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["Metadata","Values (examples)"]
[]
["Asset Title ","Data for phaseplane plot of oscillating ATP and NADH concentrations in oscillating yeast extracts"]
["Uploader","Franco du Preez"]
["Uploader SEEK ID",355]
["Project","SysMO-DB",""]
[]
["ASSAY"]
["Assay SEEK ID",219]
["Assay Title","Detailed kinetic model of yeast glycolytic oscillation"]
["Assay_type","discontinuousEnzymatic"]
["Technology_type","enzymatic activity measurements",""]
["Description","Concentration of glycolytic intermediates were determined by enzymatic assays"]
["Experimentalist","Joachim Das and Heinrich-Gustav Busse"]
["Date",1991]
["SOP",""]
["Publication (optional)","Das, J. and Busse, H.G. (1991) Biopyshical Journal 60:369-379"]
[]
["Experimental_conditions"]
["Item","temperature","pH"]
["Compound (if concentration)",null,""]
["Unit"]
["Start_value (optional)",25,"6.5"]
["End_value (optional)",25,"6.5"]
["Comments"]
[]
["Culture growth","Batch"]
[]
["FACTORS_STUDIED"]
["Item","concentration"]
["Compound (if concentration)","Glucose"]
["Unit","umol/ml"]
["Start_value (optional)",50]
["End_value (optional)",50]
["SD (optional)"]
["Comments","Semi-aerobic. Cultures were harvested in the early stationary phase. The oscillations were induced and sustained by continuous feeding of \nthe extract with 50 umol glucose/ml extract/h(or 0.83 umol/ml/ min) \nfrom a stock solution of 3M glucose in 0.1M potassium phosphate \nbuffer(pH6 .5) by an autoburette"]

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["Sample Name",{"$nulls":6},"Treatments (Factors Studied)"]
[null,"Organism ","NCBI_ID","Strain","Genotype","Phenotype","Respiration","concentration"]
["sample","Saccharomyces cerevisiae",4932,"ATCC 9080",null,null,"semi-aerobic","Glucose 30uM/ml"]
[""]
[""]
[""]
["",""]
[""]
[""]
[""]
[""]
[""]

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["Metabolites"," Steady state data",null," measured unit: Arbitrary (NADH absorbance)",{"$nulls":6},"Note: Both units are concentration related as this is the data for plotting the phase plane of ATP vs NADH during oscillation"]
[]
[null,"Concentration of ATP (mM)"]
[null,0.67,0.701,0.726,0.771,0.705,0.673,0.572,0.569,0.331,0.171,0.07,0.031,0.3,0.471,0.635]
["1,3-biphosphoglycerate"]
["2-phospho-D-glyceric acid"]
["3-phospho-D-glyceric acid"]
["acetaldehyde"]
["ADP"]
["alpha, alpha-trehalose"]
["alpha, alpha-trehalose 6-phosphate"]
["alpha, alpha-trehalose_out"]
["ATP"]
["beta-D-glucose 6-phosphate"]
["carbon dioxide"]
["D-fructose 1,6-biphosphate"]
["D-fructose 2,6-biphosphate"]
["D-fructose 6-phosphate"]
["D-glucose"]
["D-glucose 1-phosphate"]
["D-glucose 6-phosphate"]
["D-glucose_out"]
["dihydroxyacetone phosphate"]
["diphosphate"]
["ethanol"]
["ethanol_out"]
["fructose 1,6-biphosphate"]
["fructose 6-phosphate"]
["glucose 6-phosphate"]
["glyceraldehyde 3-phosphate"]
["glycerol"]
["glycerol_out"]
["glycerone phosphate"]
["H+"]
["H+_out"]
["NAD(+)"]
["NADH",0.126,0.131,0.14,0.146,0.156,0.171,0.224,0.23,0.26,0.285,0.28,0.274,0.244,0.23,0.135]
["phosphate"]
["phosphoenolpyruvate"]
["pyruvate"]
["pyruvate_out"]
["sn-glycerol 3-phosphate"]
["UDP"]
["UDP-D-glucose"]
["UTP"]
["water"]
["AMP"]
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[-2.739,0.20354999999999998,-2.739,0.22949999999999998,0.6959999999999997,0.1983]
[-2.6959999999999997,0.23085,-2.5650000000000004,0.25305,1.1300000000000008,0.20475]
[-2.5650000000000004,0.2517,-2.391,0.2778,1.3480000000000008,0.2022]
[-2.4779999999999998,0.2283,-2.3040000000000003,0.2595,1.6519999999999992,0.20745]
[-2.4349999999999996,0.18645,-2.261,0.23864999999999997,1.9570000000000007,0.20354999999999998]
[-2.348,0.17865,-2.13,0.23085,2.2170000000000005,0.21]
[-2.261,0.19305,-2,0.23745,2.4350000000000005,0.2061]
[-2.1740000000000004,0.2178,-1.9569999999999999,0.25305,2.609,0.20354999999999998]
[-2.13,0.2478,-1.87,0.27525,2.7829999999999995,0.20865]
[-2.043,0.2505,-1.8259999999999996,0.28049999999999997,2.9570000000000007,0.21389999999999998]
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[-1.8259999999999996,0.1878,-1.5220000000000002,0.22694999999999999,3.5220000000000002,0.21915]
[-1.7830000000000004,0.18255,-1.391,0.24255,3.609,0.22049999999999997]
[-1.6959999999999997,0.18645,-1.3479999999999999,0.26084999999999997,3.6959999999999997,0.2178]
[-1.6520000000000001,0.20354999999999998,-1.2610000000000001,0.27915,3.8260000000000005,0.1995]
[-1.5650000000000004,0.2244,-1.2169999999999996,0.28169999999999995,3.9130000000000003,0.1956]
[-1.5220000000000002,0.2478,-1.1740000000000004,0.27525,4,0.20085]
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[-1.391,0.2478,-1,0.23085,4.260999999999999,0.22949999999999998]
[-1.3479999999999999,0.2178,-0.9130000000000003,0.2256,4.304,0.2256]
[-1.3479999999999999,0.20475,-0.8259999999999996,0.23220000000000002,4.478,0.19305]
[-1.2610000000000001,0.19169999999999998,-0.6959999999999997,0.2661,4.5649999999999995,0.1905]
[-1.1740000000000004,0.1878,-0.6520000000000001,0.28049999999999997,4.651999999999999,0.19305]
[-1.0430000000000001,0.19305,-0.5650000000000004,0.28559999999999997,4.739000000000001,0.21389999999999998]
