td>\n </tr>\n <tr>\n <th>CO2:MITOCHONDRIAL_MATRIX</th>\n <td>0.000100</td>\n <td>False</td>\n </tr>\n <tr>\n <th>H2O:CYTOSOL</th>\n <td>55.500000</td>\n <td>False</td>\n </tr>\n <tr>\n <th>H2O:MITOCHONDRIAL_MATRIX</th>\n <td>55.500000</td>\n <td>False</td>\n </tr>\n <tr>\n <th>ADP:MITOCHONDRIAL_MATRIX</th>\n <td>0.000560</td>\n <td>False</td>\n </tr>\n <tr>\n <th>ORTHOPHOSPHATE:MITOCHONDRIAL_MATRIX</th>\n <td>0.020000</td>\n <td>False</td>\n </tr>\n <tr>\n <th>NADH:CYTOSOL</th>\n <td>0.000083</td>\n <td>False</td>\n </tr>\n <tr>\n <th>COA:MITOCHONDRIAL_MATRIX</th>\n <td>0.001400</td>\n <td>False</td>\n </tr>\n <tr>\n <th>NAD+:CYTOSOL</th>\n <td>0.002600</td>\n <td>False</td>\n </tr>\n <tr>\n <th>ORTHOPHOSPHATE:CYTOSOL</th>\n <td>0.020000</td>\n <td>False</td>\n </tr>\n <tr>\n <th>NAD+:MITOCHONDRIAL_MATRIX</th>\n <td>0.002600</td>\n <td>False</td>\n </tr>\n <tr>\n <th>OXYGEN:MITOCHONDRIAL_MATRIX</th>\n <td>0.000100</td>\n <td>False</td>\n </tr>\n <tr>\n <th>ATP:MITOCHONDRIAL_MATRIX</th>\n <td>0.009600</td>\n <td>False</td>\n </tr>\n <tr>\n <th>ADP:CYTOSOL</th>\n <td>0.000560</td>\n <td>False</td>\n </tr>\n </tbody>\n</table>\n</div>"
  1051. },
  1052. "metadata": {}
  1053. }
  1054. ]
  1055. },
  1056. {
  1057. "metadata": {},
  1058. "cell_type": "markdown",
  1059. "source": "## Prepare model for optimization"
  1060. },
  1061. {
  1062. "metadata": {},
  1063. "cell_type": "markdown",
  1064. "source": "- Adjust S Matrix to use only reactions with activity > 0, if necessary.\n- Water stoichiometry in the stiochiometric matrix needs to be set to zero since water is held constant.\n- The initial concentrations of the variable metabolites are random.\n- All concentrations are changed to log counts.\n- Equilibrium constants are calculated from standard free energies of reaction.\n- R (reactant) and P (product) matrices are derived from S."
  1065. },
  1066. {
  1067. "metadata": {
  1068. "trusted": true
  1069. },
  1070. "cell_type": "code",
  1071. "source": "# Make sure all the indices and columns are in the correct order:\nactive_reactions = reactions[reactions[enzyme_level] > 0.0]\ndisplay(reactions)\nSactive_index = S_active.index\n#Sactive_columns = S_active.columns\nactive_reactions.reindex(index = Sactive_index, copy = False)\nS_active = S_active.reindex(columns = metabolites.index, copy = False)\nS_active['H2O:MITOCHONDRIAL_MATRIX'] = 0\nS_active['H2O:CYTOSOL'] = 0\ndisplay(S_active)\nS = S_active.values\n\ndisplay(nvar)\n\n#variable_concs = np.array(metabolites['Conc'].iloc[0:nvar].values, dtype=np.float64)\nv_log_concs = -10 + 10*np.random.rand(nvar) #Vary between 1 M to 1.0e-10 M\nv_concs = np.exp(v_log_concs)\nv_log_counts = np.log(v_concs*Concentration2Count)\nv_log_counts0 = v_log_counts\ndisplay(v_log_counts)\n\nfixed_concs = np.array(metabolites['Conc'].iloc[nvar:].values, dtype=np.float64)\nfixed_counts = fixed_concs*Concentration2Count\nf_log_counts = np.log(fixed_counts)\ndisplay(f_log_counts)\n\nK = np.exp(-active_reactions[deltag0].astype('float')/RT)\ndisplay(K)\nK = K.values\n\nP = np.where(S>0,S,0)\nR = np.where(S<0, S, 0)\nE_regulation = np.ones(K.size) # THis is the vector of enzyme activities, Range: 0 to 1.\ndelta = np.zeros(metabolites['Conc'].values.size);\n\nmu0 = 1 #Dummy parameter for now; reserved for free energies of formation",
  1072. "execution_count": 10,
  1073. "outputs": [
  1074. {
  1075. "output_type": "display_data",
  1076. "data": {
  1077. "text/plain": " LEFT \\\nREACTION \nME1m (S)-MALATE + NAD+ \nME2m (S)-MALATE + NADP+ \nCSm OXALOACETATE + ACETYL-COA + H2O \nACONTm CITRATE \nICDHxm ISOCITRATE + NAD+ \nAKGDm 2-OXOGLUTARATE + COA + NAD+ \nSUCOASm SUCCINYL-COA + ADP + ORTHOPHOSPHATE \nSUCD1m SUCCINATE:MITOCHONDRIAL_MATRIX + OXYGEN + NADH \nFUMm FUMARATE + H2O \nMDHm (S)-MALATE + NAD+ \nGAPD D-GLYCERALDEHYDE-3-PHOSPHATE + ORTHOPHOSPHATE ... \nPGK 3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + ADP \nTPI GLYCERONE_PHOSPHATE \nMDH (S)-MALATE + NAD+ \nPEP_Carboxylase OXALOACETATE + ORTHOPHOSPHATE \nPPCK OXALOACETATE + ATP \nFBA D-FRUCTOSE_1,6-BISPHOSPHATE \nFBP D-FRUCTOSE_6-PHOSPHATE + ORTHOPHOSPHATE \nTKT2 D-FRUCTOSE_6-PHOSPHATE + D-GLYCERALDEHYDE-3-PH... \nRPE D-XYLULOSE-5-PHOSPHATE \nXylulokinase D-XYLULOSE + ATP \nPYK_org ADP + PHOSPHOENOLPYRUVATE \nPYK ADP + PHOSPHOENOLPYRUVATE \nRPI D-RIBOSE-5-PHOSPHATE \nTKT1 SEDOHEPTULOSE_7-PHOSPHATE + D-GLYCERALDEHYDE-3... \nTALA D-GLYCERALDEHYDE-3-PHOSPHATE + SEDOHEPTULOSE_7... \nPGM 3-PHOSPHO-D-GLYCERATE \nENO 2-PHOSPHO-D-GLYCERATE \nGND NADPH + D-RIBULOSE-5-PHOSPHATE + CO2 \nPGL 6-PHOSPHO-D-GLUCONATE \nHEX1 BETA-D-GLUCOSE + ATP \nPGI BETA-D-GLUCOSE-6-PHOSPHATE \nG6PDH2r BETA-D-GLUCOSE-6-PHOSPHATE + NADP+ \nPFK D-FRUCTOSE_6-PHOSPHATE + ATP \nPYRt2m PYRUVATE \nPDHm COA + NAD+ + PYRUVATE \nICL ISOCITRATE \nMAS ACETYL-COA + GLYOXYLATE + H2O \nPYRDC PYRUVATE \nALDD2y ACETALDEHYDE + NADP+ + H2O \nALCD2X_copy1 ACETALDEHYDE + NADH \nLactateDehydrogenase PYRUVATE + NADH \nMitochondrial complex I/NADH ubiquinone oxidore... NADH:MITOCHONDRIAL_MATRIX + UBIQUINONE-6:MITOC... \nMitochondrial complex III UBIQUINOL-6 + 2 FERRICYTOCHROME_C \nMitochondrial complex IV 4 FERROCYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + O... \n\n RIGHT \\\nREACTION \nME1m PYRUVATE + NADH + CO2 \nME2m PYRUVATE + NADPH + CO2 \nCSm CITRATE + COA \nACONTm ISOCITRATE \nICDHxm 2-OXOGLUTARATE + NADH + CO2 \nAKGDm SUCCINYL-COA + CO2 + NADH \nSUCOASm SUCCINATE + ATP + COA \nSUCD1m FUMARATE:MITOCHONDRIAL_MATRIX + 2 H2O + NAD+ \nFUMm (S)-MALATE \nMDHm OXALOACETATE + NADH \nGAPD 3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + NADH \nPGK 3-PHOSPHO-D-GLYCERATE + ATP \nTPI D-GLYCERALDEHYDE-3-PHOSPHATE \nMDH OXALOACETATE + NADH \nPEP_Carboxylase PHOSPHOENOLPYRUVATE + CO2 + H2O \nPPCK PHOSPHOENOLPYRUVATE + ADP + CO2 \nFBA GLYCERONE_PHOSPHATE + D-GLYCERALDEHYDE-3-PHOSP... \nFBP H2O + D-FRUCTOSE_1,6-BISPHOSPHATE \nTKT2 D-ERYTHROSE-4-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE \nRPE D-RIBULOSE-5-PHOSPHATE \nXylulokinase D-XYLULOSE-5-PHOSPHATE + ADP \nPYK_org PYRUVATE + ATP \nPYK PYRUVATE + ATP \nRPI D-RIBULOSE-5-PHOSPHATE \nTKT1 D-RIBOSE-5-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE \nTALA D-FRUCTOSE_6-PHOSPHATE + D-ERYTHROSE-4-PHOSPHATE \nPGM 2-PHOSPHO-D-GLYCERATE \nENO PHOSPHOENOLPYRUVATE + H2O \nGND NADP+ + 6-PHOSPHO-D-GLUCONATE \nPGL D-GLUCONO-1,5-LACTONE_6-PHOSPHATE + H2O \nHEX1 BETA-D-GLUCOSE-6-PHOSPHATE + ADP \nPGI D-FRUCTOSE_6-PHOSPHATE \nG6PDH2r D-GLUCONO-1,5-LACTONE_6-PHOSPHATE + NADPH \nPFK ADP + D-FRUCTOSE_1,6-BISPHOSPHATE \nPYRt2m PYRUVATE \nPDHm ACETYL-COA + CO2 + NADH \nICL GLYOXYLATE + SUCCINATE \nMAS (S)-MALATE + COA \nPYRDC ACETALDEHYDE + CO2 \nALDD2y ACETATE + NADPH \nALCD2X_copy1 ETHANOL + NAD+ \nLactateDehydrogenase LACTATE + NAD+ \nMitochondrial complex I/NADH ubiquinone oxidore... NAD+:MITOCHONDRIAL_MATRIX + UBIQUINOL-6:MITOCH... \nMitochondrial complex III UBIQUINONE-6 + 2 FERROCYTOCHROME_C \nMitochondrial complex IV 4 FERRICYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + 2... \n\n LEFT_COMPARTMENT \\\nREACTION \nME1m MITOCHONDRIAL_MATRIX \nME2m MITOCHONDRIAL_MATRIX \nCSm MITOCHONDRIAL_MATRIX \nACONTm MITOCHONDRIAL_MATRIX \nICDHxm MITOCHONDRIAL_MATRIX \nAKGDm MITOCHONDRIAL_MATRIX \nSUCOASm MITOCHONDRIAL_MATRIX \nSUCD1m :MITOCHONDRIAL_MATRIX \nFUMm MITOCHONDRIAL_MATRIX \nMDHm MITOCHONDRIAL_MATRIX \nGAPD CYTOSOL \nPGK CYTOSOL \nTPI CYTOSOL \nMDH CYTOSOL \nPEP_Carboxylase CYTOSOL \nPPCK CYTOSOL \nFBA CYTOSOL \nFBP CYTOSOL \nTKT2 CYTOSOL \nRPE CYTOSOL \nXylulokinase CYTOSOL \nPYK_org CYTOSOL \nPYK CYTOSOL \nRPI CYTOSOL \nTKT1 CYTOSOL \nTALA CYTOSOL \nPGM CYTOSOL \nENO CYTOSOL \nGND CYTOSOL \nPGL CYTOSOL \nHEX1 CYTOSOL \nPGI CYTOSOL \nG6PDH2r CYTOSOL \nPFK CYTOSOL \nPYRt2m CYTOSOL \nPDHm MITOCHONDRIAL_MATRIX \nICL GLYOXYSOME \nMAS GLYOXYSOME \nPYRDC CYTOSOL \nALDD2y CYTOSOL \nALCD2X_copy1 CYTOSOL \nLactateDehydrogenase CYTOSOL \nMitochondrial complex I/NADH ubiquinone oxidore... NaN \nMitochondrial complex III Mitochondrial_Membrane \nMitochondrial complex IV NaN \n\n RIGHT_COMPARTMENT \\\nREACTION \nME1m MITOCHONDRIAL_MATRIX \nME2m MITOCHONDRIAL_MATRIX \nCSm MITOCHONDRIAL_MATRIX \nACONTm MITOCHONDRIAL_MATRIX \nICDHxm MITOCHONDRIAL_MATRIX \nAKGDm MITOCHONDRIAL_MATRIX \nSUCOASm MITOCHONDRIAL_MATRIX \nSUCD1m :MITOCHONDRIAL_MATRIX \nFUMm MITOCHONDRIAL_MATRIX \nMDHm MITOCHONDRIAL_MATRIX \nGAPD CYTOSOL \nPGK CYTOSOL \nTPI CYTOSOL \nMDH CYTOSOL \nPEP_Carboxylase CYTOSOL \nPPCK CYTOSOL \nFBA CYTOSOL \nFBP CYTOSOL \nTKT2 CYTOSOL \nRPE CYTOSOL \nXylulokinase CYTOSOL \nPYK_org CYTOSOL \nPYK CYTOSOL \nRPI CYTOSOL \nTKT1 CYTOSOL \nTALA CYTOSOL \nPGM CYTOSOL \nENO CYTOSOL \nGND CYTOSOL \nPGL CYTOSOL \nHEX1 CYTOSOL \nPGI CYTOSOL \nG6PDH2r CYTOSOL \nPFK CYTOSOL \nPYRt2m MITOCHONDRIAL_MATRIX \nPDHm MITOCHONDRIAL_MATRIX \nICL GLYOXYSOME \nMAS GLYOXYSOME \nPYRDC CYTOSOL \nALDD2y CYTOSOL \nALCD2X_copy1 CYTOSOL \nLactateDehydrogenase CYTOSOL \nMitochondrial complex I/NADH ubiquinone oxidore... NaN \nMitochondrial complex III Mitochondrial_Membrane \nMitochondrial complex IV NaN \n\n ENZYME_LEVEL DGZERO \\\nREACTION \nME1m 0 4.56353 \nME2m 0 5.21174 \nCSm 1 -35.1166 \nACONTm 1 7.62949 \nICDHxm 1 -2.872 \nAKGDm 1 -36.3549 \nSUCOASm 1 1.92448 \nSUCD1m 1 -380.023 \nFUMm 1 -3.44873 \nMDHm 1 29.9942 \nGAPD 1 6.68673 \nPGK 1 -18.4733 \nTPI 1 5.48642 \nMDH 0 29.9942 \nPEP_Carboxylase 0 28.2337 \nPPCK 0 2.10596 \nFBA 1 20.5096 \nFBP 0 10.6728 \nTKT2 0 10.0094 \nRPE 0 3.37 \nXylulokinase 0 -23.0181 \nPYK_org 0 -27.5366 \nPYK 1 -27.5366 \nRPI 0 1.94759 \nTKT1 0 3.79253 \nTALA 0 -0.728767 \nPGM 1 4.19953 \nENO 1 -4.08222 \nGND 0 -2.5528 \nPGL 0 21.4202 \nHEX1 1 -17.0578 \nPGI 1 2.52401 \nG6PDH2r 0 -2.9946 \nPFK 1 -15.4549 \nPYRt2m 1 -5.70769 \nPDHm 1 -43.9219 \nICL 0 8.9806 \nMAS 0 -33.0524 \nPYRDC 0 -26.5847 \nALDD2y 0 -46.8416 \nALCD2X_copy1 0 -21.3437 \nLactateDehydrogenase 0 -27.1344 \nMitochondrial complex I/NADH ubiquinone oxidore... 0 -118.696 \nMitochondrial complex III 0 54.7291 \nMitochondrial complex IV 0 -314.91 \n\n DGZERO StdDev \\\nREACTION \nME1m 7.60174 \nME2m 7.61042 \nCSm 0.930552 \nACONTm 0.733847 \nICDHxm 7.62095 \nAKGDm 7.97121 \nSUCOASm 1.48197 \nSUCD1m 7.8098 \nFUMm 0.607693 \nMDHm 0.422376 \nGAPD 0.895659 \nPGK 0.889982 \nTPI 0.753116 \nMDH 0.422376 \nPEP_Carboxylase 7.64087 \nPPCK 7.63913 \nFBA 0.87227 \nFBP 0.818386 \nTKT2 2.08682 \nRPE 1.16485 \nXylulokinase 2.29158 \nPYK_org 0.939774 \nPYK 0.939774 \nRPI 1.16321 \nTKT1 2.16133 \nTALA 1.62106 \nPGM 0.65542 \nENO 0.734193 \nGND 7.60864 \nPGL 2.62825 \nHEX1 0.715237 \nPGI 0.596775 \nG6PDH2r 2.11855 \nPFK 0.886629 \nPYRt2m 0 \nPDHm 7.66459 \nICL 1.66465 \nMAS 2.32814 \nPYRDC 7.65275 \nALDD2y 1.53234 \nALCD2X_copy1 0.590246 \nLactateDehydrogenase 0.546575 \nMitochondrial complex I/NADH ubiquinone oxidore... 6.11392 \nMitochondrial complex III 565685 \nMitochondrial complex IV 1.13137e+06 \n\n Same Compartment? \\\nREACTION \nME1m True \nME2m True \nCSm True \nACONTm True \nICDHxm True \nAKGDm True \nSUCOASm True \nSUCD1m True \nFUMm True \nMDHm True \nGAPD True \nPGK True \nTPI True \nMDH True \nPEP_Carboxylase True \nPPCK True \nFBA True \nFBP True \nTKT2 True \nRPE True \nXylulokinase True \nPYK_org True \nPYK True \nRPI True \nTKT1 True \nTALA True \nPGM True \nENO True \nGND True \nPGL True \nHEX1 True \nPGI True \nG6PDH2r True \nPFK True \nPYRt2m False \nPDHm True \nICL True \nMAS True \nPYRDC True \nALDD2y True \nALCD2X_copy1 True \nLactateDehydrogenase True \nMitochondrial complex I/NADH ubiquinone oxidore... False \nMitochondrial complex III True \nMitochondrial complex IV False \n\n Full Rxn \nREACTION \nME1m (S)-MALATE + NAD+ = PYRUVATE + NADH + CO2 \nME2m (S)-MALATE + NADP+ = PYRUVATE + NADPH + CO2 \nCSm OXALOACETATE + ACETYL-COA + H2O = CITRATE + COA \nACONTm CITRATE = ISOCITRATE \nICDHxm ISOCITRATE + NAD+ = 2-OXOGLUTARATE + NADH + CO2 \nAKGDm 2-OXOGLUTARATE + COA + NAD+ = SUCCINYL-COA + C... \nSUCOASm SUCCINYL-COA + ADP + ORTHOPHOSPHATE = SUCCINAT... \nSUCD1m SUCCINATE:MITOCHONDRIAL_MATRIX + OXYGEN + NADH... \nFUMm FUMARATE + H2O = (S)-MALATE \nMDHm (S)-MALATE + NAD+ = OXALOACETATE + NADH \nGAPD D-GLYCERALDEHYDE-3-PHOSPHATE + ORTHOPHOSPHATE ... \nPGK 3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + ADP = 3-PHOS... \nTPI GLYCERONE_PHOSPHATE = D-GLYCERALDEHYDE-3-PHOSP... \nMDH (S)-MALATE + NAD+ = OXALOACETATE + NADH \nPEP_Carboxylase OXALOACETATE + ORTHOPHOSPHATE = PHOSPHOENOLPYR... \nPPCK OXALOACETATE + ATP = PHOSPHOENOLPYRUVATE + ADP... \nFBA D-FRUCTOSE_1,6-BISPHOSPHATE = GLYCERONE_PHOSPH... \nFBP D-FRUCTOSE_6-PHOSPHATE + ORTHOPHOSPHATE = H2O ... \nTKT2 D-FRUCTOSE_6-PHOSPHATE + D-GLYCERALDEHYDE-3-PH... \nRPE D-XYLULOSE-5-PHOSPHATE = D-RIBULOSE-5-PHOSPHATE \nXylulokinase D-XYLULOSE + ATP = D-XYLULOSE-5-PHOSPHATE + ADP \nPYK_org ADP + PHOSPHOENOLPYRUVATE = PYRUVATE + ATP \nPYK ADP + PHOSPHOENOLPYRUVATE = PYRUVATE + ATP \nRPI D-RIBOSE-5-PHOSPHATE = D-RIBULOSE-5-PHOSPHATE \nTKT1 SEDOHEPTULOSE_7-PHOSPHATE + D-GLYCERALDEHYDE-3... \nTALA D-GLYCERALDEHYDE-3-PHOSPHATE + SEDOHEPTULOSE_7... \nPGM 3-PHOSPHO-D-GLYCERATE = 2-PHOSPHO-D-GLYCERATE \nENO 2-PHOSPHO-D-GLYCERATE = PHOSPHOENOLPYRUVATE + H2O \nGND NADPH + D-RIBULOSE-5-PHOSPHATE + CO2 = NADP+ +... \nPGL 6-PHOSPHO-D-GLUCONATE = D-GLUCONO-1,5-LACTONE_... \nHEX1 BETA-D-GLUCOSE + ATP = BETA-D-GLUCOSE-6-PHOSPH... \nPGI BETA-D-GLUCOSE-6-PHOSPHATE = D-FRUCTOSE_6-PHOS... \nG6PDH2r BETA-D-GLUCOSE-6-PHOSPHATE + NADP+ = D-GLUCONO... \nPFK D-FRUCTOSE_6-PHOSPHATE + ATP = ADP + D-FRUCTOS... \nPYRt2m PYRUVATE = PYRUVATE \nPDHm COA + NAD+ + PYRUVATE = ACETYL-COA + CO2 + NADH \nICL ISOCITRATE = GLYOXYLATE + SUCCINATE \nMAS ACETYL-COA + GLYOXYLATE + H2O = (S)-MALATE + COA \nPYRDC PYRUVATE = ACETALDEHYDE + CO2 \nALDD2y ACETALDEHYDE + NADP+ + H2O = ACETATE + NADPH \nALCD2X_copy1 ACETALDEHYDE + NADH = ETHANOL + NAD+ \nLactateDehydrogenase PYRUVATE + NADH = LACTATE + NAD+ \nMitochondrial complex I/NADH ubiquinone oxidore... NADH:MITOCHONDRIAL_MATRIX + UBIQUINONE-6:MITOC... \nMitochondrial complex III UBIQUINOL-6 + 2 FERRICYTOCHROME_C = UBIQUINONE... \nMitochondrial complex IV 4 FERROCYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + O... ",
