{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# MediaScan example" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "import cobra\n", "from cobra.flux_analysis.parsimonious import pfba\n", "import cobrakbase\n", "import sys\n", "sys.path.append(\"/Users/chenry/code/ModelSEEDpy\")\n", "from modelseedpy import KBaseMediaPkg\n" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "tags": [] }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Media\tGrowth\n", "\n", "Sulfate-L-Arabitol\t0.0\n", "Sulfate-Cystathionine\t0.0\n", "Sulfate-N-Acetyl-D-galactosamine\t0.0\n", "Sulfate-Uridine\t0.0\n", "Phosphate-Cytidine-2-Monophosphate\t0.0\n", "Nitrogen-L-Pyroglutamic-Acid\t0.0\n", "Sulfate-L-Lysine\t0.0\n", "Sulfate-D-Arabitol\t0.0\n", "Carbon-L-Malic-Acid\t0.0\n", "Carbon-D-Psicose\t0.0\n", "Carbon-N-Acetyl-L-Glutamic-Acid\t0.0\n", "Nitrogen-Nitrite\t0.0\n", "Nitrogen-Xanthine\t0.0\n", "Sulfate-Tyramine\t0.0\n", "Carbon-Mucic-Acid\t0.0\n", "Sulfate-Citrate\t0.0\n", "Sulfate-Maltotriose\t0.0\n", "Sulfate-1H-Imidazole-4-ethanamin\t0.0\n", "Nitrogen-L-Glutamine\t0.0\n", "Sulfate-Glycerone\t0.0\n", "Nitrogen-b-Phenylethylamine\t0.0\n", "Sulfate-Cysteamine\t0.0\n", "Sulfate-6-Deoxy-D-galactose\t0.0\n", "Carbon-D-Gluconic-Acid\t0.0\n", "Nitrogen-L-Proline\t0.0\n", "Nitrogen-Glycine\t0.0\n", "Nitrogen-Nitrate\t0.0\n", "Sulfate-Dextrin\t0.0\n", "Carbon-L-Asparagine\t0.0\n", "Phosphate-D-2-Phospho-Glyceric-Acid\t0.0\n", "Carbon-Tyramine\t0.0\n", "Sulfate-NH3\t0.0\n", "Sulfate-Galactitol\t0.0\n", "Complete\t0.0\n", "Nitrogen-L-Asparagine\t0.0\n", "Sulfate-Biuret\t0.0\n", "Sulfate-L-Histidine\t0.0\n", "Sulfate-D-Alanine\t0.0\n", "Nitrogen-L-Tyrosine\t0.0\n", "Nitrogen-Ala-Asp\t0.0\n", "Carbon-d-Amino-Valeric-Acid\t0.0\n", "Sulfate-L-Isoleucine\t0.0\n", "Sulfate-R-R-Tartaric-Acid\t0.0\n", "Sulfate-L-Valine\t0.0\n", "Nitrogen-Inosine\t0.0\n", "Carbon-Citric-Acid\t0.0\n", "Carbon-2-3-Butanone\t0.0\n", "Sulfate-L-Rhamnose\t0.0\n", "Sulfate-Xylitol\t0.0\n", "Carbon-D-Fructose-6-Phosphate\t0.0\n", "Sulfate-Amygdalin\t0.0\n", "Phosphate-D-Mannose-6-Phosphate\t0.0\n", "Carbon-Glycyl-L-Proline\t0.0\n", "Carbon-Quinic-Acid\t0.0\n", "Carbon-Salicin\t0.0\n", "Carbon-Acetic-Acid\t0.0\n", "Carbon-D-Mannose\t0.0\n", "Sulfate-Acetamide\