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[-0.391,0.23085,0,0,5.609,0.24645]
[-0.2610000000000001,0.23609999999999998,0,0,5.696,0.24135]
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[-0.1299999999999999,0.18255,0,0,6,0.19169999999999998]
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[0.04300000000000015,0.1722,0,0,6.2170000000000005,0.24645]
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[0,0,0,0,6.391,0.2439]
[0,0,0,0,6.478,0.21134999999999998]
[0,0,0,0,6.522,0.1956]
[0,0,0,0,6.609,0.18914999999999998]
[0,0,0,0,6.696,0.19695]
[0,0,0,0,6.8260000000000005,0.2256]
[0,0,0,0,6.913,0.25305]
[0,0,0,0,7,0.26084999999999997]
[0,0,0,0,7.087,0.2505]
[0,0,0,0,7.2170000000000005,0.20354999999999998]
[0,0,0,0,7.304,0.1983]
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["<http://www.mygrid.org.uk/ontology/JERMOntology#flux_balance_analysis>","flux balance analysis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#fluxomics>","fluxomics"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#gene_expression_profiling>","gene expression profiling"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#genome-scale_enzyme_activity_profiling>","genome-scale enzyme activity profiling"]
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["<http://www.mygrid.org.uk/ontology/JERMOntology#microRNA_profiling>","microRNA profiling"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Next_Generation_sequencing_analysis>","Next Generation sequencing analysis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#organism_or_strain_characterisation>","organism or strain characterisation"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#post-translational_modification>","post-translational modification"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#primer_design>","primer design"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#protein_expression_profiling>","protein expression profiling"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#protein_identification>","protein identification"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#protein_purification>","protein purification"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#protein_structural_analysis>","protein structural analysis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#protein-protein_interaction>","protein-protein interaction"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#protein-protein_interaction_profiling>","protein-protein interaction profiling"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#proteomics>","proteomics"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#reactomics>","reactomics"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#RNA-seq_profiling>","RNA-seq profiling"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#RNAi>","RNAi"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#single_cell>","single cell"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#small-molecule_microarray>","small-molecule microarray"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#SNP_detection>","SNP detection"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Substrate_utilization>","Substrate utilization"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#tiling_path>","tiling path"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#transcriptional_profiling>","transcriptional profiling"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#transcriptomics>","transcriptomics"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#translational_profiling>","translational profiling"]

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["INDIVIDUALS","<http://www.mygrid.org.uk/ontology/JERMOntology#Project>",null,"<http://www.mygrid.org.uk/ontology/JERMOntology#is_investigated_by>"]
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["<http://www.mygrid.org.uk/ontology/JERMOntology#BaCell>","BaCell"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#COSMIC>","COSMIC"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#KOSMOBAC>","KOSMOBAC"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#MOSES>","MOSES"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Noisy-Strep>","Noisy-Strep"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#PSYSMO>","PSYSMO"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#ScaRAB>","ScaRAB"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#SilicoTryp>","SilicoTryp"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#STREAM>","STREAM"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#SulfoSys>","SulfoSys"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#SUMO>","SUMO"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#SysMO-DB>","SysMO-DB"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#SysmoLab>","SysmoLab"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Translucent>","Translucent"]

