Repository
Overview
This repository makes published experimental data required for kinetic modeling and associated models with the data (i.e. experimental data on which the model building and/or validation are based) into publicly accessible centralized, to facilitate both search and access. Detailed experimental information is provided with the data. It also allows data and associated models to remain private or provides optional access to collaborators. KiMoSys repository will be routinely updated and expanded as new dataset and models become available.
Search/browse data and associated models from publications that are stored in KiMoSys.
You may search by,
Examples: PubMed ID (e.g. '17590932'); Organism (e.g. 'Clostridium acetobutylicum'); EntryID (e.g. 'EntryID41')
| Data EntryID | Organism | Strain | Data type | Project name | Access | Associated models | All metadata | Year | Culture mode | Process condition | Keywords | Chebi/KEGG |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 30 | Escherichia coli | K-12 W3110 | time-series data of metabolites | — |  |
[yes ]|[more] | [30, "Escherichia coli", "K-12 W3110", "2", "KIMODATAID30_v1.xlsx", "17590932", "Biotechnology and Bioengineering", "Dynamic modeling of the central carbon metabolism of Escherichia coli.", "Christophe Chassagnole, Naruemol Noisommit-Rizzi, Joachim W. Schmid, Klaus Mauch, Matthias Reuss", "Institute of Biochemical Engineering, University of Stuttgart", "Chassagnole_2002.pdf", "application/pdf", 255701, "2013-04-23T17:30:11.890Z", "35.0", "7.0", "glucose", "chemostat", "0.1", nil, nil, true, "", nil, "1.5", "8.7", nil, "manually every 3 seconds with vacuum-sealed, precooled glass tubes containing the quenching solution", "liquid nitrogen (-196 ºC) and perchloric acid", "---\n- perchloric acid\n", "---\n- enzymatic\n- HPLC/HIC\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "mM", "dynamic model, Escherichia coli, intracellular metabolites, transient conditions, control and stability analysis", false, "17234", 2002, nil, "ChEBI:17634, ChEBI:4170, ChEBI:15946, ChEBI:40595, ChEBI:14336, ChEBI:44897, ChEBI:32816, ChEBI:48928, ChEBI:16077, CHEBI:15422, CHEBI:16761, ChEBI:16027, CHEBI:15846, CHEBI:16908, CHEBI:18009, CHEBI:16474", "doi.org/10.34619/7pa6-va85"] Administrator KiMoSys Data AccessID30 / EntryID30 [13, 30, "Original model source: in BioModels database.", "Chassagnole_2002.pdf", nil, "2013-03-06T19:18:54.796Z", "Metabolism", "---\n- Model building\n- Model validation\n", "ordinary differential equations", "17590932", "0.1", "Chassagnole2002_Carbon_Metabolism", "Dynamic modeling of the central carbon metabolism of Escherichia coli.", "Christophe Chassagnole, Naruemol Noisommit-Rizzi, Joachim W. Schmid, Klaus Mauch, Matthias Reuss", "Biotechnology and Bioengineering", "Institute of Biochemical Engineering, University of Stuttgart ", "", "BIOMD0000000051", "dynamic model, Escherichia coli, parameter fitting, flux control coefficients", "", "2014-03-19T14:31:21.179Z", "Escherichia coli", 2002, "COMBINE_KIMOMODELID13.omex", "application/omex+xml", 249522, "2014-06-30T17:38:01.875Z", nil, nil] Administrator KiMoSys Model AccessID13 / EntryID13 | 2002 | chemostat | aerobic | dynamic model, Escherichia coli, intracellular metabolites, transient conditions, control and stability analysis | ChEBI:17634, ChEBI:4170, ChEBI:15946, ChEBI:40595, ChEBI:14336, ChEBI:44897, ChEBI:32816, ChEBI:48928, ChEBI:16077, CHEBI:15422, CHEBI:16761, ChEBI:16027, CHEBI:15846, CHEBI:16908, CHEBI:18009, CHEBI:16474 |
| 35 | Escherichia coli | WT K-12 BW25113 and mutants | flux measurements | — | |
[yes ]|[more] | [35, "Escherichia coli", "WT K-12 BW25113 and mutants", "3", "KIMODATAID35_v3.xlsx", "17379776", "Science", "Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations.", "Nobuyoshi Ishii, Kenji Nakahigashi, Tomoya Baba, Martin Robert, Tomoyoshi Soga, Akio Kanai, Takashi Hirasawa, Miki Naba, Kenta Hirai, Aminul Hoque, Pei Yee Ho, Yuji Kakazu, Kaori Sugawara, Saori Igarashi, Satoshi Harada, Takeshi Masuda, Naoyuki Sugiyama, Takashi Togashi, Miki Hasegawa, Yuki Takai, Katsuyuki Yugi, Kazuharu Arakawa, Nayuta Iwata, Yoshihiro Toya, Yoichi Nakayama, Takaaki Nishioka, Kazuyuki Shimizu, Hirotada Mori, Masaru Tomita", "Institute for Advanced Biosciences, Keio University", nil, nil, nil, nil, "37.0", "7.0", "glucose", "chemostat", "0.1, 0.2, 0.4, 0.5 and 0.7", nil, nil, true, "", nil, "1.0", "See Supplementary files of the original article (Tabel S3).", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- GC-MS\n", "aerobic", "--- []\n", "(mmol/gDW/h)", "Escherichia coli, perturbations response, chemostat, single knockouts", false, "CHEBI:17234", 2007, nil, "R02738, R02740, R04779, R01070, R01015, R01061, R00200, R00209, R01528, R01529, R01056, R01641, R01827, R01830, R00351, R01324, R00267, R08549, R00412, R01082, R00342, R00341, R00214, R00479, R00472, R01064, R00227, R00704", "doi.org/10.34619/whwf-wb07"] Administrator KiMoSys Data AccessID35 / EntryID35 [36, nil, "", "Khodayari_2014.pdf", nil, "2014-11-04T23:47:28.858Z", "Metabolism", "---\n- Model building\n- Model validation\n", "ordinary differential equations", "24928774", "", "Kinetic model of Escherichia coli core metabolism", "A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data.", "Ali Khodayari, Ali R. Zomorrodi, James C.Liao, Costas D. Maranas", "Metabolic Engineering", "Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA", "", "", "ensemble modeling, kinetic modeling, metabolic network", "http://www.matlab.com (MATLAB)", nil, "Escherichia coli", 2014, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID36 / EntryID36 [38, nil, "MATLAB version of the model is available at http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html. ", "Jahan_2016.pdf", nil, "2018-07-12T12:32:20.605Z", "Metabolism", "---\n- Model building\n- Model validation\n", "ordinary differential equations", "27329289", "0.2, 0.4, 0.5 and 0.7", "E. coli Central Carbon Metabolism", "Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli", "Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto and Hiroyuki Kurata", "Microbial Cell Factories", "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680‑4 Kawazu, Iizuka, Fukuoka 820‑8502, Japan", "", "", "Systems biology, Rational design, Dynamic model, Enzyme kinetics, Transcription factor, Signal transduction, Allosteric enzyme", "MATLAB2007 or higher", "2018-07-20T16:47:46.311Z", "Escherichia coli", 2016, "COMBINE_KIMOMODELID38.omex", "application/octet-stream", 6603649, "2018-07-23T21:38:00.461Z", nil, nil] Administrator KiMoSys Model AccessID38 / EntryID38 [41, nil, "Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.", "Kurata_2018.pdf", nil, "2018-07-20T16:54:23.186Z", "Metabolism", "---\n- Model building\n- Model validation\n", "ordinary differential equations", "29054464", "0.2, 0.4, 0.5 and 0.7", "Continuous kinetic model of Escherichia coli", "Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures", "Hiroyuki Kurata and Yurie Sugimoto", "Journal of Bioscience and Bioengineering", "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan", "", "", "Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli", "MATLAB (MathWorks)", "2018-07-24T15:46:04.831Z", "Escherichia coli", 2018, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID41 / EntryID41 [42, nil, "For the analysis and evaluation of the kinetic model, the solver ode15s was used.", "Mannan_2015.PDF", nil, "2018-07-22T12:01:48.329Z", "Metabolism", "---\n- Model building\n", "ordinary differential equations", "26469081", "0.2", "kinetic model of the central carbon metabolism of E. coli ", "Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.", "Ahmad A. Mannan, Yoshihiro Toya, Kazuyuki Shimizu, Johnjoe McFadden, Andrzej M. Kierzek , Andrea Rocco", "Plos One", "Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, United Kingdom ", "", "", "E. coli, Bistability, Central Metabolism", "MATLAB® R2007b (version 7.5.0)", nil, "Escherichia coli", 2015, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID42 / EntryID42 | 2007 | chemostat | aerobic | Escherichia coli, perturbations response, chemostat, single knockouts | R02738, R02740, R04779, R01070, R01015, R01061, R00200, R00209, R01528, R01529, R01056, R01641, R01827, R01830, R00351, R01324, R00267, R08549, R00412, R01082, R00342, R00341, R00214, R00479, R00472, R01064, R00227, R00704 |
| 37 | Lactococcus lactis | MG1363 | time-series data of metabolites | PneumoSyS | |
[yes ]|[more] | [37, "Lactococcus lactis", "MG1363", "2", "KIMODATAID37_v1.xlsx", "12011086", "The Journal of Biological Chemistry", "Is the glycolytic flux in Lactococcus lactis primarily controlled by the redox charge? Kinetics of NAD(+) and NADH pools determined in vivo by 13C NMR.", "Ana Rute Neves, Rita Ventura, Nahla Mansour, Claire Shearman, Michael J. Gasson, Christopher Maycock, Ana Ramos and Helena Santos", "Instituto de Teconcologia Química e Biológica, Universidade Nova de Lisboa and Instituto de Biologia Experimental e Tecnológico, Oeiras, Portugal", "Neves_2002.pdf", "application/pdf", 662982, "2013-04-30T18:51:58.812Z", "30.0", "6.5", "glucose", "batch", "", nil, nil, true, "PneumoSyS", nil, "0.050", "", nil, " Cells were harvested in logarithmic growth phase (A 600 = 2.2)", "Centrifuges, washed, and suspended to a protein concentration of 16,5 mg/ml in 50mM Kpi or Mes/KOA buffer, pH 6,5, for 13C or 31P NMR respectively.", "---\n- boiling ethanol\n", "---\n- NMR\n", "--- []\n", "--- []\n", "anaerobic", "--- []\n", "", "Lactococcus lactis, metabolism of glucose, NMR, in vivo", false, "CHEBI:17234", 2002, nil, "ChEBI:17634, ChEBI:24996, ChEBI:30089, ChEBI:17050, ChEBI:4170, ChEBI:65056, ChEBI:17634, ChEBI:24996, ChEBI:30089, CHEBI:15846, CHEBI:16908, ChEBI:44897, ChEBI:17050, ChEBI:65056, CHEBI:15422, CHEBI:24838, ChEBI:17634, ChEBI:24996, ChEBI:30089, ChEBI:52684, CHEBI:15846, CHEBI:16908, ChEBI:44897, ChEBI:17050, ChEBI:65056", "doi.org/10.34619/3eze-qz73"] Administrator KiMoSys Data AccessID37 / EntryID37 [23, 37, "Original model source: in JWS online database.", "Levering_2012.pdf", nil, "2013-05-06T15:37:33.781Z", "Metabolism", "---\n- Model building\n- Model validation\n", "ordinary differential equations", "22325620", "", "glycolysis Lactococcus lactis", "Role of phosphate in the central metabolism of two lactic acid bacteria - a comparative systems biology approach.", "Jennifer Levering, Mark W. J. M. Musters, Martijn Bekker, Domenico Bellomo, Tomas Fiedler, Willem M. de Vos, Jeroen Hugenholtz, Bernd Kreikemeyer, Ursula Kummer and Bas Teusink", "FEBS Journal", "Department of Modeling of Biological Processes, COS Heidelberg ⁄ BIOQUANT, University of Heidelberg, Germany", "", "levering1", "Lactococcus lactis, metabolism of glucose, NMR, in vivo", "http://www.copasi.org (COPASI)", "2014-03-10T11:18:15.244Z", "Lactococcus lactis", 2012, "COMBINE_KIMOMODELID23.omex", "application/omex+xml", 1068365, "2014-06-30T17:53:53.205Z", nil, nil] Administrator KiMoSys Model AccessID23 / EntryID23 [24, 37, "Archive containing all files to run and plot simulations. Requires MATLAB.", "Vinga_2010.pdf", nil, "2013-05-06T18:05:17.187Z", "Metabolism", "---\n- Model building\n", "ordinary differential equations", "20921043", "", "DEB L. lactis model", "Subcellular metabolic organization in the context of dynamic energy budget and biochemical systems theories", "Susana Vinga, Ana R. Neves, Helena Santos, B. W. Brandt and S. A. L. M. Kooijman", "Philosophical transactions of the royal society B", "Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID)", "", "", "Lactococcus lactis, metabolism of glucose, NMR, in vivo", "http://www.matlab.com (MATLAB)", "2014-05-15T09:26:26.874Z", "Lactococcus lactis", 2010, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID24 / EntryID24 [35, nil, " Copasi model file used to produce manuscript figures.", "Costa_2014.pdf", nil, "2014-07-21T10:15:55.788Z", "Metabolism", "---\n- Model building\n- Model validation\n", "ordinary differential equations", "24413179", "—", "glycolysis Lactococcus lactis for mannitol and 2,3-butanediol production", "An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production", "Rafael S. Costa, Andras Hartmann, Paula Gaspar, Ana R. Neves and Susana Vinga", "Molecular BioSystems", "Instituto de Engenharia de Sistemas e Computadores, Investigacão e Desenvolvimento (INESC-ID), R Alves Redol 9, 1000-029 Lisboa, Portugal.", "PneumoSyS", "", "L. lactis, extended model, mannitol and 2,3-butanediol production, control analysis", "http://www.copasi.org (COPASI)", "2014-07-21T10:18:41.595Z", "Lactococcus lactis", 2014, nil, nil, nil, nil, nil, nil] Rafael Costa Model AccessID35 / EntryID35 [37, nil, "", nil, nil, "2015-04-12T16:04:40.278Z", "Metabolism", "---\n- Model building\n", "ordinary differential equations", "", "", "flavonoid biosynthetic pathway in L. lactis", "Modeling Lactococcus lactis for synthetic biology", "Costa, R.S.", "", "", "", nil, "flavonoid pathway, L. lactis, Naringenin", "", nil, "Lactococcus lactis", nil, nil, nil, nil, nil, nil, nil] Rafael Costa Model AccessID37 / EntryID37 | 2002 | batch | anaerobic | Lactococcus lactis, metabolism of glucose, NMR, in vivo | ChEBI:17634, ChEBI:24996, ChEBI:30089, ChEBI:17050, ChEBI:4170, ChEBI:65056, ChEBI:17634, ChEBI:24996, ChEBI:30089, CHEBI:15846, CHEBI:16908, ChEBI:44897, ChEBI:17050, ChEBI:65056, CHEBI:15422, CHEBI:24838, ChEBI:17634, ChEBI:24996, ChEBI:30089, ChEBI:52684, CHEBI:15846, CHEBI:16908, ChEBI:44897, ChEBI:17050, ChEBI:65056 |
| 38 | Escherichia coli | K-12 BW25113 and ppc, pyk mutants | time-series data of metabolites | — | |
[yes ]|[more] | [38, "Escherichia coli", "K-12 BW25113 and ppc, pyk mutants", "2", "KIMODATAID38_v1.xlsx", "21092096", "Microbial Cell Factories", "Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.", "Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu", "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Japan ", "Kadir_2010.pdf", "application/pdf", 2038907, "2013-04-24T14:40:24.921Z", "37.0", "7.0", "glucose", "batch", "—", nil, nil, true, "", nil, "1.0", "", nil, "5ml from the culture broth", "15ml of 60% (v/v) aqueous methanol containing 70mM HEPES at -80ºC", "---\n- enzymatic\n- perchloric acid\n", "---\n- enzymatic\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "g/L", "Specific Growth Rate, Flux Balance Analysis, Oxidative Pentose Phosphate Pathway, Main Metabolic Pathway, Isotopomer Distribution", false, "CHEBI:17234", 2010, nil, "ChEBI:17234, ChEBI:30089", "doi.org/10.34619/2gtb-se09"] Administrator KiMoSys Data AccessID38 / EntryID38 [16, 38, "", "Kadir_2010.pdf", nil, "2013-04-24T15:07:11.046Z", "Metabolism", "---\n- Model validation\n", "ordinary differential equations", "21092096", "—", "glycolysis Escherichia coli model", "Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.", "Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu", "Microbial Cell Factories", "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", "", "", "Escherichia coli, single-gene knockouts, main central metabolism and TCA", "http://www.matlab.com (MATLAB)", "2018-07-21T20:34:09.507Z", "Escherichia coli", 2010, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID16 / EntryID16 [38, nil, "MATLAB version of the model is available at http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html. ", "Jahan_2016.pdf", nil, "2018-07-12T12:32:20.605Z", "Metabolism", "---\n- Model building\n- Model validation\n", "ordinary differential equations", "27329289", "0.2, 0.4, 0.5 and 0.7", "E. coli Central Carbon Metabolism", "Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli", "Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto and Hiroyuki Kurata", "Microbial Cell Factories", "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680‑4 Kawazu, Iizuka, Fukuoka 820‑8502, Japan", "", "", "Systems biology, Rational design, Dynamic model, Enzyme kinetics, Transcription factor, Signal transduction, Allosteric enzyme", "MATLAB2007 or higher", "2018-07-20T16:47:46.311Z", "Escherichia coli", 2016, "COMBINE_KIMOMODELID38.omex", "application/octet-stream", 6603649, "2018-07-23T21:38:00.461Z", nil, nil] Administrator KiMoSys Model AccessID38 / EntryID38 [45, nil, "Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.", "Kurata_2018.pdf", nil, "2018-07-24T16:03:02.038Z", "Metabolism", "---\n- Model building\n", "ordinary differential equations", "29054464", "—", "Batch kinetic model of Escherichia coli", "Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures", "Hiroyuki Kurata and Yurie Sugimoto", "Journal of Bioscience and Bioengineering", "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan", "", "", "Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli", "MATLAB (MathWorks)", nil, "Escherichia coli", 2018, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID45 / EntryID45 | 2010 | batch | aerobic | Specific Growth Rate, Flux Balance Analysis, Oxidative Pentose Phosphate Pathway, Main Metabolic Pathway, Isotopomer Distribution | ChEBI:17234, ChEBI:30089 |
| 41 | Escherichia coli | WT K-12 BW25113 and mutants | metabolites at steady-state | — | |
[yes ]|[more] | [41, "Escherichia coli", "WT K-12 BW25113 and mutants", "1", "KIMODATAID41_v1.xlsx", "17379776", "Science", "Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations.", "Nobuyoshi Ishii, Kenji Nakahigashi, Tomoya Baba, Martin Robert, Tomoyoshi Soga, Akio Kanai, Takashi Hirasawa, Miki Naba, Kenta Hirai, Aminul Hoque, Pei Yee Ho, Yuji Kakazu, Kaori Sugawara, Saori Igarashi, Satoshi Harada, Takeshi Masuda, Naoyuki Sugiyama, Takashi Togashi, Miki Hasegawa, Yuki Takai, Katsuyuki Yugi, Kazuharu Arakawa, Nayuta Iwata, Yoshihiro Toya, Yoichi Nakayama, Takaaki Nishioka, Kazuyuki Shimizu, Hirotada Mori, Masaru Tomita", "Institute for Advanced Biosciences, Keio University", nil, nil, nil, nil, "37.0", "7.0", "glucose", "chemostat", "0.1, 0.2, 0.4, 0.5 and 0.7", nil, nil, true, "", nil, "1.0", "See Supplementary files of the original article (Tabel S3).", nil, "Aliquots of 10 mL were withdrawn at OD600 0.85", "Cells were filter (0.45-µm), washed with 10 mL of Milli-Q water and plunged into 1 mL of methanol containing 10µL of 0.56 mM PIPES", "---\n- chloroform\n", "---\n- CE-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "mM", "Escheirchia coli, perturbations response, chemostat, single knockouts", false, "CHEBI:17234", 2007, nil, "ChEBI:36655, ChEBI:17272, ChEBI:29805, ChEBI:35899, ChEBI:15361, ChEBI:17968, ChEBI:58363, ChEBI:24996, ChEBI:25224, ChEBI:48942, ChEBI:30795, ChEBI:18071, ChEBI:16659, ChEBI:27660, ChEBI:17760, ChEBI:16739, ChEBI:39150, ChEBI:28644, ChEBI:60630, ChEBI:16150, ChEBI:32544, ChEBI:61904, ChEBI:27804, ChEBI:30838, ChEBI:17865, ChEBI:32362, ChEBI:16682, ChEBI:55535, ChEBI:32383, ChEBI:15732, ChEBI:30916, ChEBI:18280, ChEBI:51057, ChEBI:36557, ChEBI:25147, ChEBI:58044, ChEBI:30867, ChEBI:32361, ChEBI:23410, ChEBI:26092, ChEBI:30801, ChEBI:8100, ChEBI:46957, ChEBI:16331, ChEBI:18021, ChEBI:32804, ChEBI:16632, ChEBI:58090, ChEBI:16108, ChEBI:27689, ChEBI:18386, ChEBI:17786, ChEBI:37548, ChEBI:16383, ChEBI:15708, ChEBI:36208, ChEBI:16953, ChEBI:32814, ChEBI:17536, ChEBI:28107, ChEBI:16552, ChEBI:45658, ChEBI:36242, ChEBI:15829, ChEBI:37712, ChEBI:61304, ChEBI:32369, ChEBI:78208, ChEBI:11305, ChEBI:71028, ChEBI:21557, ChEBI:29751, ChEBI:24175, ChEBI:24297, ChEBI:24265, ChEBI:48153, ChEBI:18262, ChEBI:16309, ChEBI:76283, ChEBI:71201, ChEBI:4907, ChEBI:30313, ChEBI:21626, ChEBI:16054, ChEBI:16532, ChEBI:43355, ChEBI:19569, ChEBI:17440, ChEBI:16454, ChEBI:30023, ChEBI:17381, ChEBI:17363, ChEBI:58273, ChEBI:76273, ChEBI:15956, ChEBI:18405, ChEBI:15873, ChEBI:29042, ChEBI:15946, ChEBI:17665, ChEBI:17044, ChEBI:19324, ChEBI:60083, ChEBI:15721, ChEBI:15682, ChEBI:47979, ChEBI:44395, ChEBI:57513, ChEBI:35418, ChEBI:16710, ChEBI:29025, ChEBI:16905, ChEBI:606564, ChEBI:57404, ChEBI:15842, ChEBI:29747, ChEBI:18283, ChEBI:67011, ChEBI:15919, ChEBI:29746, ChEBI:17573, ChEBI:17179, ChEBI:36261, ChEBI:9407, ChEBI:36257, ChEBI:27413, ChEBI:16628, ChEBI:15997, ChEBI:15725, ChEBI:15724, ChEBI:44423, ChEBI:17434, ChEBI:17141, ChEBI:16227, ChEBI:16898, ChEBI:5141, ChEBI:18049, ChEBI:28568, ChEBI:43689, ChEBI:15611, ChEBI:17296, ChEBI:16540, ChEBI:28123, ChEBI:16040, ChEBI:16028, ChEBI:30653, ChEBI:17154, ChEBI:16010, ChEBI:18257, ChEBI:16708, ChEBI:17368, ChEBI:16255, ChEBI:16610, ChEBI:16235, ChEBI:26374, ChEBI:16543, ChEBI:18211, ChEBI:23671, ChEBI:18335, ChEBI:16335, ChEBI:17596, ChEBI:16750, ChEBI:16856, ChEBI:15694, ChEBI:15414, ChEBI:77120, ChEBI:16695, ChEBI:17489, ChEBI:16027, ChEBI:28846, ChEBI:61377, ChEBI:17239, ChEBI:17297, ChEBI:15351, ChEBI:15479, ChEBI:16761, ChEBI:15531, ChEBI:17808, ChEBI:17552, ChEBI:17621, ChEBI:16311, ChEBI:63550, ChEBI:17677, ChEBI:15713, ChEBI:16284, ChEBI:15422, ChEBI:16039, ChEBI:15996, ChEBI:16960, ChEBI:18066, ChEBI:17200, ChEBI:16264, ChEBI:13389, ChEBI:25523", "doi.org/10.34619/c6ts-sv76"] Administrator KiMoSys Data AccessID41 / EntryID41 [42, nil, "For the analysis and evaluation of the kinetic model, the solver ode15s was used.", "Mannan_2015.PDF", nil, "2018-07-22T12:01:48.329Z", "Metabolism", "---\n- Model building\n", "ordinary differential equations", "26469081", "0.2", "kinetic model of the central carbon metabolism of E. coli ", "Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.", "Ahmad A. Mannan, Yoshihiro Toya, Kazuyuki Shimizu, Johnjoe McFadden, Andrzej M. Kierzek , Andrea Rocco", "Plos One", "Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, United Kingdom ", "", "", "E. coli, Bistability, Central Metabolism", "MATLAB® R2007b (version 7.5.0)", nil, "Escherichia coli", 2015, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID42 / EntryID42 | 2007 | chemostat | aerobic | Escheirchia coli, perturbations response, chemostat, single knockouts | ChEBI:36655, ChEBI:17272, ChEBI:29805, ChEBI:35899, ChEBI:15361, ChEBI:17968, ChEBI:58363, ChEBI:24996, ChEBI:25224, ChEBI:48942, ChEBI:30795, ChEBI:18071, ChEBI:16659, ChEBI:27660, ChEBI:17760, ChEBI:16739, ChEBI:39150, ChEBI:28644, ChEBI:60630, ChEBI:16150, ChEBI:32544, ChEBI:61904, ChEBI:27804, ChEBI:30838, ChEBI:17865, ChEBI:32362, ChEBI:16682, ChEBI:55535, ChEBI:32383, ChEBI:15732, ChEBI:30916, ChEBI:18280, ChEBI:51057, ChEBI:36557, ChEBI:25147, ChEBI:58044, ChEBI:30867, ChEBI:32361, ChEBI:23410, ChEBI:26092, ChEBI:30801, ChEBI:8100, ChEBI:46957, ChEBI:16331, ChEBI:18021, ChEBI:32804, ChEBI:16632, ChEBI:58090, ChEBI:16108, ChEBI:27689, ChEBI:18386, ChEBI:17786, ChEBI:37548, ChEBI:16383, ChEBI:15708, ChEBI:36208, ChEBI:16953, ChEBI:32814, ChEBI:17536, ChEBI:28107, ChEBI:16552, ChEBI:45658, ChEBI:36242, ChEBI:15829, ChEBI:37712, ChEBI:61304, ChEBI:32369, ChEBI:78208, ChEBI:11305, ChEBI:71028, ChEBI:21557, ChEBI:29751, ChEBI:24175, ChEBI:24297, ChEBI:24265, ChEBI:48153, ChEBI:18262, ChEBI:16309, ChEBI:76283, ChEBI:71201, ChEBI:4907, ChEBI:30313, ChEBI:21626, ChEBI:16054, ChEBI:16532, ChEBI:43355, ChEBI:19569, ChEBI:17440, ChEBI:16454, ChEBI:30023, ChEBI:17381, ChEBI:17363, ChEBI:58273, ChEBI:76273, ChEBI:15956, ChEBI:18405, ChEBI:15873, ChEBI:29042, ChEBI:15946, ChEBI:17665, ChEBI:17044, ChEBI:19324, ChEBI:60083, ChEBI:15721, ChEBI:15682, ChEBI:47979, ChEBI:44395, ChEBI:57513, ChEBI:35418, ChEBI:16710, ChEBI:29025, ChEBI:16905, ChEBI:606564, ChEBI:57404, ChEBI:15842, ChEBI:29747, ChEBI:18283, ChEBI:67011, ChEBI:15919, ChEBI:29746, ChEBI:17573, ChEBI:17179, ChEBI:36261, ChEBI:9407, ChEBI:36257, ChEBI:27413, ChEBI:16628, ChEBI:15997, ChEBI:15725, ChEBI:15724, ChEBI:44423, ChEBI:17434, ChEBI:17141, ChEBI:16227, ChEBI:16898, ChEBI:5141, ChEBI:18049, ChEBI:28568, ChEBI:43689, ChEBI:15611, ChEBI:17296, ChEBI:16540, ChEBI:28123, ChEBI:16040, ChEBI:16028, ChEBI:30653, ChEBI:17154, ChEBI:16010, ChEBI:18257, ChEBI:16708, ChEBI:17368, ChEBI:16255, ChEBI:16610, ChEBI:16235, ChEBI:26374, ChEBI:16543, ChEBI:18211, ChEBI:23671, ChEBI:18335, ChEBI:16335, ChEBI:17596, ChEBI:16750, ChEBI:16856, ChEBI:15694, ChEBI:15414, ChEBI:77120, ChEBI:16695, ChEBI:17489, ChEBI:16027, ChEBI:28846, ChEBI:61377, ChEBI:17239, ChEBI:17297, ChEBI:15351, ChEBI:15479, ChEBI:16761, ChEBI:15531, ChEBI:17808, ChEBI:17552, ChEBI:17621, ChEBI:16311, ChEBI:63550, ChEBI:17677, ChEBI:15713, ChEBI:16284, ChEBI:15422, ChEBI:16039, ChEBI:15996, ChEBI:16960, ChEBI:18066, ChEBI:17200, ChEBI:16264, ChEBI:13389, ChEBI:25523 |
| 42 | Clostridium acetobutylicum | ATCC824 | time-series data of metabolites | — | |
[yes ]|[more] | [42, "Clostridium acetobutylicum", "ATCC824", "2", "KIMODATAID42_v0.xlsx", "21247470", "BMC Systems Biology", "A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.", "Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer", "University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics", "Haus_2011.pdf", "application/pdf", 588418, "2014-04-11T17:19:41.791Z", "37.0", "5.7 and 4.5", "glucose", "chemostat", "0.1", nil, nil, true, "", nil, "1.0", "", nil, "2 ml of C. acetobutylicum cell suspensions were collected and quickly sedimented at 16,000 g for 30s at 4°C in a benchtop centrifuge.", "—", "---\n- not used\n", "---\n- GC-MS\n", "--- []\n", "--- []\n", "anaerobic", "--- []\n", "mM", "Clostridium acetobutylicum, continuous culture, effect of pH, solvent production", false, "CHEBI:17234", 2011, nil, "ChEBI:16236, ChEBI:15347, ChEBI:30089, ChEBI:28885, ChEBI:17968", "doi.org/10.34619/xn4t-0651"] Administrator KiMoSys Data AccessID42 / EntryID42 [19, 42, "", "Haus_2011.pdf", nil, "2013-05-03T13:15:51.718Z", "Metabolism", "---\n- Model building\n", "ordinary differential equations", "21247470", "0.1", "first forward shift", "A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.", "Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer", "BMC Systems Biology", "University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics", "", "", "Clostridium acetobutylicum, continuous culture, effect of pH, solvent production", " http://www.sbtoolbox.org (SBToolbox)", "2014-04-11T17:25:43.341Z", "Clostridium acetobutylicum", 2011, "COMBINE_KIMOMODELID19.omex", "application/omex+xml", 401646, "2014-06-30T20:38:42.907Z", nil, nil] Administrator KiMoSys Model AccessID19 / EntryID19 [20, 42, "", "Haus_2011.pdf", nil, "2013-05-03T13:24:53.859Z", "Metabolism", "---\n- Model building\n", "ordinary differential equations", "21247470", "0.1", "second forward shift", "A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.", "Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer", "BMC Systems Biology", "University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics", "", "", "Clostridium acetobutylicum, continuous culture, effect of pH, solvent production", "http://www.sbtoolbox.org (SBToolbox)", "2014-04-11T17:26:19.201Z", "Clostridium acetobutylicum", 2011, "COMBINE_KIMOMODELID20.omex", "application/omex+xml", 401633, "2014-06-30T20:39:10.028Z", nil, nil] Administrator KiMoSys Model AccessID20 / EntryID20 [21, 42, "", "Haus_2011.pdf", nil, "2013-05-03T13:31:42.406Z", "Metabolism", "---\n- Model building\n", "ordinary differential equations", "21247470", "0.1", "third forward shift", "A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.", "Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer", "BMC Systems Biology", "University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics", "", "", "Clostridium acetobutylicum, continuous culture, effect of pH, solvent production", "http://www.sbtoolbox.org (SBToolbox)", "2014-04-11T17:24:43.452Z", "Clostridium acetobutylicum", 2011, "COMBINE_KIMOMODELID21.omex", "application/omex+xml", 401643, "2014-06-30T20:39:32.642Z", nil, nil] Administrator KiMoSys Model AccessID21 / EntryID21 [22, 42, "", "Haus_2011.pdf", nil, "2013-05-03T13:40:10.812Z", "Metabolism", "---\n- Model building\n", "ordinary differential equations", "21247470", "0.1", "reverse forward shift", "A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.", "Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer", "BMC Systems Biology", "University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics", "", "", "Clostridium acetobutylicum, continuous culture, effect of pH, solvent production", "http://www.sbtoolbox.org (SBToolbox)", "2014-04-11T17:27:26.964Z", "Clostridium acetobutylicum", 2011, "COMBINE_KIMOMODELID22.omex", "application/omex+xml", 401628, "2014-06-30T20:39:48.510Z", nil, nil] Administrator KiMoSys Model AccessID22 / EntryID22 | 2011 | chemostat | anaerobic | Clostridium acetobutylicum, continuous culture, effect of pH, solvent production | ChEBI:16236, ChEBI:15347, ChEBI:30089, ChEBI:28885, ChEBI:17968 |