t0.0\n", "Sulfate-Lanthionine\t0.0\n", "Carbon-m-Tartaric-Acid\t0.0\n", "Biolog-C-lac-N-dna-P-dna\t0.0\n", "Phosphate-O-Phospho-D-Tyrosine\t0.0\n", "Nitrogen-Ethylamine\t0.0\n", "Sulfate-Quinate\t0.0\n", "Sulfate-Stachyose\t0.0\n", "Nitrogen-Cytidine\t0.0\n", "Sulfate-L-Proline\t0.0\n", "Sulfate-p-Amino-Benzene-Sulfonic-Acid\t0.0\n", "Carbon-Oxalic-Acid\t0.0\n", "Carbon-Tween-80\t0.0\n", "Nitrogen-L-Aspartic-Acid\t0.0\n", "7H9\t0.0\n", "Phosphate-O-Phospho-L-Threonine\t0.0\n", "Carbon-D-Saccharic-Acid\t0.0\n", "Carbon-D-Glucosamine\t0.0\n", "Carbon-D-Arabitol\t0.0\n", "Carbon-g-Hydroxy-Butyric-Acid\t0.0\n", "Carbon-D-Fucose\t0.0\n", "Phosphate-Uridine-2-Monophosphate\t0.0\n", "MinimalGrowthNMS\t0.0\n", "Carbon-p-Hydroxy-Phenylacetic-Acid\t0.0\n", "Sulfate-L-alanylglycine\t0.0\n", "Carbon-L-Glutamine\t0.0\n", "Carbon-Uridine\t0.0\n", "Sulfate-L-Ornithine\t0.0\n", "Carbon-D-L-Octopamine\t0.0\n", "Nitrogen-D-Glutamic-Acid\t0.0\n", "Carbon-Glycyl-L-Glutamic-Acid\t0.0\n", "Biolog-C-ser-l-N-ser-l\t0.0\n", "LB\t0.0\n", "Phosphate-Phosphono-Acetic-Acid\t0.0\n", "Carbon-Thymidine\t0.0\n", "Carbon-2-3-Butanediol\t0.0\n", "Sulfate-D-Glucarate\t0.0\n", "Sulfate-D-Mannosamine\t0.0\n", "Nitrogen-Acetamide\t0.0\n", "Carbon-b-Methyl-D-Glucoside\t0.0\n", "Carbon-4-Hydroxy-L-Proline-trans\t0.0\n", "Carbon-Xylitol\t0.0\n", "Nitrogen-Ala-Glu\t0.0\n", "Nitrogen-N-Acetyl-D-Mannosamine\t0.0\n", "Nitrogen-Adenosine\t0.0\n", "Carbon-Citraconic-Acid\t0.0\n", "Carbon-Dextrin\t0.0\n", "Nitrogen-L-Valine\t0.0\n", "Nitrogen-Uracil\t0.0\n", "Carbon-a-Keto-Glutaric-Acid\t0.0\n", "Sulfate-Acetoin\t0.0\n", "Sulfate-Thymine\t0.0\n", "Phosphate-Uridine-5-Monophosphate\t0.0\n", "Nitrogen-L-Isoleucine\t0.0\n", "Nitrogen-Ala-Leu\t0.0\n", "Carbon-Adenosine\t0.0\n", "Sulfate-L-Djenkolic-Acid\t0.0\n", "Sulfate-D-Aspartate\t0.0\n", "Phosphate-Guanosine-5-Monophosphate\t0.0\n", "Carbon-a-Hydroxy-Butyric-Acid\t0.0\n", "Phosphate-D-Glucose-6-Phosphate\t0.0\n", "Carbon-L-Arabitol\t0.0\n", "Phosphate-Cytidine-2-3-Cyclic-Monophosphate\t0.0\n", "Carbon-D-Cellobiose\t0.0\n", "Sulfate-L-Phenylalanine\t0.0\n", "Nitrogen-L-Alanine\t0.0\n", "Sulfate-Cytidine\t0.0\n", "Carbon-L-Leucine\t0.0\n", "Carbon-D-Xylose\t0.0\n", "Sulfate-Pyruvate\t0.0\n", "Nitrogen-Urea\t0.0\n", "Phosphate-6-Phospho-Gluconic-Acid\t0.0\n", "Carbon-Itaconic-Acid\t0.0\n", "Phosphate-D-Mannose-1-Phosphate\t0.0\n", "Nitrogen-L-Cysteine\t0.0\n", "Biolog-C-ile-l-N-ile-l\t0.0\n", "MR1Aerobic\t0.0\n", "Sulfate-L-Cysteine-Sulfinic-Acid\t0.0\n", "Carbon-Fumaric-Acid\t0.0\n", "Sulfate-L-Sorbose\t0.0\n", "Carbon-D-Glucose-Palsson\t0.0\n", "Carbon-L-Tartaric-Acid\t0.0\n", "Carbon-b-Methyl-D-Galactoside\t0.0\n", "Carbon-Gelatin\t0.0\n", "ArgonneNMSMedia\t0.0\n", "Carbon-D-Serine\t0.0\n", "Nitrogen-g-Amino-N-Butyric-Acid\t0.0\n", "Sulfate-L-Methionine-Sulfoxide\t0.0\n", "Carbon-L-Arabinose\t0.0\n", "Biolog-C-acgam-N--acgam\t0.0\n", "Phosphate-Trimetaphosphate\t0.0\n", "Sulfate-Thiosulfate\t0.0\n", "Sulfate-N-Acetylneuraminate\t0.0\n", "Sulfate-Formate\t0.0\n", "Phosphate-Phospho-Glycolic-Acid\t0.0\n", "Nitrogen-D-Lysine\t0.0\n", "Carbon-L-Lyxose\t0.0\n", "Nitrogen-N-Acetyl-D-Glucosamine\t0.0\n", "Nitrogen-Thymidine\t0.0\n", "Carbon-L-Histidine\t0.0\n", "Carbon-Glycyl-L-Aspartic-Acid\t0.0\n", "Biolog-C-lac-N-ala-l\t0.0\n", "Carbon-a-Methyl-D-Galactoside\t0.0\n", "Sulfate-D-Arabinose\t0.0\n", "Sulfate-L-Serine\t0.0\n", "Sulfate-L-Arginine\t0.0\n", "Carbon-D-Aspartic-Acid\t0.0\n", "Nitrogen-N-Acetyl-D-Galactosamine\t0.0\n", "Phosphate-Uridine-3-Monophosphate\t0.0\n", "Sulfate-L-Aspartate\t0.0\n", "Nitrogen-D-Asparagine\t0.0\n", "Nitrogen-L-Citrulline\t0.0\n", "Phosphate-Adenosine-5-Monophosphate\t0.0\n", "Carbon-D-Tagatose\t0.0\n", "Sulfate-Glycogen\t0.0\n", "Biolog-C-lac-N-ptrc\t0.0\n", "Carbon-L-Phenylalanine\t0.0\n", "Sulfate-Palatinose\t0.0\n", "Nitrogen-D-Valine\t0.0\n", "Carbon-g-Amino-Butyric-Acid\t0.0\n", "Nitrogen-Guanine\t0.0\n", "Sulfate-Butane-Sulfonic-Acid\t0.0\n", "Nitrogen-D-Alanine\t0.0\n", "Carbon-L-Lactic-Acid\t0.0\n", "NoBounds\t0.0\n", "Nitrogen-D-Serine\t0.0\n", "Carbon-L-Arginine\t0.0\n", "Phosphate-Adenosine-2-Monophosphate\t0.0\n", "Carbon-Maltotriose\t0.0\n", "MR1Anaerobic\t0.0\n", "Sulfate-Ethanolamine\t0.0\n", "Phosphate-Guanosine-3-Monophosphate\t0.0\n", "Biolog-C-cytd-N-cytd\t0.0\n", "Carbon-a-Keto-Butyric-Acid\t0.0\n", "Sulfate-Inosine\t0.0\n", "Phosphate-Phosphoenol-Pyruvate\t0.0\n", "Nitrogen-Ala-Gly\t0.0\n", "Sulfate-Methane-Sulfonic-Acid\t0.0\n", "Nitrogen-L-Ornithine\t0.0\n", "Sulfate-Gly