  1078. "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>LEFT</th>\n <th>RIGHT</th>\n <th>LEFT_COMPARTMENT</th>\n <th>RIGHT_COMPARTMENT</th>\n <th>ENZYME_LEVEL</th>\n <th>DGZERO</th>\n <th>DGZERO StdDev</th>\n <th>Same Compartment?</th>\n <th>Full Rxn</th>\n </tr>\n <tr>\n <th>REACTION</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>ME1m</th>\n <td>(S)-MALATE + NAD+</td>\n <td>PYRUVATE + NADH + CO2</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>0</td>\n <td>4.56353</td>\n <td>7.60174</td>\n <td>True</td>\n <td>(S)-MALATE + NAD+ = PYRUVATE + NADH + CO2</td>\n </tr>\n <tr>\n <th>ME2m</th>\n <td>(S)-MALATE + NADP+</td>\n <td>PYRUVATE + NADPH + CO2</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>0</td>\n <td>5.21174</td>\n <td>7.61042</td>\n <td>True</td>\n <td>(S)-MALATE + NADP+ = PYRUVATE + NADPH + CO2</td>\n </tr>\n <tr>\n <th>CSm</th>\n <td>OXALOACETATE + ACETYL-COA + H2O</td>\n <td>CITRATE + COA</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>-35.1166</td>\n <td>0.930552</td>\n <td>True</td>\n <td>OXALOACETATE + ACETYL-COA + H2O = CITRATE + COA</td>\n </tr>\n <tr>\n <th>ACONTm</th>\n <td>CITRATE</td>\n <td>ISOCITRATE</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>7.62949</td>\n <td>0.733847</td>\n <td>True</td>\n <td>CITRATE = ISOCITRATE</td>\n </tr>\n <tr>\n <th>ICDHxm</th>\n <td>ISOCITRATE + NAD+</td>\n <td>2-OXOGLUTARATE + NADH + CO2</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>-2.872</td>\n <td>7.62095</td>\n <td>True</td>\n <td>ISOCITRATE + NAD+ = 2-OXOGLUTARATE + NADH + CO2</td>\n </tr>\n <tr>\n <th>AKGDm</th>\n <td>2-OXOGLUTARATE + COA + NAD+</td>\n <td>SUCCINYL-COA + CO2 + NADH</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>-36.3549</td>\n <td>7.97121</td>\n <td>True</td>\n <td>2-OXOGLUTARATE + COA + NAD+ = SUCCINYL-COA + C...</td>\n </tr>\n <tr>\n <th>SUCOASm</th>\n <td>SUCCINYL-COA + ADP + ORTHOPHOSPHATE</td>\n <td>SUCCINATE + ATP + COA</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>1.92448</td>\n <td>1.48197</td>\n <td>True</td>\n <td>SUCCINYL-COA + ADP + ORTHOPHOSPHATE = SUCCINAT...</td>\n </tr>\n <tr>\n <th>SUCD1m</th>\n <td>SUCCINATE:MITOCHONDRIAL_MATRIX + OXYGEN + NADH</td>\n <td>FUMARATE:MITOCHONDRIAL_MATRIX + 2 H2O + NAD+</td>\n <td>:MITOCHONDRIAL_MATRIX</td>\n <td>:MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>-380.023</td>\n <td>7.8098</td>\n <td>True</td>\n <td>SUCCINATE:MITOCHONDRIAL_MATRIX + OXYGEN + NADH...</td>\n </tr>\n <tr>\n <th>FUMm</th>\n <td>FUMARATE + H2O</td>\n <td>(S)-MALATE</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>-3.44873</td>\n <td>0.607693</td>\n <td>True</td>\n <td>FUMARATE + H2O = (S)-MALATE</td>\n </tr>\n <tr>\n <th>MDHm</th>\n <td>(S)-MALATE + NAD+</td>\n <td>OXALOACETATE + NADH</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>29.9942</td>\n <td>0.422376</td>\n <td>True</td>\n <td>(S)-MALATE + NAD+ = OXALOACETATE + NADH</td>\n </tr>\n <tr>\n <th>GAPD</th>\n <td>D-GLYCERALDEHYDE-3-PHOSPHATE + ORTHOPHOSPHATE ...</td>\n <td>3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + NADH</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>6.68673</td>\n <td>0.895659</td>\n <td>True</td>\n <td>D-GLYCERALDEHYDE-3-PHOSPHATE + ORTHOPHOSPHATE ...</td>\n </tr>\n <tr>\n <th>PGK</th>\n <td>3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + ADP</td>\n <td>3-PHOSPHO-D-GLYCERATE + ATP</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>-18.4733</td>\n <td>0.889982</td>\n <td>True</td>\n <td>3-PHOSPHO-D-GLYCEROYL_PHOSPHATE + ADP = 3-PHOS...</td>\n </tr>\n <tr>\n <th>TPI</th>\n <td>GLYCERONE_PHOSPHATE</td>\n <td>D-GLYCERALDEHYDE-3-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>5.48642</td>\n <td>0.753116</td>\n <td>True</td>\n <td>GLYCERONE_PHOSPHATE = D-GLYCERALDEHYDE-3-PHOSP...</td>\n </tr>\n <tr>\n <th>MDH</th>\n <td>(S)-MALATE + NAD+</td>\n <td>OXALOACETATE + NADH</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>29.9942</td>\n <td>0.422376</td>\n <td>True</td>\n <td>(S)-MALATE + NAD+ = OXALOACETATE + NADH</td>\n </tr>\n <tr>\n <th>PEP_Carboxylase</th>\n <td>OXALOACETATE + ORTHOPHOSPHATE</td>\n <td>PHOSPHOENOLPYRUVATE + CO2 + H2O</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>28.2337</td>\n <td>7.64087</td>\n <td>True</td>\n <td>OXALOACETATE + ORTHOPHOSPHATE = PHOSPHOENOLPYR...</td>\n </tr>\n <tr>\n <th>PPCK</th>\n <td>OXALOACETATE + ATP</td>\n <td>PHOSPHOENOLPYRUVATE + ADP + CO2</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>2.10596</td>\n <td>7.63913</td>\n <td>True</td>\n <td>OXALOACETATE + ATP = PHOSPHOENOLPYRUVATE + ADP...</td>\n </tr>\n <tr>\n <th>FBA</th>\n <td>D-FRUCTOSE_1,6-BISPHOSPHATE</td>\n <td>GLYCERONE_PHOSPHATE + D-GLYCERALDEHYDE-3-PHOSP...</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>20.5096</td>\n <td>0.87227</td>\n <td>True</td>\n <td>D-FRUCTOSE_1,6-BISPHOSPHATE = GLYCERONE_PHOSPH...</td>\n </tr>\n <tr>\n <th>FBP</th>\n <td>D-FRUCTOSE_6-PHOSPHATE + ORTHOPHOSPHATE</td>\n <td>H2O + D-FRUCTOSE_1,6-BISPHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>10.6728</td>\n <td>0.818386</td>\n <td>True</td>\n <td>D-FRUCTOSE_6-PHOSPHATE + ORTHOPHOSPHATE = H2O ...</td>\n </tr>\n <tr>\n <th>TKT2</th>\n <td>D-FRUCTOSE_6-PHOSPHATE + D-GLYCERALDEHYDE-3-PH...</td>\n <td>D-ERYTHROSE-4-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>10.0094</td>\n <td>2.08682</td>\n <td>True</td>\n <td>D-FRUCTOSE_6-PHOSPHATE + D-GLYCERALDEHYDE-3-PH...</td>\n </tr>\n <tr>\n <th>RPE</th>\n <td>D-XYLULOSE-5-PHOSPHATE</td>\n <td>D-RIBULOSE-5-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>3.37</td>\n <td>1.16485</td>\n <td>True</td>\n <td>D-XYLULOSE-5-PHOSPHATE = D-RIBULOSE-5-PHOSPHATE</td>\n </tr>\n <tr>\n <th>Xylulokinase</th>\n <td>D-XYLULOSE + ATP</td>\n <td>D-XYLULOSE-5-PHOSPHATE + ADP</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-23.0181</td>\n <td>2.29158</td>\n <td>True</td>\n <td>D-XYLULOSE + ATP = D-XYLULOSE-5-PHOSPHATE + ADP</td>\n </tr>\n <tr>\n <th>PYK_org</th>\n <td>ADP + PHOSPHOENOLPYRUVATE</td>\n <td>PYRUVATE + ATP</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-27.5366</td>\n <td>0.939774</td>\n <td>True</td>\n <td>ADP + PHOSPHOENOLPYRUVATE = PYRUVATE + ATP</td>\n </tr>\n <tr>\n <th>PYK</th>\n <td>ADP + PHOSPHOENOLPYRUVATE</td>\n <td>PYRUVATE + ATP</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>-27.5366</td>\n <td>0.939774</td>\n <td>True</td>\n <td>ADP + PHOSPHOENOLPYRUVATE = PYRUVATE + ATP</td>\n </tr>\n <tr>\n <th>RPI</th>\n <td>D-RIBOSE-5-PHOSPHATE</td>\n <td>D-RIBULOSE-5-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>1.94759</td>\n <td>1.16321</td>\n <td>True</td>\n <td>D-RIBOSE-5-PHOSPHATE = D-RIBULOSE-5-PHOSPHATE</td>\n </tr>\n <tr>\n <th>TKT1</th>\n <td>SEDOHEPTULOSE_7-PHOSPHATE + D-GLYCERALDEHYDE-3...