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["ontology","<http://www.mygrid.org.uk/ontology/JERMOntology>","<http://www.mygrid.org.uk/ontology/JERMOntology>","OBJECT_PROPERTY"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#13C_radiolabelling>","13C radiolabelling"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#2-hybrid_system>","2-hybrid system"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#2D_gel_electrophoresis>","2D gel electrophoresis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Accelerator_Mass_Spectrometry>","Accelerator Mass Spectrometry"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#affinity_chromatography>","affinity chromatography"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Algebraic_equation>","Algebraic equation"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#bait_protein_tagging>","bait protein tagging"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#binding>","binding"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#capillary_electrophoresis>","capillary electrophoresis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#chemostat_measurements>","chemostat measurements"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#ChIP-on-chip>","ChIP-on-chip"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Chip-Seq>","Chip-Seq"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#chromatography>","chromatography"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#custom_Array>","custom Array"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#DNA_Methylation>","DNA Methylation"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#electrophoresis>","electrophoresis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#enzymatic_activity_measurements>","enzymatic activity measurements"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Exon_array>","Exon array"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#FACS>","FACS"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#flow_cytometry>","flow cytometry"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#FRAP>","FRAP"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#gas_chromatography>","gas chromatography"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Gas_Chromatography_Mass_Spectrometry>","Gas Chromatography Mass Spectrometry"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#gel_electrophoresis>","gel electrophoresis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#gel_filtration>","gel filtration"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#HPLC>","HPLC"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#imaging>","imaging"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Inductively_Coupled_Plasma_Mass_Spectrometry>","Inductively Coupled Plasma Mass Spectrometry"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#initial_rate_experiment>","initial rate experiment"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Ion_Mobility_Spectrometry_Mass_Spectrometry>","Ion Mobility Spectrometry Mass Spectrometry"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Isotope_Ratio_Mass_Spectrometry>","Isotope Ratio Mass Spectrometry"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Linear_equation>","Linear equation"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Liquid_chromatography_Mass_Spectrometry>","Liquid chromatography Mass Spectrometry"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#liquid_chromatography-tandem_mass_spectrometry>","liquid chromatography-tandem mass spectrometry"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#MALDI_TOF>","MALDI TOF"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#mass_Spectrometry>","mass Spectrometry"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#mathematical_modelType>","mathematical modelType"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#microarray>","microarray"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#miRNA_microarray>","miRNA microarray"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#molecule_labelling>","molecule labelling"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Next_Generation_Sequencing>","Next Generation Sequencing"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#NMR>","NMR"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Ordinary_differential_equation>","Ordinary differential equation"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Partial_differential_equation>","Partial differential equation"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#PCR>","PCR"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#progressive_curve_experiment>","progressive curve experiment"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#qPCR>","qPCR"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#qRT-PCR>","qRT-PCR"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#radioactive_labelling>","radioactive labelling"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#RNA-Seq>","RNA-Seq"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#SDS_PAGE>","SDS PAGE"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#SELDI_TOF>","SELDI TOF"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#sequencing>","sequencing"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#small_molecule_microarray>","small molecule microarray"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#SNP_array>","SNP array"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#structural_methods>","structural methods"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#surface_plasmon_resonance>","surface plasmon resonance"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Tandem_Mass_Spectrometry>","Tandem Mass Spectrometry"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#tiling_array>","tiling array"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#UPLC>","UPLC"]