-Gln\t0.0\n", "Carbon-Arbutin\t0.0\n", "Carbon-1-2-Propanediol\t0.0\n", "Sulfate-Propanoate\t0.0\n", "Biolog-C-lac-N-thr-l\t0.0\n", "Carbon-D-L-Citramalic-Acid\t0.0\n", "Sulfate-D-Tagatose\t0.0\n", "Sulfate-L-Citrulline\t0.0\n", "Carbon-L-Homoserine\t0.0\n", "Carbon-2-Hydroxy-Benzoic-Acid\t0.0\n", "SP4\t0.0\n", "Sulfate-Ethylamine\t0.0\n", "Sulfate-Salicin\t0.0\n", "Phosphate-2-Deoxy-D-Glucose-6-Phosphate\t0.0\n", "Carbon-Putrescine\t0.0\n", "Carbon-D-Threonine\t0.0\n", "Carbon-Pectin\t0.0\n", "MethanogenMedia\t0.0\n", "Carbon-Gentiobiose\t0.0\n", "Sulfate-D-Cysteine\t0.0\n", "Biolog-C-dna-N-dna-P-dna\t0.0\n", "Carbon-a-D-Glucose\t0.0\n", "Carbon-Oxalomalic-Acid\t0.0\n", "Carbon-b-Hydroxy-Butyric-Acid\t0.0\n", "Nitrogen-Met-Ala\t0.0\n", "Biolog-C-lac-N-asp-l\t0.0\n", "Carbon-Amygdalin\t0.0\n", "Carbon-D-Tartaric-Acid\t0.0\n", "Sulfate-Pectin\t0.0\n", "Nitrogen-L-Homoserine\t0.0\n", "Carbon-L-Ornithine\t0.0\n", "Carbon-Chondroitin\t0.0\n", "Carbon-tricarballylate\t0.0\n", "Sulfate-Thymidine\t0.0\n", "Phosphate-O-Phospho-L-Serine\t0.0\n", "Sulfate-L-Methionine\t0.0\n", "Sulfate-D-Galactose\t0.0\n", "Phosphate-Adenosine-2-3-Cyclic-Monophosphate\t0.0\n", "Sulfate-Xanthosine\t0.0\n", "Sulfate-D-Psicose\t0.0\n", "Carbon-L-Rhamnose\t0.0\n", "Nitrogen-Uric-Acid\t0.0\n", "Biolog-C-lac-N-met-l\t0.0\n", "Sulfate-D-Glucuronate\t0.0\n", "Carbon-L-Alanine\t0.0\n", "Nitrogen-Tyramine\t0.0\n", "Carbon-b-Phenylethylamine\t0.0\n", "Phosphate-Phosphate\t0.0\n", "Nitrogen-Ethanolamine\t0.0\n", "Carbon-N-Acetyl-D-Glucosamine\t0.0\n", "Sulfate-L-Glutamate\t0.0\n", "Biolog-C-lac-N-glu-l\t0.0\n", "Sulfate-Glutathione\t0.0\n", "Sulfate-D-Galactosamine\t0.0\n", "Sulfate-D-L-Lipoamide\t0.0\n", "Carbon-Butylamine-sec\t0.0\n", "NMS\t0.0\n", "Nitrogen-N-Acetyl-D-L-Glutamic-Acid\t0.0\n", "Sulfate-6-Deoxy-L-galactose\t0.0\n", "Sulfate-Tween-20\t0.0\n", "Sulfate-N-Acetyl-D-L-Methionine\t0.0\n", "Biolog-C-lac-N-ile-l\t0.0\n", "Sulfate-Ribitol\t0.0\n", "Nitrogen-Uridine\t0.0\n", "Sulfate-D-Fructose\t0.0\n", "Carbon-L-Aspartic-Acid\t0.0\n", "Sulfate-L-Alanine\t0.0\n", "Carbon-L-Glutamic-Acid\t0.0\n", "Sulfate-L-Cystine\t0.0\n", "MinimalGrowthNoMedia\t0.0\n", "ArgonneLBMedia\t0.0\n", "Nitrogen-D-Galactosamine\t0.0\n", "PlantAutotrophicMedia\t0.0\n", "Biolog-C-dna\t0.0\n", "Sulfate-Sucrose\t0.0\n", "Carbon-b-D-Allose\t0.0\n", "Nitrogen-L-Lysine\t0.0\n", "Nitrogen-Gly-Gln\t0.0\n", "Sulfate-Ala-His\t0.0\n", "Nitrogen-L-Glutamic-Acid\t0.0\n", "Carbon-Mannan\t0.0\n", "PlantHeterotrophicMedia\t0.0\n", "Sulfate-L-Arabinose\t0.0\n", "Sulfate-Gentiobiose\t0.0\n", "Carbon-D-Malic-Acid\t0.0\n", "Carbon-Maltose\t0.0\n", "Carbon-Sucrose\t0.0\n", "Sulfate-Taurine\t0.0\n", "Sulfate-Arbutin\t0.0\n", "Carbon-N-Acetyl-D-Galactosamine\t0.0\n", "Sulfate-Uracil\t0.0\n", "Sulfate-Propane-1-2-diol\t0.0\n", "Biolog-C-lac-N-acgam\t0.0\n", "Carbon-D-Melezitose\t0.0\n", "Sulfate-D-Ribose\t0.0\n", "Carbon-D-Ribose\t0.0\n", "Nitrogen-L-Methionine\t0.0\n", "Phosphate-Tripolyphosphate\t0.0\n", "Sulfate-D-Asparagine\t0.0\n", "Sulfate-2-Hydroxyethane-Sulfonic-Acid\t0.0\n", "Carbon-L-Alanyl-Glycine\t0.0\n", "Nitrogen-Histamine\t0.0\n", "Biolog-C-lac-N-adn\t0.0\n", "Sulfate-Guanosine\t0.0\n", "Carbon-D-Glucose-1-Phosphate\t0.0\n", "Sulfate-tricarballylate\t0.0\n", "Phosphate-Cytidine-3-Monophosphate\t0.0\n", "Nitrogen-D-Glucosamine\t0.0\n", "Sulfate-D-Methionine\t0.0\n", "Carbon-D-Lactitol\t0.0\n", "Biolog-C-lac-S-cys-l\t0.0\n", "Carbon-sorbate\t0.0\n", "Sulfate-N-Acetyl-D-glucosamine\t0.0\n", "Carbon-a-Methyl-D-Glucoside\t0.0\n", "Phosphate-2-Aminoethyl-Phosphonic-Acid\t0.0\n", "Sulfate-Galactarate\t0.0\n", "Carbon-L-Pyroglutamic-Acid\t0.0\n", "Phosphate-b-Glycerol-Phosphate\t0.0\n", "Sulfate-Glycerol\t0.0\n", "Sulfate-Acetate\t0.0\n", "Sulfate-Ala-Gln\t0.0\n", "Carbon-D-Mannitol\t0.0\n", "Phosphate-O-Phospho-D-Serine\t0.0\n", "Carbon-D-L-Carnitine\t0.0\n", "Sulfate-D-Xylose\t0.0\n", "Sulfate-Cytosine\t0.0\n", "Carbon-L-Threonine\t0.0\n", "Sulfate-Maltose\t0.0\n", "Phosphate-D-3-Phospho-Glyceric-Acid\t0.0\n", "Carbon-N-Acetyl-b-D-Mannosamine\t0.0\n", "Sulfate-Adenine\t0.0\n", "Biolog-C-lac-N-his-l\t0.0\n", "Carbon-D-Melibiose\t0.0\n", "Sulfate-4-Hydroxybenzoate\t0.0\n", "Biolog-C-lac-N-gly\t0.0\n", "Carbon-Capric-Acid\t0.0\n", "Sulfate-Butanoic-Acid\t0.0\n", "Sulfate-D-Sorbitol\t0.0\n", "Sulfate-Deoxyribose\t0.0\n", "Nitrogen-D-L-a-Amino-N-Butyric-Acid\t0.0\n", "Carbon-Glycogen\t0.0\n", "Sulfate-Gelatine\t0.0\n", "Sulfate-L-Cysteinyl-Glycine\t0.0\n", "Biolog-C-lac-N-phe-l\t0.0\n", "Biolog-C-