</td>\n <td>D-RIBOSE-5-PHOSPHATE + D-XYLULOSE-5-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>3.79253</td>\n <td>2.16133</td>\n <td>True</td>\n <td>SEDOHEPTULOSE_7-PHOSPHATE + D-GLYCERALDEHYDE-3...</td>\n </tr>\n <tr>\n <th>TALA</th>\n <td>D-GLYCERALDEHYDE-3-PHOSPHATE + SEDOHEPTULOSE_7...</td>\n <td>D-FRUCTOSE_6-PHOSPHATE + D-ERYTHROSE-4-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-0.728767</td>\n <td>1.62106</td>\n <td>True</td>\n <td>D-GLYCERALDEHYDE-3-PHOSPHATE + SEDOHEPTULOSE_7...</td>\n </tr>\n <tr>\n <th>PGM</th>\n <td>3-PHOSPHO-D-GLYCERATE</td>\n <td>2-PHOSPHO-D-GLYCERATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>4.19953</td>\n <td>0.65542</td>\n <td>True</td>\n <td>3-PHOSPHO-D-GLYCERATE = 2-PHOSPHO-D-GLYCERATE</td>\n </tr>\n <tr>\n <th>ENO</th>\n <td>2-PHOSPHO-D-GLYCERATE</td>\n <td>PHOSPHOENOLPYRUVATE + H2O</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>-4.08222</td>\n <td>0.734193</td>\n <td>True</td>\n <td>2-PHOSPHO-D-GLYCERATE = PHOSPHOENOLPYRUVATE + H2O</td>\n </tr>\n <tr>\n <th>GND</th>\n <td>NADPH + D-RIBULOSE-5-PHOSPHATE + CO2</td>\n <td>NADP+ + 6-PHOSPHO-D-GLUCONATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-2.5528</td>\n <td>7.60864</td>\n <td>True</td>\n <td>NADPH + D-RIBULOSE-5-PHOSPHATE + CO2 = NADP+ +...</td>\n </tr>\n <tr>\n <th>PGL</th>\n <td>6-PHOSPHO-D-GLUCONATE</td>\n <td>D-GLUCONO-1,5-LACTONE_6-PHOSPHATE + H2O</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>21.4202</td>\n <td>2.62825</td>\n <td>True</td>\n <td>6-PHOSPHO-D-GLUCONATE = D-GLUCONO-1,5-LACTONE_...</td>\n </tr>\n <tr>\n <th>HEX1</th>\n <td>BETA-D-GLUCOSE + ATP</td>\n <td>BETA-D-GLUCOSE-6-PHOSPHATE + ADP</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>-17.0578</td>\n <td>0.715237</td>\n <td>True</td>\n <td>BETA-D-GLUCOSE + ATP = BETA-D-GLUCOSE-6-PHOSPH...</td>\n </tr>\n <tr>\n <th>PGI</th>\n <td>BETA-D-GLUCOSE-6-PHOSPHATE</td>\n <td>D-FRUCTOSE_6-PHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>2.52401</td>\n <td>0.596775</td>\n <td>True</td>\n <td>BETA-D-GLUCOSE-6-PHOSPHATE = D-FRUCTOSE_6-PHOS...</td>\n </tr>\n <tr>\n <th>G6PDH2r</th>\n <td>BETA-D-GLUCOSE-6-PHOSPHATE + NADP+</td>\n <td>D-GLUCONO-1,5-LACTONE_6-PHOSPHATE + NADPH</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-2.9946</td>\n <td>2.11855</td>\n <td>True</td>\n <td>BETA-D-GLUCOSE-6-PHOSPHATE + NADP+ = D-GLUCONO...</td>\n </tr>\n <tr>\n <th>PFK</th>\n <td>D-FRUCTOSE_6-PHOSPHATE + ATP</td>\n <td>ADP + D-FRUCTOSE_1,6-BISPHOSPHATE</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>1</td>\n <td>-15.4549</td>\n <td>0.886629</td>\n <td>True</td>\n <td>D-FRUCTOSE_6-PHOSPHATE + ATP = ADP + D-FRUCTOS...</td>\n </tr>\n <tr>\n <th>PYRt2m</th>\n <td>PYRUVATE</td>\n <td>PYRUVATE</td>\n <td>CYTOSOL</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>-5.70769</td>\n <td>0</td>\n <td>False</td>\n <td>PYRUVATE = PYRUVATE</td>\n </tr>\n <tr>\n <th>PDHm</th>\n <td>COA + NAD+ + PYRUVATE</td>\n <td>ACETYL-COA + CO2 + NADH</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>MITOCHONDRIAL_MATRIX</td>\n <td>1</td>\n <td>-43.9219</td>\n <td>7.66459</td>\n <td>True</td>\n <td>COA + NAD+ + PYRUVATE = ACETYL-COA + CO2 + NADH</td>\n </tr>\n <tr>\n <th>ICL</th>\n <td>ISOCITRATE</td>\n <td>GLYOXYLATE + SUCCINATE</td>\n <td>GLYOXYSOME</td>\n <td>GLYOXYSOME</td>\n <td>0</td>\n <td>8.9806</td>\n <td>1.66465</td>\n <td>True</td>\n <td>ISOCITRATE = GLYOXYLATE + SUCCINATE</td>\n </tr>\n <tr>\n <th>MAS</th>\n <td>ACETYL-COA + GLYOXYLATE + H2O</td>\n <td>(S)-MALATE + COA</td>\n <td>GLYOXYSOME</td>\n <td>GLYOXYSOME</td>\n <td>0</td>\n <td>-33.0524</td>\n <td>2.32814</td>\n <td>True</td>\n <td>ACETYL-COA + GLYOXYLATE + H2O = (S)-MALATE + COA</td>\n </tr>\n <tr>\n <th>PYRDC</th>\n <td>PYRUVATE</td>\n <td>ACETALDEHYDE + CO2</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-26.5847</td>\n <td>7.65275</td>\n <td>True</td>\n <td>PYRUVATE = ACETALDEHYDE + CO2</td>\n </tr>\n <tr>\n <th>ALDD2y</th>\n <td>ACETALDEHYDE + NADP+ + H2O</td>\n <td>ACETATE + NADPH</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-46.8416</td>\n <td>1.53234</td>\n <td>True</td>\n <td>ACETALDEHYDE + NADP+ + H2O = ACETATE + NADPH</td>\n </tr>\n <tr>\n <th>ALCD2X_copy1</th>\n <td>ACETALDEHYDE + NADH</td>\n <td>ETHANOL + NAD+</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-21.3437</td>\n <td>0.590246</td>\n <td>True</td>\n <td>ACETALDEHYDE + NADH = ETHANOL + NAD+</td>\n </tr>\n <tr>\n <th>LactateDehydrogenase</th>\n <td>PYRUVATE + NADH</td>\n <td>LACTATE + NAD+</td>\n <td>CYTOSOL</td>\n <td>CYTOSOL</td>\n <td>0</td>\n <td>-27.1344</td>\n <td>0.546575</td>\n <td>True</td>\n <td>PYRUVATE + NADH = LACTATE + NAD+</td>\n </tr>\n <tr>\n <th>Mitochondrial complex I/NADH ubiquinone oxidoredectase</th>\n <td>NADH:MITOCHONDRIAL_MATRIX + UBIQUINONE-6:MITOC...</td>\n <td>NAD+:MITOCHONDRIAL_MATRIX + UBIQUINOL-6:MITOCH...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>0</td>\n <td>-118.696</td>\n <td>6.11392</td>\n <td>False</td>\n <td>NADH:MITOCHONDRIAL_MATRIX + UBIQUINONE-6:MITOC...</td>\n </tr>\n <tr>\n <th>Mitochondrial complex III</th>\n <td>UBIQUINOL-6 + 2 FERRICYTOCHROME_C</td>\n <td>UBIQUINONE-6 + 2 FERROCYTOCHROME_C</td>\n <td>Mitochondrial_Membrane</td>\n <td>Mitochondrial_Membrane</td>\n <td>0</td>\n <td>54.7291</td>\n <td>565685</td>\n <td>True</td>\n <td>UBIQUINOL-6 + 2 FERRICYTOCHROME_C = UBIQUINONE...</td>\n </tr>\n <tr>\n <th>Mitochondrial complex IV</th>\n <td>4 FERROCYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + O...</td>\n <td>4 FERRICYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + 2...</td>\n <td>NaN</td>\n <td>NaN</td>\n <td>0</td>\n <td>-314.91</td>\n <td>1.13137e+06</td>\n <td>False</td>\n <td>4 FERROCYTOCHROME_C:MITOCHONDRIAL_MEMBRANE + O...</td>\n </tr>\n </tbody>\n</table>\n</div>"
  1079. },
  1080. "metadata": {}
  1081. },
  1082. {
  1083. "output_type": "display_data",
  1084. "data": {