| 44 | Escherichia coli | WT K-12 BW25113 and mutants | enzyme/protein concentrations | — | |
[yes ]|[more] | [44, "Escherichia coli", "WT K-12 BW25113 and mutants", "4", "KIMODATAID44_v0.xlsx", "17379776", "Science", "Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations.", "Nobuyoshi Ishii, Kenji Nakahigashi, Tomoya Baba, Martin Robert, Tomoyoshi Soga, Akio Kanai, Takashi Hirasawa, Miki Naba, Kenta Hirai, Aminul Hoque, Pei Yee Ho, Yuji Kakazu, Kaori Sugawara, Saori Igarashi, Satoshi Harada, Takeshi Masuda, Naoyuki Sugiyama, Takashi Togashi, Miki Hasegawa, Yuki Takai, Katsuyuki Yugi, Kazuharu Arakawa, Nayuta Iwata, Yoshihiro Toya, Yoichi Nakayama, Takaaki Nishioka, Kazuyuki Shimizu, Hirotada Mori, Masaru Tomita", "Institute for Advanced Biosciences, Keio University", nil, nil, nil, nil, "37.0", "7.0", "glucose", "chemostat", "0.1, 0.2, 0.4, 0.5 and 0.7", nil, nil, true, "", nil, "1.0", "See Supplementary files of the original article (Tabel S3).", nil, "", "", "[\"\"]", "[\"\"]", "[\"\"]", "[\"\"]", "aerobic", "[\"\", \"LC-MS/MS\", \"2D gel-MALDI-TOF\"]", "(mg-protein/g-dry cell weight)", "Escheirchia coli, perturbations response, chemostat, single knockouts", false, "CHEBI:17234", 2007, nil, "P0A9C3, P0A6V8, P36938, P0A6T1, P0A796, P06999, P0A993, P0AB71, P0A858, P0A9B2, P0A799, P62707, P0A6P9, P21599, P0AD61, P23538, P0AC53, P52697, P00350, P0AG07, P0A7Z0, P37351, P27302, P33570, P0A867, P0A870, P0ADF6, P0A955, P0AFG8, P06959, P0A9P0, P22259, P00864, C6UHN7, P0ABH7, P25516, P36683, P08200, P0AFG3, P0AFG6, P0A836, P0AGE9, P0AC41, P07014, P00363, P0AC33, P14407, P05042, P61889, P0A9G6, P08997, P37330, P27550, P31660, P52643, P33232, P07003, P0A9N4, P09373, P32675, P0A9Q7, P0A9M8, P0A6A3, P69441, P0AA04, P08839", "doi.org/10.34619/vf58-qq82"] Administrator KiMoSys Data AccessID44 / EntryID44 [42, nil, "For the analysis and evaluation of the kinetic model, the solver ode15s was used.", "Mannan_2015.PDF", nil, "2018-07-22T12:01:48.329Z", "Metabolism", "---\n- Model building\n", "ordinary differential equations", "26469081", "0.2", "kinetic model of the central carbon metabolism of E. coli ", "Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.", "Ahmad A. Mannan, Yoshihiro Toya, Kazuyuki Shimizu, Johnjoe McFadden, Andrzej M. Kierzek , Andrea Rocco", "Plos One", "Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, United Kingdom ", "", "", "E. coli, Bistability, Central Metabolism", "MATLAB® R2007b (version 7.5.0)", nil, "Escherichia coli", 2015, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID42 / EntryID42 | 2007 | chemostat | aerobic | Escheirchia coli, perturbations response, chemostat, single knockouts | P0A9C3, P0A6V8, P36938, P0A6T1, P0A796, P06999, P0A993, P0AB71, P0A858, P0A9B2, P0A799, P62707, P0A6P9, P21599, P0AD61, P23538, P0AC53, P52697, P00350, P0AG07, P0A7Z0, P37351, P27302, P33570, P0A867, P0A870, P0ADF6, P0A955, P0AFG8, P06959, P0A9P0, P22259, P00864, C6UHN7, P0ABH7, P25516, P36683, P08200, P0AFG3, P0AFG6, P0A836, P0AGE9, P0AC41, P07014, P00363, P0AC33, P14407, P05042, P61889, P0A9G6, P08997, P37330, P27550, P31660, P52643, P33232, P07003, P0A9N4, P09373, P32675, P0A9Q7, P0A9M8, P0A6A3, P69441, P0AA04, P08839 |
| 51 | Escherichia coli | K-12 AG1 | time-series data of metabolites | — | |
[no] | [51, "Escherichia coli", "K-12 AG1", "2", "KIMODATAID51_v0.xlsx", "17239859", "FEBS Letters", "Dynamic simulation of an in vitro multi-enzyme system.", "Nobuyoshi Ishii, Yoshihiro Suga, Akiko Hagiya, Hisami Watanabe, Hirotada Mori, Masataka Yoshino, Masaru Tomita", "Institute for Advanced Biosciences, Keio University, Japan", "Ishii_2007.pdf", "application/pdf", 142546, "2014-04-23T10:27:14.149Z", "37.0", "not specified", "glucose", "batch", "—", nil, nil, true, "", nil, "0.2", "", nil, "Samples were obtained 2 h after addition of 0.1 mM isopropyl-b-D-thiogalactopyranoside (IPTG)", "cells were collected by centrifugation (6000 r.p.m., 5 min at 4 ºC) and resuspended in 10 ml of cold buffer I [50 mM sodium phosphate (pH 7.0), 200 mM NaCl, Protease inhibitor (Complete Mini EDTA-Free, Roche Diagnostics, Basel, Switzerland)].", "---\n- sonication\n", "---\n- enzymatic\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "mM", "dynamic simulation, enzyme kinetics, metabolism, glycolysis, in vitro", false, "CHEBI:17234", 2007, nil, "ChEBI:17634, ChEBI:15946, ChEBI:17665, ChEBI:16905", "doi.org/10.34619/6tjg-pp39"] Administrator KiMoSys Data AccessID51 / EntryID51 | 2007 | batch | aerobic | dynamic simulation, enzyme kinetics, metabolism, glycolysis, in vitro | ChEBI:17634, ChEBI:15946, ChEBI:17665, ChEBI:16905 |
| 52 | Escherichia coli | K-12 DSM 498 | metabolites at steady-state | — | |
[no] | [52, "Escherichia coli", "K-12 DSM 498", "1", "KIMODATAID52_v0.xlsx", "17479221", "Biotechnology Letters", "Metabolic profiling of Escherichia coli cultivations: evaluation of extraction and metabolite analysis procedures.", "Julia Hiller, Ezequiel Franco-Lara, Dirk Weuster-Botz", "Institut fuer Bioverfahrenstechnik, Technische Universitaet Braunschweig, Gausstrasse 17, 38106 Braunschwieg, Germany", nil, nil, nil, nil, "37.0", "7.0", "glucose", "chemostat", "0.125", nil, nil, true, "", nil, "3.0", "", nil, "6g cell suspension, 25 g 60% MeOH-H2O 30mM TEA, pH=7.5, T=40ºC", "centrifugation at -19 ºC, 6000g, 3min", "---\n- freezing-thawing in methanol\n", "---\n- enzymatic\n- LC-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "mM", "extraction methods, metabolic profiling and multi-substrate", false, "CHEBI:17234", 2007, nil, "ChEBI:18009, ChEBI:15846, ChEBI:16238, ChEBI:15422, ChEBI:16761, ChEBI:16027, ChEBI:17489, ChEBI:17665, ChEBI:15946, ChEBI:40595, ChEBI:17138, ChEBI:16108, ChEBI:44897, ChEBI:32816, ChEBI:15351", "doi.org/10.34619/28xq-2n73"] Administrator KiMoSys Data AccessID52 / EntryID52 | 2007 | chemostat | aerobic | extraction methods, metabolic profiling and multi-substrate | ChEBI:18009, ChEBI:15846, ChEBI:16238, ChEBI:15422, ChEBI:16761, ChEBI:16027, ChEBI:17489, ChEBI:17665, ChEBI:15946, ChEBI:40595, ChEBI:17138, ChEBI:16108, ChEBI:44897, ChEBI:32816, ChEBI:15351 |
| 54 | Escherichia coli | K-12 DSM | metabolites at steady-state | — | |
[no] | [54, "Escherichia coli", "K-12 DSM", "1", "KIMODATAID54_v0.xlsx", "11488613", "Analytical Biochemistry", "Quantification of intracellular metabolites in Escherichia coli K12 using liquid chromatographic-electrospray ionization tandem mass spectrometric techniques.", "Arne Buchholz, Ralf Takors, and Christian Wandrey", "Institute of Biotechnology, Research Center Juelich, 52425 Juelich, Germany", nil, nil, nil, nil, "not specified", "not specified", "glucose", "chemostat", "0.125", nil, nil, true, "", nil, "0.4", "", nil, "Samples are taken after the cultures have remained constant at a cell density of 10.0 g/L for at least three residence times, thus ensuring steady-state conditions.", "Sampling was performed using precooled syringes containing 15 ml of the quenching fluid, 60%, v/v, aqueous methanol containing 70 mM Hepes (2-[4-(2-hydroxyethyl)- 1-piperazinyl]ethanesulfonic acid).", "---\n- methanol-water\n", "---\n- LC-ESI-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "mM", "Escherichia coli, intracellular metabolites, ESI, extraction, LC-MS, quantification", false, "CHEBI:17234", 2001, nil, "ChEBI:48928, ChEBI:15996, ChEBI:15946, ChEBI:17665, ChEBI:17797, ChEBI:17552, ChEBI:15422, ChEBI:18009, ChEBI:16761, ChEBI:15351, ChEBI:16238, ChEBI:40595, ChEBI:16027, ChEBI:18009", "doi.org/10.34619/3ktp-1816"] Administrator KiMoSys Data AccessID54 / EntryID54 | 2001 | chemostat | aerobic | Escherichia coli, intracellular metabolites, ESI, extraction, LC-MS, quantification | ChEBI:48928, ChEBI:15996, ChEBI:15946, ChEBI:17665, ChEBI:17797, ChEBI:17552, ChEBI:15422, ChEBI:18009, ChEBI:16761, ChEBI:15351, ChEBI:16238, ChEBI:40595, ChEBI:16027, ChEBI:18009 |
| 55 | Pichia pastoris | X-33 | metabolites at steady-state | — | |
[no] | [55, "Pichia pastoris", "X-33", "1", "KIMODATAID55_v0.xlsx", "23448228", "BMC Systems Biology", "Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary 13C flux analysis.", "Joel Jordà, Camilo Suarez, Marc Carnicer, Angela ten Pierick, Joseph J Heijnen, Walter van Gulik, Pau Ferrer, Joan Albiol and Aljoscha Wahl", "Department of Chemical Engineering, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallès, Spain", "Jorda_2013.pdf", "application/pdf", 779343, "2014-04-23T10:41:24.455Z", "25.0", "5.0", "glucose", "chemostat", "0.09", nil, nil, true, "", nil, "1.0", "4.0", nil, " One hour before the switch to the labelled feed using a dedicated rapid-sampling setup.", "Approximately 1 g of broth were rapidly withdrawn and immediately mixed with 5 ml of precooled quenching solution at -40°C. ", "---\n- boiling ethanol\n", "---\n- GC-MS\n- LC-MS\n- HPLC-UV/RI\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "(µmol/l) and (µmol/gDW)", "Pichia pastoris, intracellular, extracellular, glucose, glucose:methanol", false, "CHEBI:17234", 2013, nil, "CHEBI:18012, CHEBI:15741, CHEBI:30797, CHEBI:44897, CHEBI:17634, CHEBI:17138 , CHEBI:30769, CHEBI:24344, CHEBI:30887, CHEBI:16108, CHEBI:17050, CHEBI:48153, CHEBI:17797, CHEBI:17363, CHEBI:16332, CHEBI:15946, CHEBI:17665, CHEBI:15721, CHEBI:40595, CHEBI:18283, CHEBI:27082, CHEBI:32816, CHEBI:16977, CHEBI:15428, CHEBI:16414, CHEBI:15603, CHEBI:17191, CHEBI:17203, CHEBI:17115, CHEBI:16857, CHEBI:22660, CHEBI:58095, CHEBI:18257, CHEBI:16015, CHEBI:18019, CHEBI:17196, CHEBI:18050, CHEBI:17895, CHEBI:15971, CHEBI:16828, CHEBI:16643, CHEBI:15846 + CHEBI:16908, CHEBI:18009 + CHEBI:16474, CHEBI:15351, CHEBI:16238, CHEBI:15422, CHEBI:16761 , CHEBI:15996, CHEBI:17345, CHEBI:16027 , CHEBI:17552, CHEBI:17489, CHEBI:27082, CHEBI:17665, CHEBI:30769, CHEBI:15721, CHEBI:15946, CHEBI:30797, CHEBI:15741, CHEBI:17050, CHEBI:32816, CHEBI:44897, CHEBI:17634, CHEBI:17138 , CHEBI:24344, CHEBI:30887, CHEBI:16108, CHEBI:48153, CHEBI:17797, CHEBI:17363, CHEBI:16332, CHEBI:18012, CHEBI:40595, CHEBI:18283, CHEBI:16015, CHEBI:18050, CHEBI:22660, CHEBI:18257, CHEBI:16977, CHEBI:18019, CHEBI:17115, CHEBI:17196, CHEBI:15971, CHEBI:15428, CHEBI:16414, CHEBI:15603, CHEBI:17191, CHEBI:17203, CHEBI:16857, CHEBI:58095, CHEBI:17895, CHEBI:16828, CHEBI:16643", "doi.org/10.34619/5zhw-s051"] Administrator KiMoSys Data AccessID55 / EntryID55 | 2013 | chemostat | aerobic | Pichia pastoris, intracellular, extracellular, glucose, glucose:methanol | CHEBI:18012, CHEBI:15741, CHEBI:30797, CHEBI:44897, CHEBI:17634, CHEBI:17138 , CHEBI:30769, CHEBI:24344, CHEBI:30887, CHEBI:16108, CHEBI:17050, CHEBI:48153, CHEBI:17797, CHEBI:17363, CHEBI:16332, CHEBI:15946, CHEBI:17665, CHEBI:15721, CHEBI:40595, CHEBI:18283, CHEBI:27082, CHEBI:32816, CHEBI:16977, CHEBI:15428, CHEBI:16414, CHEBI:15603, CHEBI:17191, CHEBI:17203, CHEBI:17115, CHEBI:16857, CHEBI:22660, CHEBI:58095, CHEBI:18257, CHEBI:16015, CHEBI:18019, CHEBI:17196, CHEBI:18050, CHEBI:17895, CHEBI:15971, CHEBI:16828, CHEBI:16643, CHEBI:15846 + CHEBI:16908, CHEBI:18009 + CHEBI:16474, CHEBI:15351, CHEBI:16238, CHEBI:15422, CHEBI:16761 , CHEBI:15996, CHEBI:17345, CHEBI:16027 , CHEBI:17552, CHEBI:17489, CHEBI:27082, CHEBI:17665, CHEBI:30769, CHEBI:15721, CHEBI:15946, CHEBI:30797, CHEBI:15741, CHEBI:17050, CHEBI:32816, CHEBI:44897, CHEBI:17634, CHEBI:17138 , CHEBI:24344, CHEBI:30887, CHEBI:16108, CHEBI:48153, CHEBI:17797, CHEBI:17363, CHEBI:16332, CHEBI:18012, CHEBI:40595, CHEBI:18283, CHEBI:16015, CHEBI:18050, CHEBI:22660, CHEBI:18257, CHEBI:16977, CHEBI:18019, CHEBI:17115, CHEBI:17196, CHEBI:15971, CHEBI:15428, CHEBI:16414, CHEBI:15603, CHEBI:17191, CHEBI:17203, CHEBI:16857, CHEBI:58095, CHEBI:17895, CHEBI:16828, CHEBI:16643 |
| 57 | Pichia pastoris | X-33 | flux measurements | — | |
[no] | [57, "Pichia pastoris", "X-33", "3", "KIMODATAID57_v0.xlsx", "23448228", "BMC Systems Biology", "Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics ans instationary 13C flux analysis.", "Joel Jordà, Camilo Suarez, Marc Carnicer, Angela ten Pierick, Joseph J Heijnen, Walter van Gulik, Pau Ferrer, Joan Albiol and Aljoscha Wahl", "Department of Chemical Engineering, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallès, Spain", "Jorda_2013.pdf", "application/pdf", 779383, "2014-04-15T10:39:34.480Z", "25.0", "5.0", "glucose", "chemostat", "0.09", nil, nil, true, "", nil, "1.0", "4.0", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- GC-MS\n- LC-MS\n", "aerobic", "--- []\n", "(mmol/gDW.h)", "Pichia pastoris, instationary 13C-metabolic flux analysis, GC-MS, LC-MS", false, "CHEBI:17234", 2013, nil, "", "doi.org/10.34619/8tbx-m638"] Administrator KiMoSys Data AccessID57 / EntryID57 | 2013 | chemostat | aerobic | Pichia pastoris, instationary 13C-metabolic flux analysis, GC-MS, LC-MS | |
| 58 | Homo sapiens | HepG2 (ATCC number HB-8065) | metabolites at steady-state | — | |
[no] | [58, "Homo sapiens", "HepG2 (ATCC number HB-8065)", "1", "KIMODATAID58_v0.xlsx", "20426867", "BMC Systems Biology", "Dynamics and control of the central carbon metabolism in Hepatoma cells.", "Klaus Maier, Ute Hofmann, Mathias Reuss and Klaus Mauch", "Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany", "Maier_2010.pdf", "application/pdf", 1005199, "2013-06-06T13:47:09.177Z", "37.0", "not specified", "glucose", "batch", "—", nil, nil, true, "", nil, "not specified", "not specified", nil, "Removal of cell culture medium by suction (5 seconds).", "hot air", "---\n- hot water\n", "---\n- GC-MS\n- LC-MS\n- HPLC-UV/RI\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "(mmol/L)", "Hepatoma Cells, in vivo Dynamics, Dynamic Model, Control", false, "CHEBI:17234", 2010, nil, "CHEBI:16977, CHEBI:48928, CHEBI:15721, CHEBI:44897, CHEBI:40595, CHEBI:17138 , CHEBI:16108, CHEBI:17665, CHEBI:17797, CHEBI:17363, CHEBI:16761 , CHEBI:15422, CHEBI:16027 , CHEBI:18009, CHEBI:16474, CHEBI:15846, CHEBI:16908, CHEBI:18012, CHEBI:30797, CHEBI:17634, CHEBI:30887, CHEBI:30769, CHEBI:17634, CHEBI:32816, CHEBI:24996, CHEBI:16977, CHEBI:17634, CHEBI:32816, CHEBI:24996, CHEBI:17822", "doi.org/10.34619/054k-yg38"] Administrator KiMoSys Data AccessID58 / EntryID58 | 2010 | batch | aerobic | Hepatoma Cells, in vivo Dynamics, Dynamic Model, Control | CHEBI:16977, CHEBI:48928, CHEBI:15721, CHEBI:44897, CHEBI:40595, CHEBI:17138 , CHEBI:16108, CHEBI:17665, CHEBI:17797, CHEBI:17363, CHEBI:16761 , CHEBI:15422, CHEBI:16027 , CHEBI:18009, CHEBI:16474, CHEBI:15846, CHEBI:16908, CHEBI:18012, CHEBI:30797, CHEBI:17634, CHEBI:30887, CHEBI:30769, CHEBI:17634, CHEBI:32816, CHEBI:24996, CHEBI:16977, CHEBI:17634, CHEBI:32816, CHEBI:24996, CHEBI:17822 |
| 59 | Rattus | not specified | time-series data of metabolites | — | |
[no] | [59, "Rattus", "not specified", "2", "KIMODATAID59_v0.xlsx", "23670537", "Molecular Sytems Biology", "The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns.", "Rei Noguchi, Hiroyuki Kubota, Katsuyuki Yugi, Yu Toyoshima, Yasunori Komori, Tomoyoshi Soga, Shinya Kuroda", "Department of Computational Biology, Graduate School of Frontier Sciencies, The University of Tokyo, Kashiwa, Chiba, Japan", "Rei_2013.pdf", "application/pdf", 918733, "2013-06-07T13:36:43.315Z", "not specified", "not specified", "glucose", "batch", "—", nil, nil, true, "", nil, "not specified", "not specified", nil, "collected manually", "Stimulated cells washed twice with 5% mannitl and incubated for 10 min in 1ml of methanol containing 25 mM each of the three internal standards (L-methionine sulphone, D-camphor-10-sulphonic acid and 2-(N-morpholin-o)ethanesulfonic acid).", "---\n- chloroform-methanol\n", "---\n- enzymatic\n- CE-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "µM", "glucose metabolism, insulin, computational model, network motif, temporal coding", false, "CHEBI:17234", 2013, nil, "ChEBI:17665, ChEBI:40595, ChEBI:16108, ChEBI:17050, ChEBI:19324, ChEBI:44897, ChEBI:16004, ChEBI:16077, ChEBI:18066, ChEBI:28087, ChEBI:15361, ChEBI:17634, ChEBI:28087, ChEBI:28087, ChEBI:28087, ChEBI:17634, ChEBI:17634, ChEBI:17634", "doi.org/10.34619/9rzz-7550"] Administrator KiMoSys Data AccessID59 / EntryID59 | 2013 | batch | aerobic | glucose metabolism, insulin, computational model, network motif, temporal coding | ChEBI:17665, ChEBI:40595, ChEBI:16108, ChEBI:17050, ChEBI:19324, ChEBI:44897, ChEBI:16004, ChEBI:16077, ChEBI:18066, ChEBI:28087, ChEBI:15361, ChEBI:17634, ChEBI:28087, ChEBI:28087, ChEBI:28087, ChEBI:17634, ChEBI:17634, ChEBI:17634 |
| 61 | Saccharomyces cerevisiae | FY4 | time-series data of metabolites | — | |
[no] | [61, "Saccharomyces cerevisiae", "FY4", "2", "KIMODATAID61_v0.xlsx", "23549479", "Molecular Systems Biology", "Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast.", "Guillermo G Zampar, Anne Kümmel, Jennifer Ewald, Stefan Jol, Bastian Niebel, Paola Picotti, Ruedi Aebersold, Uwe Sauer, Nicola Zamboni and Matthias Heinemann", "ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland", "Zampar_2013.pdf", "application/pdf", 2754858, "2014-04-15T11:42:39.451Z", "30.0", "5.0", "glucose", "batch", "—", nil, nil, true, "", nil, "2.0", "correlation of OD with biomass: 0.486 gDW/L OD", nil, "1 ml samples and centrifuged for 4 min at 4000, r.p.m at 4 ºC", "—", "---\n- not used\n", "---\n- HPLC-UV/RI\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "(mM) and (gDW/L)", "diauxic shift, metabolome, S. cerevisiae, extracelullar", false, "CHEBI:17234", 2013, nil, "ChEBI:30089, ChEBI:30089, ChEBI:30089, ChEBI:16236, ChEBI:16236, ChEBI:16236, ChEBI:17634, ChEBI:17634, ChEBI:17634, ChEBI: 17754, ChEBI: 17754, ChEBI: 17754, ChEBI: 32816, ChEBI: 32816, ChEBI: 32816, ChEBI: 15741, ChEBI: 15741", "doi.org/10.34619/pzwd-f936"] Administrator KiMoSys Data AccessID61 / EntryID61 | 2013 | batch | aerobic | diauxic shift, metabolome, S. cerevisiae, extracelullar | ChEBI:30089, ChEBI:30089, ChEBI:30089, ChEBI:16236, ChEBI:16236, ChEBI:16236, ChEBI:17634, ChEBI:17634, ChEBI:17634, ChEBI: 17754, ChEBI: 17754, ChEBI: 17754, ChEBI: 32816, ChEBI: 32816, ChEBI: 32816, ChEBI: 15741, ChEBI: 15741 |
| 62 | Saccharomyces cerevisiae | FY4 | time-series data of metabolites | — | |
[no] | [62, "Saccharomyces cerevisiae", "FY4", "2", "KIMODATAID62_v0.xlsx", "23549479", "Molecular Systems Biology", "Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast.", "Guillermo G Zampar, Anne Kümmel, Jennifer Ewald, Stefan Jol, Bastian Niebel, Paola Picotti, Ruedi Aebersold, Uwe Sauer, Nicola Zamboni and Matthias Heinemann", "ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland", "Zampar_2013.pdf", "application/pdf", 2754858, "2014-04-15T12:42:25.715Z", "30.0", "5.0", "glucose", "batch", "—", nil, nil, true, "", nil, "2.0", "correlation of OD with biomass: 0.486 gDW/L OD", nil, "withdrawn from the culture at specific time points.", "four samples of 1-4ml at each sampling time point were quenched in 4 volumes of 60% methanol in 10mM ammonium acetate pH 7.5 at -40ºC. After centrifuging for 3min at 14000 rpm and -9ºC, frozen in liquid nitrogen and stored at -80ºC.", "---\n- hot ethanol\n", "---\n- LC-MS\n- GC-TOF\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "(mmol/L) of total cell volume", "diauxic shift, metabolome, S. cerevisiae, intracellular", false, "CHEBI:17234", 2013, nil, "CHEBI:16001, CHEBI:17835, CHEBI:48928, CHEBI:15351, CHEBI:16761 , CHEBI:30915, CHEBI:16977, CHEBI:16027 , CHEBI:16467, CHEBI:17196, CHEBI:22660, CHEBI:15422, CHEBI:16356, CHEBI:30769 + CHEBI:30887, CHEBI:15346, CHEBI:17677, CHEBI:17561, CHEBI:16040, CHEBI:16311, CHEBI:16108, CHEBI:18105, CHEBI:15946, CHEBI:15946 + CHEBI:16077, CHEBI:40595, CHEBI:18012, CHEBI:17665, CHEBI:17138 , CHEBI:17552, CHEBI:18050, CHEBI:16015, CHEBI:15428, CHEBI:5445, CHEBI:14336, CHEBI:16891, CHEBI:17345, CHEBI:15996, CHEBI:15971, CHEBI:15699, CHEBI:422 + CHEBI:42111, CHEBI:17191, CHEBI:15603, CHEBI:18019, CHEBI:30797, CHEBI:15454, CHEBI:18167, CHEBI:16643, CHEBI:15846, CHEBI:16908, CHEBI:18009, CHEBI:16474, CHEBI:18257, CHEBI:30744, CHEBI:44897, CHEBI:58095 , CHEBI:17203, CHEBI:32816, CHEBI:17797, CHEBI:17363, CHEBI:15721, CHEBI:17115, CHEBI:16119, CHEBI:15741, CHEBI:15380, CHEBI:16857, CHEBI:16828, CHEBI:17895, CHEBI:17568, CHEBI:16414", "doi.org/10.34619/387t-p428"] Administrator KiMoSys Data AccessID62 / EntryID62 | 2013 | batch | aerobic | diauxic shift, metabolome, S. cerevisiae, intracellular | CHEBI:16001, CHEBI:17835, CHEBI:48928, CHEBI:15351, CHEBI:16761 , CHEBI:30915, CHEBI:16977, CHEBI:16027 , CHEBI:16467, CHEBI:17196, CHEBI:22660, CHEBI:15422, CHEBI:16356, CHEBI:30769 + CHEBI:30887, CHEBI:15346, CHEBI:17677, CHEBI:17561, CHEBI:16040, CHEBI:16311, CHEBI:16108, CHEBI:18105, CHEBI:15946, CHEBI:15946 + CHEBI:16077, CHEBI:40595, CHEBI:18012, CHEBI:17665, CHEBI:17138 , CHEBI:17552, CHEBI:18050, CHEBI:16015, CHEBI:15428, CHEBI:5445, CHEBI:14336, CHEBI:16891, CHEBI:17345, CHEBI:15996, CHEBI:15971, CHEBI:15699, CHEBI:422 + CHEBI:42111, CHEBI:17191, CHEBI:15603, CHEBI:18019, CHEBI:30797, CHEBI:15454, CHEBI:18167, CHEBI:16643, CHEBI:15846, CHEBI:16908, CHEBI:18009, CHEBI:16474, CHEBI:18257, CHEBI:30744, CHEBI:44897, CHEBI:58095 , CHEBI:17203, CHEBI:32816, CHEBI:17797, CHEBI:17363, CHEBI:15721, CHEBI:17115, CHEBI:16119, CHEBI:15741, CHEBI:15380, CHEBI:16857, CHEBI:16828, CHEBI:17895, CHEBI:17568, CHEBI:16414 |
| 63 | Escherichia coli | NCM 3722 and mutants | time-series data of metabolites | — | |
[yes ]|[more] | [63, "Escherichia coli", "NCM 3722 and mutants", "2", "KIMODATAID63_v0.xlsx", "19690571", "Molecular Systems Biology", "Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.", "Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen and Joshua D Rabinowitz", "Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA and Department of Chemistry, Princeton University, Princeton, NJ, USA", "Yuan_2009.pdf", "application/pdf", 742006, "2014-04-11T17:39:37.583Z", "37.0", "≈ 7.0", "glucose", "batch", "—", nil, nil, true, "", nil, "", "", nil, "filter cultures were prepared by passing 5 ml of exponentially growing liquid batch culture through membrane filters.", "filters were submerged directly into -75 ºC methanol or -20 ºC 40:40:20 acetonitrile:methanol:water with 0.1 % formic acid.", "---\n- methanol\n", "---\n- LC-ESI-MS\n", "--- []\n", "--- []\n", "anaerobic", "--- []\n", "mM", "E. coli, ammonia assimilation, nitrogen upshift", false, "CHEBI:17234", 2009, nil, "ChEBI:16015, ChEBI:18050, ChEBI:16810, ChEBI:30797, ChEBI:22660", "doi.org/10.34619/bspb-ek47"] Administrator KiMoSys Data AccessID63 / EntryID63 [25, 63, "", "Yuan_2009.pdf", nil, "2013-06-12T13:43:10.970Z", "Metabolism", "---\n- Model building\n- Model validation\n", "ordinary differential equations", "19690571", "—", "Nitrogen assimilation model", "Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.", "Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen and Joshua D Rabinowitz", "Molecular Systems Biology", "Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA and Department of Chemistry, Princeton University, Princeton, NJ, USA", "", "", "E. coli, ammonia assimilation, nitrogen upshift, differential equations, sensitivity analysis", "written in C++", "2014-04-11T17:38:32.527Z", "Escherichia coli", 2009, "COMBINE_KIMOMODELID25.omex", "application/omex+xml", 645413, "2014-06-30T17:56:44.644Z", nil, nil] Administrator KiMoSys Model AccessID25 / EntryID25 | 2009 | batch | anaerobic | E. coli, ammonia assimilation, nitrogen upshift | ChEBI:16015, ChEBI:18050, ChEBI:16810, ChEBI:30797, ChEBI:22660 |
| 64 | Escherichia coli | BW25113 and mutants | flux measurements | — | |
[no] | [64, "Escherichia coli", "BW25113 and mutants ", "3", "KIMODATAID64_v0.xlsx", "15838044", "Journal of Bacteriology", "Impact of global transcriptional regulation by arcA, arcB, cra, crp, cya, fnr, and mlc on glucose catabolism in Escherichia coli.", "Annik Perrenoud and Uwe Sauer", "Institute of Biotechnology, ETH, Zurich, Switzerland", "Perrenoud_2005.pdf", "application/pdf", 390295, "2014-04-15T13:57:52.836Z", "37.0", "not specified", "glucose", "batch", "—", nil, nil, true, "", nil, "0.030-0.050", "not specified", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- GC-MS\n", "aerobic", "--- []\n", "(mmol/g.h)", "Escherichia coli, aerobic glucose catabolism", false, "CHEBI:17234", 2005, nil, "R02738, R01528, R10221, R02740, R05605, R01067, R01827, R00200, R01196, R00267, R01082, R00342, R00214, R00341, R00341, R00229, R00105", "doi.org/10.34619/z4tb-zk02"] Administrator KiMoSys Data AccessID64 / EntryID64 | 2005 | batch | aerobic | Escherichia coli, aerobic glucose catabolism | R02738, R01528, R10221, R02740, R05605, R01067, R01827, R00200, R01196, R00267, R01082, R00342, R00214, R00341, R00341, R00229, R00105 |
| 65 | Escherichia coli | MG1655 | flux measurements | — | |
[no] | [65, "Escherichia coli", "MG1655", "3", "KIMODATAID65_v0.xlsx", "16461663", "Applied and Environmental Microbiology", "Nonlinear dependency of intracellular fluxes on growth rate in miniaturized continuous cultures of Escherichia coli.", "Annik Nanchen, Alexander Schicker and Uwe Sauer", "Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland", "Nanchen_2006.pdf", "application/pdf", 453495, "2013-06-12T15:55:08.749Z", "37.0", "7.0", "glucose", "chemostat", "several dilution rates", nil, nil, true, "", nil, "0.010", "0.2-0.5", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- GC-MS\n", "aerobic", "--- []\n", "(mmol/gDW.h)", "Escherichia coli, continuous culture, intracellular fluxes", false, "CHEBI:17234", 2006, nil, "R02738, R01528, R10221, R02740, R05605, R01067, R01827, R00200, R01196, R00267, R01082, R00342, R00214, R00341, R00341, R00229, R00105", "doi.org/10.34619/5n39-r321"] Administrator KiMoSys Data AccessID65 / EntryID65 | 2006 | chemostat | aerobic | Escherichia coli, continuous culture, intracellular fluxes | R02738, R01528, R10221, R02740, R05605, R01067, R01827, R00200, R01196, R00267, R01082, R00342, R00214, R00341, R00341, R00229, R00105 |
| 66 | Shewanella oneidensis | MR-1 | flux measurements | — | |