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["<http://www.mygrid.org.uk/ontology/JERMOntology#dry_biomass>","dry biomass"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#enzymeActivity>","enzymeActivity"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#expression>","expression"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#extracellular_concentration>","extracellular concentration"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#gas_flow>","gas flow"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#growth_medium>","growth medium"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#intracellular_concentration>","intracellular concentration"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#mass>","mass"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#optical_density>","optical density"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#optical_density_600>","optical density 600"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#pH>","pH"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#pressure>","pressure"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#specific_concentration>","specific concentration"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#temperature>","temperature"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#volume>","volume"]

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["<http://www.mygrid.org.uk/ontology/JERMOntology#growth_medium>","growth medium"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#intracellular_concentration>","intracellular concentration"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#mass>","mass"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#optical_density>","optical density"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#optical_density_600>","optical density 600"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#pH>","pH"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#pressure>","pressure"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#specific_concentration>","specific concentration"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#temperature>","temperature"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#volume>","volume"]

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["<http://www.mygrid.org.uk/ontology/JERMOntology#Bacillus_subtilis>","Bacillus subtilis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Clostridium_acetobutylicum>","Clostridium acetobutylicum"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Enterococcus_faecalis>","Enterococcus faecalis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Escherichia_coli>","Escherichia coli"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Lactococcus_lactis>","Lactococcus lactis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Pseudomonas_fluorescens>","Pseudomonas fluorescens"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Pseudomonas_putida>","Pseudomonas putida"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Saccharomyces_cerevisiae>","Saccharomyces cerevisiae"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Streptococcus_pneumoniae>","Streptococcus pneumoniae"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Streptococcus_pyogenes>","Streptococcus pyogenes"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Streptomyces_coelicolor>","Streptomyces coelicolor"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Sulfolobus_solfataricus>","Sulfolobus solfataricus"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Trypanosoma_brucei>","Trypanosoma brucei"]

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["<http://www.mygrid.org.uk/ontology/JERMOntology#turbidostat>","turbidostat"]

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["<http://www.mygrid.org.uk/ontology/JERMOntology#optical_density>","optical density"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#optical_density_600>","optical density 600"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#pH>","pH"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#pressure>","pressure"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#specific_concentration>","specific concentration"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#temperature>","temperature"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#volume>","volume"]

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["This is sheet displays the nomenclature of the genes, reaction, etc, that needs to be used for this excel file"]
["Name","Gene(s)","Gene Names","Reaction","Metabolites","Notes"]
["Hexose transport","YDL245C","HXT15","D-glucose_out = D-glucose","D-glucose_out","In the minimal model we add only one reaction, but later should one for each permease. These permeases also transport other hexoses, like fructose."]