gln-l-N-gln-l\t0.0\n", "Nitrogen-D-Aspartic-Acid\t0.0\n", "Sulfate-Putrescine\t0.0\n", "Phosphate-Guanosine-3-5-Cyclic-Monophosphate\t0.0\n", "Phosphate-Pyrophosphate\t0.0\n", "Sulfate-L-Cysteic-Acid\t0.0\n", "Sulfate-Nitrite\t0.0\n", "Nitrogen-Biuret\t0.0\n", "Sulfate-D-Mannose\t0.0\n", "Sulfate-L-Glutamine\t0.0\n", "Nitrogen-Gly-Glu\t0.0\n", "Sulfate-Sulfate\t0.0\n", "Nitrogen-Ala-His\t0.0\n", "Carbon-D-Glucosaminic-Acid\t0.0\n", "Nitrogen-Gly-Asn\t0.0\n", "Sulfate-Tetrathionate\t0.0\n", "Nitrogen-Formamide\t0.0\n", "Nitrogen-Allantoin\t0.0\n", "Carbon-L-Proline\t0.0\n", "Biolog-C-cytd\t0.0\n", "Carbon-D-Glucose-6-Phosphate\t0.0\n", "Phosphate-D-Glucose-1-Phosphate\t0.0\n", "Carbon-D-L-a-Glycerol-Phosphate\t0.0\n", "Nitrogen-L-Threonine\t0.0\n", "Sulfate-N-Acetyl-D-mannosamine\t0.0\n", "Carbon-L-Xylose\t0.0\n", "Carbon-Palatinose\t0.0\n", "Carbon-3-Hydroxy-2-Butanone\t0.0\n", "Biolog-C-lac-N-dna\t0.0\n", "Carbon-Urocanic-Acid\t0.0\n", "Carbon-Butyric-Acid\t0.0\n", "Sulfate-L-Lyxose\t0.0\n", "Carbon-Caproic-Acid\t0.0\n", "Phosphate-Cytidine-5-Monophosphate\t0.0\n", "Nitrogen-L-Phenylalanine\t0.0\n", "Phosphate-Carbamyl-Phosphate\t0.0\n", "Carbon-Dihydroxy-Acetone\t0.0\n", "Carbon-D-Galacturonic-Acid\t0.0\n", "Nitrogen-Ammonia\t0.0\n", "Carbon-Pyruvic-Acid\t0.0\n", "Carbon-Stachyose\t0.0\n", "Nitrogen-L-Arginine\t0.0\n", "Biolog-C-lac-S-gthrd\t0.0\n", "Carbon-D-Alanine\t0.0\n", "Carbon-D-L-Malic-Acid\t0.0\n", "Sulfate-2-Amino-2-deoxy-D-glucon\t0.0\n", "Carbon-D-Galactonic-Acid-g-Lactone\t0.0\n", "Carbon-Glyoxylic-Acid\t0.0\n", "Sulfate-Carbon\t0.0\n", "Carbon-D-Raffinose\t0.0\n", "Sulfate-Mannan\t0.0\n", "Sulfate-Ala-Leu\t0.0\n", "Biolog-C-dna-P-dna\t0.0\n", "Carbon-Glycolic-Acid\t0.0\n", "Carbon-Formic-Acid\t0.0\n", "Sulfate-Methylamine\t0.0\n", "Sulfate-Xanthine\t0.0\n", "Biolog-C-lac-N-pro-l\t0.0\n", "Carbon-2-Deoxy-Adenosine\t0.0\n", "Nitrogen-L-Tryptophan\t0.0\n", "Sulfate-Succinate\t0.0\n", "Sulfate-Gly-Met\t0.0\n", "Carbon-Dulcitol\t0.0\n", "Carbon-a-D-Lactose\t0.0\n", "Sulfate-Laminarin\t0.0\n", "Carbon-L-Lysine\t0.0\n", "Nitrogen-Hydroxylamine\t0.0\n", "Sulfate-Taurocholic-Acid\t0.0\n", "Sulfate-S-Lactate\t0.0\n", "Phosphate-Guanosine-2-3-Cyclic-Monophosphate\t0.0\n", "Nitrogen-Guanosine\t0.0\n", "Sulfate