[no] | [66, "Shewanella oneidensis", "MR-1", "3", "KIMODATAID66_v0.xlsx", "19610125", "Biotechnology Progress", "Invariability of central metabolic flux distribution in Shewanella oneidensis MR-1 under environmental or genetic perturbations.", "Yinjie J. Tang, Hector Garcia Martin, Adam Deutchbauer, Xueyang Feng, Rick Huang, Xavier Llora, Adam Arkin, Jay D. Keasling", "Dept. of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO63130 and Dept. of Chemical Engineering, University of California, Berkeley, CA", nil, nil, nil, nil, "30.0", "7.0", "lactate", "batch", "—", nil, nil, true, "", nil, "0.012", "0.1 - 1.0", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- GC-MS\n", "aerobic", "--- []\n", "% of substrate uptake", "Shewanella oneidensis, 13C-based, secondary metabolism", false, "CHEBI:24996", 2009, nil, "R00196, R00200, R02740, R01528, R00210, R00351, R01324, R00709, R01252, R00402, R01082, R00342, R00227, R01827, R01641, R00214, R00341, R00472", "doi.org/10.34619/1d7d-0664"] Administrator KiMoSys Data AccessID66 / EntryID66 | 2009 | batch | aerobic | Shewanella oneidensis, 13C-based, secondary metabolism | R00196, R00200, R02740, R01528, R00210, R00351, R01324, R00709, R01252, R00402, R01082, R00342, R00227, R01827, R01641, R00214, R00341, R00472 |
| 67 | Escherichia coli | MG1655 | flux measurements | — | |
[no] | [67, "Escherichia coli", "MG1655", "3", "KIMODATAID67_v0.xlsx", "23036703", "Metabolic Engineering", "An integrated computational and experimental study for overproducing fatty acids in Escherichia coli.", "Sridhar Ranganathan, Ting Wei Teeb, Anupam Chowdhuryc, Ali R. Zomorrodic, Jong Moon Yoon, Yanfen Fu, Jacqueline V. Shanksb, Costas D. Maranas", "Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, USA and Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA", "Ranganathan_2012.pdf", "application/pdf", 3485823, "2013-06-20T16:59:55.902Z", "37.0", "7.0", "glucose", "batch", "—", nil, nil, true, "", nil, "0.4", "0.36 (gDW/L) = 1 OD550 ", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- NMR\n", "aerobic", "--- []\n", "% substrate uptake", "Metabolic flux analysis, E. coli, fatty acids overproduction, MG1655", false, "CHEBI:17234", 2012, nil, "R02738, R02739, R01015, R00200, R05605, R01641, R01067, R01827, R00210, R01082, R00342, R00227, R00341, R00214, R00472, R00220, R00253, R00907, R00355", "doi.org/10.34619/7bxr-2h93"] Administrator KiMoSys Data AccessID67 / EntryID67 | 2012 | batch | aerobic | Metabolic flux analysis, E. coli, fatty acids overproduction, MG1655 | R02738, R02739, R01015, R00200, R05605, R01641, R01067, R01827, R00210, R01082, R00342, R00227, R00341, R00214, R00472, R00220, R00253, R00907, R00355 |
| 68 | Escherichia coli | ML103 | flux measurements | — | |
[no] | [68, "Escherichia coli", "ML103", "3", "KIMODATAID68_v1.xlsx", "23036703", "Metabolic Engineering", "An integrated computational and experimental study for overproducing fatty acids in Escherichia coli.", "Sridhar Ranganathan, Ting Wei Teeb, Anupam Chowdhuryc, Ali R. Zomorrodic, Jong Moon Yoon, Yanfen Fu, Jacqueline V. Shanksb, Costas D. Maranas", "Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, USA and Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA", "Ranganathan_2012.pdf", "application/pdf", 3485823, "2013-06-20T17:42:27.578Z", "30.0", "7.0", "glucose", "batch", "—", nil, nil, true, "", nil, "0.4", "0.36 (gDW/L) = 1 OD550", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- NMR\n", "aerobic", "--- []\n", "mmol/gDW.h", "Metabolic flux analysis, E. Coli, fatty acids overproduction, ML103", false, "CHEBI:17234", 2012, nil, "R02738, R02739, R01015, R00200, R05605, R01641, R01067, R01827, R00210, R01082, R00342, R00227, R00341, R00214, R00472, R00220, R00253, R00907, R00355", "doi.org/10.34619/pnrg-2a80"] Administrator KiMoSys Data AccessID68 / EntryID68 | 2012 | batch | aerobic | Metabolic flux analysis, E. Coli, fatty acids overproduction, ML103 | R02738, R02739, R01015, R00200, R05605, R01641, R01067, R01827, R00210, R01082, R00342, R00227, R00341, R00214, R00472, R00220, R00253, R00907, R00355 |
| 69 | Saccharomyces cerevisiae | CEN.PK2-1C (W.T.), HXT1, HXT7 and TM6 | time-series data of metabolites | — | |
[yes ]|[more] | [69, "Saccharomyces cerevisiae", "CEN.PK2-1C (W.T.), HXT1, HXT7 and TM6", "2", "KIMODATAID69_v1.xlsx", "18042231", "FEMS Yeast Research", "Characterization of glucose transport mutants of Saccharomyces cerevisiae during a nutritional upshift reveals a correlation between metabolite levels and glycolytic flux.", "Daniel Bosch, Mikael Johansson, Cecilia Ferndahl, Carl Johan Franzén, Christer Larsson and Lena Gustafsson", "Molecular Biotechnology and Chemical reaction Engineering, Department of Chemical and Biological Engineering, Chalmers University of Technology, Goeteborg, Sweden", "Bosch_2008.pdf", "application/pdf", 426078, "2013-11-21T18:09:15.332Z", "30.0", "5.0", "ethanol", "chemostat", "0.1", nil, nil, true, "", nil, "2.0", "correlation of OD with biomass: 0.486 gDW/L OD", nil, "duplicate samples of 1ml each were steril filtered (0.22 µm), frozen in liquid N2 and stored at \u0002-20 ºC.", "—", "---\n- not used\n", "---\n- enzymatic\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "(mM)", "Saccharomyces cerevisiae, extracellular, metabolites, glucose and fructose pulse", false, "CHEBI:16236", 2008, nil, "ChEBI:17634, ChEBI:16236, ChEBI:17754, ChEBI:15824, ChEBI:16236, ChEBI:17754", "doi.org/10.34619/rt41-rr71"] Administrator KiMoSys Data AccessID69 / EntryID69 [28, 69, "", "Bosch_2008.pdf", nil, "2013-06-27T09:17:15.784Z", "Metabolism", "---\n- Model building\n", "ordinary differential equations", "18042231", "—", "Model for respiro-fermentative growth on glucose", "Characterization of glucose transport mutants of Saccharomyces cerevisiae during a nutritional upshift reveals a correlation between metabolite levels and glycolytic flux.", "Daniel Bosch, Mikael Johansson, Cecilia Ferndahl, Carl Johan Franzén, Christer Larsson and Lena Gustafsson", "FEMS Yeast Research", "Molecular Biotechnology and Chemical reaction Engineering, Department of Chemical and Biological Engineering, Chalmers University of Technology, Goeteborg, Sweden", "", "", "fitting, glucose pulse, Saccharomyce cerevisae, respiro-fermentative growth on glucose,", "http://www.matlab.com (MATLAB)", "2014-04-11T17:42:47.759Z", "Saccharomyces cerevisiae", 2008, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID28 / EntryID28 | 2008 | chemostat | aerobic | Saccharomyces cerevisiae, extracellular, metabolites, glucose and fructose pulse | ChEBI:17634, ChEBI:16236, ChEBI:17754, ChEBI:15824, ChEBI:16236, ChEBI:17754 |
| 70 | Saccharomyces cerevisiae | CEN.PK2-1C (W.T.), HXT1, HXT7 and TM6 | time-series data of metabolites | — | |
[yes ]|[more] | [70, "Saccharomyces cerevisiae", "CEN.PK2-1C (W.T.), HXT1, HXT7 and TM6", "2", "KIMODATAID70_v1.xlsx", "18042231", "FEMS Yeast Research", "Characterization of glucose transport mutants of Saccharomyces cerevisiae during a nutritional upshift reveals a correlation between metabolite levels and glycolytic flux.", "Daniel Bosch, Mikael Johansson, Cecilia Ferndahl, Carl Johan Franzén, Christer Larsson and Lena Gustafsson", "Molecular Biotechnology and Chemical reaction Engineering, Department of Chemical and Biological Engineering, Chalmers University of Technology, Goeteborg, Sweden", "Bosch_2008.pdf", "application/pdf", 426078, "2013-11-21T18:09:41.633Z", "30.0", "5.0", "ethanol", "chemostat", "0.1", nil, nil, true, "", nil, "2.0", "correlation of OD with biomass: 0.486 gDW/L OD", nil, "for all metabolites, except ATP, six samples of 3 mL each", "samples were directly transferred into tubes with 10mL of methanol maintained at -48ºC; the final concentration of methanol (v/v) was about 75%.", "---\n- methanol\n", "---\n- enzymatic\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "(mM)", "Saccharomyces cerevisiae, intracellular, metabolites, glucose and fructose pulse", false, "CHEBI:16236", 2008, nil, "ChEBI:17665, ChEBI:15946, ChEBI:40595, ChEBI:32816, ChEBI:16761, ChEBI:16027, ChEBI:15846, ChEBI:15422", "doi.org/10.34619/3525-sw41"] Administrator KiMoSys Data AccessID70 / EntryID70 [28, 69, "", "Bosch_2008.pdf", nil, "2013-06-27T09:17:15.784Z", "Metabolism", "---\n- Model building\n", "ordinary differential equations", "18042231", "—", "Model for respiro-fermentative growth on glucose", "Characterization of glucose transport mutants of Saccharomyces cerevisiae during a nutritional upshift reveals a correlation between metabolite levels and glycolytic flux.", "Daniel Bosch, Mikael Johansson, Cecilia Ferndahl, Carl Johan Franzén, Christer Larsson and Lena Gustafsson", "FEMS Yeast Research", "Molecular Biotechnology and Chemical reaction Engineering, Department of Chemical and Biological Engineering, Chalmers University of Technology, Goeteborg, Sweden", "", "", "fitting, glucose pulse, Saccharomyce cerevisae, respiro-fermentative growth on glucose,", "http://www.matlab.com (MATLAB)", "2014-04-11T17:42:47.759Z", "Saccharomyces cerevisiae", 2008, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID28 / EntryID28 | 2008 | chemostat | aerobic | Saccharomyces cerevisiae, intracellular, metabolites, glucose and fructose pulse | ChEBI:17665, ChEBI:15946, ChEBI:40595, ChEBI:32816, ChEBI:16761, ChEBI:16027, ChEBI:15846, ChEBI:15422 |
| 71 | Penicillium chrysogenum | DS12975 | time-series data of metabolites | — | |
[no] | [71, "Penicillium chrysogenum", "DS12975", "2", "KIMODATAID71_v0.xlsx", "16807032", "Metabolic Engineering", "Generating short-term kinetic responses of primary metabolism of Penicillium chrysogenum through glucose perturbation in the bioscope mini reactor.", "U. Nasution, W.M. Van Gulik, A. Proell, W.A. van Winden, J.J. Heijnen", "Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, Netherlands", "Nasution_2006.pdf", "application/pdf", 292170, "2013-06-21T17:04:51.029Z", "25.0", "6.5", "glucose", "chemostat", "0.05", nil, nil, true, "", nil, "4.0", "6.21 ± 0.16", nil, " rapid sampling of broth for measurement of intracellular metabolites was carried out at 5, 10, 15, 20, 25, 35, 50, 70 and 90 s after injection of the glucose solution.", "60 w/w % analytical grade methanol (ARCOS, Geel, Belgium) and water purified in a milli-QUFplus system (Millipore, Bedford, MA), buffered with 10 mM HEPES (Merck, Darmstadt, Germany) and adjusted to pH 7.5 with 3M KOA (Baker, Deventer, The Netherlands).", "---\n- hot ethanol\n", "---\n- HPLC-UV/RI\n- LC-ESI-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "(µmol/gDW)", "glucose pulse, in vivo kinetics, metabolome, Penicillium chrysogenum", false, "CHEBI:17234", 2006, nil, "ChEBI: 17634, ChEBI:17665, ChEBI:15946, CHEBI:16077, CHEBI:17835&17794, CHEBI:15741, ChEBI:40595, CHEBI:44897, ChEBI:32816, CHEBI:30769, CHEBI:30915, CHEBI:18012, CHEBI:18167, CHEBI:15422, CHEBI:16761 , CHEBI:16027 ", "doi.org/10.34619/r8qn-5r05"] Administrator KiMoSys Data AccessID71 / EntryID71 | 2006 | chemostat | aerobic | glucose pulse, in vivo kinetics, metabolome, Penicillium chrysogenum | ChEBI: 17634, ChEBI:17665, ChEBI:15946, CHEBI:16077, CHEBI:17835&17794, CHEBI:15741, ChEBI:40595, CHEBI:44897, ChEBI:32816, CHEBI:30769, CHEBI:30915, CHEBI:18012, CHEBI:18167, CHEBI:15422, CHEBI:16761 , CHEBI:16027 |
| 72 | Aspergillus niger | SKANip8 (W.T.) and SKAn1015 | flux measurements | — | |
[no] | [72, "Aspergillus niger", "SKANip8 (W.T.) and SKAn1015", "3", "KIMODATAID72_v0.xlsx", "22115737", "Metabolic Engineering", "Integration of in vivo and in silico metabolic fluxes for improvement of recombinant protein production.", "Habib Driouch, Guido Melzer, Christoph Wittmann", "Institute of Biochemical Engineering, Technische Universitat Braunschweig, Gaussstrasse 17, Braunschweig, Germany", "Driouch_2012.pdf", "application/pdf", 1268569, "2013-06-22T14:35:53.746Z", "37.0", "5.0", "glucose", "batch", "—", nil, nil, true, "", nil, "0.025", "", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- GC-MS\n", "aerobic", "--- []\n", "(mmol/gh)", "Aspergillus niger, 13C metabolic flux, fructofuranosidase", false, "CHEBI:17234", 2012, nil, "R02778, R00299, R02740, R01067, R01819, R01512, R00217, R00341, R00338, R00214, R00351, R01324, R00709, R00265, R02164, R01082, R00342", "doi.org/10.34619/ztch-6j87"] Administrator KiMoSys Data AccessID72 / EntryID72 | 2012 | batch | aerobic | Aspergillus niger, 13C metabolic flux, fructofuranosidase | R02778, R00299, R02740, R01067, R01819, R01512, R00217, R00341, R00338, R00214, R00351, R01324, R00709, R00265, R02164, R01082, R00342 |
| 73 | Aspergillus niger | N402 (W.T.) and icl overexpression | flux measurements | — | |
[no] | [73, "Aspergillus niger", "N402 (W.T.) and icl overexpression", "3", "KIMODATAID73_v0.xlsx", "19271267", "Metabolic Engineering", "Overexpression of isocitrate lyase-glyoxylate bypass influence on metabolism in Aspergillus niger.", "S. Meijer, J Otero, R. Olivares, M.R. Andersen, L. Olsson, J. Nielsen", "Department for Systems Biology, Center for Microbial Biotechnology, Building 223, Technical University of Denmark, Lyngby, Denmark.", "Meijer_2009.pdf", "application/pdf", 793540, "2013-06-23T12:31:56.744Z", "30.0", "2.5", "glucose", "batch", "", nil, nil, true, "", nil, "2.0", "2.0-4.0", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- GC-MS\n", "aerobic", "--- []\n", "% substrate uptake", "Aspergillus niger, isocitrate lyase over-expression, glyoxylate bypass", false, "CHEBI:17234", 2009, nil, "R02778, R00299, R02740, R01067, R01819, R01512, R00217, R00341, R00338, R00214, R00351, R01324, R00709, R00265, R02164, R01082, R00342", "doi.org/10.34619/9pzn-h470"] Administrator KiMoSys Data AccessID73 / EntryID73 | 2009 | batch | aerobic | Aspergillus niger, isocitrate lyase over-expression, glyoxylate bypass | R02778, R00299, R02740, R01067, R01819, R01512, R00217, R00341, R00338, R00214, R00351, R01324, R00709, R00265, R02164, R01082, R00342 |
| 74 | Escherichia coli | K-12 MG1655 | metabolites at steady-state | — | |
[no] | [74, "Escherichia coli", "K-12 MG1655", "1", "KIMODATAID74_v0.xlsx", "20447466", "Metabolic Engineering", "Catching prompt metabolite dynamics in Escherichia coli with the BioScope at oxygen rich conditions.", "Marjan De Mey, Hilal Taymaz-Nikerel, Gino Baart, Hendrik Waegeman, Jo Maertens, Joseph J. Heijnen, Walter M. Van Gulik", "Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium and Department of Biotechnology, Delft University of Technology, Kluyver Center for Genomics of Industrial Fermentation, 2628 BC Delft, The Netherlands", "DeMey_2010.pdf", "application/pdf", 1348974, "2013-06-25T14:31:11.271Z", "37.0", "5.0", "glucose", "chemostat", "0.1", nil, nil, true, "", nil, "4.0", "8.4 (Experiment 1) and 8.02 (Experiment 2)", nil, "1ml of broth rapidly withdrawn from the bioreactor.", "tubes containing 5ml of 60% aqueous methanol, pre-cooled at -40 ºC and immediately mixed after sampling by vortexing.", "---\n- boiling ethanol\n", "---\n- LC-ESI-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "(µmol/gDW)", "Escherichia coli, glucose pulse, BioScope, chemostat", false, "CHEBI:17234", 2010, nil, "CHEBI:17665, CHEBI:15946, CHEBI:43896, CHEBI:16298, CHEBI:48928, CHEBI:40595, CHEBI:17835 + CHEBI:17794, CHEBI:44897, CHEBI:32816, CHEBI:30769, CHEBI:15741, CHEBI:18012, CHEBI:30797, CHEBI:16761 , CHEBI:15422, CHEBI:17552, CHEBI:15996, CHEBI:17297, CHEBI:15713", "doi.org/10.34619/rqz2-xj86"] Administrator KiMoSys Data AccessID74 / EntryID74 | 2010 | chemostat | aerobic | Escherichia coli, glucose pulse, BioScope, chemostat | CHEBI:17665, CHEBI:15946, CHEBI:43896, CHEBI:16298, CHEBI:48928, CHEBI:40595, CHEBI:17835 + CHEBI:17794, CHEBI:44897, CHEBI:32816, CHEBI:30769, CHEBI:15741, CHEBI:18012, CHEBI:30797, CHEBI:16761 , CHEBI:15422, CHEBI:17552, CHEBI:15996, CHEBI:17297, CHEBI:15713 |
| 75 | Escherichia coli | K-12 MG1655 | time-series data of metabolites | — | |
[no] | [75, "Escherichia coli", "K-12 MG1655", "2", "KIMODATAID75_v1.xlsx", "23370343", "Metabolic Engineering", "Changes in substrate availability in Escherichia coli lead to rapid metabolite, flux and growth rate responses.", "Hilal Taymaz-Nikerel, Marjan De Mey, Gino Baart, Jo Maertens, Joseph J. Heijnen, Walter M. Van Gulik", "Department of Biotechnoloy, Delft University of Technology, Kluyver Center for Genomics of Industrial Fermentation Julianalaan 67, 2628 BC Delft, The Netherlands", "Nikerel_2013.pdf", "application/pdf", 2224811, "2013-06-25T15:06:47.746Z", "37.0", "7.0", "glucose", "chemostat", "0.1", nil, nil, true, "", nil, "4.0", "8.36 (Experiment 1) and 8.02 (Experiment 2)", nil, "differential method", "not specified", "---\n- boiling ethanol\n", "---\n- enzymatic\n- GC-MS\n- LC-MS\n- HPLC-UV/RI\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "(µmol/gDW)", "Escherichia coli, intracellular metabolites, stimulus response", false, "CHEBI:17234", 2013, nil, "CHEBI:17665, CHEBI:15946, CHEBI:43896, CHEBI:48928, CHEBI:16298, CHEBI:17794, CHEBI:40595, CHEBI:28602, CHEBI:17835 + CHEBI:17794, CHEBI:44897, CHEBI:32816, CHEBI:30769, CHEBI:30915, CHEBI:15741, CHEBI:18012, CHEBI:30797, CHEBI:16977, CHEBI:17196, CHEBI:22660, CHEBI:17561, CHEBI:16015, CHEBI:18050, CHEBI:15428, CHEBI:27570, CHEBI:17191, CHEBI:15603, CHEBI:18019, CHEBI:16643, CHEBI:58095 , CHEBI:17203, CHEBI:17115, CHEBI:16857, CHEBI:16828, CHEBI:17895, CHEBI:16414, CHEBI:18257, CHEBI:15422, CHEBI:16761 , CHEBI:16027 ", "doi.org/10.34619/3y5p-9947"] Administrator KiMoSys Data AccessID75 / EntryID75 | 2013 | chemostat | aerobic | Escherichia coli, intracellular metabolites, stimulus response | CHEBI:17665, CHEBI:15946, CHEBI:43896, CHEBI:48928, CHEBI:16298, CHEBI:17794, CHEBI:40595, CHEBI:28602, CHEBI:17835 + CHEBI:17794, CHEBI:44897, CHEBI:32816, CHEBI:30769, CHEBI:30915, CHEBI:15741, CHEBI:18012, CHEBI:30797, CHEBI:16977, CHEBI:17196, CHEBI:22660, CHEBI:17561, CHEBI:16015, CHEBI:18050, CHEBI:15428, CHEBI:27570, CHEBI:17191, CHEBI:15603, CHEBI:18019, CHEBI:16643, CHEBI:58095 , CHEBI:17203, CHEBI:17115, CHEBI:16857, CHEBI:16828, CHEBI:17895, CHEBI:16414, CHEBI:18257, CHEBI:15422, CHEBI:16761 , CHEBI:16027 |
| 76 | Streptomyces coelicolor | M145 (W.T.) and phoP mutant (INB201) | time-series data of metabolites | — | |
[no] | [76, "Streptomyces coelicolor", "M145 (W.T.) and phoP mutant (INB201)", "2", "KIMODATAID76_v0.xlsx", "", "Metabolites", "Intracellular metabolite pool changes in response to nutrient depletion induced metabolic switching in Streptomyces coelicolor.", "Alexander Wentzel, Harvard Sletta, Stream Consortium, Trond E. Ellingsen and Per Bruheim", "Department of Biotechnology, SINTEF Materials and Chemistry, Sem Saelandsvei 2a, N-7465 Trondheim, Norway and Department of Biotechnology, Norwegian University of Science and Technology, Sem Saelandsvei 6/8, N-7491 Trondheim, Norway ", "Wentzel_2012.pdf", "application/pdf", 1290587, "2013-06-28T14:43:07.538Z", "30.0", "not specified", "glucose", "batch", "—", nil, nil, true, "", nil, "1.8", "see worksheets", nil, " Samples for metabolite profiling were withdrawn from the cultivations in 1–2 h time intervals.", "Quenching procedure: 5 mL culture sample was withdrawn from the fermentation vessel and immediately applied to a 0.8 μm Supor 800 filter (Pall). On the filter disc, the cells were subsequently washed twice with one volume 2.63% (w/v) NaCl solution each. ", "---\n- methanol\n", "---\n- GC-MS\n- LC-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "µM", "Streptomyces coelicolor, transition phase, metabolic switching metabolite profiling", false, "CHEBI:17234", 2012, nil, "CHEBI:15422, CHEBI:17677, CHEBI:15996, CHEBI:63550, CHEBI:15713, CHEBI:16761 , CHEBI:17239, CHEBI:17552, CHEBI:17297, CHEBI:16027 , CHEBI:16356, CHEBI:17345, CHEBI:16695, CHEBI:15846, CHEBI:18009, CHEBI:48928, CHEBI:17797, CHEBI:40595, CHEBI:16298, CHEBI:16108, CHEBI:17138 , CHEBI:17050, CHEBI:44897", "doi.org/10.34619/dbzd-fs68"] Administrator KiMoSys Data AccessID76 / EntryID76 | 2012 | batch | aerobic | Streptomyces coelicolor, transition phase, metabolic switching metabolite profiling | CHEBI:15422, CHEBI:17677, CHEBI:15996, CHEBI:63550, CHEBI:15713, CHEBI:16761 , CHEBI:17239, CHEBI:17552, CHEBI:17297, CHEBI:16027 , CHEBI:16356, CHEBI:17345, CHEBI:16695, CHEBI:15846, CHEBI:18009, CHEBI:48928, CHEBI:17797, CHEBI:40595, CHEBI:16298, CHEBI:16108, CHEBI:17138 , CHEBI:17050, CHEBI:44897 |
| 77 | Shewanella oneidensis | MR-1 (ATCC 70050) | time-series data of metabolites | — | |
[yes ]|[more] | [77, "Shewanella oneidensis", "MR-1 (ATCC 70050)", "2", "KIMODATAID77_v0.xlsx", "22319437", "PLOS Computational Biology", "Integrating flux balance analysis into kinetic models to decipher the dynamic metabolism of Shewanella oneidensis.", "Xueyang Feng, You Xu, Yixin Chen, Yinjie J. Tang", "Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, Missouri, United States of America", "Feng_2012.pdf", "application/pdf", 1271214, "2013-07-03T16:40:55.695Z", "30.0", "not specified", "lactate", "batch", "—", nil, nil, true, "", nil, "0.1", "≈ 0.3 - 0.5", nil, "manually at different time", "—", "---\n- not used\n", "---\n- enzymatic\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "(g/L) and (mM)", "Shewanella oneidensis, dynamic metabolism, extracellular", false, "CHEBI:24996", 2012, nil, "CHEBI:28358, CHEBI:15366, CHEBI:32816", "doi.org/10.34619/nqsj-kh55"] Administrator KiMoSys Data AccessID77 / EntryID77 [30, 77, "", "Feng_2012.pdf", nil, "2013-07-03T16:54:30.800Z", "Metabolism", "---\n- Model building\n- Model validation\n", "ordinary differential equations", "22319437", "—", "Kinetic model of Shewanella oneidensis MR-1 ", "Integrating flux balance analysis into kinetic models to decipher the dynamic metabolism of Shewanella oneidensis MR-1.", "Xueyang Feng, You Xu, Yixin Chen, Yinjie J. Tang", "PLOS Computational Biology", "", "", "", "DFBA, kinetic model", "http://www.matlab.com (MATLAB)", "2014-04-11T17:54:44.161Z", "Shewanella oneidensis", 2012, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID30 / EntryID30 | 2012 | batch | aerobic | Shewanella oneidensis, dynamic metabolism, extracellular | CHEBI:28358, CHEBI:15366, CHEBI:32816 |
| 78 | Escherichia coli | K-12 overproduce 1,3-propanediol | time-series data of metabolites | — | |
[no] | [78, "Escherichia coli", "K-12 overproduce 1,3-propanediol", "2", "KIMODATAID78_v0.xlsx", "17400499", "Metabolic Engineering", "Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol.", "Maciek R. Antoniewicz, David F. Kraynie, Lisa A. Laffend, Joanna González-Lergier, Joanne K. Kelleher and Gregory Stephanopoulos", "Department of Chemical Engineering, Bioinformatics and Metabolic Engineering Laboratory, Massachusetts Institute of Technology, Cambridge", "Antoniewicz_2007.pdf", "application/pdf", 1081894, "2013-07-05T14:28:29.382Z", "34.0", "6.8 ± 0.04", "glucose", "fed-batch", "—", nil, nil, true, "", nil, "1.0", "3.0 ", nil, "Periodically taken during the fed-batch ", "—", "---\n- not used\n", "---\n- HPLC-UV/RI\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "mM", "E. coli, extracelullar metabolites, HPLC", false, "CHEBI:17234", 2007, nil, "CHEBI:17634, CHEBI:17754, CHEBI:15366, CHEBI:16109, CHEBI:30769", "doi.org/10.34619/2j9t-rp92"] Administrator KiMoSys Data AccessID78 / EntryID78 | 2007 | fed-batch | aerobic | E. coli, extracelullar metabolites, HPLC | CHEBI:17634, CHEBI:17754, CHEBI:15366, CHEBI:16109, CHEBI:30769 |
| 79 | Escherichia coli | BW25113 and arcA mutant | metabolites at steady-state | — | |
[no] | [79, "Escherichia coli", "BW25113 and arcA mutant", "1", "KIMODATAID79_v0.xlsx", "22790675", "Molecular BioSystems", "Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data.", "Yoshihiro Toya, Kenji Nakahigashi, Masaru Tomita and Kazuyuki Shimizu", "Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan", nil, nil, nil, nil, "37.0", "7.0", "glucose", "chemostat", "0.2", nil, nil, true, "", nil, "1.0", "", nil, "5 mg of cells were passed through a 0.45 mm pore filter (Millipore) filled with saline.", "filter washed twice with 10 mL of Milli-Q water and quickly plunged into 5 mL of methanol containing 2 mM CSA and methionine sulfone as internal standards within 1 min.", "---\n- chloroform\n- sonication\n", "---\n- CE-TOF-MS\n", "--- []\n", "--- []\n", "aerobic and anaerobic", "--- []\n", "(µM)", "Escherichia coli, intracelullar metabolites", false, "CHEBI:17234", 2012, nil, "CHEBI:17665, CHEBI:15946, CHEBI:40595, CHEBI:16108, CHEBI:17794, CHEBI:44897, CHEBI:48928, CHEBI:17363, CHEBI:17797, CHEBI:15721, CHEBI:15351, CHEBI:30769, CHEBI:18012, CHEBI:15741, CHEBI:30797, CHEBI:16027 , CHEBI:16761 , CHEBI:15422, CHEBI:15428, CHEBI:16977, CHEBI:17115, CHEBI:17203, CHEBI:16414, CHEBI:16857, CHEBI:17191, CHEBI:15603, CHEBI:17196, CHEBI:22660, CHEBI:18050, CHEBI:18019, CHEBI:16015, CHEBI:16643, CHEBI:15971, CHEBI:58095 , CHEBI:16467, CHEBI:17895, CHEBI:15946, CHEBI:40595, CHEBI:16108, CHEBI:17794, CHEBI:44897, CHEBI:48928, CHEBI:17363, CHEBI:17797, CHEBI:15721, CHEBI:15351, CHEBI:30769, CHEBI:18012, CHEBI:15741, CHEBI:30797, CHEBI:16027 , CHEBI:16761 , CHEBI:15422, CHEBI:15428, CHEBI:16977, CHEBI:17115, CHEBI:17203, CHEBI:16414, CHEBI:16857, CHEBI:17191, CHEBI:15603, CHEBI:17196, CHEBI:22660, CHEBI:18050, CHEBI:18019, CHEBI:16015, CHEBI:16643, CHEBI:15971, CHEBI:58095 , CHEBI:16467, CHEBI:17895", "doi.org/10.34619/jacx-ww91"] Administrator KiMoSys Data AccessID79 / EntryID79 | 2012 | chemostat | aerobic and anaerobic | Escherichia coli, intracelullar metabolites | CHEBI:17665, CHEBI:15946, CHEBI:40595, CHEBI:16108, CHEBI:17794, CHEBI:44897, CHEBI:48928, CHEBI:17363, CHEBI:17797, CHEBI:15721, CHEBI:15351, CHEBI:30769, CHEBI:18012, CHEBI:15741, CHEBI:30797, CHEBI:16027 , CHEBI:16761 , CHEBI:15422, CHEBI:15428, CHEBI:16977, CHEBI:17115, CHEBI:17203, CHEBI:16414, CHEBI:16857, CHEBI:17191, CHEBI:15603, CHEBI:17196, CHEBI:22660, CHEBI:18050, CHEBI:18019, CHEBI:16015, CHEBI:16643, CHEBI:15971, CHEBI:58095 , CHEBI:16467, CHEBI:17895, CHEBI:15946, CHEBI:40595, CHEBI:16108, CHEBI:17794, CHEBI:44897, CHEBI:48928, CHEBI:17363, CHEBI:17797, CHEBI:15721, CHEBI:15351, CHEBI:30769, CHEBI:18012, CHEBI:15741, CHEBI:30797, CHEBI:16027 , CHEBI:16761 , CHEBI:15422, CHEBI:15428, CHEBI:16977, CHEBI:17115, CHEBI:17203, CHEBI:16414, CHEBI:16857, CHEBI:17191, CHEBI:15603, CHEBI:17196, CHEBI:22660, CHEBI:18050, CHEBI:18019, CHEBI:16015, CHEBI:16643, CHEBI:15971, CHEBI:58095 , CHEBI:16467, CHEBI:17895 |
| 80 | Escherichia coli | BW25113 and arcA mutant | flux measurements | — | |
[no] | [80, "Escherichia coli", "BW25113 and arcA mutant", "3", "KIMODATAID80_v0.xlsx", "22790675", "Molecular BioSystems", "Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data.", "Yoshihiro Toya, Kenji Nakahigashi, Masaru Tomita and Kazuyuki Shimizu", "Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan", nil, nil, nil, nil, "37.0", "7.0", "glucose", "chemostat", "0.2", nil, nil, true, "", nil, "1.0", "", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- MALDI-TOF\n", "aerobic and anaerobic", "--- []\n", "(mmol/gDW.h)", "Escherichia coli, metabolic flux distributions", false, "CHEBI:17234", 2012, nil, "R02738, R02740, R09084, R01070, R01015, R01061, R00200, R00210, R00212, R00703, R00341, R01528, R01529, R01056, R01641, R01827, R01067, R00351, R01324, R00267, R00272, R00408, R01082, R00342, R00479, R00472, R01064, R00227", "doi.org/10.34619/xabb-1845"] Administrator KiMoSys Data AccessID80 / EntryID80 | 2012 | chemostat | aerobic and anaerobic | Escherichia coli, metabolic flux distributions | R02738, R02740, R09084, R01070, R01015, R01061, R00200, R00210, R00212, R00703, R00341, R01528, R01529, R01056, R01641, R01827, R01067, R00351, R01324, R00267, R00272, R00408, R01082, R00342, R00479, R00472, R01064, R00227 |
| 81 | Mus musculus | E13.5 Balb/c | enzyme/protein concentrations | — | |