  1085. "text/plain": " (S)-MALATE:MITOCHONDRIAL_MATRIX SUCCINYL-COA:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 1.0 \nSUCOASm 0.0 -1.0 \nSUCD1m 0.0 0.0 \nFUMm 1.0 0.0 \nMDHm -1.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 0.0 \n\n 2-PHOSPHO-D-GLYCERATE:CYTOSOL PYRUVATE:CYTOSOL \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 1.0 \nPGM 1.0 0.0 \nENO -1.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 -1.0 \nPDHm 0.0 0.0 \n\n D-FRUCTOSE_6-PHOSPHATE:CYTOSOL D-FRUCTOSE_1,6-BISPHOSPHATE:CYTOSOL \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 -1.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 1.0 0.0 \nPFK -1.0 1.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 0.0 \n\n PHOSPHOENOLPYRUVATE:CYTOSOL GLYCERONE_PHOSPHATE:CYTOSOL \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 -1.0 \nFBA 0.0 1.0 \nPYK -1.0 0.0 \nPGM 0.0 0.0 \nENO 1.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 0.0 \n\n 3-PHOSPHO-D-GLYCERATE:CYTOSOL \\\nREACTION \nCSm 0.0 \nACONTm 0.0 \nICDHxm 0.0 \nAKGDm 0.0 \nSUCOASm 0.0 \nSUCD1m 0.0 \nFUMm 0.0 \nMDHm 0.0 \nGAPD 0.0 \nPGK 1.0 \nTPI 0.0 \nFBA 0.0 \nPYK 0.0 \nPGM -1.0 \nENO 0.0 \nHEX1 0.0 \nPGI 0.0 \nPFK 0.0 \nPYRt2m 0.0 \nPDHm 0.0 \n\n 3-PHOSPHO-D-GLYCEROYL_PHOSPHATE:CYTOSOL \\\nREACTION \nCSm 0.0 \nACONTm 0.0 \nICDHxm 0.0 \nAKGDm 0.0 \nSUCOASm 0.0 \nSUCD1m 0.0 \nFUMm 0.0 \nMDHm 0.0 \nGAPD 1.0 \nPGK -1.0 \nTPI 0.0 \nFBA 0.0 \nPYK 0.0 \nPGM 0.0 \nENO 0.0 \nHEX1 0.0 \nPGI 0.0 \nPFK 0.0 \nPYRt2m 0.0 \nPDHm 0.0 \n\n D-GLYCERALDEHYDE-3-PHOSPHATE:CYTOSOL \\\nREACTION \nCSm 0.0 \nACONTm 0.0 \nICDHxm 0.0 \nAKGDm 0.0 \nSUCOASm 0.0 \nSUCD1m 0.0 \nFUMm 0.0 \nMDHm 0.0 \nGAPD -1.0 \nPGK 0.0 \nTPI 1.0 \nFBA 1.0 \nPYK 0.0 \nPGM 0.0 \nENO 0.0 \nHEX1 0.0 \nPGI 0.0 \nPFK 0.0 \nPYRt2m 0.0 \nPDHm 0.0 \n\n SUCCINATE:MITOCHONDRIAL_MATRIX FUMARATE:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm 1.0 0.0 \nSUCD1m -1.0 1.0 \nFUMm 0.0 -1.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 0.0 \n\n BETA-D-GLUCOSE-6-PHOSPHATE:CYTOSOL \\\nREACTION \nCSm 0.0 \nACONTm 0.0 \nICDHxm 0.0 \nAKGDm 0.0 \nSUCOASm 0.0 \nSUCD1m 0.0 \nFUMm 0.0 \nMDHm 0.0 \nGAPD 0.0 \nPGK 0.0 \nTPI 0.0 \nFBA 0.0 \nPYK 0.0 \nPGM 0.0 \nENO 0.0 \nHEX1 1.0 \nPGI -1.0 \nPFK 0.0 \nPYRt2m 0.0 \nPDHm 0.0 \n\n 2-OXOGLUTARATE:MITOCHONDRIAL_MATRIX PYRUVATE:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 1.0 0.0 \nAKGDm -1.0 0.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 1.0 \nPDHm 0.0 -1.0 \n\n ISOCITRATE:MITOCHONDRIAL_MATRIX OXALOACETATE:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 -1.0 \nACONTm 1.0 0.0 \nICDHxm -1.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 1.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 0.0 \n\n ACETYL-COA:MITOCHONDRIAL_MATRIX CITRATE:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm -1.0 1.0 \nACONTm 0.0 -1.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 1.0 0.0 \n\n ATP:CYTOSOL BETA-D-GLUCOSE:CYTOSOL NADH:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 0.0 0.0 \nACONTm 0.0 0.0 0.0 \nICDHxm 0.0 0.0 1.0 \nAKGDm 0.0 0.0 1.0 \nSUCOASm 0.0 0.0 0.0 \nSUCD1m 0.0 0.0 -1.0 \nFUMm 0.0 0.0 0.0 \nMDHm 0.0 0.0 1.0 \nGAPD 0.0 0.0 0.0 \nPGK 1.0 0.0 0.0 \nTPI 0.0 0.0 0.0 \nFBA 0.0 0.0 0.0 \nPYK 1.0 0.0 0.0 \nPGM 0.0 0.0 0.0 \nENO 0.0 0.0 0.0 \nHEX1 -1.0 -1.0 0.0 \nPGI 0.0 0.0 0.0 \nPFK -1.0 0.0 0.0 \nPYRt2m 0.0 0.0 0.0 \nPDHm 0.0 0.0 1.0 \n\n CO2:MITOCHONDRIAL_MATRIX H2O:CYTOSOL H2O:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 0 0 \nACONTm 0.0 0 0 \nICDHxm 1.0 0 0 \nAKGDm 1.0 0 0 \nSUCOASm 0.0 0 0 \nSUCD1m 0.0 0 0 \nFUMm 0.0 0 0 \nMDHm 0.0 0 0 \nGAPD 0.0 0 0 \nPGK 0.0 0 0 \nTPI 0.0 0 0 \nFBA 0.0 0 0 \nPYK 0.0 0 0 \nPGM 0.0 0 0 \nENO 0.0 0 0 \nHEX1 0.0 0 0 \nPGI 0.0 0 0 \nPFK 0.0 0 0 \nPYRt2m 0.0 0 0 \nPDHm 1.0 0 0 \n\n ADP:MITOCHONDRIAL_MATRIX ORTHOPHOSPHATE:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 0.0 \nAKGDm 0.0 0.0 \nSUCOASm -1.0 -1.0 \nSUCD1m 0.0 0.0 \nFUMm 0.0 0.0 \nMDHm 0.0 0.0 \nGAPD 0.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 0.0 \n\n NADH:CYTOSOL COA:MITOCHONDRIAL_MATRIX NAD+:CYTOSOL \\\nREACTION \nCSm 0.0 1.0 0.0 \nACONTm 0.0 0.0 0.0 \nICDHxm 0.0 0.0 0.0 \nAKGDm 0.0 -1.0 0.0 \nSUCOASm 0.0 1.0 0.0 \nSUCD1m 0.0 0.0 0.0 \nFUMm 0.0 0.0 0.0 \nMDHm 0.0 0.0 0.0 \nGAPD 1.0 0.0 -1.0 \nPGK 0.0 0.0 0.0 \nTPI 0.0 0.0 0.0 \nFBA 0.0 0.0 0.0 \nPYK 0.0 0.0 0.0 \nPGM 0.0 0.0 0.0 \nENO 0.0 0.0 0.0 \nHEX1 0.0 0.0 0.0 \nPGI 0.0 0.0 0.0 \nPFK 0.0 0.0 0.0 \nPYRt2m 0.0 0.0 0.0 \nPDHm 0.0 -1.0 0.0 \n\n ORTHOPHOSPHATE:CYTOSOL NAD+:MITOCHONDRIAL_MATRIX \\\nREACTION \nCSm 0.0 0.0 \nACONTm 0.0 0.0 \nICDHxm 0.0 -1.0 \nAKGDm 0.0 -1.0 \nSUCOASm 0.0 0.0 \nSUCD1m 0.0 1.0 \nFUMm 0.0 0.0 \nMDHm 0.0 -1.0 \nGAPD -1.0 0.0 \nPGK 0.0 0.0 \nTPI 0.0 0.0 \nFBA 0.0 0.0 \nPYK 0.0 0.0 \nPGM 0.0 0.0 \nENO 0.0 0.0 \nHEX1 0.0 0.0 \nPGI 0.0 0.0 \nPFK 0.0 0.0 \nPYRt2m 0.0 0.0 \nPDHm 0.0 -1.0 \n\n OXYGEN:MITOCHONDRIAL_MATRIX ATP:MITOCHONDRIAL_MATRIX ADP:CYTOSOL \nREACTION \nCSm 0.0 0.0 0.0 \nACONTm 0.0 0.0 0.0 \nICDHxm 0.0 0.0 0.0 \nAKGDm 0.0 0.0 0.0 \nSUCOASm 0.0 1.0 0.0 \nSUCD1m -1.0 0.0 0.0 \nFUMm 0.0 0.0 0.0 \nMDHm 0.0 0.0 0.0 \nGAPD 0.0 0.0 0.0 \nPGK 0.0 0.0 -1.0 \nTPI 0.0 0.0 0.0 \nFBA 0.0 0.0 0.0 \nPYK 0.0 0.0 -1.0 \nPGM 0.0 0.0 0.0 \nENO 0.0 0.0 0.0 \nHEX1 0.0 0.0 1.0 \nPGI 0.0 0.0 0.0 \nPFK 0.0 0.0 1.0 \nPYRt2m 0.0 0.0 0.0 \nPDHm 0.0 0.0 0.0 ",
  1086. "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>(S)-MALATE:MITOCHONDRIAL_MATRIX</th>\n <th>SUCCINYL-COA:MITOCHONDRIAL_MATRIX</th>\n <th>2-PHOSPHO-D-GLYCERATE:CYTOSOL</th>\n <th>PYRUVATE:CYTOSOL</th>\n <th>D-FRUCTOSE_6-PHOSPHATE:CYTOSOL</th>\n <th>D-FRUCTOSE_1,6-BISPHOSPHATE:CYTOSOL</th>\n <th>PHOSPHOENOLPYRUVATE:CYTOSOL</th>\n <th>GLYCERONE_PHOSPHATE:CYTOSOL</th>\n <th>3-PHOSPHO-D-GLYCERATE:CYTOSOL</th>\n <th>3-PHOSPHO-D-GLYCEROYL_PHOSPHATE:CYTOSOL</th>\n <th>D-GLYCERALDEHYDE-3-PHOSPHATE:CYTOSOL</th>\n <th>SUCCINATE:MITOCHONDRIAL_MATRIX</th>\n <th>FUMARATE:MITOCHONDRIAL_MATRIX</th>\n <th>BETA-D-GLUCOSE-6-PHOSPHATE:CYTOSOL</th>\n <th>2-OXOGLUTARATE:MITOCHONDRIAL_MATRIX</th>\n <th>PYRUVATE:MITOCHONDRIAL_MATRIX</th>\n <th>ISOCITRATE:MITOCHONDRIAL_MATRIX</th>\n <th>OXALOACETATE:MITOCHONDRIAL_MATRIX</th>\n <th>ACETYL-COA:MITOCHONDRIAL_MATRIX</th>\n <th>CITRATE:MITOCHONDRIAL_MATRIX</th>\n <th>ATP:CYTOSOL</th>\n <th>BETA-D-GLUCOSE:CYTOSOL</th>\n <th>NADH:MITOCHONDRIAL_MATRIX</th>\n <th>CO2:MITOCHONDRIAL_MATRIX</th>\n <th>H2O:CYTOSOL</th>\n <th>H2O:MITOCHONDRIAL_MATRIX</th>\n <th>ADP:MITOCHONDRIAL_MATRIX</th>\n <th>ORTHOPHOSPHATE:MITOCHONDRIAL_MATRIX</th>\n <th>NADH:CYTOSOL</th>\n <th>COA:MITOCHONDRIAL_MATRIX</th>\n <th>NAD+:CYTOSOL</th>\n <th>ORTHOPHOSPHATE:CYTOSOL</th>\n <th>NAD+:MITOCHONDRIAL_MATRIX</th>\n <th>OXYGEN:MITOCHONDRIAL_MATRIX</th>\n <th>ATP:MITOCHONDRIAL_MATRIX</th>\n <th>ADP:CYTOSOL</th>\n </tr>\n <tr>\n <th>REACTION</th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <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>CSm</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>-1.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>ACONTm</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>ICDHxm</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>1.