-Oxalate\t0.0\n", "Sulfate-Malonate\t0.0\n", "Sulfate-D-Serine\t0.0\n", "Nitrogen-L-Leucine\t0.0\n", "Sulfate-Adenosine\t0.0\n", "Biolog-C-lac-N-ser-l\t0.0\n", "Sulfate-Tween-80\t0.0\n", "Carbon-D-Fructose\t0.0\n", "Nitrogen-Ala-Thr\t0.0\n", "Biolog-C-lac-N-arg-l\t0.0\n", "Carbon-4-Hydroxy-Benzoic-Acid\t0.0\n", "Carbon-Laminarin\t0.0\n", "Carbon-L-Isoleucine\t0.0\n", "Carbon-N-Acetyl-Neuraminic-Acid\t0.0\n", "Empty\t0.0\n", "Carbon-L-Methionine\t0.0\n", "Phosphate-Phosphocreatine\t0.0\n", "Carbon-D-Galactose\t0.0\n", "Sulfate-Urea\t0.0\n", "Biolog-C-lac-N-leu-l\t0.0\n", "Sulfate-sorbate\t0.0\n", "Sulfate-Allantoin\t0.0\n", "Carbon-a-Keto-Valeric-Acid\t0.0\n", "Carbon-L-Fucose\t0.0\n", "Sulfate-Hypotaurine\t0.0\n", "Nitrogen-Cytosine\t0.0\n", "Sulfate-L-Cysteine\t0.0\n", "Nitrogen-Putrescine\t0.0\n", "Nitrogen-L-Serine\t0.0\n", "Carbon-i-Erythritol\t0.0\n", "Biolog-C-lac-N-asn-l\t0.0\n", "Carbon-m-Inositol\t0.0\n", "Sulfate-Sebacic-acid\t0.0\n", "Phosphate-Thymidine-5-Monophosphate\t0.0\n", "Sulfate-L-Asparagine\t0.0\n", "Carbon-Propionic-Acid\t0.0\n", "Sulfate-D-Valine\t0.0\n", "Carbon-2-Deoxy-D-Ribose\t0.0\n", "Phosphate-O-Phosphoryl-Ethanolamine\t0.0\n", "Carbon-Lactulose\t0.0\n", "Nitrogen-D-Mannosamine\t0.0\n", "Carbon-Succinic-Acid\t0.0\n", "Sulfate-D-Lysine\t0.0\n", "Sulfate-L-Leucine\t0.0\n", "Biolog-C-lac-N-gln-l\t0.0\n", "Sulfate-S-Malate\t0.0\n", "Sulfate-2-Methylmaleate\t0.0\n", "Sulfate-Glyoxylate\t0.0\n", "Sulfate-b-Methyl-D-Glucoside\t0.0\n", "Carbon-Inosine\t0.0\n", "Nitrogen-Ala-Gln\t0.0\n", "Phosphate-Phosphoryl-Choline\t0.0\n", "Carbon-Sebacic-Acid\t0.0\n", "Carbon-D-Arabinose\t0.0\n", "Sulfate-N-Acetyl-L-glutamate\t0.0\n", "Nitrogen-e-Amino-N-Caproic-Acid\t0.0\n", "Biolog-C-lac-S-tsul\t0.0\n", "Nitrogen-Adenine\t0.0\n", "Carbon-D-Glucuronic-Acid\t0.0\n", "Carbon-Chondroitin-Sulfate-C\t0.0\n", "Carbon-D-Glucose\t0.0\n", "Carbon-L-Serine\t0.0\n", "Phosphate-Adenosine-3-Monophosphate\t0.0\n", "Sulfate-Mannitol\t0.0\n", "Nitrogen-L-Histidine\t0.0\n", "Phosphate-Uridine-2-3-Cyclic-Monophosphate\t0.0\n", "Phosphate-Phospho-L-Arginine\t0.0\n", "Biolog-C-lac-S-so3\t0.0\n", "Nitrogen-Gly-Met\t0.0\n", "Sulfate-Thiourea\t0.0\n", "Nitrogen-Methylamine\t0.0\n", "Sulfate-L-Homoserine\t0.0\n", "Carbon-Malonic-