[yes ]|[more] | [81, "Mus musculus", "E13.5 Balb/c", "4", "KIMODATAID81_v0.xlsx", "21772264", "Molecular Systems Biology", "Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range.", "Julie Bachmann, Andreas Raue, Marcel Schilling, Martin E. Boehm, Clemens Kreutz, Daniel Kaschek, Hauke Busch, Norbert Gretz, Wolf D. Lehmann, Jens Timmer and Ursula Klingmueller", "Division of Systems Biology of Signal Transduction, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany", "Bachmann_2011.pdf", "application/pdf", 1464156, "2014-04-23T17:40:13.098Z", "37.0", "not specified", "", "batch", "—", nil, nil, true, "", nil, "", "4.0×10^7 (cells/L)", nil, "", "", "--- []\n", "--- []\n", "--- []\n", "--- []\n", "", "---\n- immunoblotting\n", "(a.u.)", "apoptosis, erythropoietin, mathematical modeling, negative feedback, SOCS, simulation and data analysis, signal transduction", false, "", 2011, nil, "", "doi.org/10.34619/q4zs-y049"] Administrator KiMoSys Data AccessID81 / EntryID81 [31, nil, "", "Bachmann_2011.pdf", nil, "2014-04-23T17:30:03.354Z", "Signal", "---\n- Model building\n", "ordinary differential equations", "21772264", "", "transcriptional model of JAK2/STAT5 signaling", "Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range.", "Julie Bachmann, Andreas Raue, Marcel Schilling, Martin E. Boehm, Clemens Kreutz, Daniel Kaschek, Hauke Busch, Norbert Gretz, Wolf D. Lehmann, Jens Timmer and Ursula Klingmueller", "Molecular Systems Biology", "Division of Systems Biology of Signal Transduction, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany", "", "", "apoptosis, erythropoietin, mathematical modeling, negative feedback, SOCS, simulation and data analysis, signal transduction", "http://www.matlab.com (MATLAB)", nil, "Mouse", 2011, "COMBINE_KIMOMODELID31.omex", "application/omex+xml", 1445888, "2014-06-30T17:59:26.698Z", nil, nil] Administrator KiMoSys Model AccessID31 / EntryID31 | 2011 | batch | apoptosis, erythropoietin, mathematical modeling, negative feedback, SOCS, simulation and data analysis, signal transduction | ||
| 82 | Homo sapiens | colorectal cancer cell lines SW480, SW403, HCT116, RKO, LIM1215 and HT29 | enzyme/protein concentrations | — | |
[no] | [82, "Homo sapiens", "colorectal cancer cell lines SW480, SW403, HCT116, RKO, LIM1215 and HT29", "4", "KIMODATAID82_v0.xlsx", "23752269", "Molecular Systems Biology", "Network quantification of EGFR signaling unveils potential for targeted combination therapy.", "Bertram Klinger, Anja Sieber, Raphaela Fritsche-Guenther, Franziska Witzel, Leanne Berry, Dirk Schumacher, Yibing Yan, Pawel Durek1, Mark Merchant, Reinhold Schaefer, Christine Sers and Nils Bluethgen", "Laboratory of Molecular Tumour Pathology, Institute of Pathology, Charité - Universitatsmedizin Berlin, Berlin, Germany, and Institute for Theoretical Biology, Humboldt University Berlin, Berlin, Germany", "Klinger_2013.pdf", "application/pdf", 402404, "2014-04-23T17:56:27.559Z", "37.0", "not specified", "", "batch", "—", nil, nil, true, "", nil, "", "", nil, "", "", "--- []\n", "--- []\n", "--- []\n", "--- []\n", "aerobic", "---\n- immunoblotting\n", "(a.u.)", "cancer, EGFR signaling, modular response analysis, signal transduction", false, "", 2013, nil, "", "doi.org/10.34619/xcp1-mq63"] Administrator KiMoSys Data AccessID82 / EntryID82 | 2013 | batch | aerobic | cancer, EGFR signaling, modular response analysis, signal transduction | |
| 86 | Escherichia coli | K-12 MG1655 | flux measurements | — | |
[no] | [86, "Escherichia coli", "K-12 MG1655", "3", "KIMODATAID86_v2.xlsx", "25102204", "Analytical Biochemistry", "Sampling of intracellular metabolites for stationary and non-stationary 13C metabolic flux analysis in Escherichia coli", "Pierre Millard, Stéphane Massou, Christoph wittmann, Jean-Charles Portais, Fabien Létisse", "Université de Toulouse, INSA, UPS, INP, LISBP, F-31077 Toulouse, France; INRA, UMR 792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR 5504, F-31400 Toulouse, France", "Millard_2014.pdf", "application/pdf", 1574738, "2015-04-20T14:43:51.613Z", "37.0", "7.0", "glucose", "batch", "—", nil, nil, true, "", nil, "0.150", "", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- NMR\n- GC-MS\n- LC-MS\n", "aerobic", "--- []\n", "% substrate uptake", "(13)C-labeling experiments, Isotopes, Isotopologue, Mass isotopomer, Metabolism, Sampling procedures", false, "17234", 2014, nil, "R01786, R02738, R04779, R01070, R01015, R00658, R00200, R00209, R00835 , R01528, R05605, R00341, R00351, R00342, R00227, R01786, R02740, R04779, R01070, R01015, R01061, R01512, R01518, R00658, R00835 , R00835 , R01528, R01529, R01056, R02036, R05605", "doi.org/10.34619/5ayx-q773"] Administrator KiMoSys Data AccessID86 / EntryID86 | 2014 | batch | aerobic | (13)C-labeling experiments, Isotopes, Isotopologue, Mass isotopomer, Metabolism, Sampling procedures | R01786, R02738, R04779, R01070, R01015, R00658, R00200, R00209, R00835 , R01528, R05605, R00341, R00351, R00342, R00227, R01786, R02740, R04779, R01070, R01015, R01061, R01512, R01518, R00658, R00835 , R00835 , R01528, R01529, R01056, R02036, R05605 |
| 87 | Escherichia coli | K-12 MG1655 | metabolites at steady-state | — | |
[no] | [87, "Escherichia coli", "K-12 MG1655", "1", "KIMODATAID87_v0.xlsx", "25102204", "Analytical Biochemistry", "Sampling of intracellular metabolites for stationary and non-stationary 13C metabolic flux analysis in Escherichia coli", "Pierre Millard, Stéphane Massou, Christoph wittmann, Jean-Charles Portais, Fabien Létisse", "Université de Toulouse, INSA, UPS, INP, LISBP, F-31077 Toulouse, France; INRA, UMR 792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR 5504, F-31400 Toulouse, France", "Millard_2014.pdf", "application/pdf", 1574738, "2015-05-01T11:55:03.047Z", "37.0", "7.0", "glucose", "batch", "—", nil, nil, true, "", nil, "0.150", "—", nil, "different methods (see Figure 1).", "different methods (see Figure 1).", "---\n- hot ethanol\n", "---\n- NMR\n- GC-MS\n- LC-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "mM", "Quantitative metabolomics, Metabolism, Sampling procedures", false, "17234", 2014, nil, "CHEBI:17665, CHEBI:15946, CHEBI:40595, ChEBI:14336, CHEBI:16108, CHEBI:19324, CHEBI:17794, CHEBI:17835, CHEBI:44897, CHEBI:48928, CHEBI:17797, CHEBI:17363, CHEBI:16332, CHEBI:15721, CHEBI:48153", "doi.org/10.34619/kbcj-8q13"] Administrator KiMoSys Data AccessID87 / EntryID87 | 2014 | batch | aerobic | Quantitative metabolomics, Metabolism, Sampling procedures | CHEBI:17665, CHEBI:15946, CHEBI:40595, ChEBI:14336, CHEBI:16108, CHEBI:19324, CHEBI:17794, CHEBI:17835, CHEBI:44897, CHEBI:48928, CHEBI:17797, CHEBI:17363, CHEBI:16332, CHEBI:15721, CHEBI:48153 |
| 88 | Bacillus subtilis | BSB168 | metabolites at steady-state | — | |
[no] | [88, "Bacillus subtilis", "BSB168", "1", "KIMODATAID88_v3.xlsx", "24281055", "Molecular Systems Biology", "Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis", "Victor Chubukov, Markus Uhr, Ludovic Le Chat, Roelco J Kleijn, Matthieu Jules, Hannes Link, Stephane Aymerich, Joerg Stelling and Uwe Sauer", "Institute of Molecular System Biology, ETH Zurich, Zurich, Switzerland.", "Chubukov_2013.pdf", "application/pdf", 559480, "2015-05-05T16:47:23.880Z", "37.0", "—", "glucose, fructose, gluconate, succinate+glutamate, glycerol, malate, malate, malate+glucose, pyruvate", "batch", "—", nil, nil, true, "", nil, "0.03", "3.0 g cells/OD600", nil, "Sampling method: Two samples for intracellular metabolite quantification were taken within 5 min of each other from the shake flask cultures during exponential growth at an OD600 between 0.8 and 1.2.", "—", "---\n- hot ethanol\n", "---\n- HPLC-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "mMol/L cell volume", "central carbon metabolism, metabolic flux, transcriptional regulation", false, "", 2013, nil, "ChEBI:29016, ChEBI:22653, ChEBI:28300, ChEBI:36233, ChEBI:18186, ChEBI:16708, ChEBI:28044, ChEBI:29990, ChEBI:29986, ChEBI:17665, ChEBI:78679, ChEBI:15978, ChEBI:29027, ChEBI:27354, ChEBI:35425, ChEBI:74948, ChEBI:16454, ChEBI:16027, ChEBI:30779, ChEBI:6650, ChEBI:37154, ChEBI:16863, ChEBI:17552, CHEBI:16761, ChEBI:44897, ChEBI:40595, ChEBI:35804, ChEBI:30887, ChEBI:15996, CHEBI:15422", "doi.org/10.34619/vmff-m240"] Administrator KiMoSys Data AccessID88 / EntryID88 | 2013 | batch | aerobic | central carbon metabolism, metabolic flux, transcriptional regulation | ChEBI:29016, ChEBI:22653, ChEBI:28300, ChEBI:36233, ChEBI:18186, ChEBI:16708, ChEBI:28044, ChEBI:29990, ChEBI:29986, ChEBI:17665, ChEBI:78679, ChEBI:15978, ChEBI:29027, ChEBI:27354, ChEBI:35425, ChEBI:74948, ChEBI:16454, ChEBI:16027, ChEBI:30779, ChEBI:6650, ChEBI:37154, ChEBI:16863, ChEBI:17552, CHEBI:16761, ChEBI:44897, ChEBI:40595, ChEBI:35804, ChEBI:30887, ChEBI:15996, CHEBI:15422 |
| 89 | Bacillus subtilis | BSB168 | flux measurements | — | |
[no] | [89, "Bacillus subtilis", "BSB168", "3", "KIMODATAID89_v0.xlsx", "24281055", "Molecular Systems Biology", "Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis.", "Victor Chubukov, Markus Uhr, Ludovic Le Chat, Roelco J Kleijn, Matthieu Jules, Hannes Link, Stephane Aymerich, Joerg Stelling and Uwe Sauer", "Institute of Molecular System Biology, ETH Zurich, Zurich, Switzerland.", "Chubukov_2013.pdf", "application/pdf", 559480, "2015-05-12T15:24:47.143Z", "37.0", "—", "glucose, fructose, gluconate, succinate+glutamate, glycerol, malate, malate, malate+glucose, pyruvate", "batch", "—", nil, nil, true, "", nil, "0.03", "3.0 g cells/OD600", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- GC-MS\n", "aerobic", "--- []\n", "mmol/g/h", "central carbon metabolism, metabolic flux, transcriptional regulation", false, "", 2013, nil, "R00771, R04779, R00762 , R01068, R01015 , R01061 , R01061 , R00200, R02736, R01528, R01529 , R01056 , R01641, R01067, R01827, R00210, R00267, R00342, R00341, R00344", "doi.org/10.34619/8qsg-rd27"] Administrator KiMoSys Data AccessID89 / EntryID89 | 2013 | batch | aerobic | central carbon metabolism, metabolic flux, transcriptional regulation | R00771, R04779, R00762 , R01068, R01015 , R01061 , R01061 , R00200, R02736, R01528, R01529 , R01056 , R01641, R01067, R01827, R00210, R00267, R00342, R00341, R00344 |
| 90 | Thermus thermophilus | HB8 (ATCC 27634) | flux measurements | — | |
[no] | [90, "Thermus thermophilus", "HB8 (ATCC 27634)", "3", "KIMODATAID90_v0.xlsx", "24909362", "Metabolic Engineering", "Metabolic network reconstruction, growth characterization and 13C-metabolic flux analysis of the extremophile Thermus thermophilus HB8", "Aditi Swarup, Jimg Lu, Kathleen C. DeWoody, Maciek R. Antoniewicz", "Department of Chemical & Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark DE 19716, USA", "Swarup_2014.pdf", "application/pdf", 1039072, "2015-09-22T12:48:07.141Z", "70", "7.9", "glucose", "batch", "—", nil, nil, true, "", nil, "0.01", "0.39 (g/L)/OD600 cell dry weight and 25.3 g/C-mol for the molecular weight of dry biomass", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- GC-MS\n", "aerobic", "--- []\n", "% substrate uptake", "Extremophile, Thermophilic bacterium, Optimal growth, Metabolic network model, Isotopic labeling", false, "17234", 2014, nil, "R01786, R02740, R04779, R01070, R01015, R01061, R01512, R01518, R00658, R00200, R00209, R00351, R01324, R00267, R08549, R00405, R00402, R01082, R00342, R02736, R02035, R01528, R01529, R01056, R01641, R01827, R01830, R02036, R05605, R00341, R00214, R00479, R00472", "doi.org/10.34619/j1n4-cs29"] Administrator KiMoSys Data AccessID90 / EntryID90 | 2014 | batch | aerobic | Extremophile, Thermophilic bacterium, Optimal growth, Metabolic network model, Isotopic labeling | R01786, R02740, R04779, R01070, R01015, R01061, R01512, R01518, R00658, R00200, R00209, R00351, R01324, R00267, R08549, R00405, R00402, R01082, R00342, R02736, R02035, R01528, R01529, R01056, R01641, R01827, R01830, R02036, R05605, R00341, R00214, R00479, R00472 |
| 91 | Rattus | C57BLKS/J-m+/+db and mutants | metabolites at steady-state | — | |
[no] | [91, "Rattus", "C57BLKS/J-m+/+db and mutants", "1", "KIMODATAID91_v2.xlsx", "", "Molecular brain", "Metabonomic profiles delineate potential role of glutamate-glutamine cycle in db/db mice with diabetes-associated cognitive decline", "Yongquan Zheng, Yunjun Yang, Baijun Dong, Hong Zheng, Xiaodong Lin, Du Yao, Xiaokun Li, Liangcai Zhao, Hongchang Gao", "Radiology Department of the First Affiliated Hospital, Wenzhou Medical University;School of Pharmaceutical Sciences, Wenzhou Medical University, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine.", "Zheng_2016.pdf", "application/pdf", 3790994, "2016-04-26T15:38:14.037Z", "25", "7", "glucose", "batch", "", nil, nil, true, "", nil, "0.0005", "", nil, " The mice were sacrificed by decapitation at 17-wk of age, and specimens of hippocampus were collected manually.", "specimens of hippocampus were dissected immediately, snap-frozen in liquid nitrogen and stored at -80 °C until use.", "---\n- chloroform\n", "---\n- NMR\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "unitless", "Diabetes-associated cognition decline, Nuclear magnetic resonance, Metabonomics, Glutamate-glutamine cycle", false, "17234", 2016, nil, "CHEBI:15428, CHEBI:17268, CHEBI:15891, CHEBI:15354, CHEBI:16919, CHEBI:29993, CHEBI:30769, CHEBI:28300, CHEBI:15741, CHEBI:29985, CHEBI:32816, CHEBI:16865, CHEBI:21547, CHEBI:16449, CHEBI:24996", "doi.org/10.34619/vacj-fn92"] Administrator KiMoSys Data AccessID91 / EntryID91 | 2016 | batch | aerobic | Diabetes-associated cognition decline, Nuclear magnetic resonance, Metabonomics, Glutamate-glutamine cycle | CHEBI:15428, CHEBI:17268, CHEBI:15891, CHEBI:15354, CHEBI:16919, CHEBI:29993, CHEBI:30769, CHEBI:28300, CHEBI:15741, CHEBI:29985, CHEBI:32816, CHEBI:16865, CHEBI:21547, CHEBI:16449, CHEBI:24996 |
| 92 | Escherichia coli | WT K-12 strain NCM3722 of E. coli | metabolites at steady-state | — | |
[no] | [92, "Escherichia coli", "WT K-12 strain NCM3722 of E. coli", "1", "KIMODATAID92_v2.xlsx", "19561621", "Nature Chemical Biology", "Absolute Metabolite Concentrations and Implied Enzyme Active Site Occupancy in Escherichia coli.", "Bryson D Bennett, Elizabeth H Kimball, Melissa Gao, Robin Osterhout, Stephen J Van Dien, and Joshua D Rabinowitz", "Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton", nil, nil, nil, nil, "37", "not specified", "glucose, glycerol, acetate", "batch", "-", nil, nil, true, "", nil, "0.05", "Cultures were grown to OD650 of 0.35.", nil, "This liquid culture was grown to OD650~0.1, at which time it was transferred to filter culture as follows:for each filter culture, 5 mL of liquid culture was passed through an 82 mm diameter round nylon filter and the placed cell-side up onto a plate.", "Cells were filter (0.45-µm), washed with 10 mL of Milli-Q water and plunged into 1 mL of methanol containing 10µL of 0.56 mM PIPES.", "---\n- acidic acetonitrile-methanol\n", "---\n- NMR\n- LC-ESI-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "mM", "", false, "", 2009, nil, "ChEBI:15422, ChEBI:13389, ChEBI:16908, ChEBI:16474, ChEBI:25523, ChEBI:16761, ChEBI:15351, ChEBI:17297, ChEBI:16238, ChEBI:18405, ChEBI:15414, ChEBI:16027, ChEBI:16680, ChEBI:15361, ChEBI:15351, ChEBI:29985, ChEBI:30916, ChEBI:18066, ChEBI:17552, ChEBI:15428, ChEBI:16977, ChEBI:26806, ChEBI:16264, ChEBI:15996, ChEBI:18019, ChEBI:29991, ChEBI:16856, ChEBI:20878, ChEBI:17621, ChEBI:16467, ChEBI:17677, ChEBI:18050, ChEBI:17115, ChEBI:16643, ChEBI:18021, ChEBI:15713, ChEBI:15729, ChEBI:16828, ChEBI:17295, ChEBI:16039, ChEBI:17895, ChEBI:15531, ChEBI:61553, ChEBI:15380, ChEBI:16809, ChEBI:15978, ChEBI:17561, ChEBI:16958, ChEBI:26296, ChEBI:16218, ChEBI:17808, ChEBI:16567, ChEBI:57642, ChEBI:17239, ChEBI:78679, ChEBI:29052, ChEBI:68689, ChEBI:37154, ChEBI:15603, ChEBI:12936, ChEBI:17858, ChEBI:62303, ChEBI:17202, ChEBI:16284 , ChEBI:17148, ChEBI:15971, ChEBI:17268, ChEBI:16708, ChEBI:17203, ChEBI:17196, ChEBI:17154, ChEBI:17879, ChEBI:35804, ChEBI:26008, ChEBI:17200, ChEBI:16150, ChEBI:16414, ChEBI:16651, ChEBI:16857, ChEBI:36654, ChEBI:17794, ChEBI:16217, ChEBI:17363, ChEBI:16174, ChEBI:17306, ChEBI:16335, ChEBI:17709, ChEBI:13711, ChEBI:16332, ChEBI:16001, ChEBI:16235, ChEBI:17015, ChEBI:33198, ChEBI:16659, ChEBI:17368, ChEBI:15699, ChEBI:48153, ChEBI:17596, ChEBI:30839, ChEBI:26490, ChEBI:16704, ChEBI:16919, ChEBI:16960, ChEBI:30887, ChEBI:16709, ChEBI:17126, ChEBI:16349, ChEBI:17315, ChEBI:17172, ChEBI:15345, ChEBI:30864, ChEBI:16863, ChEBI:12962, ChEBI:37736, ChEBI:15784, ChEBI:18075, ChEBI:17013, ChEBI:16040, ChEBI:16750, ChEBI:17191, ChEBI:30633, ChEBI:16383, ChEBI:15669, ChEBI:86496, ChEBI:32814, ChEBI:16311, ChEBI:18077, ChEBI:17562, ChEBI:15760, ChEBI:36208, ChEBI:17256, ChEBI:17489, ChEBI:17533, ChEBI:18335, ChEBI:16026, ChEBI:16132, ChEBI:28846, ChEBI:25115, ChEBI:26374, ChEBI:16227, ChEBI:27247, ChEBI:16737, ChEBI:16255, ChEBI:16454, ChEBI:16356, ChEBI:58672, ChEBI:17981, ChEBI:15811, ChEBI:18240, ChEBI:17724, ChEBI:27911, ChEBI:86392, ChEBI:16953, ChEBI:9533, ChEBI:78736, ChEBI:17044, ChEBI:15724, ChEBI:133040, ChEBI:5390, ChEBI:30776, ChEBI:7728, ChEBI:18049, ChEBI:17485, ChEBI:16010, ChEBI:15355, ChEBI:30861 , ChEBI:30719 , ChEBI:27860 , ChEBI:27551, ChEBI:16020, ChEBI:43689 , ChEBI:4676, ChEBI:17760 , ChEBI:17768, ChEBI:15997 , ChEBI:15968, ChEBI:23809, ChEBI:48950, ChEBI:18188, ChEBI:19324, ChEBI:15682, ChEBI:15694, ChEBI:7417, ChEBI:17543, ChEBI:21519, ChEBI:17963, ChEBI:28483, ChEBI:15721, ChEBI:19030, ChEBI:33033, ChEBI:28837, ChEBI:27469, ChEBI:18316, ChEBI:28621, ChEBI:28123, ChEBI:28502, ChEBI:9754, ChEBI:48131, ChEBI:41865, ChEBI:27915, ChEBI:16054, ChEBI:8607, ChEBI:1026, ChEBI:6415, ChEBI:45571", "doi.org/10.34619/fjpw-md86"] Administrator KiMoSys Data AccessID92 / EntryID92 | 2009 | batch | aerobic | ChEBI:15422, ChEBI:13389, ChEBI:16908, ChEBI:16474, ChEBI:25523, ChEBI:16761, ChEBI:15351, ChEBI:17297, ChEBI:16238, ChEBI:18405, ChEBI:15414, ChEBI:16027, ChEBI:16680, ChEBI:15361, ChEBI:15351, ChEBI:29985, ChEBI:30916, ChEBI:18066, ChEBI:17552, ChEBI:15428, ChEBI:16977, ChEBI:26806, ChEBI:16264, ChEBI:15996, ChEBI:18019, ChEBI:29991, ChEBI:16856, ChEBI:20878, ChEBI:17621, ChEBI:16467, ChEBI:17677, ChEBI:18050, ChEBI:17115, ChEBI:16643, ChEBI:18021, ChEBI:15713, ChEBI:15729, ChEBI:16828, ChEBI:17295, ChEBI:16039, ChEBI:17895, ChEBI:15531, ChEBI:61553, ChEBI:15380, ChEBI:16809, ChEBI:15978, ChEBI:17561, ChEBI:16958, ChEBI:26296, ChEBI:16218, ChEBI:17808, ChEBI:16567, ChEBI:57642, ChEBI:17239, ChEBI:78679, ChEBI:29052, ChEBI:68689, ChEBI:37154, ChEBI:15603, ChEBI:12936, ChEBI:17858, ChEBI:62303, ChEBI:17202, ChEBI:16284 , ChEBI:17148, ChEBI:15971, ChEBI:17268, ChEBI:16708, ChEBI:17203, ChEBI:17196, ChEBI:17154, ChEBI:17879, ChEBI:35804, ChEBI:26008, ChEBI:17200, ChEBI:16150, ChEBI:16414, ChEBI:16651, ChEBI:16857, ChEBI:36654, ChEBI:17794, ChEBI:16217, ChEBI:17363, ChEBI:16174, ChEBI:17306, ChEBI:16335, ChEBI:17709, ChEBI:13711, ChEBI:16332, ChEBI:16001, ChEBI:16235, ChEBI:17015, ChEBI:33198, ChEBI:16659, ChEBI:17368, ChEBI:15699, ChEBI:48153, ChEBI:17596, ChEBI:30839, ChEBI:26490, ChEBI:16704, ChEBI:16919, ChEBI:16960, ChEBI:30887, ChEBI:16709, ChEBI:17126, ChEBI:16349, ChEBI:17315, ChEBI:17172, ChEBI:15345, ChEBI:30864, ChEBI:16863, ChEBI:12962, ChEBI:37736, ChEBI:15784, ChEBI:18075, ChEBI:17013, ChEBI:16040, ChEBI:16750, ChEBI:17191, ChEBI:30633, ChEBI:16383, ChEBI:15669, ChEBI:86496, ChEBI:32814, ChEBI:16311, ChEBI:18077, ChEBI:17562, ChEBI:15760, ChEBI:36208, ChEBI:17256, ChEBI:17489, ChEBI:17533, ChEBI:18335, ChEBI:16026, ChEBI:16132, ChEBI:28846, ChEBI:25115, ChEBI:26374, ChEBI:16227, ChEBI:27247, ChEBI:16737, ChEBI:16255, ChEBI:16454, ChEBI:16356, ChEBI:58672, ChEBI:17981, ChEBI:15811, ChEBI:18240, ChEBI:17724, ChEBI:27911, ChEBI:86392, ChEBI:16953, ChEBI:9533, ChEBI:78736, ChEBI:17044, ChEBI:15724, ChEBI:133040, ChEBI:5390, ChEBI:30776, ChEBI:7728, ChEBI:18049, ChEBI:17485, ChEBI:16010, ChEBI:15355, ChEBI:30861 , ChEBI:30719 , ChEBI:27860 , ChEBI:27551, ChEBI:16020, ChEBI:43689 , ChEBI:4676, ChEBI:17760 , ChEBI:17768, ChEBI:15997 , ChEBI:15968, ChEBI:23809, ChEBI:48950, ChEBI:18188, ChEBI:19324, ChEBI:15682, ChEBI:15694, ChEBI:7417, ChEBI:17543, ChEBI:21519, ChEBI:17963, ChEBI:28483, ChEBI:15721, ChEBI:19030, ChEBI:33033, ChEBI:28837, ChEBI:27469, ChEBI:18316, ChEBI:28621, ChEBI:28123, ChEBI:28502, ChEBI:9754, ChEBI:48131, ChEBI:41865, ChEBI:27915, ChEBI:16054, ChEBI:8607, ChEBI:1026, ChEBI:6415, ChEBI:45571 | |
| 93 | Saccharomyces cerevisiae | CEN.PK 113-7D, CEN.PK/JT4, FY4 | metabolites at steady-state | — | |
[no] | [93, "Saccharomyces cerevisiae", "CEN.PK 113-7D, CEN.PK/JT4, FY4 ", "1", "KIMODATAID93_v1.xlsx", "20199578", "FEMS Yeast Research", "Differential glucose repression in common yeast strains in response to HXK2 deletion.", "Anne Kümmel, Jennifer Christina Ewald, Sarah‐Maria Fendt, Stefan Jasper Jol, Paola Picotti, Ruedi Aebersold, Uwe Sauer, Nicola Zamboni, Matthias Heinemann", "Institute of Molecular Systems Biology, ETH Zurich", "Kummel_2010.pdf", "application/pdf", 260572, "2018-07-07T21:16:38.518Z", "30", "5.0", "glucose", "batch", "-", nil, nil, true, "", nil, "not specified", "Calculated using an earlier determined OD-to-biomass DW correlation coefficient of 0.486 gDWL/OD for FY4 and 0.52 gDWL/OD for CEN.PK strains.", nil, "Intracellular metabolite concentrations of two biological and two technical replicates were determined from samples withdrawn from culture at an OD of approximately 1.5. Samples of 1–4mL were taken at each sampling time point.", "quenched in methanol at -40 ºC. For the determination of the cAMP concentrations, a sample volume of 10mL was taken. After centrifuging for 3 min at 15 550 g in a rotor precooled to -9 ºC, the samples were frozen at -40 ºC.", "---\n- hot ethanol\n", "---\n- LC-MS\n- GC-TOF\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "mM", "glucose repression; hexokinase 2; FY4; CEN.PK; PKA; metabolomics", false, "17234", 2010, nil, "ChEBI:13389, ChEBI:16761, ChEBI:16027, ChEBI:18050, ChEBI:30916, ChEBI:15428, ChEBI:16977, ChEBI:26806, ChEBI:18019, ChEBI:29991, ChEBI:17115, ChEBI:16643, ChEBI:18021, ChEBI:17295, ChEBI:17895, ChEBI:61553, ChEBI:16809, ChEBI:57642, ChEBI:78679, ChEBI:37154, ChEBI:15603, ChEBI:15971, ChEBI:17203, ChEBI:17196, ChEBI:35804, ChEBI:16414, ChEBI:16857, ChEBI:17794, ChEBI:17363, ChEBI:16332, ChEBI:16863, ChEBI:37736, ChEBI:17191, ChEBI:17489, ChEBI:25115, ChEBI:78736", "doi.org/10.34619/1cke-3f59"] Administrator KiMoSys Data AccessID93 / EntryID93 | 2010 | batch | aerobic | glucose repression; hexokinase 2; FY4; CEN.PK; PKA; metabolomics | ChEBI:13389, ChEBI:16761, ChEBI:16027, ChEBI:18050, ChEBI:30916, ChEBI:15428, ChEBI:16977, ChEBI:26806, ChEBI:18019, ChEBI:29991, ChEBI:17115, ChEBI:16643, ChEBI:18021, ChEBI:17295, ChEBI:17895, ChEBI:61553, ChEBI:16809, ChEBI:57642, ChEBI:78679, ChEBI:37154, ChEBI:15603, ChEBI:15971, ChEBI:17203, ChEBI:17196, ChEBI:35804, ChEBI:16414, ChEBI:16857, ChEBI:17794, ChEBI:17363, ChEBI:16332, ChEBI:16863, ChEBI:37736, ChEBI:17191, ChEBI:17489, ChEBI:25115, ChEBI:78736 |
| 94 | Bacillus subtilis | Wild-type BSB168 trp+ | metabolites at steady-state | — | |
[no] | [94, "Bacillus subtilis", "Wild-type BSB168 trp+", "1", "KIMODATAID94_v2.xlsx", "19917605", "The Journal of Biological Chemistry", "Metabolic Fluxes during Strong Carbon Catabolite Repression by Malate in Bacillus subtilis.", "Roelco J. Kleijn, Joerg M. Buescher, Ludovic Le Chat, Matthieu Jules, Stephane Aymerich and Uwe Sauer", "Institute of Molecular System Biology, ETH Zurich, CH-8093 Zurich, Switzerland", "Kleijn_2010.pdf", "application/pdf", 1325603, "2018-07-09T20:51:51.690Z", "37", "not specified", "glucose, glucose + malate, malate", "batch", "-", nil, nil, true, "", nil, "0.03", "0.5", nil, "Liquid culture was grown to OD650 of ~0.1, at which time it was transferred to filter culture as follows: for each filter culture, 5 mL of liquid culture was passed through an 82mm diameter round nylon filter and placed cell-side up onto a agarose plate", "rapid centrifugation method where 1 ml of culture broth was transferred into a 1.5-ml tube and centrifuged for 15 s at 14,000×g in a tabletop centrifuge. The supernatant was decanted, and the pellet was frozen in liquid nitrogen.", "---\n- hot ethanol\n", "---\n- LC-MS\n- GC-TOF\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "mM", "Metabolism, Metabolism/Gluconeogenesis, Metabolism/Intermediary, Metabolism/Regulation, Metabolism/Tricarboxylic Acid Cycle, Methods/Mass Spectrometry, flux analysis, metabolomics", false, "", 2009, nil, "ChEBI:15351, ChEBI:15361, ChEBI:15351, ChEBI:18237, ChEBI:30915, ChEBI:16449, ChEBI:15741, ChEBI:22660, ChEBI:28300, ChEBI:17822, ChEBI:16811, ChEBI:18021, ChEBI:27897, ChEBI:28044, ChEBI:18186, ChEBI:61553, ChEBI:16809, ChEBI:16890, ChEBI:16218, ChEBI:57642, ChEBI:78679, ChEBI:17138, ChEBI:18012, ChEBI:25017, ChEBI:27266, ChEBI:422, ChEBI:26986, ChEBI:17363 + 27354, ChEBI:30887, ChEBI:18211, ChEBI:48928, ChEBI:78682, ChEBI:24898, ChEBI:36208, ChEBI:6650, ChEBI:28907", "doi.org/10.34619/y0mr-bg52"] Administrator KiMoSys Data AccessID94 / EntryID94 | 2009 | batch | aerobic | Metabolism, Metabolism/Gluconeogenesis, Metabolism/Intermediary, Metabolism/Regulation, Metabolism/Tricarboxylic Acid Cycle, Methods/Mass Spectrometry, flux analysis, metabolomics | ChEBI:15351, ChEBI:15361, ChEBI:15351, ChEBI:18237, ChEBI:30915, ChEBI:16449, ChEBI:15741, ChEBI:22660, ChEBI:28300, ChEBI:17822, ChEBI:16811, ChEBI:18021, ChEBI:27897, ChEBI:28044, ChEBI:18186, ChEBI:61553, ChEBI:16809, ChEBI:16890, ChEBI:16218, ChEBI:57642, ChEBI:78679, ChEBI:17138, ChEBI:18012, ChEBI:25017, ChEBI:27266, ChEBI:422, ChEBI:26986, ChEBI:17363 + 27354, ChEBI:30887, ChEBI:18211, ChEBI:48928, ChEBI:78682, ChEBI:24898, ChEBI:36208, ChEBI:6650, ChEBI:28907 |
| 95 | Bacillus subtilis | Wild-type BSB168 trp+ | flux measurements | — | |
[no] | [95, "Bacillus subtilis", "Wild-type BSB168 trp+", "3", "KIMODATAID95_v4.xlsx", "19917605", "The Journal of Biological Chemistry", "Metabolic Fluxes during Strong Carbon Catabolite Repression by Malate in Bacillus subtilis.", "Roelco J. Kleijn, Joerg M. Buescher, Ludovic Le Chat, Matthieu Jules, Stephane Aymerich and Uwe Sauer", "Institute of Molecular System Biology, ETH Zurich, CH-8093 Zurich, Switzerland", "Kleijn_2010.pdf", "application/pdf", 1325603, "2018-07-11T22:06:12.974Z", "37", "not specified", "glucose, glucose + malate, malate", "batch", "-", nil, nil, true, "", nil, "0.03", "dry weight was inferred from a predetermined conversion factor of 0.48 g of cells/A600", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- GC-MS\n", "aerobic", "--- []\n", "", "Metabolism, Metabolism/Gluconeogenesis, Metabolism/Intermediary, Metabolism/Regulation, Metabolism/Tricarboxylic Acid Cycle, Methods/Mass Spectrometry, flux analysis, metabolomics", false, "", 2010, nil, "R02740, R02740, R00756 , R00756 , R01068, R01068, R01015, R01015, R01061 , R01061 , R00661, R00661, R00200, R00200, R00835 , R01641, R01641, R01067, R01067, R08575, R08575, R00210, R00351, R00267, R00267, R08549, R00406, R00406, R00342, R00342, R00341, R00341, R00214, R00214, R00217", "doi.org/10.34619/dcvx-q138"] Administrator KiMoSys Data AccessID95 / EntryID95 | 2010 | batch | aerobic | Metabolism, Metabolism/Gluconeogenesis, Metabolism/Intermediary, Metabolism/Regulation, Metabolism/Tricarboxylic Acid Cycle, Methods/Mass Spectrometry, flux analysis, metabolomics | R02740, R02740, R00756 , R00756 , R01068, R01068, R01015, R01015, R01061 , R01061 , R00661, R00661, R00200, R00200, R00835 , R01641, R01641, R01067, R01067, R08575, R08575, R00210, R00351, R00267, R00267, R08549, R00406, R00406, R00342, R00342, R00341, R00341, R00214, R00214, R00217 |