[null,"YDR342C","HXT7",null,"D-glucose"]
[null,"YDR343C","HXT6"]
[null,"YDR345C","HXT3"]
[null,"YDR536W","STL1"]
[null,"YEL069C","HXT13"]
[null,"YFL011W","HXT10"]
[null,"YHR092C","HXT4"]
[null,"YHR094C","HXT1"]
[null,"YHR096C","HXT5"]
[null,"YJL214W","HXT8"]
[null,"YJL219W","HXT9"]
[null,"YJR158W","HXT16"]
[null,"YLR081W","GAL2"]
[null,"YMR011W","HXT2"]
[null,"YNR072W","HXT17"]
[null,"YOL156W","HXT11"]
[]
["Glucokinase","YCL040W","GLK1","ATP + D-glucose = ADP + beta-D-glucose 6-phosphate + H+","ATP"]
[{"$nulls":4},"ADP"]
[{"$nulls":4},"D-glucose"]
[{"$nulls":4},"beta-D-glucose 6-phosphate"]
[{"$nulls":4},"H+"]
[]
["Hexokinase 1","YFR053C","HXK1","ATP + D-glucose = ADP + beta-D-glucose 6-phosphate + H+","ATP"]
[{"$nulls":4},"ADP"]
[{"$nulls":4},"D-glucose"]
[{"$nulls":4},"beta-D-glucose 6-phosphate"]
[{"$nulls":4},"H+"]
[]
["Hexokinase 2","YGL253W","HXK2","ATP + D-glucose = ADP + beta-D-glucose 6-phosphate + H+","ATP"]
[{"$nulls":4},"ADP"]
[{"$nulls":4},"D-glucose"]
[{"$nulls":4},"beta-D-glucose 6-phosphate"]
[{"$nulls":4},"H+"]
[]
["Phosphoglucose isomerase","YBR196C","PGI1","glucose 6-phosphate = fructose 6-phosphate","glucose 6-phosphate"]
[{"$nulls":4},"fructose 6-phosphate"]
[]
["Phosphofructokinase","YGR240C","PFK1","ATP + fructose 6-phosphate -> ADP + fructose 1,6-bisphosphate\" + H+","ATP","The enzyme is a hetero-multimer (octamer) of two different polypeptides (2 genes). The binding of these polypeptides could be represented in the model"]
[null,"YMR205C","PFK2",null,"ADP"]
[{"$nulls":4},"fructose 6-phosphate"]
[{"$nulls":4},"fructose 1,6-biphosphate"]
[{"$nulls":4},"H+"]
[]
["Fructosebisphosphate aldolase","YKL060C","FBA1","fructose 1,6-bisphosphate = dihydroxyacetone phosphate + glyceraldehyde 3-phosphate","fructose 1,6-biphosphate"]
[{"$nulls":4},"dihydroxyacetone phosphate"]
[{"$nulls":4},"glyceraldehyde 3-phosphate"]
[]
["Triosephosphate isomerase","YDR050C","TPI1","dihydroxyacetone phosphate = glyceraldehyde 3-phosphate","dihydroxyacetone phosphate"]
[{"$nulls":4},"glyceraldehyde 3-phosphate"]
[]
["Glyceraldehyde phosphate dehydrogenase","YJL052W","TDH1","glyceraldehyde 3-phosphate + NAD + phosphate = 1,3-bisphosphoglycerate + NADH + H+","glyceraldehyde 3-phosphate"]
[{"$nulls":4},"NAD"]
[{"$nulls":4},"phosphate"]
[{"$nulls":4},"1,3-biphosphoglycerate"]
[{"$nulls":4},"NADH"]
[{"$nulls":4},"H+"]
[]
["Glyceraldehyde phosphate dehydrogenase","YJR009C","TDH2","glyceraldehyde 3-phosphate + NAD + phosphate = 1,3-bisphosphoglycerate + NADH + H+","glyceraldehyde 3-phosphate"]
[{"$nulls":4},"NAD"]
[{"$nulls":4},"phosphate"]
[{"$nulls":4},"1,3-biphosphoglycerate"]
[{"$nulls":4},"NADH"]
[{"$nulls":4},"H+"]