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>AKGDm</th>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>1.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>SUCOASm</th>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>-1.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>SUCD1m</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>FUMm</th>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>MDHm</th>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>GAPD</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>PGK</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n </tr>\n <tr>\n <th>TPI</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>FBA</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>PYK</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n </tr>\n <tr>\n <th>PGM</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>ENO</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>HEX1</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n </tr>\n <tr>\n <th>PGI</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>PFK</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n </tr>\n <tr>\n <th>PYRt2m</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n <tr>\n <th>PDHm</th>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>1.0</td>\n <td>1.0</td>\n <td>0</td>\n <td>0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>-1.0</td>\n <td>0.0</td>\n <td>0.0</td>\n <td>0.0</td>\n </tr>\n </tbody>\n</table>\n</div>"
  1087. },
  1088. "metadata": {}
  1089. },
  1090. {
  1091. "output_type": "display_data",
  1092. "data": {
  1093. "text/plain": "20"
  1094. },
  1095. "metadata": {}
  1096. },
  1097. {
  1098. "output_type": "display_data",
  1099. "data": {
  1100. "text/plain": "array([10.7271265 , 17.89891189, 15.31650625, 11.20640219, 18.77069648,\n 13.09995288, 12.87397651, 13.55269687, 15.1330066 , 16.23779835,\n 16.33338291, 16.63175862, 10.46207157, 12.86312937, 11.9408733 ,\n 17.92427395, 17.35636198, 10.44930748, 11.43382475, 16.88106601])"
  1101. },
  1102. "metadata": {}
  1103. },
  1104. {
  1105. "output_type": "display_data",
  1106. "data": {
  1107. "text/plain": "array([15.57013138, 14.00151547, 10.81945361, 11.00578319, 24.23250658,\n 24.23250658, 12.72854979, 16.30410056, 10.81945361, 13.64484052,\n 14.26387973, 16.30410056, 14.26387973, 11.00578319, 15.57013138,\n 12.72854979])"
  1108. },
  1109. "metadata": {}
  1110. },
  1111. {
  1112. "output_type": "display_data",
  1113. "data": {
  1114. "text/plain": "REACTION\nCSm 1.420710e+06\nACONTm 4.605706e-02\nICDHxm 3.185528e+00\nAKGDm 2.341333e+06\nSUCOASm 4.600726e-01\nSUCD1m 3.809967e+66\nFUMm 4.019990e+00\nMDHm 5.558462e-06\nGAPD 6.737062e-02\nPGK 1.724098e+03\nTPI 1.093368e-01\nFBA 2.550739e-04\nPYK 6.675328e+04\nPGM 1.837526e-01\nENO 5.190563e+00\nHEX1 9.739958e+02\nPGI 3.612341e-01\nPFK 5.101948e+02\nPYRt2m 1.000000e+01\nPDHm 4.956973e+07\nName: DGZERO, dtype: float64"
  1115. },
  1116. "metadata": {}
  1117. }
  1118. ]
  1119. },
  1120. {
  1121. "metadata": {
  1122. "trusted": true
  1123. },
  1124. "cell_type": "code",
  1125. "source": "def derivatives(vcounts,fcounts,mu0,S, R, P, delta, Keq, E_Regulation):\n nvar = vcounts.size\n metabolites = np.append(vcounts,fcounts)\n KQ_f = odds(metabolites,mu0,S, R, P, delta, Keq, 1);\n Keq_inverse = np.power(Keq,-1);\n KQ_r = odds(metabolites,mu0,-S, P, R, delta, Keq_inverse, -1);\n deriv = S.T.dot((E_Regulation *(KQ_f - KQ_r)).T);\n #deriv = S.T.dot(((KQ_f - KQ_r)).T);\n deriv = deriv[0:nvar]\n return(deriv.reshape(deriv.size,))",
  1126. "execution_count": 11,
  1127. "outputs": []
  1128. },
  1129. {
  1130. "metadata": {
  1131. "trusted": true
  1132. },
  1133. "cell_type": "code",
  1134. "source": "def odds(log_counts,mu0,S, R, P, delta, K, direction = 1):\n counts = np.exp(log_counts)\n delta_counts = counts+delta;\n log_delta = np.log(delta_counts);\n Q_inv = np.exp(-direction*(R.dot(log_counts) + P.dot(log_delta)))\n KQ = np.multiply(K,Q_inv);\n return(KQ)",
  1135. "execution_count": 12,
  1136. "outputs": []
  1137. },
  1138. {
  1139. "metadata": {
  1140. "trusted": true
  1141. },
  1142. "cell_type": "code",
  1143. "source": "def oddsDiff(vcounts,fcounts,mu0,S, R, P, delta,Keq,E_Regulation):\n metabolites = np.append(vcounts,fcounts)\n KQ_f = odds(metabolites,mu0,S, R, P, delta,Keq);\n Keq_inverse = np.power(Keq,-1);\n KQ_r = odds(metabolites,mu0,-S, P, R, delta,Keq_inverse,-1);\n \n #WARNING: Multiply regulation here, not on individual Keq values.\n KQdiff = E_Regulation * (KQ_f - KQ_r);\n return(KQdiff)",
  1144. "execution_count": 13,
  1145. "outputs": []
  1146. },
  1147. {
  1148. "metadata": {
  1149. "trusted": true
  1150. },
  1151. "cell_type": "code",
  1152. "source": "def calc_delta_S(vcounts, fcounts, P):\n #WARNING To avoid negative numbers do not use log concs\n metab = np.append(vcounts, fcounts)\n target_metab = np.ones(vcounts.size) * np.log(0.001*Concentration2Count);\n target_metab = np.append(target_metab, fcounts)\n delta_S = P.dot(metab) - P.dot(target_metab)\n return(delta_S)",
  1153. "execution_count": 14,
  1154. "outputs": []
  1155. },
  1156. {
  1157. "metadata": {
  1158. "trusted": true
  1159. },
  1160. "cell_type": "code",
  1161. "source": "def calc_E_step(E, vcounts, fcounts):\n newE = E -E/2\n return(newE)",
  1162. "execution_count": 15,
  1163. "outputs": []
  1164. },
  1165. {
  1166. "metadata": {},
  1167. "cell_type": "markdown",
  1168. "source": "# Nonlinear Least Squares Optimization of Concentrations"
  1169. },
  1170. {
  1171. "metadata": {
  1172. "trusted": true
  1173. },
  1174. "cell_type": "code",
  1175. "source": "from scipy.optimize import least_squares\n#r_log_counts = -10 + 10*np.random.rand(v_log_counts.size)\n#v_log_counts = r_log_counts\nprint('====== Without adjusting K ======')\n#display(v_log_counts)\nres_lsq = least_squares(derivatives, v_log_counts, method='lm',xtol=1e-20, args=(f_log_counts, mu0, S, R, P, delta, K, E_regulation))\ndisplay(res_lsq.x)\n\nrxn_flux = oddsDiff(res_lsq.x, f_log_counts, mu0, S, R, P, delta, K, E_regulation)\nprint(res_lsq.optimality)\nprint(res_lsq.x)\nprint(rxn_flux)",
  1176. "execution_count": 16,
  1177. "outputs": [
  1178. {
  1179. "output_type": "stream",
  1180. "text": "====== Without adjusting K ======\n",
  1181. "name": "stdout"
  1182. },
  1183. {
  1184. "output_type": "stream",