| 96 | Escherichia coli | Wild‐type E. coli BW25113, Pyk and Pgi mutants | time-series data of metabolites | — | |
[yes ]|[more] | [96, "Escherichia coli", "Wild‐type E. coli BW25113, Pyk and Pgi mutants", "2", "KIMODATAID96_v1.xlsx", "20730757", "Biotechnology Progress", "13C‐metabolic flux analysis for batch culture of Escherichia coli and its pyk and pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites.", "Yoshihiro Toya, Nobuyoshi Ishii, Kenji Nakahigashi, Takashi Hirasawa, Tomoyoshi Soga, Masaru Tomita, Kazuyuki Shimizu", "Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan", "Toya_2010.pdf", "application/pdf", 1380598, "2018-07-13T11:15:07.495Z", "37", "7.0", "glucose", "batch", "—", nil, nil, true, "", nil, "1.2", "1 OD600 = 0.3 g/L", nil, "An aliquot of culture broth containing 0.015 g of cells was passed through a 0.45‐μm pore size filter.", "cells washed with 20 mL of Milli‐Q water at 37°C and metabolism was stopped by submerging in 4 mL of methanol at 4°C containing 2 μM 2‐(N‐morpholino)ethanesulfonic acid, 2 μM trimesate, 2 μM methionine sulfone and 2 μM 3‐aminopyrrolidine as standard.", "---\n- chloroform-methanol\n", "---\n- CE-TOF-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "g/L and mM", "13C-metabolic flux analysis, batch culture, Escherichia coli, Pyk mutant, Pgi", false, "17234", 2010, nil, "ChEBI:17234, ChEBI:30089, ChEBI:15361, ChEBI:25115, ChEBI:18021, ChEBI:16108, ChEBI:61304, ChEBI:17363, ChEBI:58273, ChEBI:17665, ChEBI:48928, ChEBI:15721, ChEBI:78682", "doi.org/10.34619/78qa-a695"] Administrator KiMoSys Data AccessID96 / EntryID96 [38, nil, "MATLAB version of the model is available at http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html. ", "Jahan_2016.pdf", nil, "2018-07-12T12:32:20.605Z", "Metabolism", "---\n- Model building\n- Model validation\n", "ordinary differential equations", "27329289", "0.2, 0.4, 0.5 and 0.7", "E. coli Central Carbon Metabolism", "Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli", "Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto and Hiroyuki Kurata", "Microbial Cell Factories", "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680‑4 Kawazu, Iizuka, Fukuoka 820‑8502, Japan", "", "", "Systems biology, Rational design, Dynamic model, Enzyme kinetics, Transcription factor, Signal transduction, Allosteric enzyme", "MATLAB2007 or higher", "2018-07-20T16:47:46.311Z", "Escherichia coli", 2016, "COMBINE_KIMOMODELID38.omex", "application/octet-stream", 6603649, "2018-07-23T21:38:00.461Z", nil, nil] Administrator KiMoSys Model AccessID38 / EntryID38 [40, nil, "Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.", "Matsuoka_2017.pdf", nil, "2018-07-19T15:05:36.967Z", "Metabolism", "---\n- Model building\n- Model validation\n", "ordinary differential equations", "28725263", "—", "E. coli redox regulation model", "Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations.", "Yu Matsuoka and Hiroyuki Kurata", "Biotechnology for Biofuels", " Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan", "", "", "Kinetic modeling, Fermentation, Dissolved oxygen limitation, Redox regulation, ArcA, Fnr, Respiratory chain, NADH/NAD+ ratio, Escherichia coli ", "MATLAB (MathWorks) was used for all simulations.", "2018-07-20T16:25:00.495Z", "Escherichia coli", 2017, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID40 / EntryID40 [45, nil, "Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.", "Kurata_2018.pdf", nil, "2018-07-24T16:03:02.038Z", "Metabolism", "---\n- Model building\n", "ordinary differential equations", "29054464", "—", "Batch kinetic model of Escherichia coli", "Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures", "Hiroyuki Kurata and Yurie Sugimoto", "Journal of Bioscience and Bioengineering", "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan", "", "", "Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli", "MATLAB (MathWorks)", nil, "Escherichia coli", 2018, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID45 / EntryID45 | 2010 | batch | aerobic | 13C-metabolic flux analysis, batch culture, Escherichia coli, Pyk mutant, Pgi | ChEBI:17234, ChEBI:30089, ChEBI:15361, ChEBI:25115, ChEBI:18021, ChEBI:16108, ChEBI:61304, ChEBI:17363, ChEBI:58273, ChEBI:17665, ChEBI:48928, ChEBI:15721, ChEBI:78682 |
| 97 | Saccharomyces cerevisiae | Y23925 | enzyme/protein concentrations | — | |
[yes ]|[more] | [97, "Saccharomyces cerevisiae", "Y23925", "4", "KIMODATAID97_v4.xlsx", "23831062", "FEBS Letters", "A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.", "Kieran Smallbone, Hanan L. Messiha, Kathleen M. Carroll, Catherine L. Winder, Naglis Malys, Warwick B. Dunn, Ettore Murabito, Neil Swainston, Joseph O. Dada, Farid Khan, Pınar Pir, Evangelos Simeonidis, Irena Spasić, Jill Wishart, Dieter Weichart, Neil W. Hayes, Daniel Jameson, David S. Broomhead, Stephen G. Oliver, Simon J. Gaskell, John E.G. McCarthy, Norman W. Paton, Hans V. Westerhoff, Douglas B. Kell, Pedro Mendes", "Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK", "Smallbone_2013.pdf", "application/pdf", 755835, "2018-07-15T21:24:27.956Z", "not specified", "not specified", "glucose", "chemostat", "µmax", nil, nil, true, "", nil, "not specified", "monitored by measuring the electrical capacitance of the culture.", nil, "", "", "--- []\n", "--- []\n", "--- []\n", "--- []\n", "aerobic", "---\n- LC-MS/MS\n", "molecules/cell", "Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling", false, "17234", 2013, nil, "P00330, P38113, P00924, P00925, P14540, P00950, P17709, P04806, P04807, P06169, P16467, P26263, P16861, P16862, P12709, P00560, P00549, P52489, P00360, P00358, P00359, P00942", "doi.org/10.34619/d41y-ws04"] Administrator KiMoSys Data AccessID97 / EntryID97 [39, nil, "Original model source: in JWS online database.", "Smallbone_2013.pdf", nil, "2018-07-16T19:34:20.703Z", "Metabolism", "---\n- Model validation\n", "ordinary differential equations", "23831062", "", "smallbone18", "A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.", "Kieran Smallbone, Hanan L. Messiha, Kathleen M. Carroll, Catherine L. Winder, Naglis Malys, Warwick B. Dunn, Ettore Murabito, Neil Swainston, Joseph O. Dada, Farid Khan, Pınar Pir, Evangelos Simeonidis, Irena Spasić, Jill Wishart, Dieter Weichart, Neil W.", "FEBS Letters", "Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK", "", "smallbone18", "Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling", "Copasi (www.copasi.org)", nil, "Saccharomyces cerevisiae", 2013, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID39 / EntryID39 | 2013 | chemostat | aerobic | Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling | P00330, P38113, P00924, P00925, P14540, P00950, P17709, P04806, P04807, P06169, P16467, P26263, P16861, P16862, P12709, P00560, P00549, P52489, P00360, P00358, P00359, P00942 |
| 98 | Saccharomyces cerevisiae | TAP-tagged strain | enzyme/protein concentrations | — | |
[yes ]|[more] | [98, "Saccharomyces cerevisiae", "TAP-tagged strain ", "4", "KIMODATAID98_v0.xlsx", "14562106", "Nature", "Global analysis of protein expression in yeast.", "Sina Ghaemmaghami, Won-Ki Huh, Kiowa Bower, Russell W. Howson, Archana Belle, Noah Dephoure, Erin K. O'Shea & Jonathan S. Weissman", "Howard Hughes Medical Institute, University of California–San Francisco, San Francisco, California 94143-2240, USA", "Ghaemmaghami_2003.pdf", "application/pdf", 873183, "2018-07-16T15:29:11.376Z", "30", "not specified", "glucose", "chemostat", "—", nil, nil, true, "", nil, "0.0017", "OD of ~0.7 ", nil, "", "", "--- []\n", "--- []\n", "--- []\n", "--- []\n", "aerobic", "---\n- LC-MS/MS\n", "molecules/cell", "yeast, protein expression, S. cerevisiae", false, "17234", 2003, nil, "P00330, P38113, P00924, P00925, P14540, P00950, P17709, P04806, P04807, P06169, P16467, P26263, P16861, P16862, P12709, P00560, P00549, P52489, P00360, P00358, P00359, P00942", "doi.org/10.34619/m32r-1q02"] Administrator KiMoSys Data AccessID98 / EntryID98 [39, nil, "Original model source: in JWS online database.", "Smallbone_2013.pdf", nil, "2018-07-16T19:34:20.703Z", "Metabolism", "---\n- Model validation\n", "ordinary differential equations", "23831062", "", "smallbone18", "A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.", "Kieran Smallbone, Hanan L. Messiha, Kathleen M. Carroll, Catherine L. Winder, Naglis Malys, Warwick B. Dunn, Ettore Murabito, Neil Swainston, Joseph O. Dada, Farid Khan, Pınar Pir, Evangelos Simeonidis, Irena Spasić, Jill Wishart, Dieter Weichart, Neil W.", "FEBS Letters", "Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK", "", "smallbone18", "Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling", "Copasi (www.copasi.org)", nil, "Saccharomyces cerevisiae", 2013, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID39 / EntryID39 | 2003 | chemostat | aerobic | yeast, protein expression, S. cerevisiae | P00330, P38113, P00924, P00925, P14540, P00950, P17709, P04806, P04807, P06169, P16467, P26263, P16861, P16862, P12709, P00560, P00549, P52489, P00360, P00358, P00359, P00942 |
| 99 | Saccharomyces cerevisiae | Y23925 | metabolites at steady-state | — | |
[yes ]|[more] | [99, "Saccharomyces cerevisiae", "Y23925", "1", "KIMODATAID99_v2.xlsx", "23831062", "FEBS Letters", "A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.", "Kieran Smallbone, Hanan L. Messiha, Kathleen M. Carroll, Catherine L. Winder, Naglis Malys, Warwick B. Dunn, Ettore Murabito, Neil Swainston, Joseph O. Dada, Farid Khan, Pınar Pir, Evangelos Simeonidis, Irena Spasić, Jill Wishart, Dieter Weichart, Neil W. Hayes, Daniel Jameson, David S. Broomhead, Stephen G. Oliver, Simon J. Gaskell, John E.G. McCarthy, Norman W. Paton, Hans V. Westerhoff, Douglas B. Kell, Pedro Mendes", "Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK", "Smallbone_2013.pdf", "application/pdf", 755835, "2018-07-16T15:49:58.630Z", "not specified", "not specified", "glucose", "chemostat", "µmax", nil, nil, true, "—", nil, "not specified", "monitored by measuring the electrical capacitance of the culture.", nil, "10 ml of culture.", "10 ml of culture solution into 40 ml of a 60:40 methanol/water solution [1] stored at a temperature of −47 °C [2]. Immediate separation of cells was performed by applying centrifugation (4000 g for 5 min) followed by removal of the quenching solution. ", "---\n- freezing-thawing in methanol\n- methanol-water\n", "---\n- GC-MS\n- LC-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "molecules/cell", "Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling", false, "17234", 2013, nil, "ChEBI:16108, ChEBI:28013, ChEBI:16084, ChEBI:15 978, ChEBI:17 665, ChEBI:29 052, ChEBI:4167, ChEBI:18021, ChEBI:15361, ChEBI:17835", "doi.org/10.34619/eck4-3541"] Administrator KiMoSys Data AccessID99 / EntryID99 [39, nil, "Original model source: in JWS online database.", "Smallbone_2013.pdf", nil, "2018-07-16T19:34:20.703Z", "Metabolism", "---\n- Model validation\n", "ordinary differential equations", "23831062", "", "smallbone18", "A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.", "Kieran Smallbone, Hanan L. Messiha, Kathleen M. Carroll, Catherine L. Winder, Naglis Malys, Warwick B. Dunn, Ettore Murabito, Neil Swainston, Joseph O. Dada, Farid Khan, Pınar Pir, Evangelos Simeonidis, Irena Spasić, Jill Wishart, Dieter Weichart, Neil W.", "FEBS Letters", "Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK", "", "smallbone18", "Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling", "Copasi (www.copasi.org)", nil, "Saccharomyces cerevisiae", 2013, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID39 / EntryID39 | 2013 | chemostat | aerobic | Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling | ChEBI:16108, ChEBI:28013, ChEBI:16084, ChEBI:15 978, ChEBI:17 665, ChEBI:29 052, ChEBI:4167, ChEBI:18021, ChEBI:15361, ChEBI:17835 |
| 100 | Saccharomyces cerevisiae | CEN.PK113-1A | enzyme/protein concentrations | — | |
[no] | [100, "Saccharomyces cerevisiae", "CEN.PK113-1A", "4", "KIMODATAID100_v1.xlsx", "19804647", "BMC Genomics", "Low oxygen levels as a trigger for enhancement of respiratory metabolism in Saccharomyces cerevisiae.", "Eija Rintala, Mervi Toivari, Juha-Pekka Pitkänen, Marilyn G Wiebe, Laura Ruohonen and Merja Penttilä", "VTT Technical Research Centre of Finland, Finland", "Rintala_2009.pdf", "application/pdf", 2927778, "2018-07-18T12:56:46.134Z", "30", "5", "glucose", "chemostat", "0.1 ± 0.02", nil, nil, true, "", nil, "2.5", "not specified", nil, "", "", "--- []\n", "--- []\n", "--- []\n", "--- []\n", "aerobic and anaerobic", "---\n- 2D gel-MALDI-TOF\n", "―", "Aerobic Condition, MAPK Signalling, Pathway Central Carbon Metabolism, Filamentous Growth, Ergosterol Biosynthesis", false, "17234", 2009, nil, "P32471, P32471, P19414, P19414, J6EBK9, J6EBK9, P60010, P27616, P38009, P07245, P07245, P00330, P00330, P00330, P00331, P00331, P00331, P07246, P07170, P47143, P47143, P43567, P54114, P46367, P46367, P54115, P54115, P38115, P22768, P22768, P28777, P14843, P53090, P38011, P49089, P07251, P07251, P07251, P00830, P38077, P09457, P30902, P38891, P29311, P07991, Q05791, P00890, P07256, P35176, P00175, P00175, P31373, P32582, P32582, P32582, P54838, P06634, P32891, P39976, P39976, P38791, P32471, P32324, P00924, P00924, P00924, P00924, P00924, P00924, P00925, P00925, P00925, P00925, P54839, P25087, P24521, P38071, P39518, P39518, P14540, P14540, Q08911, P38777, P08417, P18562, P14065, P07262, P07262, P39708, P17709, Q00055, P00950, P00950, P00950, P38088, P32835, P38625, P15454, P32191, Q05775, P11353, P32471, P13663, P38274, P31539, P31539, P15992, P15992, P15992, P07263, P04806, P04806, P28240, P28834, P28241, P21954, P41939, P07342, P07342, P06168, P11986, P00817, P35844, P07264, P04173, P09624, P09624, P53598, P53312, P38998, Q12122, Q12122, P38999, P36013, P11914, P36060, P36060, P22133, P06106, P06106, P06106, P05694, P05694, P05694, P05694, Q07938, P30952, P40364, P35719, P40029, P32471, P53081, P53081, P04147, P04147, P06169, Q12428, P00560, P04840, P04840, P27796, Q12335, P07257, P41277, P08067, Q12189, P07703, P38886, P26783, P19358, P19358, P21243, Q00711, P07283, P33330, Q12118, P37292, P25294, Q03144, P00447, P11484, P11484, P0CS90, P0CS90, P32589, P32589, P15705, P15705, P15705, P15705, P02994, P02994, P14306, P34167, P33315, P23644, P00942, P29509, P34760, P02557, P02992, P21734, P17649, P16140, Q12363, Q07551, P32614, P40093, P23180, P47115, P35691, Q05016", "doi.org/10.34619/a1sc-q830"] Administrator KiMoSys Data AccessID100 / EntryID100 | 2009 | chemostat | aerobic and anaerobic | Aerobic Condition, MAPK Signalling, Pathway Central Carbon Metabolism, Filamentous Growth, Ergosterol Biosynthesis | P32471, P32471, P19414, P19414, J6EBK9, J6EBK9, P60010, P27616, P38009, P07245, P07245, P00330, P00330, P00330, P00331, P00331, P00331, P07246, P07170, P47143, P47143, P43567, P54114, P46367, P46367, P54115, P54115, P38115, P22768, P22768, P28777, P14843, P53090, P38011, P49089, P07251, P07251, P07251, P00830, P38077, P09457, P30902, P38891, P29311, P07991, Q05791, P00890, P07256, P35176, P00175, P00175, P31373, P32582, P32582, P32582, P54838, P06634, P32891, P39976, P39976, P38791, P32471, P32324, P00924, P00924, P00924, P00924, P00924, P00924, P00925, P00925, P00925, P00925, P54839, P25087, P24521, P38071, P39518, P39518, P14540, P14540, Q08911, P38777, P08417, P18562, P14065, P07262, P07262, P39708, P17709, Q00055, P00950, P00950, P00950, P38088, P32835, P38625, P15454, P32191, Q05775, P11353, P32471, P13663, P38274, P31539, P31539, P15992, P15992, P15992, P07263, P04806, P04806, P28240, P28834, P28241, P21954, P41939, P07342, P07342, P06168, P11986, P00817, P35844, P07264, P04173, P09624, P09624, P53598, P53312, P38998, Q12122, Q12122, P38999, P36013, P11914, P36060, P36060, P22133, P06106, P06106, P06106, P05694, P05694, P05694, P05694, Q07938, P30952, P40364, P35719, P40029, P32471, P53081, P53081, P04147, P04147, P06169, Q12428, P00560, P04840, P04840, P27796, Q12335, P07257, P41277, P08067, Q12189, P07703, P38886, P26783, P19358, P19358, P21243, Q00711, P07283, P33330, Q12118, P37292, P25294, Q03144, P00447, P11484, P11484, P0CS90, P0CS90, P32589, P32589, P15705, P15705, P15705, P15705, P02994, P02994, P14306, P34167, P33315, P23644, P00942, P29509, P34760, P02557, P02992, P21734, P17649, P16140, Q12363, Q07551, P32614, P40093, P23180, P47115, P35691, Q05016 |
| 101 | Escherichia coli | BW25113, pflA, pta, ppc, adhE and pykF mutants | metabolites at steady-state | — | |
[yes ]|[more] | [101, "Escherichia coli", "BW25113, pflA, pta, ppc, adhE and pykF mutants", "1", "KIMODATAID101_v1.xlsx", "15781419", "Metabolic Engineering", "Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic condition.", "Jiangfeng Zhu, Kazuyuki Shimizu", "Department of Biochemical Engineering & Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", "Zhu_2005.pdf", "application/pdf", 292546, "2018-07-19T14:32:27.511Z", "37", "7.0", "glucose", "batch", "—", nil, nil, true, "", nil, "1.0", "See worksheet for the different strains. Cell dry weight was determined by measuring the optical density at 600 nm. ", nil, " Samples were centrifuged for 10 min at 4 °C and 6000×g to remove the cells for extracellular metabolite analysis. ", "—", "---\n- not used\n", "---\n- enzymatic\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "yield on glucose (g/g)%", "Escherichia coli, Enzyme activity, Metabolite concentration, Metabolic flux analysis, Lactate production, Pyruvate metabolism", false, "17234", 2005, nil, "CHEBI:24996, CHEBI:30089, CHEBI:15740, CHEBI:26806, CHEBI:16236, CHEBI:15361", "doi.org/10.34619/tnq8-4n54"] Administrator KiMoSys Data AccessID101 / EntryID101 [40, nil, "Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.", "Matsuoka_2017.pdf", nil, "2018-07-19T15:05:36.967Z", "Metabolism", "---\n- Model building\n- Model validation\n", "ordinary differential equations", "28725263", "—", "E. coli redox regulation model", "Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations.", "Yu Matsuoka and Hiroyuki Kurata", "Biotechnology for Biofuels", " Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan", "", "", "Kinetic modeling, Fermentation, Dissolved oxygen limitation, Redox regulation, ArcA, Fnr, Respiratory chain, NADH/NAD+ ratio, Escherichia coli ", "MATLAB (MathWorks) was used for all simulations.", "2018-07-20T16:25:00.495Z", "Escherichia coli", 2017, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID40 / EntryID40 | 2005 | batch | aerobic | Escherichia coli, Enzyme activity, Metabolite concentration, Metabolic flux analysis, Lactate production, Pyruvate metabolism | CHEBI:24996, CHEBI:30089, CHEBI:15740, CHEBI:26806, CHEBI:16236, CHEBI:15361 |
| 102 | Escherichia coli | BW25113, pflA, pta, ppc, adhE and pykF mutants | enzyme/protein concentrations | — | |
[no] | [102, "Escherichia coli", "BW25113, pflA, pta, ppc, adhE and pykF mutants", "4", "KIMODATAID102_v2.xlsx", "15781419", "Metabolic Engineering", "Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic condition.", "Jiangfeng Zhu, Kazuyuki Shimizu", "Department of Biochemical Engineering & Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan.", "Zhu_2005.pdf", "application/pdf", 292546, "2018-07-20T13:04:40.907Z", "37", "7.0", "glucose", "batch", "—", nil, nil, true, "", nil, "1.0", "Cell dry weight was determined by measuring the optical density at 600 nm. See worksheet.", nil, "", "", "[\"\"]", "[\"\"]", "[\"\"]", "[\"\"]", "aerobic", "[\"\", \"colorimetric assays\"]", "mmol/min mg protein", "Escherichia coli, Enzyme activity, Metabolite concentration, Metabolic flux analysis, Lactate production, Pyruvate metabolism", false, "17234", 2005, nil, "P0AC53, P00350, P0A9B2, P0AD61, P33232, P00864, P0A9N4, P0AC60, Q7DL18", "doi.org/10.34619/24cm-8d34"] Administrator KiMoSys Data AccessID102 / EntryID102 | 2005 | batch | aerobic | Escherichia coli, Enzyme activity, Metabolite concentration, Metabolic flux analysis, Lactate production, Pyruvate metabolism | P0AC53, P00350, P0A9B2, P0AD61, P33232, P00864, P0A9N4, P0AC60, Q7DL18 |
| 103 | Escherichia coli | BW25113, pflA, pta, ppc, adhE and pykF mutants | metabolites at steady-state | — | |
[no] | [103, "Escherichia coli", "BW25113, pflA, pta, ppc, adhE and pykF mutants", "1", "KIMODATAID103_v1.xlsx", "15781419", "Metabolic Engineering", "Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic condition.", "Jiangfeng Zhu, Kazuyuki Shimizu", "Department of Biochemical Engineering & Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", "Zhu_2005.pdf", "application/pdf", 292546, "2018-07-20T14:51:02.492Z", "37", "7.0", "glucose", "batch", "—", nil, nil, true, "", nil, "1.0", "Cell dry weight was determined by measuring the optical density at 600 nm.", nil, "About 10 ml of the culture broth was quickly taken as the sample, and immediately injected into 40 ml of pre-cooled 60% methanol. The mixture was kept at −20 °C. ", "The quenched samples were centrifuged at 10,000×g at a temperature of −15 °C for 10 min. The pellets were kept at −20 °C for 30 min and then lyophilized. The dried biomass was kept in a −20 °C freezer for further processing.", "---\n- perchloric acid\n- boiling ethanol\n", "---\n- enzymatic\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "mM/g DCW", "Escherichia coli, Enzyme activity, Metabolite concentration, Metabolic flux analysis, Lactate production, Pyruvate metabolism", false, "17234", 2005, nil, "CHEBI:14314, CHEBI:78682, CHEBI:18021, CHEBI:15361, CHEBI:15351, CHEBI:15422, CHEBI:16761, CHEBI:16027 , CHEBI:16908, CHEBI:13389", "doi.org/10.34619/3xrc-9n56"] Administrator KiMoSys Data AccessID103 / EntryID103 | 2005 | batch | aerobic | Escherichia coli, Enzyme activity, Metabolite concentration, Metabolic flux analysis, Lactate production, Pyruvate metabolism | CHEBI:14314, CHEBI:78682, CHEBI:18021, CHEBI:15361, CHEBI:15351, CHEBI:15422, CHEBI:16761, CHEBI:16027 , CHEBI:16908, CHEBI:13389 |
| 104 | Escherichia coli | K-12 BW25113 and ppc, pck, pyk mutants | flux measurements | — | |
[yes ]|[more] | [104, "Escherichia coli", "K-12 BW25113 and ppc, pck, pyk mutants", "3", "KIMODATAID104_v1.xlsx", "21092096", "Microbial Cell Factories", "Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.", "Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu", "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", "Kadir_2010.pdf", "application/pdf", 2038907, "2018-07-21T11:27:22.623Z", "37", "7.0", "glucose", "chemostat", "0.2", nil, nil, true, "", nil, "1.0", "not specified", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- GC-MS\n", "aerobic", "--- []\n", "(mmol/g-dry cell weight/h)", "Specific Growth Rate, Flux Balance Analysis, Oxidative Pentose Phosphate Pathway, Main Metabolic Pathway, Isotopomer Distribution", false, "17234", 2010, nil, "R02738, R02740, R04779, R01070, R00200, R00209, R00835, R01528, R01529, R01056, R01641, R01827, R01830, R00267, R08549, R00412, R01082, R00342, R00341, R00341, R00214, R00479, R00472, R00227, R00704, R00235", "doi.org/10.34619/1wnt-3696"] Administrator KiMoSys Data AccessID104 / EntryID104 [41, nil, "Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.", "Kurata_2018.pdf", nil, "2018-07-20T16:54:23.186Z", "Metabolism", "---\n- Model building\n- Model validation\n", "ordinary differential equations", "29054464", "0.2, 0.4, 0.5 and 0.7", "Continuous kinetic model of Escherichia coli", "Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures", "Hiroyuki Kurata and Yurie Sugimoto", "Journal of Bioscience and Bioengineering", "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan", "", "", "Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli", "MATLAB (MathWorks)", "2018-07-24T15:46:04.831Z", "Escherichia coli", 2018, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID41 / EntryID41 | 2010 | chemostat | aerobic | Specific Growth Rate, Flux Balance Analysis, Oxidative Pentose Phosphate Pathway, Main Metabolic Pathway, Isotopomer Distribution | R02738, R02740, R04779, R01070, R00200, R00209, R00835, R01528, R01529, R01056, R01641, R01827, R01830, R00267, R08549, R00412, R01082, R00342, R00341, R00341, R00214, R00479, R00472, R00227, R00704, R00235 |
| 105 | Escherichia coli | BW25113 and ppc mutant | flux measurements | — | |
[yes ]|[more] | [105, "Escherichia coli", "BW25113 and ppc mutant", "3", "KIMODATAID105_v2.xlsx", "15158257", "FEMS Microbiology Letters", "Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements.", "Lifeng Peng, Marcos J. Arauzo-Bravo, Kazuyuki Shimizu", "Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", "Peng_2004.pdf", "application/pdf", 271660, "2018-07-21T14:36:12.067Z", "37", "7.0", "glucose", "chemostat", "0.2", nil, nil, true, "", nil, "1.0", "see worksheet.", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- NMR\n- GC-MS\n", "aerobic", "--- []\n", "(mmol/g-dry cell weight/h)", "ppc mutant Escherichia coli, 2-Dimensional nuclear magnetic resonance, Gas chromatography-mass spectrometry, Metabolic flux analysis", false, "17234", 2004, nil, "R02738, R02740, R04779, R00200, R00209, R00835, R01528, R01529, R01056, R01641, R01827, R01830, R00267, R08549, R00412, R00342, R00341, R00341, R00479, R00472, R00227, R00704", "doi.org/10.34619/1yzf-1r95"] Administrator KiMoSys Data AccessID105 / EntryID105 [16, 38, "", "Kadir_2010.pdf", nil, "2013-04-24T15:07:11.046Z", "Metabolism", "---\n- Model validation\n", "ordinary differential equations", "21092096", "—", "glycolysis Escherichia coli model", "Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.", "Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu", "Microbial Cell Factories", "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", "", "", "Escherichia coli, single-gene knockouts, main central metabolism and TCA", "http://www.matlab.com (MATLAB)", "2018-07-21T20:34:09.507Z", "Escherichia coli", 2010, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID16 / EntryID16 [41, nil, "Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.", "Kurata_2018.pdf", nil, "2018-07-20T16:54:23.186Z", "Metabolism", "---\n- Model building\n- Model validation\n", "ordinary differential equations", "29054464", "0.2, 0.4, 0.5 and 0.7", "Continuous kinetic model of Escherichia coli", "Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures", "Hiroyuki Kurata and Yurie Sugimoto", "Journal of Bioscience and Bioengineering", "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan", "", "", "Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli", "MATLAB (MathWorks)", "2018-07-24T15:46:04.831Z", "Escherichia coli", 2018, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID41 / EntryID41 | 2004 | chemostat | aerobic | ppc mutant Escherichia coli, 2-Dimensional nuclear magnetic resonance, Gas chromatography-mass spectrometry, Metabolic flux analysis | R02738, R02740, R04779, R00200, R00209, R00835, R01528, R01529, R01056, R01641, R01827, R01830, R00267, R08549, R00412, R00342, R00341, R00341, R00479, R00472, R00227, R00704 |
| 106 | Escherichia coli | W3110 and pck mutant | flux measurements | — | |