[]
["Glyceraldehyde phosphate dehydrogenase","YGR192C","TDH3","glyceraldehyde 3-phosphate + NAD + phosphate = 1,3-bisphosphoglycerate + NADH + H+","glyceraldehyde 3-phosphate"]
[{"$nulls":4},"NAD"]
[{"$nulls":4},"phosphate"]
[{"$nulls":4},"1,3-biphosphoglycerate"]
[{"$nulls":4},"NADH"]
[{"$nulls":4},"H+"]
[]
["Phosphoglycerate kinase","YCR012W","PGK1","1,3-bisphosphoglycerate + ADP = 3-phospho-D-glyceric acid + ATP","1,3-biphosphoglycerate"]
[{"$nulls":4},"ADP"]
[{"$nulls":4},"3-phospho-D-glyceric acid"]
[{"$nulls":4},"ATP"]
[]
["Phosphoglycerate mutase","YKL152C","GPM1","3-phospho-D-glyceric acid  = 2-phospho-D-glyceric acid","3-phospho-D-glyceric acid","This enzyme also catalyzes a reaction of 1,3-bisphosphoglycerate to 2,3- bisphosphoglycerate"]
[{"$nulls":4},"2-phospho-D-glyceric acid"]
[]
[]
["Enolase","YGR254W","ENO1","2-phospho-D-glyceric acid  = phosphoenolpyruvate + water","2-phospho-D-glyceric acid"]
[{"$nulls":4},"phosphoenolpyruvate"]
[{"$nulls":4},"water"]
[]
["Enolase","YHR174W","ENO2","2-phospho-D-glyceric acid  = phosphoenolpyruvate + water","2-phospho-D-glyceric acid"]
[{"$nulls":4},"phosphoenolpyruvate"]
[{"$nulls":4},"water"]
[]
["pyruvate kinase","YAL038W","PYK1","ADP + H+  + phosphoenolpyruvate  = ATP + pyruvate","ATP"]
[{"$nulls":4},"ADP"]
[{"$nulls":4},"H+"]
[{"$nulls":4},"phosphoenolpyruvate"]
[{"$nulls":4},"pyruvate"]
[]
["Pyruvate kinase","YOR347C","PYK2","ADP + H+  + phosphoenolpyruvate  = ATP + pyruvate","ATP"]
[{"$nulls":4},"ADP"]
[{"$nulls":4},"H+"]
[{"$nulls":4},"phosphoenolpyruvate"]
[{"$nulls":4},"pyruvate"]
[]
["Pyruvate decarboxylase","YLR044C","PDC1","H+ + pyruvate = acetaldehyde  + carbon dioxide","H+"]
[{"$nulls":4},"pyruvate"]
[{"$nulls":4},"acetaldehyde"]
[{"$nulls":4},"carbon dioxide"]
[]
["Pyruvate decarboxylase","YLR134W","PDC5","H+ + pyruvate = acetaldehyde  + carbon dioxide","H+"]
[{"$nulls":4},"pyruvate"]
[{"$nulls":4},"acetaldehyde"]
[{"$nulls":4},"carbon dioxide"]
[]
["Pyruvate decarboxylase","YGR087C","PDC6","H+ + pyruvate = acetaldehyde  + carbon dioxide","H+"]
[{"$nulls":4},"pyruvate"]
[{"$nulls":4},"acetaldehyde"]
[{"$nulls":4},"carbon dioxide"]
[]
["Alcohol dehydrogenase","YOL086C","ADH1","Acetaldehyde + H+ + NADH = ethanol  + NAD(+)","acetaldehyde"]
[{"$nulls":4},"H+"]
[{"$nulls":4},"NADH"]
[{"$nulls":4},"ethanol"]
[{"$nulls":4},"NAD(+)"]
[]
["Alcohol dehydrogenase","YGL256W","ADH4","Acetaldehyde + H+ + NADH = ethanol  + NAD(+)","acetaldehyde"]
[{"$nulls":4},"H+"]
[{"$nulls":4},"NADH"]
[{"$nulls":4},"ethanol"]
[{"$nulls":4},"NAD(+)"]
[]
["Alcohol dehydrogenase","YBR145W","ADH5","Acetaldehyde + H+ + NADH = ethanol  + NAD(+)","acetaldehyde"]