  1185. "text": "/Users/d3k137/.pyenv/versions/anaconda3-4.3.0/lib/python3.6/site-packages/scipy/optimize/_lsq/least_squares.py:114: UserWarning: `xtol` is too low, setting to machine epsilon 2.220446049250313e-16.\n warn(message.format(\"`xtol`\", EPS))\n/Users/d3k137/.pyenv/versions/anaconda3-4.3.0/lib/python3.6/site-packages/ipykernel_launcher.py:2: RuntimeWarning: overflow encountered in exp\n \n/Users/d3k137/.pyenv/versions/anaconda3-4.3.0/lib/python3.6/site-packages/ipykernel_launcher.py:4: RuntimeWarning: divide by zero encountered in log\n after removing the cwd from sys.path.\n/Users/d3k137/.pyenv/versions/anaconda3-4.3.0/lib/python3.6/site-packages/ipykernel_launcher.py:5: RuntimeWarning: overflow encountered in exp\n \"\"\"\n",
  1186. "name": "stderr"
  1187. },
  1188. {
  1189. "output_type": "display_data",
  1190. "data": {
  1191. "text/plain": "array([162.21272369, 40.81989804, -40.81890478, -57.5111222 ,\n -2.51366733, -6.04726425, -52.47518096, -6.05394979,\n -25.82162147, -17.1293806 , -20.87724273, 26.55808728,\n 174.12456266, 11.11453295, 33.37330173, -68.51165542,\n 53.07915913, 140.25384239, -58.0123993 , 69.46015164])"
  1192. },
  1193. "metadata": {}
  1194. },
  1195. {
  1196. "output_type": "stream",
  1197. "text": "0.020782475857719994\n[162.21272369 40.81989804 -40.81890478 -57.5111222 -2.51366733\n -6.04726425 -52.47518096 -6.05394979 -25.82162147 -17.1293806\n -20.87724273 26.55808728 174.12456266 11.11453295 33.37330173\n -68.51165542 53.07915913 140.25384239 -58.0123993 69.46015164]\n[599060.7599283 599060.7599283 599060.7599283 599060.7599283\n 599060.75992831 599060.7599283 599060.7599283 599060.75992831\n 599060.7599283 599060.7599283 299530.37996415 299530.37996415\n 599060.7599283 599060.7599283 599060.7599283 299530.37996415\n 299530.37996415 299530.37996415 599060.7599283 599060.7599283 ]\n",
  1198. "name": "stdout"
  1199. }
  1200. ]
  1201. },
  1202. {
  1203. "metadata": {},
  1204. "cell_type": "markdown",
  1205. "source": "If an equilibrium constant is too large, then the optimization will fail unless one starts in the vicinity of the minimum. One solution to this is to reduce the magnitude of the problematic equilibrium constant to a reasonable value, and then optimize. Then one can increase the size of the problematic equilibrium constant, re-optimize. Iterating through this procedure until the equilibrium constant is back to its original value, one can obtain an optimal solution in this way.\n\nAdjust equilibrium constants if they are too large:"
  1206. },
  1207. {
  1208. "metadata": {
  1209. "trusted": true
  1210. },
  1211. "cell_type": "code",
  1212. "source": "K5 = K[5]\nK[5] = 1.0e+02\nattempts = 40\ni = 0\noptimality = 1.0e+01\nv_log_counts = v_log_counts0\nwhile((i < attempts) and (optimality > 1.0e-15) and (K[5] < 1.0e+66)):\n K[5] = K[5]*1.0e+10\n if(K[5] > 1.0e+66): \n K[5] = K5\n res_lsq = least_squares(derivatives, v_log_counts, method='lm', ftol=1.0e-3000, xtol=1.0e-200, args=(f_log_counts, mu0, S, R, P, delta, K, E_regulation))\n v_log_counts = res_lsq.x\n optimality = res_lsq.optimality\n i = i + 1\n rxn_flux = oddsDiff(res_lsq.x, f_log_counts, mu0, S, R, P, delta, K, E_regulation)\n F = 0.5*np.sum(np.power(res_lsq.fun,2))\nprint(i)\nprint(K[5])\nprint(res_lsq.optimality)\nprint(rxn_flux)",
  1213. "execution_count": 17,
  1214. "outputs": [
  1215. {
  1216. "output_type": "stream",
  1217. "text": "/Users/d3k137/.pyenv/versions/anaconda3-4.3.0/lib/python3.6/site-packages/scipy/optimize/_lsq/least_squares.py:111: UserWarning: `ftol` is too low, setting to machine epsilon 2.220446049250313e-16.\n warn(message.format(\"`ftol`\", EPS))\n/Users/d3k137/.pyenv/versions/anaconda3-4.3.0/lib/python3.6/site-packages/scipy/optimize/_lsq/least_squares.py:114: UserWarning: `xtol` is too low, setting to machine epsilon 2.220446049250313e-16.\n warn(message.format(\"`xtol`\", EPS))\n/Users/d3k137/.pyenv/versions/anaconda3-4.3.0/lib/python3.6/site-packages/ipykernel_launcher.py:4: RuntimeWarning: divide by zero encountered in log\n after removing the cwd from sys.path.\n",
  1218. "name": "stderr"
  1219. },
  1220. {
  1221. "output_type": "stream",
  1222. "text": "7\n3.809966807068541e+66\n0.013041353466981095\n[599060.7599283 599060.7599283 599060.7599283 599060.75992831\n 599060.7599283 599060.7599283 599060.7599283 599060.7599283\n 599060.7599283 599060.7599283 299530.37996415 299530.37996415\n 599060.7599283 599060.7599283 599060.7599283 299530.37996415\n 299530.37996415 299530.37996415 599060.7599283 599060.7599283 ]\n",
  1223. "name": "stdout"
  1224. }
  1225. ]
  1226. },
  1227. {
  1228. "metadata": {},
  1229. "cell_type": "markdown",
  1230. "source": "## Apply Regulation and Optimize"
  1231. },
  1232. {
  1233. "metadata": {
  1234. "trusted": true
  1235. },
  1236. "cell_type": "code",
  1237. "source": "v_log_counts = res_lsq.x\napply_regulation = True;\nrxn_order = np.array([16, 17, 18, 12, 11, 9, 10, 14, 15, 13, 19, 20, 1, 2, 3, 4, 5, 6, 7, 8])\nrxn_order = rxn_order - 1\nenzymeRegulation = np.ones(K.size)\ni = 0\ndeltaS_value = 10\nwhile(i < 2*attempts and deltaS_value > 0):\n res_lsq = least_squares(derivatives, v_log_counts, method='lm',args=(f_log_counts, mu0, S, R, P, delta, K, E_regulation))\n v_log_counts = res_lsq.x\n rxn_flux = oddsDiff(v_log_counts, f_log_counts, mu0, S, R, P, delta, K, E_regulation)\n delta_S = calc_delta_S(v_log_counts,f_log_counts, P)\n #print(res_lsq.optimality)\n #print(rxn_flux)\n metab_log_counts = np.append(v_log_counts, f_log_counts)\n Pdotmetab = P*metab_log_counts\n #print(np.exp(Pdotmetab[15,20:24])/Concentration2Count)\n #print(np.exp(metab_log_counts[20:24])/Concentration2Count)\n #print(metabolites_status.iloc[20:24])\n \n temp_index = np.where(delta_S[rxn_order] > 0)\n rxn_index = rxn_order[temp_index]\n if rxn_index.any():\n index = rxn_index[0]\n \n \n current_EnzActivity = E_regulation[index];\n \n newEnzReg = calc_E_step(current_EnzActivity, v_log_counts, f_log_counts)\n E_regulation[index] = newEnzReg\n deltaS_value = delta_S[index]\n #print(delta_S)\n #print(index+1, newEnzReg,delta_S[index])\n #print('======Next======')\n i = i+1\ndisplay(rxn_flux)\ndisplay(E_regulation)\ndisplay(delta_S)\ndisplay(deltaS_value)\ndisplay(np.exp(v_log_counts)/Concentration2Count) ",
  1238. "execution_count": 19,
  1239. "outputs": [
  1240. {
  1241. "output_type": "display_data",
  1242. "data": {
  1243. "text/plain": "array([599060.7599283 , 599060.7599283 , 599060.7599283 , 599060.75992831,\n 599060.7599283 , 599060.7599283 , 599060.7599283 , 599060.7599283 ,\n 599060.7599283 , 599060.7599283 , 299530.37996415, 299530.37996415,\n 599060.7599283 , 599060.7599283 , 599060.7599283 , 299530.37996415,\n 299530.37996415, 299530.37996415, 599060.7599283 , 599060.7599283 ])"
  1244. },
  1245. "metadata": {}
  1246. },
  1247. {
  1248. "output_type": "display_data",
  1249. "data": {
  1250. "text/plain": "array([1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.,\n 1., 1., 1.])"