[yes ]|[more] | [106, "Escherichia coli", "W3110 and pck mutant", "3", "KIMODATAID106_v1.xlsx", "12966569", "Biotechnology and Bioengineering", "Analysis of Escherichia coli Anaplerotic Metabolism and Its Regulation Mechanisms From the Metabolic Responses to Altered Dilution Rates and Phosphoenolpyruvate Carboxykinase Knockout.", "Yang C, Hua Q, Baba T, Mori H, Shimizu K", "Metabolome Unit, Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.", "Yang2003.pdf", "application/pdf", 372915, "2018-07-31T09:18:03.417Z", "37", "7.0", "glucose", "chemostat", "0.1, 0.32, 0.55 (WT ) and 0.1 (pck)", nil, nil, true, "", nil, "1.0", "see worksheet.", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- NMR\n", "aerobic", "--- []\n", "(mmol/g-dry cell weight/h)", "Escherichia coli; metabolic flux; 13C labeling; anaplerotic reaction; phosphoenolpyruvate carboxykinase; in vivo regulation", false, "17234", 2003, nil, "R02738, R02740, R04779, R00200, R00209, R00835, R01641, R01827, R01830, R00267, R08549, R00412, R01082, R00342, R00341, R00341, R00214, R00479, R00472", "doi.org/10.34619/x28q-1x57"] Administrator KiMoSys Data AccessID106 / EntryID106 [16, 38, "", "Kadir_2010.pdf", nil, "2013-04-24T15:07:11.046Z", "Metabolism", "---\n- Model validation\n", "ordinary differential equations", "21092096", "—", "glycolysis Escherichia coli model", "Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.", "Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu", "Microbial Cell Factories", "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", "", "", "Escherichia coli, single-gene knockouts, main central metabolism and TCA", "http://www.matlab.com (MATLAB)", "2018-07-21T20:34:09.507Z", "Escherichia coli", 2010, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID16 / EntryID16 | 2003 | chemostat | aerobic | Escherichia coli; metabolic flux; 13C labeling; anaplerotic reaction; phosphoenolpyruvate carboxykinase; in vivo regulation | R02738, R02740, R04779, R00200, R00209, R00835, R01641, R01827, R01830, R00267, R08549, R00412, R01082, R00342, R00341, R00341, R00214, R00479, R00472 |
| 107 | Escherichia coli | BW25113 and pyk mutant | flux measurements | — | |
[yes ]|[more] | [107, "Escherichia coli", "BW25113 and pyk mutant", "3", "KIMODATAID107_v1.xlsx", "12802531", "Appl Micriobiol Biotechnology", "Metabolic flux analysis of pykF gene knockout Escherichia coli based on 13C-labeling experiments together with measurements of enzyme activities and intracellular metabolite concentrations.", "Al Zaid Siddiquee K, Arauzo-Bravo MJ, Shimizu K.", "Department of Biochemical Engineering and Science, Kyushu Institute of Technology,Iizuka, 820–8502 Fukuoka, Japan", nil, nil, nil, nil, "37", "7.0", "glucose", "chemostat", "0.1", nil, nil, true, "", nil, "0.5", "see worksheet.", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- NMR\n- GC-MS\n", "aerobic", "--- []\n", "(mmol/g-dry cell weight/h)", "Dilution Ratem Intracellular Metabolite, Metabolic Flux Analysis, Oxidative Pentose Phosphate Pathway, Proteinogenic Amino Acid ", false, "17234", 2004, nil, "R02738, R02740, R01070, R00200, R00209, R00835, R01528, R01529, R01056, R01641, R01827, R01830, R00267, R08549, R00342, R00341, R00214, R00704", "doi.org/10.34619/v4p3-2g68"] Administrator KiMoSys Data AccessID107 / EntryID107 [16, 38, "", "Kadir_2010.pdf", nil, "2013-04-24T15:07:11.046Z", "Metabolism", "---\n- Model validation\n", "ordinary differential equations", "21092096", "—", "glycolysis Escherichia coli model", "Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.", "Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu", "Microbial Cell Factories", "Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", "", "", "Escherichia coli, single-gene knockouts, main central metabolism and TCA", "http://www.matlab.com (MATLAB)", "2018-07-21T20:34:09.507Z", "Escherichia coli", 2010, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID16 / EntryID16 | 2004 | chemostat | aerobic | Dilution Ratem Intracellular Metabolite, Metabolic Flux Analysis, Oxidative Pentose Phosphate Pathway, Proteinogenic Amino Acid | R02738, R02740, R01070, R00200, R00209, R00835, R01528, R01529, R01056, R01641, R01827, R01830, R00267, R08549, R00342, R00341, R00214, R00704 |
| 108 | Escherichia coli | K-12 | flux measurements | — | |
[yes ]|[more] | [108, "Escherichia coli", "K-12", "3", "KIMODATAID108_v1.xlsx", "12568740", "Journal of Biotechnology", "Metabolic flux analysis of Escherichia coli K12 grown on 13C-labeled acetate and glucose using GC-MS and powerful flux calculation method.", "Jiao Zhao, Kazuyuki Shimizu", "Institute for Advanced Biosciences, Keio University, Yamagata 997-0017, Japan", nil, nil, nil, nil, "37", "7.0", "glucose", "chemostat", "0.11 and 0.22", nil, nil, true, "", nil, "0.9", "", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- GC-MS\n", "aerobic", "--- []\n", "(mmol/g.h)", "Mass isotopomer analysis, Metabolic flux analysis, Carbon source, Genetic algorithm, Levenberg-Marquardt algorithm, Escherichia coli K12", false, "17234", 2003, nil, "R00235, R00351, R00472, R01324 , R00479 , R00267 , R02164, R01082, R00342, R00431, R00658, R01512, R02740, R01528, R01056, R01529, R01641, R01067, R01827, R00216, R00209, R00945, R00299, R02740, R01512, R00658, R00200, R00209, R00235, R01528, R01529, R01056, R01641, R01827, R01067, R00945, R00351, R01324 , R00267 , R02164, R01082, R00342, R00345", "doi.org/10.34619/mcah-cq59"] Administrator KiMoSys Data AccessID108 / EntryID108 [43, nil, "Original model source: in BioModels database.", "Singh_2006.pdf", nil, "2018-07-23T10:25:20.587Z", "Metabolism", "---\n- Model validation\n", "ordinary differential equations", "16887020", "", "Singh2006_TCA_Ecoli_acetate", "Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets", "Vivek Kumar Singh and Indira Ghosh", "Theoretical Biology and Medical Modelling", "Bioinformatics Centre, University of Pune, India", "", "BIOMD0000000221", "Tuberculosis, Steady State Flux, Glyoxylate Bypass, Metabolic Control Analysis, Experimental Flux", "Jarnac 2.14 (http://jdesigner.sourceforge.net/Site/Jarnac.html)", nil, "Escherichia coli", 2006, "COMBINE_KIMOMODELID43.omex", "application/octet-stream", 253672, "2018-07-27T10:28:17.660Z", nil, nil] Administrator KiMoSys Model AccessID43 / EntryID43 [44, nil, "Original model source: in BioModels database.", "Singh_2006.pdf", nil, "2018-07-23T10:39:44.310Z", "Metabolism", "---\n- Model validation\n", "ordinary differential equations", "16887020", "", "Singh2006_TCA_Ecoli_glucose", "Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets", "Vivek Kumar Singh and Indira Ghosh", "Theoretical Biology and Medical Modelling", "Bioinformatics Centre, University of Pune, India", "", "BIOMD0000000222", "Tuberculosis, Steady State Flux, Glyoxylate Bypass, Metabolic Control Analysis, Experimental Flux", "Jarnac 2.14 (http://jdesigner.sourceforge.net/Site/Jarnac.html)", nil, "Escherichia coli", 2006, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID44 / EntryID44 | 2003 | chemostat | aerobic | Mass isotopomer analysis, Metabolic flux analysis, Carbon source, Genetic algorithm, Levenberg-Marquardt algorithm, Escherichia coli K12 | R00235, R00351, R00472, R01324 , R00479 , R00267 , R02164, R01082, R00342, R00431, R00658, R01512, R02740, R01528, R01056, R01529, R01641, R01067, R01827, R00216, R00209, R00945, R00299, R02740, R01512, R00658, R00200, R00209, R00235, R01528, R01529, R01056, R01641, R01827, R01067, R00945, R00351, R01324 , R00267 , R02164, R01082, R00342, R00345 |
| 109 | Escherichia coli | BW25113 and ppc mutant | enzyme/protein concentrations | — | |
[no] | [109, "Escherichia coli", "BW25113 and ppc mutant", "4", "KIMODATAID109_v2.xlsx", "15158257", "FEMS Microbiology Letters", "Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements.", "Lifeng Peng, Marcos J. Arauzo-Bravo, Kazuyuki Shimizu", "Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan.", "Peng_2004.pdf", "application/pdf", 271660, "2018-07-28T16:46:57.974Z", "37", "7.0", "glucose", "chemostat", "0.2", nil, nil, true, "", nil, "1.0", "Yield of biomass on glucose (g/g): 0,48 (WT) and 0,55 (ppc)", nil, "", "", "--- []\n", "--- []\n", "--- []\n", "--- []\n", "aerobic", "---\n- 2D gel-MALDI-TOF\n", "µmol/min mg(protein)", "ppc mutant Escherichia coli, 2-Dimensional nuclear magnetic resonance, Gas chromatography-mass spectrometry, Metabolic flux analysis", false, "17234", 2004, nil, "P0A6T1, P0AB71, P0A9B2, P0AD61, P00864, P22259, P76558, P26616, P0AC53, P00350, P0ABH7, P25516, P0A9G6, P08200, P61889", "doi.org/10.34619/dpv4-4w25"] Administrator KiMoSys Data AccessID109 / EntryID109 | 2004 | chemostat | aerobic | ppc mutant Escherichia coli, 2-Dimensional nuclear magnetic resonance, Gas chromatography-mass spectrometry, Metabolic flux analysis | P0A6T1, P0AB71, P0A9B2, P0AD61, P00864, P22259, P76558, P26616, P0AC53, P00350, P0ABH7, P25516, P0A9G6, P08200, P61889 |
| 110 | Escherichia coli | BW25113 and ppc mutant | metabolites at steady-state | — | |
[no] | [110, "Escherichia coli", "BW25113 and ppc mutant", "1", "KIMODATAID110_v1.xlsx", "15158257", "FEMS Microbiology Letters", "Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements.", "Lifeng Peng, Marcos J. Arauzo-Bravo, Kazuyuki Shimizu", "Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan.", nil, nil, nil, nil, "37", "7.0", "glucose", "chemostat", "0.2", nil, nil, true, "", nil, "1.0", "Yield of biomass on glucose (g/g): 0,48 (WT) and 0,55 (ppc)", nil, "Cells were harvested by centrifugation at 10,000 g for 10 min.", "Washed twice with 100 mM Tris-HCl (pH 7.0) containing 20 mM KCl, 5 mM MnSO4, 2 mM DTT and 0.1 mM EDTA, and then resuspended in the same buffer (ca. 15 g wet cells in 50 ml buffer solution).", "---\n- sonication\n", "---\n- enzymatic\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "mM", "ppc mutant Escherichia coli, 2-Dimensional nuclear magnetic resonance, Gas chromatography-mass spectrometry, Metabolic flux analysis", false, "17234", 2004, nil, "CHEBI:17665, CHEBI:88003, CHEBI:78682, CHEBI:18021, CHEBI:48928, CHEBI:15351, CHEBI:30744", "doi.org/10.34619/4dqp-g589"] Administrator KiMoSys Data AccessID110 / EntryID110 | 2004 | chemostat | aerobic | ppc mutant Escherichia coli, 2-Dimensional nuclear magnetic resonance, Gas chromatography-mass spectrometry, Metabolic flux analysis | CHEBI:17665, CHEBI:88003, CHEBI:78682, CHEBI:18021, CHEBI:48928, CHEBI:15351, CHEBI:30744 |
| 111 | Saccharomyces cerevisiae | CEN.PK113-7D | metabolites at steady-state | — | |
[yes ]|[more] | [111, "Saccharomyces cerevisiae", "CEN.PK113-7D", "1", "KIMODATAID111_v1.xlsx", "20232995", "IET Systems Biology", "Time-dependent regulation of yeast glycolysis upon nitrogen starvation depends on cell history.", "van Eunen K, Dool P, Canelas AB, Kiewiet J, Bouwman J, van Gulik WM, Westerhoff HV, Bakker BM", "Vrije Universiteit Amsterdam, Department of Molecular Cell Physiology, Amsterdam, The Netherlands.", "vanEunen_2010.pdf", "application/pdf", 756037, "2018-07-30T14:53:24.392Z", "30", "5.0 ± 0.1", "glucose", "chemostat", "0.1 and 0.35", nil, nil, true, "", nil, "1.0", "Yieldglu,X (g/g) = 0.45 ± 0.02 (D = 0.1h-1) and 0.29 ± 0.01 (D = 0.35h-1)", nil, "Samples were taken 15 min after the start of the fermentative capacity assay to the protocol described by Canelas et al. [2].", "Quenching and washing of the sample was done with 100% and 80% (v/v) methanol/water, respectively, at -40ºC.", "---\n- boiling ethanol\n", "---\n- LC-ESI-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "mM", "yeast, glycolysis, glucose-limited chemostat, nitrogen starvation", false, "17234", 2010, nil, "CHEBI:17665, CHEBI:88003, CHEBI:78682, CHEBI:132960, CHEBI:88350, CHEBI:18021, CHEBI:15361, CHEBI:17665, CHEBI:88003, CHEBI:78682, CHEBI:18021, CHEBI:15361", "doi.org/10.34619/wfa0-da34"] Administrator KiMoSys Data AccessID111 / EntryID111 [46, nil, "Original model source: in BioModels database.", "vanEunen_2012.pdf", nil, "2018-07-30T22:00:51.793Z", "Metabolism", "---\n- Model building\n- Model validation\n", "ordinary differential equations", "22570597", "", "vanEunen2012 - Yeast Glycolysis (glucose upshift)", "Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics", "Karen van Eunen, José A. L. Kiewiet, Hans V. Westerhoff, Barbara M. Bakker", "PLoS Computational Biology", "Department of Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands", "", "BIOMD1403250001", "yeast glycolysis, In Vivo and in Vitro Enzyme Kinetics, computational model", "MATLAB (MathWorks)", nil, "Saccharomyces cerevisiae", 2012, nil, nil, nil, nil, nil, nil] Administrator KiMoSys Model AccessID46 / EntryID46 | 2010 | chemostat | aerobic | yeast, glycolysis, glucose-limited chemostat, nitrogen starvation | CHEBI:17665, CHEBI:88003, CHEBI:78682, CHEBI:132960, CHEBI:88350, CHEBI:18021, CHEBI:15361, CHEBI:17665, CHEBI:88003, CHEBI:78682, CHEBI:18021, CHEBI:15361 |
| 112 | Escherichia coli | W3110 and pck mutant | metabolites at steady-state | — | |
[no] | [112, "Escherichia coli", "W3110 and pck mutant", "1", "KIMODATAID112_v0.xlsx", "12966569", "Biotechnology and Bioengineering", "Analysis of Escherichia coli Anaplerotic Metabolism and Its Regulation Mechanisms From the Metabolic Responses to Altered Dilution Rates and Phosphoenolpyruvate Carboxykinase Knockout.", "Yang C, Hua Q, Baba T, Mori H, Shimizu K", "Metabolome Unit, Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.", "Yang2003.pdf", "application/pdf", 372915, "2018-07-31T15:50:28.620Z", "37", "7.0", "glucose", "chemostat", "0.1, 0.32, 0.55 (WT ) and 0.1 (pck)", nil, nil, true, "", nil, "1.0", "Yield glu,X (g/g) = 0.40 ± 0.02 (D = 0.1h-1), 0.44 ± 0.02 (D = 0.32h-1) and 0.48 ± 0.03 (D = 0.55h-1) for WT; 0.46 ± 0.02 (D = 0.1h-1) for pck", nil, "not described", "To rapidly quench the cell metabolism, 5 mL of culture suspension was cooled to 0°C in a −50°C methanol bath within 15–20 s. Cells were separated from the culture medium by centrifugation, and resuspended in cold 100% methanol immediately.", "---\n- chloroform\n", "---\n- enzymatic\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "mM", "Escherichia coli; metabolic flux; 13C labeling; anaplerotic reaction; phosphoenolpyruvate carboxykinase; in vivo regulation", false, "17234", 2003, nil, "CHEBI:78682, CHEBI:132960, CHEBI:18021, CHEBI:15361, CHEBI:15351, CHEBI:30887, CHEBI:16810, CHEBI:25115, CHEBI:16452, CHEBI:29991, CHEBI:15422, CHEBI:16761", "doi.org/10.34619/qzt2-vk49"] Administrator KiMoSys Data AccessID112 / EntryID112 | 2003 | chemostat | aerobic | Escherichia coli; metabolic flux; 13C labeling; anaplerotic reaction; phosphoenolpyruvate carboxykinase; in vivo regulation | CHEBI:78682, CHEBI:132960, CHEBI:18021, CHEBI:15361, CHEBI:15351, CHEBI:30887, CHEBI:16810, CHEBI:25115, CHEBI:16452, CHEBI:29991, CHEBI:15422, CHEBI:16761 |
| 113 | Pichia pastoris | X-33 | metabolites at steady-state | — | |
[no] | [113, "Pichia pastoris", "X-33", "1", "KIMODATAID113_v0.xlsx", "22448155", "Metabolomics", "Development of quantitative metabolomics for Pichia pastoris.", "Marc Carnicer, Andre B. Canelas, Angela ten Pierick, Zhen Zeng, Jan van Dam, Joan Albiol, Pau Ferrer, Joseph J. Heijnen, Walter van Gulik", "Department of Chemical Engineering, Universitat Autonoma de Barcelona, 08193 Bellaterra (Cerdanyola del Valle`s), Spain", "Carnicer_2012.pdf", "application/pdf", 986763, "2018-08-01T15:36:45.690Z", "25", "5.0", "glucose", "chemostat", "0.1", nil, nil, true, "", nil, "4.0", "≈ 4.5 g/l", nil, "samples for intracellular metabolite analysis were taken using a dedicated rapid-sampling setup [2].", "approximately, 0.63 ± 0.01 g of broth was rapidly withdrawn and immediately injected in 5 ml of precooled quenching solution.", "---\n- hot ethanol\n", "---\n- GC-MS\n- LC-ESI-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "µmol/gDCW", "Pichia pastoris, Metabolite quantification, Quenching, Chemostat", false, "17234", 2012, nil, "CHEBI:17665, CHEBI:88003, CHEBI:78682, CHEBI:18021, CHEBI:30769, CHEBI:16810, CHEBI:26806, CHEBI:29806, CHEBI:25115, CHEBI:16218, CHEBI:48928, CHEBI:43896, CHEBI:18283, CHEBI:15978, CHEBI:15721, CHEBI:18066, CHEBI:16449, CHEBI:27266, CHEBI:25017, CHEBI:26986, CHEBI:26271, CHEBI:22653, CHEBI:22660, CHEBI:16811, CHEBI:18237, CHEBI:28044, CHEBI:28300, CHEBI:18257, CHEBI:25094, CHEBI:27570, CHEBI:18186, CHEBI:27897", "doi.org/10.34619/23ya-5n95"] Administrator KiMoSys Data AccessID113 / EntryID113 | 2012 | chemostat | aerobic | Pichia pastoris, Metabolite quantification, Quenching, Chemostat | CHEBI:17665, CHEBI:88003, CHEBI:78682, CHEBI:18021, CHEBI:30769, CHEBI:16810, CHEBI:26806, CHEBI:29806, CHEBI:25115, CHEBI:16218, CHEBI:48928, CHEBI:43896, CHEBI:18283, CHEBI:15978, CHEBI:15721, CHEBI:18066, CHEBI:16449, CHEBI:27266, CHEBI:25017, CHEBI:26986, CHEBI:26271, CHEBI:22653, CHEBI:22660, CHEBI:16811, CHEBI:18237, CHEBI:28044, CHEBI:28300, CHEBI:18257, CHEBI:25094, CHEBI:27570, CHEBI:18186, CHEBI:27897 |
| 114 | Pichia pastoris | X-33/pGAPaA_Fab and X-33/pGAPaA | flux measurements | — | |
[no] | [114, "Pichia pastoris", "X-33/pGAPaA_Fab and X-33/pGAPaA", "3", "KIMODATAID114_v1.xlsx", "20969759", "BMC Systems Biology", "A multi-level study of recombinant Pichia pastoris in different oxygen conditions.", "Kristin Baumann, Marc Carnicer, Martin Dragosits, Alexandra B Graf, Johannes Stadlmann, Paula Jouhten, Hannu Maaheimo, Brigitte Gasser, Joan Albiol, Diethard Mattanovich, Pau Ferrer", "Department of Chemical Engineering, Autonomous University of Barcelona, Spain", "Baumann_2010.pdf", "application/pdf", 1396363, "2018-08-18T22:44:26.432Z", "25", "5", "glucose", "chemostat", "0.1", nil, nil, true, "", nil, "1.0", "for O2 21% = 0.47 ± 0.02, for O2 11% = 0.45 ± 0.01 and for O2 8% = 0.25 ± 0.01", nil, "", "", "--- []\n", "--- []\n", "---\n- flux ratio\n- 13C constrained MFA\n", "---\n- NMR\n", "aerobic", "--- []\n", "(mmol/g.h)", "Hypoxic Condition, Unfold Protein Response, Pentose Phosphate Pathway, Metabolic Flux, Flux Ratio", false, "17234", 2010, nil, "R01092, R02740, R01641, R01830, R01827, R00209, R00351, R00267, R00342", "doi.org/10.34619/hew7-f341"] Administrator KiMoSys Data AccessID114 / EntryID114 | 2010 | chemostat | aerobic | Hypoxic Condition, Unfold Protein Response, Pentose Phosphate Pathway, Metabolic Flux, Flux Ratio | R01092, R02740, R01641, R01830, R01827, R00209, R00351, R00267, R00342 |
| 115 | Saccharomyces cerevisiae | 59A NADPH-Bdh | flux measurements | — | |
[no] | [115, "Saccharomyces cerevisiae", "59A NADPH-Bdh", "3", "KIMODATAID115_v0.xlsx", "22805527", "BMC Genomics", "A comparative transcriptomic, fluxomic and metabolomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation.", "Magalie Celton, Isabelle Sanchez, Anne Goelzer, Vincent Fromion, Carole Camarasa and Sylvie Dequin", "INRA, UMR1083 SPO, 2 place Viala, F-34060 Montpellier, France", "Celton_2012.pdf", "application/pdf", 1077632, "2018-08-19T19:03:08.183Z", "28", "5.0", "glucose", "batch", "—", nil, nil, true, "", nil, "0.01", "for acetoin 0 mM = 2.9g, for acetoin 100 mM = 2.55g, for acetoin 200 mM = 2.65g and for acetoin 300 mM = 2.17g", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- GC-MS\n", "anaerobic", "--- []\n", "mmol/100 mmol glucose", "NADPH, Pentose Phosphate Pathway, Acetoin, Intracellular Metabolite, NADPH Oxidation", false, "17234", 2012, nil, "", "doi.org/10.34619/chc4-e460"] Administrator KiMoSys Data AccessID115 / EntryID115 | 2012 | batch | anaerobic | NADPH, Pentose Phosphate Pathway, Acetoin, Intracellular Metabolite, NADPH Oxidation | |
| 116 | Escherichia coli | MG1655 and (pgi, ppc, pta, tpi) mutants | flux measurements | — | |
[no] | [116, "Escherichia coli", "MG1655 and (pgi, ppc, pta, tpi) mutants", "3", "KIMODATAID116_v2.xlsx", "16319065", "Journal of Biological Chemistry", "Latent Pathway Activation and Increased Pathway Capacity Enable Escherichia coli Adaptation to Loss of Key Metabolic Enzymes.", "Stephen S. Fong, Annik Nanchen, Bernhard O. Palsson and Uwe Sauer", "Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland", "Fong_2006.pdf", "application/pdf", 882915, "2018-08-22T22:28:56.155Z", "37", "not specified", "glucose", "batch", "—", nil, nil, true, "", nil, "0.03", "see spreadsheet", nil, "", "", "--- []\n", "--- []\n", "---\n- flux ratio\n- 13C constrained MFA\n", "---\n- GC-MS\n", "aerobic", "--- []\n", "mmol/gdw h", "Escherichia coli, latent pathway activation", false, "17234", 2006, nil, "R00835, R01528, R02740, R05605, R01641, R01067, R01827, R00661, R00200, R00209, R01082, R00342, R00214, R00341, R00341, R00235", "doi.org/10.34619/6s2r-n096"] Administrator KiMoSys Data AccessID116 / EntryID116 | 2006 | batch | aerobic | Escherichia coli, latent pathway activation | R00835, R01528, R02740, R05605, R01641, R01067, R01827, R00661, R00200, R00209, R01082, R00342, R00214, R00341, R00341, R00235 |
| 117 | Saccharomyces cerevisiae | CEN.PK113-1A | flux measurements | — | |
[no] | [117, "Saccharomyces cerevisiae", "CEN.PK113-1A", "3", "KIMODATAID117_v1.xlsx", "18613954", "BMC Systems Biology", "Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A", "Paula Jouhten, Eija Rintala, Anne Huuskonen, Anu Tamminen, Mervi Toivari, Marilyn Wiebe, Laura Ruohonen, Merja Penttilä and Hannu Maaheimo", "VTT Technical Research Centre of Finland, Espoo, Finland", "Jouhten_2008.pdf", "application/pdf", 756447, "2018-08-23T21:59:13.341Z", "30", "5.0", "glucose", "chemostat", "0.1", nil, nil, true, "", nil, "2.5", "see spreadsheet", nil, "", "", "--- []\n", "--- []\n", "---\n- flux ratio\n- 13C constrained MFA\n", "---\n- NMR\n", "aerobic and anaerobic", "--- []\n", "normalised to the specific glucose uptake rate", "Pentose Phosphate Pathway, Flux Distribution, Flux Ratio, Metabolic Flux Analysis, Central Carbon Metabolism", false, "17234", 2008, nil, "R00299, R02740, R01641, R01067, R01827, R00200, R00209, R00351, R00709, R00341, R00229, R00711, R00754", "doi.org/10.34619/x818-xy86"] Administrator KiMoSys Data AccessID117 / EntryID117 | 2008 | chemostat | aerobic and anaerobic | Pentose Phosphate Pathway, Flux Distribution, Flux Ratio, Metabolic Flux Analysis, Central Carbon Metabolism | R00299, R02740, R01641, R01067, R01827, R00200, R00209, R00351, R00709, R00341, R00229, R00711, R00754 |
| 118 | Escherichia coli | MG1655 and 2 over-expression strains (NOX, ATPase) | flux measurements | — | |
[no] | [118, "Escherichia coli", "MG1655 and 2 over-expression strains (NOX, ATPase)", "3", "KIMODATAID118_v1.xlsx", "20299454", "Journal of Biological Chemistry", "Metabolic and Transcriptional Response to Cofactor Perturbations in Escherichia coli.", "Anders K. Holm, Lars M. Blank, Marco Oldiges, Andreas Schmid, Christian Solem, Peter R. Jensen and Goutham N. Vemuri", "Department of Systems Biology, Center for Systems Microbiology, Technical University of Denmark, 2800 Denmark", "Holm_2010.pdf", "application/pdf", 1356725, "2018-08-24T18:15:24.388Z", "37", "not specified", "glucose", "batch", "—", nil, nil, true, "", nil, "0.1", "Biomass yield from glucose (g dry cell weight/g glucose): WT = 0.43 ± 0.02, NOX = 0.29 ± 0.03 and ATPase = 0.22 ± 0.00", nil, "", "", "--- []\n", "--- []\n", "---\n- flux ratio\n", "---\n- GC-MS\n- LC-MS\n", "aerobic", "--- []\n", "mmol/gdw h", "F1Fo ATPase, Glycolysis, Metabolic Regulation, Transcription Regulation, Tricarboxylic Acid (TCA) Cycle, Cofactor Perturbation, Escherichia coli, NADH Oxidase, Soluble ATPase, Systems Biology ", false, "17234", 2010, nil, "R02740, R00200, R01528, R10221, R01529, R01056, R01641, R01067, R01827, R00267, R00342, R01196, R00214, R00341, R00341, R00229, R00105", "doi.org/10.34619/qexq-m560"] Administrator KiMoSys Data AccessID118 / EntryID118 | 2010 | batch | aerobic | F1Fo ATPase, Glycolysis, Metabolic Regulation, Transcription Regulation, Tricarboxylic Acid (TCA) Cycle, Cofactor Perturbation, Escherichia coli, NADH Oxidase, Soluble ATPase, Systems Biology | R02740, R00200, R01528, R10221, R01529, R01056, R01641, R01067, R01827, R00267, R00342, R01196, R00214, R00341, R00341, R00229, R00105 |
| 119 | Escherichia coli | MG1655 and 2 over-expression strains (NOX, ATPase) | metabolites at steady-state | — | |
[no] | [119, "Escherichia coli", "MG1655 and 2 over-expression strains (NOX, ATPase)", "1", "KIMODATAID119_v0.xlsx", "20299454", "Journal of Biological Chemistry", "Metabolic and Transcriptional Response to Cofactor Perturbations in Escherichia coli.", "Anders K. Holm, Lars M. Blank, Marco Oldiges, Andreas Schmid, Christian Solem, Peter R. Jensen and Goutham N. Vemuri", "Department of Systems Biology, Center for Systems Microbiology, Technical University of Denmark, 2800 Denmark", "Holm_2010.pdf", "application/pdf", 1356725, "2018-08-25T15:22:03.610Z", "37", "not specified", "glucose", "batch", "—", nil, nil, true, "", nil, "0.1", "Biomass yield from glucose (g dry cell weight/g glucose): WT = 0.43 ± 0.02, NOX = 0.29 ± 0.03 and ATPase = 0.22 ± 0.00", nil, "aliquot of 5 ml of the culture from mid-exponential phase", "quenched in hot phenol (80 °C) and subsequently frozen at −20 °C.", "---\n- methanol-water\n", "---\n- LC-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "μmol/g DCW", "F1Fo ATPase, Glycolysis, Metabolic Regulation, Transcription Regulation, Tricarboxylic Acid (TCA) Cycle, Cofactor Perturbation, Escherichia coli, NADH Oxidase, Soluble ATPase, Systems Biology ", false, "17234", 2010, nil, "ChEBI:17665, ChEBI:15946, CHEBI:78682, CHEBI:16108, ChEBI:14336, CHEBI:44897, CHEBI:15361, ChEBI:48928, ChEBI:17797, CHEBI:15721, ChEBI:15351, ChEBI:133748, ChEBI:30887, CHEBI:15741, CHEBI:18012, ChEBI:25115, ChEBI:36655, ChEBI:16027, ChEBI:16761, ChEBI:15422, ChEBI:18009, ChEBI:16908, ChEBI:18009, ChEBI:16474, ChEBI:17345 , ChEBI:15996, ChEBI:17202, ChEBI:17677, ChEBI:18077, ChEBI:15713", "doi.org/10.34619/8qdf-kk03"] Administrator KiMoSys Data AccessID119 / EntryID119 | 2010 | batch | aerobic | F1Fo ATPase, Glycolysis, Metabolic Regulation, Transcription Regulation, Tricarboxylic Acid (TCA) Cycle, Cofactor Perturbation, Escherichia coli, NADH Oxidase, Soluble ATPase, Systems Biology | ChEBI:17665, ChEBI:15946, CHEBI:78682, CHEBI:16108, ChEBI:14336, CHEBI:44897, CHEBI:15361, ChEBI:48928, ChEBI:17797, CHEBI:15721, ChEBI:15351, ChEBI:133748, ChEBI:30887, CHEBI:15741, CHEBI:18012, ChEBI:25115, ChEBI:36655, ChEBI:16027, ChEBI:16761, ChEBI:15422, ChEBI:18009, ChEBI:16908, ChEBI:18009, ChEBI:16474, ChEBI:17345 , ChEBI:15996, ChEBI:17202, ChEBI:17677, ChEBI:18077, ChEBI:15713 |
| 120 | Saccharomyces cerevisiae | IMS0001 and IMS0002 | metabolites at steady-state | — | |
[no] | [120, "Saccharomyces cerevisiae", "IMS0001 and IMS0002 ", "1", "KIMODATAID120_v2.xlsx", "20816840", "Metabolic Engineering", "Metabolome, transcriptome and metabolic flux analysis of arabinose fermentation by engineered Saccharomyces cerevisiae", "H. Wouter Wisselink, Chiara Cipollina, Bart Oud, BarbaraCrimi, Joseph J. Heijnen, Jack T. Pronk, Antonius J.A.van Maris", "Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.", "Wisselink_2010.pdf", "application/pdf", 1219787, "2018-08-27T21:00:50.703Z", "30", "5.0", "glucose and arabinose", "chemostat", "0.03", nil, nil, true, "", nil, "1.0", "Biomass yield (g g−1) = 0.066±0.001 (IMS0001, Glucose), 0.072±0.003 (IMS0002, Glucose) and 0.075±0.001 (IMS0002, Arabinose) ", nil, "Sampling and sample preparation for analysis of intracellular metabolite concentrations was carried out as previously described in [1].", "1 ml of broth was rapidly quenched in 5 ml of −40 °C 60% (vol/vol) aqueous methanol. After centrifugation (2000g, −20 °C, 5 min), the pellet was resuspended in 5 ml of −40 °C 60% (vol/vol) aqueous methanol and centrifuged again.", "---\n- boiling ethanol\n", "---\n- GC-MS\n- LC-ESI-MS\n", "--- []\n", "--- []\n", "anaerobic", "--- []\n", "mmol/[gDW]", "Saccharomyces cerevisiae, Evolutionary engineering, Arabinose, Transcriptomics, Metabolomics, Metabolic flux ana", false, "", 2010, nil, "CHEBI:29042, CHEBI:17665, CHEBI:88003, CHEBI:78682, CHEBI:17138, CHEBI:16108, CHEBI:15361, CHEBI:15361, CHEBI:18012, CHEBI:15741, ChEBI:25115, ChEBI:30887", "doi.org/10.34619/9n86-re89"] Administrator KiMoSys Data AccessID120 / EntryID120 | 2010 | chemostat | anaerobic | Saccharomyces cerevisiae, Evolutionary engineering, Arabinose, Transcriptomics, Metabolomics, Metabolic flux ana | CHEBI:29042, CHEBI:17665, CHEBI:88003, CHEBI:78682, CHEBI:17138, CHEBI:16108, CHEBI:15361, CHEBI:15361, CHEBI:18012, CHEBI:15741, ChEBI:25115, ChEBI:30887 |