[{"$nulls":4},"H+"]
[{"$nulls":4},"NADH"]
[{"$nulls":4},"ethanol"]
[{"$nulls":4},"NAD(+)"]
[]
["Alcohol dehydrogenase","YMR303C","ADH2","ethanol  + NAD(+) = Acetaldehyde + H+ + NADH","ethanol","This isoenzyme is expected to be active in ethanol growth, thus the reaction is written in reverse direction from other ADHs"]
[{"$nulls":4},"NAD(+)"]
[{"$nulls":4},"acetaldehyde"]
[{"$nulls":4},"H+"]
[{"$nulls":4},"NADH"]
[]
["Ethanol transport",null,null,"ethanol_out = ethanol","ethanol_out","No gene identified, appears as uncatalysed transport"]
[{"$nulls":4},"ethanol"]
[]
["ATP consumption","Many, not considered explicitly",null,"ATP → ADP + phosphate","ATP","This represents a large number of processes, such as protein synthesis, ion pumps, etc."]
[{"$nulls":4},"ADP"]
[{"$nulls":4},"phosphate"]
[]
["Glycerol-3-phosphate dehydrogenase","YDL022W","GPD1","glycerone phosphate + H+ + NADH = NAD(+)  + sn-glycerol 3-phosphate","glycerone phosphate"]
[{"$nulls":4},"H+"]
[{"$nulls":4},"NADH"]
[{"$nulls":4},"NAD(+)"]
[{"$nulls":4},"sn-glycerol 3-phosphate"]
[]
["Glycerol-3-phosphate dehydrogenase","YOL059W","GPD2","glycerone phosphate + H+ + NADH = NAD(+)  + sn-glycerol 3-phosphate","glycerone phosphate"]
[{"$nulls":4},"H+"]
[{"$nulls":4},"NADH"]
[{"$nulls":4},"NAD(+)"]
[{"$nulls":4},"sn-glycerol 3-phosphate"]
[]
["Glycerol-3-phosphatase","YER062C","HOR2","sn-glycerol 3-phosphate + water  = glycerol + phosphate","sn-glycerol 3-phosphate"]
[{"$nulls":4},"water"]
[{"$nulls":4},"glycerol"]
[{"$nulls":4},"phosphate"]
[]
["Glycerol-3-phosphatase","YIL053W","RHR2","sn-glycerol 3-phosphate + water  = glycerol + phosphate","sn-glycerol 3-phosphate"]
[{"$nulls":4},"water"]
[{"$nulls":4},"glycerol"]
[{"$nulls":4},"phosphate"]
[]
["Glycerol transport","YLL043W","FPS1","glycerol = glycerol_out","glycerol","There is also a glycerol/proton symport that could be considered"]
[{"$nulls":4},"glycerol_out"]
[]
["6-phosphofructo-2-kinase","YIL107C","PFK26","D-fructose 6-phosphate + ATP = D-fructose 2,6-bisphosphate + ADP + H+","D-fructose 6-phosphate"]
[{"$nulls":4},"ATP"]
[{"$nulls":4},"D-fructose 2,6-biphosphate"]
[{"$nulls":4},"ADP"]
[{"$nulls":4},"H+"]
[]
["6-phosphofructo-2-kinase","YOL136C","PFK27","D-fructose 6-phosphate + ATP = D-fructose 2,6-bisphosphate + ADP + H+","D-fructose 6-phosphate"]
[{"$nulls":4},"ATP"]
[{"$nulls":4},"D-fructose 2,6-biphosphate"]
[{"$nulls":4},"ADP"]
[{"$nulls":4},"H+"]
[]
["Fructose-2,6-bisphosphate 2-phosphatase","YJL155C","FBP26","D-fructose 2,6-bisphosphate + water  = D-fructose 6-phosphate + phosphate","D-fructose 2,6-biphosphate"]
[{"$nulls":4},"water"]
[{"$nulls":4},"D-fructose 6-phosphate"]