  1251. },
  1252. "metadata": {}
  1253. },
  1254. {
  1255. "output_type": "display_data",
  1256. "data": {
  1257. "text/plain": "array([-104.92651715, -121.30750967, -141.01336707, -133.56677075,\n -147.82858152, -0.26210613, -12.1739451 , -34.13282641,\n -30.43774888, -39.12998976, -34.18561102, -53.54792909,\n -70.81949049, -54.12727307, -65.78354924, -2.19383534,\n -15.82203561, -19.35563253, -81.8200237 , -71.32076758])"
  1258. },
  1259. "metadata": {}
  1260. },
  1261. {
  1262. "output_type": "display_data",
  1263. "data": {
  1264. "text/plain": "10"
  1265. },
  1266. "metadata": {}
  1267. },
  1268. {
  1269. "output_type": "display_data",
  1270. "data": {
  1271. "text/plain": "array([5.16324602e-09, 9.83305563e-62, 3.11045545e-27, 1.75180624e-34,\n 1.34455088e-10, 3.92604793e-12, 2.69505457e-32, 3.89988772e-12,\n 1.01405467e-20, 6.04023198e-17, 1.42356655e-18, 6.29307315e-68,\n 7.69429357e-04, 1.11488332e-04, 5.73684092e-65, 2.92425470e-39,\n 2.07404387e-56, 1.50072750e-18, 1.06116812e-34, 2.69769343e-49])"
  1272. },
  1273. "metadata": {}
  1274. }
  1275. ]
  1276. },
  1277. {
  1278. "metadata": {},
  1279. "cell_type": "markdown",
  1280. "source": "# ODE Simulations"
  1281. },
  1282. {
  1283. "metadata": {},
  1284. "cell_type": "markdown",
  1285. "source": "## Calculate Rate Constants\nEquation 9 from Cannon, et al, Prediction of Metabolite Concentrations, Rate Constants and Post-translational Regulation using Maximum Entropy-based Simulations with Application to Central Metabolism of Neurospora crassa,\" Processes 6, 63, DOI:10.3390/pr6060063."
  1286. },
  1287. {
  1288. "metadata": {},
  1289. "cell_type": "raw",
  1290. "source": "Matlab code to translate:\nfunction [fwd_rate_constants] = calculate_rate_constants(log_counts, rxn_flux,KQ_inverse, R, E_Regulation)\n\n KQ = KQ_inverse.^-1;\n %Infer rate constants from reaction flux\n %denominator = E_Regulation.* exp(-R*log_counts).*(1);\n denominator = E_Regulation.* exp(-R*log_counts).*(1-KQ_inverse);\n % A reaction near equilibrium is problematic because (1-KQ_inverse)->0\n % By setting these reactions to be \n % rate constant = 1/product_concs we are setting the rate to 1, which\n % is the same as the thermodynamic rate = KQ.\n one_idx = find(KQ_inverse > 0.9);\n denominator(one_idx) = E_Regulation(one_idx).* exp(-R(one_idx,:)*log_counts);\n rxn_flux(one_idx) = 1;\n try\n fwd_rate_constants = rxn_flux./denominator;\n catch\n x = x;\n end\nend\n\n"
  1291. },
  1292. {
  1293. "metadata": {
  1294. "trusted": true
  1295. },
  1296. "cell_type": "code",
  1297. "source": "def calculate_rate_constants(log_counts, rxn_flux,KQ_inverse, R, E_Regulation):\n KQ = np.power(KQ_inverse,-1)\n #Infer rate constants from reaction flux\n denominator = E_Regulation* np.exp(-R.dot(log_counts))*(1-KQ_inverse)\n # A reaction near equilibrium is problematic because (1-KQ_inverse)->0\n # By setting these reactions to be \n # rate constant = 1/product_concs we are setting the rate to 1, which\n # is the same as the thermodynamic rate = KQ.\n one_idx = np.where(KQ_inverse > 0.9)\n denominator[one_idx] = E_Regulation[one_idx]* np.exp(-R[one_idx,:].dot(log_counts));\n rxn_flux[one_idx] = 1;\n fwd_rate_constants = rxn_flux/denominator;\n \n return(fwd_rate_constants)",
  1298. "execution_count": null,
  1299. "outputs": []
  1300. },
  1301. {
  1302. "metadata": {
  1303. "trusted": true
  1304. },
  1305. "cell_type": "code",
  1306. "source": "log_counts = np.append(v_log_counts,f_log_counts)\nKQ_inverse = odds(log_counts,mu0,S, R, P, delta, K, direction = -1)\nforward_rate_constants = calculate_rate_constants(log_counts, rxn_flux, KQ_inverse, R, E_regulation)\nreverse_rate_constants = forward_rate_constants/K\ndisplay(forward_rate_constants)",
  1307. "execution_count": null,
  1308. "outputs": []
  1309. },
  1310. {
  1311. "metadata": {
  1312. "trusted": true
  1313. },
  1314. "cell_type": "code",
  1315. "source": "",
  1316. "execution_count": null,
  1317. "outputs": []
  1318. },
  1319. {
  1320. "metadata": {},
  1321. "cell_type": "markdown",
  1322. "source": "## ODE Solvers: Python interface using libroadrunner to Sundials/CVODE"
  1323. }
  1324. ],
  1325. "metadata": {
  1326. "hide_input": false,
  1327. "kernelspec": {
  1328. "name": "python3",
  1329. "display_name": "Python 3",
  1330. "language": "python"
  1331. },
  1332. "language_info": {
  1333. "name": "python",
  1334. "version": "3.6.8",
  1335. "mimetype": "text/x-python",
  1336. "codemirror_mode": {
  1337. "name": "ipython",
  1338. "version": 3
  1339. },
  1340. "pygments_lexer": "ipython3",
  1341. "nbconvert_exporter": "python",
  1342. "file_extension": ".py"
  1343. },
  1344. "latex_envs": {
  1345. "eqNumInitial": 1,
  1346. "eqLabelWithNumbers": true,
  1347. "current_citInitial": 1,
  1348. "cite_by": "apalike",
  1349. "bibliofile": "whitepaper.bib",
  1350. "LaTeX_envs_menu_present": true,
  1351. "labels_anchors": false,
  1352. "latex_user_defs": false,
  1353. "user_envs_cfg": true,
  1354. "report_style_numbering": false,
  1355. "autocomplete": false,
  1356. "hotkeys": {
  1357. "equation": "Ctrl-E",
  1358. "itemize": "Ctrl-I"
  1359. }
  1360. },
  1361. "toc": {
  1362. "threshold": 4,
  1363. "number_sections": true,
  1364. "toc_cell": true,
  1365. "toc_window_display": true,
  1366. "toc_section_display": "block",
  1367. "sideBar": true,
  1368. "navigate_menu": true,
  1369. "moveMenuLeft": true,
  1370. "widenNotebook": false,
  1371. "colors": {
  1372. "hover_highlight": "#DAA520",
  1373. "selected_highlight": "#FFD700",
  1374. "running_highlight": "#FF0000"
  1375. },
  1376. "nav_menu": {
  1377. "height": "12px",
  1378. "width": "252px"
  1379. }
  1380. },
  1381. "gist": {
  1382. "id": "",
  1383. "data": {
  1384. "description": "CentralMetabolism_example.ipynb",
  1385. "public": true
  1386. }
  1387. }
  1388. },
  1389. "nbformat": 4,
  1390. "nbformat_minor": 2
  1391. }
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