| 121 | Saccharomyces cerevisiae | IMS0001 and IMS0002 | flux measurements | — | |
[no] | [121, "Saccharomyces cerevisiae", "IMS0001 and IMS0002 ", "3", "KIMODATAID121_v0.xlsx", "20816840", "Metabolic Engineering", "Metabolome, transcriptome and metabolic flux analysis of arabinose fermentation by engineered Saccharomyces cerevisiae.", "H. Wouter Wisselink, Chiara Cipollina, Bart Oud, BarbaraCrimi, Joseph J. Heijnen, Jack T. Pronk, Antonius J.A.van Maris", "Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.", "Wisselink_2010.pdf", "application/pdf", 1219787, "2018-08-28T16:39:16.470Z", "30", "5.0", "glucose and arabinose", "chemostat", "0.03", nil, nil, true, "", nil, "1.0", "Biomass yield (g g−1) = 0.066±0.001 (IMS0001, Glucose), 0.072±0.003 (IMS0002, Glucose) and 0.075±0.001 (IMS0002, Arabinose) ", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- LC-MS\n", "anaerobic", "--- []\n", "normalised to the specific glucose uptake rate", "Saccharomyces cerevisiae, Evolutionary engineering, Arabinose, Transcriptomics, Metabolomics, Metabolic flux analysis", false, "", 2010, nil, "R00299, R02740, R00756, R01015, R01061, R00658, R00200, R00842, R01056, R01529, R01067, R01641, R01827, R00014, R00754, R00209, R00344, R00351, R01082, R00342, R00342, R02439", "doi.org/10.34619/9n86-re89"] Administrator KiMoSys Data AccessID121 / EntryID121 | 2010 | chemostat | anaerobic | Saccharomyces cerevisiae, Evolutionary engineering, Arabinose, Transcriptomics, Metabolomics, Metabolic flux analysis | R00299, R02740, R00756, R01015, R01061, R00658, R00200, R00842, R01056, R01529, R01067, R01641, R01827, R00014, R00754, R00209, R00344, R00351, R01082, R00342, R00342, R02439 |
| 122 | Saccharomyces cerevisiae | WT S288C and gcn4-knockout | flux measurements | — | |
[no] | [122, "Saccharomyces cerevisiae", "WT S288C and gcn4-knockout", "3", "KIMODATAID122_v1.xlsx", "19346491", "Proc Natl Acad Sci USA", "Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p.", "Joel F. Moxley, Michael C. Jewett, Maciek R. Antoniewicz, Silas G. Villas-Boas, Hal Alper, Robert T. Wheeler, Lily Tong, Alan G. Hinnebusch, Trey Ideker, Jens Nielsen, and Gregory Stephanopoulos", "Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139", "Moxley_2009.pdf", "application/pdf", 1325393, "2018-09-12T09:46:26.473Z", "30", "5.0", "glucose", "chemostat", "0.1", nil, nil, true, "", nil, "1.0", "not specified", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- GC-MS\n", "aerobic", "--- []\n", "", "amino acid stress response, fluxomics, gcn4, systems biology", false, "17234", 2009, nil, "R00299, R02740, R00756, R00200, R00014, R00754, R00227, R00217, R00341, R00344, R00209, R00351, R00709, R00351", "doi.org/10.34619/jq2x-5s79"] Administrator KiMoSys Data AccessID122 / EntryID122 | 2009 | chemostat | aerobic | amino acid stress response, fluxomics, gcn4, systems biology | R00299, R02740, R00756, R00200, R00014, R00754, R00227, R00217, R00341, R00344, R00209, R00351, R00709, R00351 |
| 123 | Saccharomyces cerevisiae | CEN.PK113-7D ΔLYS1 | enzyme/protein concentrations | — | |
[no] | [123, "Saccharomyces cerevisiae", "CEN.PK113-7D ΔLYS1", "4", "KIMODATAID123_v0.xlsx", "28365149", "Cell Systems", "Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast.", "Petri-Jaan Lahtvee, Benjamín J. Sánchez, Agata Smialowska, Sergo Kasvandik, Ibrahim E. Elsemman, Francesco Gatto, Jens Nielsen", "Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.", "Lahtvee_2017.pdf", "application/pdf", 2550326, "2018-09-20T17:22:27.258Z", "30", "5.5", "glucose", "chemostat", "0.1", nil, nil, true, "", nil, "1", "see original paper", nil, "", "", "--- []\n", "--- []\n", "--- []\n", "--- []\n", "aerobic", "---\n- LC-MS/MS\n", "pgDW", "integrative data analysis, absolute proteome, absolute transcriptome, protein turnover, protein degradation rates, translation efficiency, genome-scale metabolic modeling, translational control", false, "17234", 2017, nil, "P32471, P39704, P31373, P31377, P31383, P31384, P10962, P28005, P39730, P39729, P00549, P11433, P39727, P39726, P39715, P39715, P39714, Q05359, P39705, P22336, P27616, P35845, P35194, P32790, P32316, P36775, P38205, P38203, P38066, P38197, P38065, P28274, P23724, P07256, P34216, P32602, P34220, P34221, Q3E7A4, P34224, P34227, P38063, P09436, P38182, P38181, P38175, P38174, P38061, P38172, P38169, P07251, P24583, P35196, P18900, P38067, P00817, P38217, P38219, P38071, P38221, P38074, P38075, P23833, P38077, P38228, P38230, P38234, P38235, P38081, P38238, P15992, P38249, P18759, P15731, P09440, O43137, P38251, P15873, P38254, P38255, P38256, P38260, P38261, P38262, P38087, P38264, P06787, P16661, Q01976, P07702, P07253, P36531, P32367, Q00764, P16140, P38112, P12385, P38113, P38120, P38115, P38281, P20434, P33313, P38286, P00546, P38288, P38116, P20049, P32590, P33755, P33754, P38122, P38295, P05755, P38127, P12709, P38132, P15807, P38314, P32327, P32473, P38137, P38323, P38144, P38333, P33734, P32449, P33759, P33317, P32570, P38145, P38339, P37292, P36532, P38349, P38351, P38352, P38149, P38353, P37302, P38153, P38152, P25560, P25605, P25555, P25559, P25374, P04173, Q96VH4, P25367, P11709, P00815, P25368, P25373, P25567, P25569, P17709, P17967, P25573, P25574, P25576, P16550, P25580, P25375, P25586, P25342, P25349, P25343, P25371, P00560, P25616, P25617, P23060, P25619, P25345, P32445, P25623, P25359, P25626, P25631, P25632, P16120, P25355, P25635, P25337, P25642, P25382, P37262, P25372, P16649, P37263, P15891, P25655, Q03435, Q12165, P40327, P15646, Q99190, Q12451, Q00055, Q12100, P32381, Q12389, P12945, P10849, P38913, Q12408, P20604, P33399, P33333, Q07362, P41940, P25386, Q07381, P41058, Q07395, P50623, Q07418, P07255, Q07451, Q07457, P0C2H8, Q07468, P32419, P05318, Q12690, Q07478, Q07505, P38985, P33775, Q12377, Q12154, P39009, P43123, Q12513, Q07527, Q07528, Q07532, P52891, Q07534, Q07540, Q07541, Q07551, Q04344, P25694, P10622, Q12122, Q12018, P23594, Q12434, P04050, P39078, Q07589, Q07589, Q12250, Q99207, P25441, P39517, Q12518, P06100, Q12055, P32771, Q12680, P32891, P46681, P01097, P48570, P17255, P54860, P38968, P38988, Q12009, P36521, P28789, Q12315, P32495, Q02774, Q07623, P33327, Q07648, Q07655, Q07657, P35197, Q07688, P19881, Q07716, P32356, P41920, P32568, P48015, Q12099, P07284, Q12335, P14843, P15180, Q03201, P11353, P32347, Q04311, P00942, Q99288, Q12355, Q12176, Q12298, P40970, P05756, P54858, Q12447, P31688, Q3E7C1, P38958, P38959, P38962, P35179, P38966, Q03195, P52490, Q03834, Q03835, P34730, Q03862, P46944, Q04599, Q04600, Q04603, P13185, P08566, P32599, P16664, Q03919, Q03761, P19262, Q03768, Q03769, P14832, P13663, P30619, Q03774, P89102, Q12030, P06101, P11075, Q12329, P05453, Q03973, Q03976, P21734, Q03981, Q04004, P39079, P22213, Q03940, P15424, P42073, Q03941, Q03942, Q03956, P32501, P12612, Q12449, P07170, P11978, Q04934, Q04935, P09950, Q04947, P49367, Q03778, P36519, P41810, Q03782, P50108, Q03784, Q03786, P37304, Q12504, P33416, Q12331, Q05583, P04803, Q05584, Q05635, Q05636, P32916, P24276, Q05567, Q06629, Q06630, P09457, Q06631, P32264, Q06632, Q06639, P35176, P49775, P32776, P38986, Q06678, Q06679, P52286, Q06682", "doi.org/10.34619/tc9g-h956"] Administrator KiMoSys Data AccessID123 / EntryID123 | 2017 | chemostat | aerobic | integrative data analysis, absolute proteome, absolute transcriptome, protein turnover, protein degradation rates, translation efficiency, genome-scale metabolic modeling, translational control | P32471, P39704, P31373, P31377, P31383, P31384, P10962, P28005, P39730, P39729, P00549, P11433, P39727, P39726, P39715, P39715, P39714, Q05359, P39705, P22336, P27616, P35845, P35194, P32790, P32316, P36775, P38205, P38203, P38066, P38197, P38065, P28274, P23724, P07256, P34216, P32602, P34220, P34221, Q3E7A4, P34224, P34227, P38063, P09436, P38182, P38181, P38175, P38174, P38061, P38172, P38169, P07251, P24583, P35196, P18900, P38067, P00817, P38217, P38219, P38071, P38221, P38074, P38075, P23833, P38077, P38228, P38230, P38234, P38235, P38081, P38238, P15992, P38249, P18759, P15731, P09440, O43137, P38251, P15873, P38254, P38255, P38256, P38260, P38261, P38262, P38087, P38264, P06787, P16661, Q01976, P07702, P07253, P36531, P32367, Q00764, P16140, P38112, P12385, P38113, P38120, P38115, P38281, P20434, P33313, P38286, P00546, P38288, P38116, P20049, P32590, P33755, P33754, P38122, P38295, P05755, P38127, P12709, P38132, P15807, P38314, P32327, P32473, P38137, P38323, P38144, P38333, P33734, P32449, P33759, P33317, P32570, P38145, P38339, P37292, P36532, P38349, P38351, P38352, P38149, P38353, P37302, P38153, P38152, P25560, P25605, P25555, P25559, P25374, P04173, Q96VH4, P25367, P11709, P00815, P25368, P25373, P25567, P25569, P17709, P17967, P25573, P25574, P25576, P16550, P25580, P25375, P25586, P25342, P25349, P25343, P25371, P00560, P25616, P25617, P23060, P25619, P25345, P32445, P25623, P25359, P25626, P25631, P25632, P16120, P25355, P25635, P25337, P25642, P25382, P37262, P25372, P16649, P37263, P15891, P25655, Q03435, Q12165, P40327, P15646, Q99190, Q12451, Q00055, Q12100, P32381, Q12389, P12945, P10849, P38913, Q12408, P20604, P33399, P33333, Q07362, P41940, P25386, Q07381, P41058, Q07395, P50623, Q07418, P07255, Q07451, Q07457, P0C2H8, Q07468, P32419, P05318, Q12690, Q07478, Q07505, P38985, P33775, Q12377, Q12154, P39009, P43123, Q12513, Q07527, Q07528, Q07532, P52891, Q07534, Q07540, Q07541, Q07551, Q04344, P25694, P10622, Q12122, Q12018, P23594, Q12434, P04050, P39078, Q07589, Q07589, Q12250, Q99207, P25441, P39517, Q12518, P06100, Q12055, P32771, Q12680, P32891, P46681, P01097, P48570, P17255, P54860, P38968, P38988, Q12009, P36521, P28789, Q12315, P32495, Q02774, Q07623, P33327, Q07648, Q07655, Q07657, P35197, Q07688, P19881, Q07716, P32356, P41920, P32568, P48015, Q12099, P07284, Q12335, P14843, P15180, Q03201, P11353, P32347, Q04311, P00942, Q99288, Q12355, Q12176, Q12298, P40970, P05756, P54858, Q12447, P31688, Q3E7C1, P38958, P38959, P38962, P35179, P38966, Q03195, P52490, Q03834, Q03835, P34730, Q03862, P46944, Q04599, Q04600, Q04603, P13185, P08566, P32599, P16664, Q03919, Q03761, P19262, Q03768, Q03769, P14832, P13663, P30619, Q03774, P89102, Q12030, P06101, P11075, Q12329, P05453, Q03973, Q03976, P21734, Q03981, Q04004, P39079, P22213, Q03940, P15424, P42073, Q03941, Q03942, Q03956, P32501, P12612, Q12449, P07170, P11978, Q04934, Q04935, P09950, Q04947, P49367, Q03778, P36519, P41810, Q03782, P50108, Q03784, Q03786, P37304, Q12504, P33416, Q12331, Q05583, P04803, Q05584, Q05635, Q05636, P32916, P24276, Q05567, Q06629, Q06630, P09457, Q06631, P32264, Q06632, Q06639, P35176, P49775, P32776, P38986, Q06678, Q06679, P52286, Q06682 |
| 124 | Saccharomyces cerevisiae | CEN.PK113-7D and 38 mutants | flux measurements | — | |
[no] | [124, "Saccharomyces cerevisiae", "CEN.PK113-7D and 38 mutants", "3", "KIMODATAID124_v2.xlsx", "15960801", "BMC Genome Biology", "Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast.", "Lars M Blank, Lars Kuepfer and Uwe Sauer", "Institute of Biotechnology, ETH Zürich, 8093 Zürich, Switzerland", "Blank_2005.pdf", "application/pdf", 318008, "2018-09-25T13:20:17.178Z", "30", "5", "glucose", "batch", "—", nil, nil, true, "", nil, "0.0012", "see worksheet", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- GC-MS\n", "aerobic", "--- []\n", "mmol/gh", "Pentose Phosphate Pathway, Flux Analysis, Glucose Uptake Rate, Oxidative Pentose Phosphate Pathway", false, "17234", 2005, nil, "R00299, R02740, R01641, R01067, R01827, R00200, R00209, R00351, R00709, R00272, R00402, R00342, R01082, R00214, R00345, R00341, R00229, R00711, R00754, R01036, R00224", "doi.org/10.34619/zm8j-kk21"] Administrator KiMoSys Data AccessID124 / EntryID124 | 2005 | batch | aerobic | Pentose Phosphate Pathway, Flux Analysis, Glucose Uptake Rate, Oxidative Pentose Phosphate Pathway | R00299, R02740, R01641, R01067, R01827, R00200, R00209, R00351, R00709, R00272, R00402, R00342, R01082, R00214, R00345, R00341, R00229, R00711, R00754, R01036, R00224 |
| 125 | Escherichia coli | BW25113 | flux measurements | — | |
[no] | [125, "Escherichia coli", "BW25113", "3", "KIMODATAID125_v2.xlsx", "27136056", "Cell Systems", "Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data.", "Luca Gerosa, Bart R.B. Haverkorn van Rijsewijk, Dimitris Christodoulou, Karl Kochanowski, Thomas S.B. Schmidt, Elad Noor, Uwe Sauer", "Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland; Systems Biology Graduate School, Zurich 8057, Switzerland. ", "Gerosa_2015.pdf", "application/pdf", 5007487, "2018-09-25T22:34:51.419Z", "37", "not specified", "acetate, fructose, galactose, glucose, glycerol, gluconate, pyruvate, succinate", "batch", "—", nil, nil, true, "", nil, "0.0035", "see worksheet", nil, "", "", "--- []\n", "--- []\n", "---\n- 13C constrained MFA\n", "---\n- LC-MS\n", "aerobic", "--- []\n", "mmol/gh", "computational biology; metabolism; metabolomics; regulation network; transcription factor", false, "", 2015, nil, "R00771, R00756, R01068, R01015, R03145, R02036, R01056, R01529, R01067, R00345, R00341, R00267, R02164, R01082, R00214", "doi.org/10.34619/3x35-dd84"] Administrator KiMoSys Data AccessID125 / EntryID125 | 2015 | batch | aerobic | computational biology; metabolism; metabolomics; regulation network; transcription factor | R00771, R00756, R01068, R01015, R03145, R02036, R01056, R01529, R01067, R00345, R00341, R00267, R02164, R01082, R00214 |
| 126 | Escherichia coli | BW25113 | metabolites at steady-state | — | |
[no] | [126, "Escherichia coli", "BW25113", "1", "KIMODATAID126_v0.xlsx", "27136056", "Cell Systems", "Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data.", "Luca Gerosa, Bart R.B., Haverkorn van Rijsewijk, Dimitris Christodoulou, Karl Kochanowski, Thomas S.B. Schmidt, Elad Noor, Uwe Sauer", "Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland; Systems Biology Graduate School, Zurich 8057, Switzerland. ", "Gerosa_2015.pdf", "application/pdf", 5007487, "2018-10-01T08:52:44.480Z", "37", "not specified", "acetate, fructose, galactose, glucose, glycerol, gluconate, pyruvate, succinate", "batch", "—", nil, nil, true, "", nil, "0.0035", "see worksheet", nil, "1 ml aliquots were taken in a 37°C room from exponential phase cultures.", "Filters were directly subjected to cold extraction (-20°C) with 40:40:20 acetonitrile/methanol/water containing 200 μl of internal standard (fully 13C-labelled S. cerevisiae extract).", "---\n- boiling ethanol\n", "---\n- LC-MS\n", "--- []\n", "--- []\n", "aerobic", "--- []\n", "µmol * gCDW-1", "computational biology; metabolism; metabolomics; regulation network; transcription factor", false, "", 2015, nil, "ChEBI:16761, ChEBI:16027, ChEBI:15422, ChEBI:29985, ChEBI:18050, ChEBI:17196, ChEBI:22660, ChEBI:18186, ChEBI:29016, ChEBI:16708, ChEBI:28044, ChEBI:17552, ChEBI:17345, ChEBI:15996, ChEBI:13389, ChEBI:16908, ChEBI:18009 , ChEBI:16474, ChEBI:57604, ChEBI:15925, ChEBI:78697, ChEBI:16108, ChEBI:14314, ChEBI:16863, ChEBI:18021, ChEBI:15361, ChEBI:78682, ChEBI:48153, ChEBI:18189, ChEBI:17363, ChEBI:15721, ChEBI:16332, ChEBI:30769, ChEBI:30769, ChEBI:26806, ChEBI:17489, ChEBI:78737, ChEBI:53025, ChEBI:15978", "doi.org/10.34619/95b1-rz37"] Administrator KiMoSys Data AccessID126 / EntryID126 | 2015 | batch | aerobic | computational biology; metabolism; metabolomics; regulation network; transcription factor | ChEBI:16761, ChEBI:16027, ChEBI:15422, ChEBI:29985, ChEBI:18050, ChEBI:17196, ChEBI:22660, ChEBI:18186, ChEBI:29016, ChEBI:16708, ChEBI:28044, ChEBI:17552, ChEBI:17345, ChEBI:15996, ChEBI:13389, ChEBI:16908, ChEBI:18009 , ChEBI:16474, ChEBI:57604, ChEBI:15925, ChEBI:78697, ChEBI:16108, ChEBI:14314, ChEBI:16863, ChEBI:18021, ChEBI:15361, ChEBI:78682, ChEBI:48153, ChEBI:18189, ChEBI:17363, ChEBI:15721, ChEBI:16332, ChEBI:30769, ChEBI:30769, ChEBI:26806, ChEBI:17489, ChEBI:78737, ChEBI:53025, ChEBI:15978 |
| 128 | Saccharomyces cerevisiae | FY4 | flux measurements | — | |
[no] | [128, "Saccharomyces cerevisiae", "FY4", "3", nil, "20167065", "BMC Systems Biology", "Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates", "Sarah-Maria Fendt, Uwe Sauer", "Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland", nil, nil, nil, nil, "30", "not applicable", "glucose, galactose, mannose, pyruvate", "batch", "not applicable", nil, nil, true, "", nil, "0,0012", "see Table 1", "2009-03-09", "", "", "[\"\"]", "[\"\"]", "[\"\", \"13C constrained MFA\"]", "[\"\", \"GC-MS\"]", "aerobic", "[\"\"]", "mmol/g*h", "Saccharomyces cerevisiae, Flux Analysis, FY4, Yeast", false, "17234, 28260, 37681, 15361", 2010, nil, "R02740, R01641, R01067, R01827, R00200, R01196, R00351, R00267, R00272, R00402, R00342, R01082, R00214, R00341, R00341, R00229, R00711, R00754, R01036, R00224", nil] Hugo Mochão Data AccessID128 / EntryID128 | 2010 | batch | aerobic | Saccharomyces cerevisiae, Flux Analysis, FY4, Yeast | R02740, R01641, R01067, R01827, R00200, R01196, R00351, R00267, R00272, R00402, R00342, R01082, R00214, R00341, R00341, R00229, R00711, R00754, R01036, R00224 |
| 129 | mus | C57bl6 | flux measurements | DNL | |
[no] | [129, "mus", "C57bl6", "3", nil, "34145255", "Nature Communication", "Measurement of Lipogenic Flux by Deuterium Resolved Mass Spectrometry", "Xiaorong Fu, Stanisław Deja, Justin A. Fletcher, Norma N. Anderson, Monika Mizerska, Gonçalo Vale, Jeffrey D Browning, Jay D. Horton, Jeffrey G. McDonald, Matthew A. Mitsche, and Shawn C. Burgess", "UT Southwestern Medical Center", nil, nil, nil, nil, "37", "7.4", "", "fed-batch", "", nil, nil, true, "DNL", nil, "", "", "0005-05-21", "", "", "[\"\"]", "[\"\"]", "[\"\"]", "[\"\"]", "", "[\"\"]", "fraction", "Lipogenesis, Liver, palmitate, fatty acid synthase, deuterated water, deuterium, orbitrap, mass spectrometry", false, "", 2021, nil, "K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665", nil] Shawn Burgess Data AccessID129 / EntryID129 | 2021 | fed-batch | Lipogenesis, Liver, palmitate, fatty acid synthase, deuterated water, deuterium, orbitrap, mass spectrometry | K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665 | |
| 130 | homo sapiens | Normal volunteers | flux measurements | DNL | |
[no] | [130, "homo sapiens", "Normal volunteers", "3", nil, "", "Nature Communication", "Measurement of Lipogenic Flux by Deuterium Resolved Mass Spectrometry", "Xiaorong Fu, Stanisław Deja, Justin A. Fletcher, Norma N. Anderson, Monika Mizerska, Gonçalo Vale, Jeffrey D Browning, Jay D. Horton, Jeffrey G. McDonald, Matthew A. Mitsche, and Shawn C. Burgess", "UT Southwestern Medical Center", nil, nil, nil, nil, "37", "7.4", "deuterated water", "batch", "", nil, nil, true, "DNL", nil, "", "", "0005-05-21", "", "", "[\"\"]", "[\"\"]", "[\"\"]", "[\"\"]", "", "[\"\"]", "fractional dnl", "Lipogenesis, Liver, palmitate, fatty acid synthase, deuterated water, deuterium, orbitrap, mass spectrometry, human", false, "15377", 2021, nil, "K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665", nil] Shawn Burgess Data AccessID130 / EntryID130 | 2021 | batch | Lipogenesis, Liver, palmitate, fatty acid synthase, deuterated water, deuterium, orbitrap, mass spectrometry, human | K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665, K00665 |
DataEntryID 30 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 13 | Chassagnole2002_Carbon_Metabolism | Metabolism | ordinary differential equations | Model building and Model validation | |
{"id":13,"organism_id":30,"comments":"Original model source: in BioModels database.","sbml_file_name":"Chassagnole_2002.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"17590932","dilution_rate":"0.1","name_of_model":"Chassagnole2002_Carbon_Metabolism","manuscript_title":"Dynamic modeling of the central carbon metabolism of Escherichia coli.","authors":"Christophe Chassagnole, Naruemol Noisommit-Rizzi, Joachim W. Schmid, Klaus Mauch, Matthias Reuss","journal":"Biotechnology and Bioengineering","affiliation":"Institute of Biochemical Engineering, University of Stuttgart ","project_name":"","biomodels_id":"BIOMD0000000051","keywords":"dynamic model, Escherichia coli, parameter fitting, flux control coefficients","software":"","control":"2014-03-19T14:31:21.179Z","main_organism":"Escherichia coli","year":2002,"combine_archive_file_name":"COMBINE_KIMOMODELID13.omex","combine_archive_content_type":"application/omex+xml","combine_archive_file_size":249522,"combine_archive_updated_at":"2014-06-30T17:38:01.875Z","review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 35 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 36 | Kinetic model of Escherichia coli core metabolism | Metabolism | ordinary differential equations | Model building and Model validation | |
{"id":36,"organism_id":null,"comments":"","sbml_file_name":"Khodayari_2014.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"24928774","dilution_rate":"","name_of_model":"Kinetic model of Escherichia coli core metabolism","manuscript_title":"A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data.","authors":"Ali Khodayari, Ali R. Zomorrodi, James C.Liao, Costas D. Maranas","journal":"Metabolic Engineering","affiliation":"Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA","project_name":"","biomodels_id":"","keywords":"ensemble modeling, kinetic modeling, metabolic network","software":"http://www.matlab.com (MATLAB)","control":null,"main_organism":"Escherichia coli","year":2014,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
| 38 | E. coli Central Carbon Metabolism | Metabolism | ordinary differential equations | Model building and Model validation | |
{"id":38,"organism_id":null,"comments":"MATLAB version of the model is available at http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html. ","sbml_file_name":"Jahan_2016.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"27329289","dilution_rate":"0.2, 0.4, 0.5 and 0.7","name_of_model":"E. coli Central Carbon Metabolism","manuscript_title":"Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli","authors":"Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto and Hiroyuki Kurata","journal":"Microbial Cell Factories","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680‑4 Kawazu, Iizuka, Fukuoka 820‑8502, Japan","project_name":"","biomodels_id":"","keywords":"Systems biology, Rational design, Dynamic model, Enzyme kinetics, Transcription factor, Signal transduction, Allosteric enzyme","software":"MATLAB2007 or higher","control":"2018-07-20T16:47:46.311Z","main_organism":"Escherichia coli","year":2016,"combine_archive_file_name":"COMBINE_KIMOMODELID38.omex","combine_archive_content_type":"application/octet-stream","combine_archive_file_size":6603649,"combine_archive_updated_at":"2018-07-23T21:38:00.461Z","review_journal_id":null,"doi":null} Administrator KiMoSys |
| 41 | Continuous kinetic model of Escherichia coli | Metabolism | ordinary differential equations | Model building and Model validation | |
{"id":41,"organism_id":null,"comments":"Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.","sbml_file_name":"Kurata_2018.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"29054464","dilution_rate":"0.2, 0.4, 0.5 and 0.7","name_of_model":"Continuous kinetic model of Escherichia coli","manuscript_title":"Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures","authors":"Hiroyuki Kurata and Yurie Sugimoto","journal":"Journal of Bioscience and Bioengineering","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan","project_name":"","biomodels_id":"","keywords":"Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli","software":"MATLAB (MathWorks)","control":"2018-07-24T15:46:04.831Z","main_organism":"Escherichia coli","year":2018,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
| 42 | kinetic model of the central carbon metabolism of E. coli | Metabolism | ordinary differential equations | Model building | |
{"id":42,"organism_id":null,"comments":"For the analysis and evaluation of the kinetic model, the solver ode15s was used.","sbml_file_name":"Mannan_2015.PDF","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"26469081","dilution_rate":"0.2","name_of_model":"kinetic model of the central carbon metabolism of E. coli ","manuscript_title":"Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.","authors":"Ahmad A. Mannan, Yoshihiro Toya, Kazuyuki Shimizu, Johnjoe McFadden, Andrzej M. Kierzek , Andrea Rocco","journal":"Plos One","affiliation":"Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, United Kingdom ","project_name":"","biomodels_id":"","keywords":"E. coli, Bistability, Central Metabolism","software":"MATLAB® R2007b (version 7.5.0)","control":null,"main_organism":"Escherichia coli","year":2015,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 37 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 23 | glycolysis Lactococcus lactis | Metabolism | ordinary differential equations | Model building and Model validation | |
{"id":23,"organism_id":37,"comments":"Original model source: in JWS online database.","sbml_file_name":"Levering_2012.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"22325620","dilution_rate":"","name_of_model":"glycolysis Lactococcus lactis","manuscript_title":"Role of phosphate in the central metabolism of two lactic acid bacteria - a comparative systems biology approach.","authors":"Jennifer Levering, Mark W. J. M. Musters, Martijn Bekker, Domenico Bellomo, Tomas Fiedler, Willem M. de Vos, Jeroen Hugenholtz, Bernd Kreikemeyer, Ursula Kummer and Bas Teusink","journal":"FEBS Journal","affiliation":"Department of Modeling of Biological Processes, COS Heidelberg ⁄ BIOQUANT, University of Heidelberg, Germany","project_name":"","biomodels_id":"levering1","keywords":"Lactococcus lactis, metabolism of glucose, NMR, in vivo","software":"http://www.copasi.org (COPASI)","control":"2014-03-10T11:18:15.244Z","main_organism":"Lactococcus lactis","year":2012,"combine_archive_file_name":"COMBINE_KIMOMODELID23.omex","combine_archive_content_type":"application/omex+xml","combine_archive_file_size":1068365,"combine_archive_updated_at":"2014-06-30T17:53:53.205Z","review_journal_id":null,"doi":null} Administrator KiMoSys |
| 24 | DEB L. lactis model | Metabolism | ordinary differential equations | Model building | |