[{"$nulls":4},"phosphate"]
[]
["Fructose bisphosphatase","YLR377C","FBP1","D-fructose 1,6-bisphosphate  + water = D-fructose 6-phosphate + phosphate","D-fructose 1,6-biphosphate"]
[{"$nulls":4},"water"]
[{"$nulls":4},"D-fructose 6-phosphate"]
[{"$nulls":4},"phosphate"]
[]
["Phosphoglucomutase","YKL127W","PGM1","D-glucose 6-phosphate = D-glucose 1-phosphate","D-fructose 6-phosphate"]
[{"$nulls":4},"D-glucose 1-phosphate"]
[]
["Phosphoglucomutase","YMR105C","PGM2","D-glucose 6-phosphate = D-glucose 1-phosphate","D-fructose 6-phosphate"]
[{"$nulls":4},"D-glucose 1-phosphate"]
[]
["UTP-glucose 1-phosphate uridylyltransferase","YKL035W","UGP1","D-glucose 1-phosphate + H+ + UTP = diphosphate + UDP-D-glucose","D-glucose 1-phosphate"]
[{"$nulls":4},"H+"]
[{"$nulls":4},"UTP"]
[{"$nulls":4},"diphosphate"]
[{"$nulls":4},"UDP-D-glucose"]
[]
["alpha,alpha-trehalose-phosphate synthase (UDP-forming)","YBR126C","TPS1","D-glucose 6-phosphate + UDP-D-glucose = alpha,alpha-trehalose 6-phosphate + H+ + UDP","D-glucose 6-phosphate","The enzyme is a hetero-multimer of three different polypeptides (3 genes). The binding of these polypeptides could be represented in the model. Also the trehalose phosphatase is part of this complex and the model could consider that (not currently so)"]
[null,"YML100W","TSL1",null,"UDP-D-glucose"]
[null,"YMR261C","TPS3",null,"alpha, alpha-trehalose 6-phosphate"]
[{"$nulls":4},"H+"]
[{"$nulls":4},"UDP"]
[]
[]
[]
["alpha,alpha-trehalose phosphatase","YDR074W","TPS2","alpha,alpha-trehalose 6-phosphate + water = alpha,alpha-trehalose + phosphate","alpha, alpha-trehalose 6-phosphate","This enzyme is part of the trehalose-phosphate synthase/trehalose phosphatase. This is not reflected here but could be done later on. (there could be channelling of these two reactions)"]
[{"$nulls":4},"water"]
[{"$nulls":4},"alpha, alpha-trehalose"]
[{"$nulls":4},"phosphate"]
[]
[]
["alpha,alpha-trehalose transport","YGR289C","MAL11","alpha,alpha-trehalose_out + H+_out = alpha,alpha-trehalose + H+","alpha, alpha-trehalose_out","Proton symport, high affinity transporter (MAL11). There is another (unidentified gene) transporter with low affinity; unknown if that is also a proton symport or not. "]
[{"$nulls":4},"alpha, alpha-trehalose"]
[{"$nulls":4},"H+_out"]
[{"$nulls":4},"H+"]
[]
[]
["alpha,alpha-trehalase","YDR001C","NTH1","alpha,alpha-trehalose + water = 2 * D-glucose","alpha, alpha-trehalose"]
[{"$nulls":4},"water"]
[{"$nulls":4},"2 * D-glucose"]
[]
["Pyruvate transport","YKL217W","JEN1","pyruvate + H+ = pyruvate_out + H+_out","pyruvate"]
[{"$nulls":4},"H+"]
[{"$nulls":4},"pyruvate_out"]
[{"$nulls":4},"H+_out"]