Acid\t0.0\n", "Carbon-Adonitol\t0.0\n", "Carbon-Inulin\t0.0\n", "Carbon-L-Valine\t0.0\n", "Carbon-D-Sorbitol\t0.0\n", "Carbon-Tween-20\t0.0\n", "Phosphate-O-Phospho-L-Tyrosine\t0.0\n", "Nitrogen-Xanthosine\t0.0\n", "Carbon-Ethanolamine\t0.0\n", "Sulfate-Fumarate\t0.0\n", "Sulfate-2-1-beta-D-Fructosyl-n\t0.0\n", "Sulfate-L-Threonine\t0.0\n", "Sulfate-D-Glucose-6-phosphate\t0.0\n", "Carbon-Glycine\t0.0\n", "Sulfate-Nitrate\t0.0\n", "Carbon-L-Sorbose\t0.0\n", "Carbon-Acetamide\t0.0\n", "Carbon-Glycerol\t0.0\n", "Sulfate-D-Galacturonate\t0.0\n", "Sulfate-Itaconate\t0.0\n", "Nitrogen-Thymine\t0.0\n", "Phosphate-Cytidine-3-5-Cyclic-Monophosphate\t0.0\n", "Sulfate-L-Tyrosine\t0.0\n", "Sulfate-N-Acetyl-L-Cysteine\t0.0\n", "Phosphate-D-L-a-Glycerol-Phosphate\t0.0\n", "Sulfate-Glycine\t0.0\n", "Nitrogen-d-Amino-N-Valeric-Acid\t0.0\n", "Sulfate-D-Glucosamine\t0.0\n", "Sulfate-5-Oxoproline\t0.0\n", "Phosphate-D-Glucosamine-6-Phosphate\t0.0\n", "Biolog-C-thr-l-N-thr-l\t0.0\n", "Carbon-Acetoacetic-Acid\t0.0\n", "Sulfate-L-Tryptophan\t0.0\n", "Sulfate-Formamide\t0.0\n", "Nitrogen-Agmatine\t0.0\n", "Sulfate-D-L-Ethionine\t0.0\n", "Biolog-C-glu-l-N-glu-l\t0.0\n", "Carbon-D-Trehalose\t0.0\n", "BU12_10\t0.0\n", "BU7_LacPrx\t0.0\n", "C-acetate\t0.0\n", "C-Citrate\t0.0\n", "C-D-Glucose\t0.0\n", "fdx2_ActOxl_t2\t0.0\n", "LB_4C_24h\t0.0\n", "C-D-Lactate\t0.0\n", "RefGlucoseMinimal\t0.0\n" ] } ], "source": [ "kbase_api = cobrakbase.KBaseAPI()\n", "#Getting B. theta model out of KBase\n", "model = kbase_api.get_from_ws(\"E_iML1515.kb\",40576)\n", "#Creating KBase media package for assigning constraints based on media\n", "kmp = KBaseMediaPkg(model)\n", "#Getting list of all media in KBase\n", "media_list = kbase_api.list_objects(\"KBaseMedia\")\n", "print(\"Media\\tGrowth\")\n", "for media_info in media_list:\n", " #Getting media object data\n", " media = kbase_api.get_from_ws(media_info[1],media_info[6])\n", " #Constraining model based on media\n", " kmp.build_package(media)\n", " #Optimizing model\n", " solution=model.optimize()\n", " #Printing predicted growth rate in media\n", " print(media_info[1]+\"\\t\"+str(solution.objective_value))" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.12" } }, "nbformat": 4, "nbformat_minor": 4 }