{"id":24,"organism_id":37,"comments":"Archive containing all files to run and plot simulations. Requires MATLAB.","sbml_file_name":"Vinga_2010.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"20921043","dilution_rate":"","name_of_model":"DEB L. lactis model","manuscript_title":"Subcellular metabolic organization in the context of dynamic energy budget and biochemical systems theories","authors":"Susana Vinga, Ana R. Neves, Helena Santos, B. W. Brandt and S. A. L. M. Kooijman","journal":"Philosophical transactions of the royal society B","affiliation":"Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID)","project_name":"","biomodels_id":"","keywords":"Lactococcus lactis, metabolism of glucose, NMR, in vivo","software":"http://www.matlab.com (MATLAB)","control":"2014-05-15T09:26:26.874Z","main_organism":"Lactococcus lactis","year":2010,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
| 35 | glycolysis Lactococcus lactis for mannitol and 2,3-butanediol production | Metabolism | ordinary differential equations | Model building and Model validation | |
{"id":35,"organism_id":null,"comments":" Copasi model file used to produce manuscript figures.","sbml_file_name":"Costa_2014.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"24413179","dilution_rate":"—","name_of_model":"glycolysis Lactococcus lactis for mannitol and 2,3-butanediol production","manuscript_title":"An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production","authors":"Rafael S. Costa, Andras Hartmann, Paula Gaspar, Ana R. Neves and Susana Vinga","journal":"Molecular BioSystems","affiliation":"Instituto de Engenharia de Sistemas e Computadores, Investigacão e Desenvolvimento (INESC-ID), R Alves Redol 9, 1000-029 Lisboa, Portugal.","project_name":"PneumoSyS","biomodels_id":"","keywords":"L. lactis, extended model, mannitol and 2,3-butanediol production, control analysis","software":"http://www.copasi.org (COPASI)","control":"2014-07-21T10:18:41.595Z","main_organism":"Lactococcus lactis","year":2014,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Rafael Costa |
DataEntryID 38 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 16 | glycolysis Escherichia coli model | Metabolism | ordinary differential equations | Model validation | |
{"id":16,"organism_id":38,"comments":"","sbml_file_name":"Kadir_2010.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"21092096","dilution_rate":"—","name_of_model":"glycolysis Escherichia coli model","manuscript_title":"Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.","authors":"Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu","journal":"Microbial Cell Factories","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan","project_name":"","biomodels_id":"","keywords":"Escherichia coli, single-gene knockouts, main central metabolism and TCA","software":"http://www.matlab.com (MATLAB)","control":"2018-07-21T20:34:09.507Z","main_organism":"Escherichia coli","year":2010,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
| 38 | E. coli Central Carbon Metabolism | Metabolism | ordinary differential equations | Model building and Model validation | |
{"id":38,"organism_id":null,"comments":"MATLAB version of the model is available at http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html. ","sbml_file_name":"Jahan_2016.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"27329289","dilution_rate":"0.2, 0.4, 0.5 and 0.7","name_of_model":"E. coli Central Carbon Metabolism","manuscript_title":"Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli","authors":"Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto and Hiroyuki Kurata","journal":"Microbial Cell Factories","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680‑4 Kawazu, Iizuka, Fukuoka 820‑8502, Japan","project_name":"","biomodels_id":"","keywords":"Systems biology, Rational design, Dynamic model, Enzyme kinetics, Transcription factor, Signal transduction, Allosteric enzyme","software":"MATLAB2007 or higher","control":"2018-07-20T16:47:46.311Z","main_organism":"Escherichia coli","year":2016,"combine_archive_file_name":"COMBINE_KIMOMODELID38.omex","combine_archive_content_type":"application/octet-stream","combine_archive_file_size":6603649,"combine_archive_updated_at":"2018-07-23T21:38:00.461Z","review_journal_id":null,"doi":null} Administrator KiMoSys |
| 45 | Batch kinetic model of Escherichia coli | Metabolism | ordinary differential equations | Model building | |
{"id":45,"organism_id":null,"comments":"Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.","sbml_file_name":"Kurata_2018.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"29054464","dilution_rate":"—","name_of_model":"Batch kinetic model of Escherichia coli","manuscript_title":"Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures","authors":"Hiroyuki Kurata and Yurie Sugimoto","journal":"Journal of Bioscience and Bioengineering","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan","project_name":"","biomodels_id":"","keywords":"Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli","software":"MATLAB (MathWorks)","control":null,"main_organism":"Escherichia coli","year":2018,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 41 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 42 | kinetic model of the central carbon metabolism of E. coli | Metabolism | ordinary differential equations | Model building | |
{"id":42,"organism_id":null,"comments":"For the analysis and evaluation of the kinetic model, the solver ode15s was used.","sbml_file_name":"Mannan_2015.PDF","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"26469081","dilution_rate":"0.2","name_of_model":"kinetic model of the central carbon metabolism of E. coli ","manuscript_title":"Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.","authors":"Ahmad A. Mannan, Yoshihiro Toya, Kazuyuki Shimizu, Johnjoe McFadden, Andrzej M. Kierzek , Andrea Rocco","journal":"Plos One","affiliation":"Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, United Kingdom ","project_name":"","biomodels_id":"","keywords":"E. coli, Bistability, Central Metabolism","software":"MATLAB® R2007b (version 7.5.0)","control":null,"main_organism":"Escherichia coli","year":2015,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 42 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 19 | first forward shift | Metabolism | ordinary differential equations | Model building | |
{"id":19,"organism_id":42,"comments":"","sbml_file_name":"Haus_2011.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"21247470","dilution_rate":"0.1","name_of_model":"first forward shift","manuscript_title":"A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.","authors":"Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer","journal":"BMC Systems Biology","affiliation":"University of Rostock, Institute of Computer Science, Department of Systems Biology \u0026 Bioinformatics","project_name":"","biomodels_id":"","keywords":"Clostridium acetobutylicum, continuous culture, effect of pH, solvent production","software":" http://www.sbtoolbox.org (SBToolbox)","control":"2014-04-11T17:25:43.341Z","main_organism":"Clostridium acetobutylicum","year":2011,"combine_archive_file_name":"COMBINE_KIMOMODELID19.omex","combine_archive_content_type":"application/omex+xml","combine_archive_file_size":401646,"combine_archive_updated_at":"2014-06-30T20:38:42.907Z","review_journal_id":null,"doi":null} Administrator KiMoSys |
| 20 | second forward shift | Metabolism | ordinary differential equations | Model building | |
{"id":20,"organism_id":42,"comments":"","sbml_file_name":"Haus_2011.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"21247470","dilution_rate":"0.1","name_of_model":"second forward shift","manuscript_title":"A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.","authors":"Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer","journal":"BMC Systems Biology","affiliation":"University of Rostock, Institute of Computer Science, Department of Systems Biology \u0026 Bioinformatics","project_name":"","biomodels_id":"","keywords":"Clostridium acetobutylicum, continuous culture, effect of pH, solvent production","software":"http://www.sbtoolbox.org (SBToolbox)","control":"2014-04-11T17:26:19.201Z","main_organism":"Clostridium acetobutylicum","year":2011,"combine_archive_file_name":"COMBINE_KIMOMODELID20.omex","combine_archive_content_type":"application/omex+xml","combine_archive_file_size":401633,"combine_archive_updated_at":"2014-06-30T20:39:10.028Z","review_journal_id":null,"doi":null} Administrator KiMoSys |
| 21 | third forward shift | Metabolism | ordinary differential equations | Model building | |
{"id":21,"organism_id":42,"comments":"","sbml_file_name":"Haus_2011.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"21247470","dilution_rate":"0.1","name_of_model":"third forward shift","manuscript_title":"A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.","authors":"Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer","journal":"BMC Systems Biology","affiliation":"University of Rostock, Institute of Computer Science, Department of Systems Biology \u0026 Bioinformatics","project_name":"","biomodels_id":"","keywords":"Clostridium acetobutylicum, continuous culture, effect of pH, solvent production","software":"http://www.sbtoolbox.org (SBToolbox)","control":"2014-04-11T17:24:43.452Z","main_organism":"Clostridium acetobutylicum","year":2011,"combine_archive_file_name":"COMBINE_KIMOMODELID21.omex","combine_archive_content_type":"application/omex+xml","combine_archive_file_size":401643,"combine_archive_updated_at":"2014-06-30T20:39:32.642Z","review_journal_id":null,"doi":null} Administrator KiMoSys |
| 22 | reverse forward shift | Metabolism | ordinary differential equations | Model building | |
{"id":22,"organism_id":42,"comments":"","sbml_file_name":"Haus_2011.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"21247470","dilution_rate":"0.1","name_of_model":"reverse forward shift","manuscript_title":"A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.","authors":"Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer","journal":"BMC Systems Biology","affiliation":"University of Rostock, Institute of Computer Science, Department of Systems Biology \u0026 Bioinformatics","project_name":"","biomodels_id":"","keywords":"Clostridium acetobutylicum, continuous culture, effect of pH, solvent production","software":"http://www.sbtoolbox.org (SBToolbox)","control":"2014-04-11T17:27:26.964Z","main_organism":"Clostridium acetobutylicum","year":2011,"combine_archive_file_name":"COMBINE_KIMOMODELID22.omex","combine_archive_content_type":"application/omex+xml","combine_archive_file_size":401628,"combine_archive_updated_at":"2014-06-30T20:39:48.510Z","review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 44 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 42 | kinetic model of the central carbon metabolism of E. coli | Metabolism | ordinary differential equations | Model building | |
{"id":42,"organism_id":null,"comments":"For the analysis and evaluation of the kinetic model, the solver ode15s was used.","sbml_file_name":"Mannan_2015.PDF","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"26469081","dilution_rate":"0.2","name_of_model":"kinetic model of the central carbon metabolism of E. coli ","manuscript_title":"Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.","authors":"Ahmad A. Mannan, Yoshihiro Toya, Kazuyuki Shimizu, Johnjoe McFadden, Andrzej M. Kierzek , Andrea Rocco","journal":"Plos One","affiliation":"Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, United Kingdom ","project_name":"","biomodels_id":"","keywords":"E. coli, Bistability, Central Metabolism","software":"MATLAB® R2007b (version 7.5.0)","control":null,"main_organism":"Escherichia coli","year":2015,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 63 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 25 | Nitrogen assimilation model | Metabolism | ordinary differential equations | Model building and Model validation | |
{"id":25,"organism_id":63,"comments":"","sbml_file_name":"Yuan_2009.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"19690571","dilution_rate":"—","name_of_model":"Nitrogen assimilation model","manuscript_title":"Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.","authors":"Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen and Joshua D Rabinowitz","journal":"Molecular Systems Biology","affiliation":"Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA and Department of Chemistry, Princeton University, Princeton, NJ, USA","project_name":"","biomodels_id":"","keywords":"E. coli, ammonia assimilation, nitrogen upshift, differential equations, sensitivity analysis","software":"written in C++","control":"2014-04-11T17:38:32.527Z","main_organism":"Escherichia coli","year":2009,"combine_archive_file_name":"COMBINE_KIMOMODELID25.omex","combine_archive_content_type":"application/omex+xml","combine_archive_file_size":645413,"combine_archive_updated_at":"2014-06-30T17:56:44.644Z","review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 69 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 28 | Model for respiro-fermentative growth on glucose | Metabolism | ordinary differential equations | Model building | |
{"id":28,"organism_id":69,"comments":"","sbml_file_name":"Bosch_2008.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"18042231","dilution_rate":"—","name_of_model":"Model for respiro-fermentative growth on glucose","manuscript_title":"Characterization of glucose transport mutants of Saccharomyces cerevisiae during a nutritional upshift reveals a correlation between metabolite levels and glycolytic flux.","authors":"Daniel Bosch, Mikael Johansson, Cecilia Ferndahl, Carl Johan Franzén, Christer Larsson and Lena Gustafsson","journal":"FEMS Yeast Research","affiliation":"Molecular Biotechnology and Chemical reaction Engineering, Department of Chemical and Biological Engineering, Chalmers University of Technology, Goeteborg, Sweden","project_name":"","biomodels_id":"","keywords":"fitting, glucose pulse, Saccharomyce cerevisae, respiro-fermentative growth on glucose,","software":"http://www.matlab.com (MATLAB)","control":"2014-04-11T17:42:47.759Z","main_organism":"Saccharomyces cerevisiae","year":2008,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 70 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 28 | Model for respiro-fermentative growth on glucose | Metabolism | ordinary differential equations | Model building | |
{"id":28,"organism_id":69,"comments":"","sbml_file_name":"Bosch_2008.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"18042231","dilution_rate":"—","name_of_model":"Model for respiro-fermentative growth on glucose","manuscript_title":"Characterization of glucose transport mutants of Saccharomyces cerevisiae during a nutritional upshift reveals a correlation between metabolite levels and glycolytic flux.","authors":"Daniel Bosch, Mikael Johansson, Cecilia Ferndahl, Carl Johan Franzén, Christer Larsson and Lena Gustafsson","journal":"FEMS Yeast Research","affiliation":"Molecular Biotechnology and Chemical reaction Engineering, Department of Chemical and Biological Engineering, Chalmers University of Technology, Goeteborg, Sweden","project_name":"","biomodels_id":"","keywords":"fitting, glucose pulse, Saccharomyce cerevisae, respiro-fermentative growth on glucose,","software":"http://www.matlab.com (MATLAB)","control":"2014-04-11T17:42:47.759Z","main_organism":"Saccharomyces cerevisiae","year":2008,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 77 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 30 | Kinetic model of Shewanella oneidensis MR-1 | Metabolism | ordinary differential equations | Model building and Model validation | |
{"id":30,"organism_id":77,"comments":"","sbml_file_name":"Feng_2012.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"22319437","dilution_rate":"—","name_of_model":"Kinetic model of Shewanella oneidensis MR-1 ","manuscript_title":"Integrating flux balance analysis into kinetic models to decipher the dynamic metabolism of Shewanella oneidensis MR-1.","authors":"Xueyang Feng, You Xu, Yixin Chen, Yinjie J. Tang","journal":"PLOS Computational Biology","affiliation":"","project_name":"","biomodels_id":"","keywords":"DFBA, kinetic model","software":"http://www.matlab.com (MATLAB)","control":"2014-04-11T17:54:44.161Z","main_organism":"Shewanella oneidensis","year":2012,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 81 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 31 | transcriptional model of JAK2/STAT5 signaling | Signal | ordinary differential equations | Model building | |
{"id":31,"organism_id":null,"comments":"","sbml_file_name":"Bachmann_2011.pdf","article_file_name":null,"category":"Signal","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"21772264","dilution_rate":"","name_of_model":"transcriptional model of JAK2/STAT5 signaling","manuscript_title":"Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range.","authors":"Julie Bachmann, Andreas Raue, Marcel Schilling, Martin E. Boehm, Clemens Kreutz, Daniel Kaschek, Hauke Busch, Norbert Gretz, Wolf D. Lehmann, Jens Timmer and Ursula Klingmueller","journal":"Molecular Systems Biology","affiliation":"Division of Systems Biology of Signal Transduction, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany","project_name":"","biomodels_id":"","keywords":"apoptosis, erythropoietin, mathematical modeling, negative feedback, SOCS, simulation and data analysis, signal transduction","software":"http://www.matlab.com (MATLAB)","control":null,"main_organism":"Mouse","year":2011,"combine_archive_file_name":"COMBINE_KIMOMODELID31.omex","combine_archive_content_type":"application/omex+xml","combine_archive_file_size":1445888,"combine_archive_updated_at":"2014-06-30T17:59:26.698Z","review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 96 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 38 | E. coli Central Carbon Metabolism | Metabolism | ordinary differential equations | Model building and Model validation | |
{"id":38,"organism_id":null,"comments":"MATLAB version of the model is available at http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html. ","sbml_file_name":"Jahan_2016.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"27329289","dilution_rate":"0.2, 0.4, 0.5 and 0.7","name_of_model":"E. coli Central Carbon Metabolism","manuscript_title":"Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli","authors":"Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto and Hiroyuki Kurata","journal":"Microbial Cell Factories","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680‑4 Kawazu, Iizuka, Fukuoka 820‑8502, Japan","project_name":"","biomodels_id":"","keywords":"Systems biology, Rational design, Dynamic model, Enzyme kinetics, Transcription factor, Signal transduction, Allosteric enzyme","software":"MATLAB2007 or higher","control":"2018-07-20T16:47:46.311Z","main_organism":"Escherichia coli","year":2016,"combine_archive_file_name":"COMBINE_KIMOMODELID38.omex","combine_archive_content_type":"application/octet-stream","combine_archive_file_size":6603649,"combine_archive_updated_at":"2018-07-23T21:38:00.461Z","review_journal_id":null,"doi":null} Administrator KiMoSys |
| 40 | E. coli redox regulation model | Metabolism | ordinary differential equations | Model building and Model validation | |
{"id":40,"organism_id":null,"comments":"Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.","sbml_file_name":"Matsuoka_2017.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"28725263","dilution_rate":"—","name_of_model":"E. coli redox regulation model","manuscript_title":"Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations.","authors":"Yu Matsuoka and Hiroyuki Kurata","journal":"Biotechnology for Biofuels","affiliation":" Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan","project_name":"","biomodels_id":"","keywords":"Kinetic modeling, Fermentation, Dissolved oxygen limitation, Redox regulation, ArcA, Fnr, Respiratory chain, NADH/NAD+ ratio, Escherichia coli ","software":"MATLAB (MathWorks) was used for all simulations.","control":"2018-07-20T16:25:00.495Z","main_organism":"Escherichia coli","year":2017,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
| 45 | Batch kinetic model of Escherichia coli | Metabolism | ordinary differential equations | Model building | |
{"id":45,"organism_id":null,"comments":"Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.","sbml_file_name":"Kurata_2018.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n","model_type":"ordinary differential equations","pubmed_id":"29054464","dilution_rate":"—","name_of_model":"Batch kinetic model of Escherichia coli","manuscript_title":"Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures","authors":"Hiroyuki Kurata and Yurie Sugimoto","journal":"Journal of Bioscience and Bioengineering","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan","project_name":"","biomodels_id":"","keywords":"Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli","software":"MATLAB (MathWorks)","control":null,"main_organism":"Escherichia coli","year":2018,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 97 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 39 | smallbone18 | Metabolism | ordinary differential equations | Model validation | |
{"id":39,"organism_id":null,"comments":"Original model source: in JWS online database.","sbml_file_name":"Smallbone_2013.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"23831062","dilution_rate":"","name_of_model":"smallbone18","manuscript_title":"A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.","authors":"Kieran Smallbone, Hanan L. Messiha, Kathleen M. Carroll, Catherine L. Winder, Naglis Malys, Warwick B. Dunn, Ettore Murabito, Neil Swainston, Joseph O. Dada, Farid Khan, Pınar Pir, Evangelos Simeonidis, Irena Spasić, Jill Wishart, Dieter Weichart, Neil W.","journal":"FEBS Letters","affiliation":"Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK","project_name":"","biomodels_id":"smallbone18","keywords":"Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling","software":"Copasi (www.copasi.org)","control":null,"main_organism":"Saccharomyces cerevisiae","year":2013,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 98 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 39 | smallbone18 | Metabolism | ordinary differential equations | Model validation | |
{"id":39,"organism_id":null,"comments":"Original model source: in JWS online database.","sbml_file_name":"Smallbone_2013.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"23831062","dilution_rate":"","name_of_model":"smallbone18","manuscript_title":"A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.","authors":"Kieran Smallbone, Hanan L. Messiha, Kathleen M. Carroll, Catherine L. Winder, Naglis Malys, Warwick B. Dunn, Ettore Murabito, Neil Swainston, Joseph O. Dada, Farid Khan, Pınar Pir, Evangelos Simeonidis, Irena Spasić, Jill Wishart, Dieter Weichart, Neil W.","journal":"FEBS Letters","affiliation":"Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK","project_name":"","biomodels_id":"smallbone18","keywords":"Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling","software":"Copasi (www.copasi.org)","control":null,"main_organism":"Saccharomyces cerevisiae","year":2013,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 99 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 39 | smallbone18 | Metabolism | ordinary differential equations | Model validation | |
{"id":39,"organism_id":null,"comments":"Original model source: in JWS online database.","sbml_file_name":"Smallbone_2013.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"23831062","dilution_rate":"","name_of_model":"smallbone18","manuscript_title":"A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.","authors":"Kieran Smallbone, Hanan L. Messiha, Kathleen M. Carroll, Catherine L. Winder, Naglis Malys, Warwick B. Dunn, Ettore Murabito, Neil Swainston, Joseph O. Dada, Farid Khan, Pınar Pir, Evangelos Simeonidis, Irena Spasić, Jill Wishart, Dieter Weichart, Neil W.","journal":"FEBS Letters","affiliation":"Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK","project_name":"","biomodels_id":"smallbone18","keywords":"Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling","software":"Copasi (www.copasi.org)","control":null,"main_organism":"Saccharomyces cerevisiae","year":2013,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 101 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 40 | E. coli redox regulation model | Metabolism | ordinary differential equations | Model building and Model validation | |
{"id":40,"organism_id":null,"comments":"Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.","sbml_file_name":"Matsuoka_2017.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"28725263","dilution_rate":"—","name_of_model":"E. coli redox regulation model","manuscript_title":"Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations.","authors":"Yu Matsuoka and Hiroyuki Kurata","journal":"Biotechnology for Biofuels","affiliation":" Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan","project_name":"","biomodels_id":"","keywords":"Kinetic modeling, Fermentation, Dissolved oxygen limitation, Redox regulation, ArcA, Fnr, Respiratory chain, NADH/NAD+ ratio, Escherichia coli ","software":"MATLAB (MathWorks) was used for all simulations.","control":"2018-07-20T16:25:00.495Z","main_organism":"Escherichia coli","year":2017,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 104 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 41 | Continuous kinetic model of Escherichia coli | Metabolism | ordinary differential equations | Model building and Model validation | |
{"id":41,"organism_id":null,"comments":"Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.","sbml_file_name":"Kurata_2018.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"29054464","dilution_rate":"0.2, 0.4, 0.5 and 0.7","name_of_model":"Continuous kinetic model of Escherichia coli","manuscript_title":"Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures","authors":"Hiroyuki Kurata and Yurie Sugimoto","journal":"Journal of Bioscience and Bioengineering","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan","project_name":"","biomodels_id":"","keywords":"Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli","software":"MATLAB (MathWorks)","control":"2018-07-24T15:46:04.831Z","main_organism":"Escherichia coli","year":2018,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 105 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 16 | glycolysis Escherichia coli model | Metabolism | ordinary differential equations | Model validation | |
{"id":16,"organism_id":38,"comments":"","sbml_file_name":"Kadir_2010.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"21092096","dilution_rate":"—","name_of_model":"glycolysis Escherichia coli model","manuscript_title":"Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.","authors":"Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu","journal":"Microbial Cell Factories","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan","project_name":"","biomodels_id":"","keywords":"Escherichia coli, single-gene knockouts, main central metabolism and TCA","software":"http://www.matlab.com (MATLAB)","control":"2018-07-21T20:34:09.507Z","main_organism":"Escherichia coli","year":2010,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
| 41 | Continuous kinetic model of Escherichia coli | Metabolism | ordinary differential equations | Model building and Model validation | |
{"id":41,"organism_id":null,"comments":"Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.","sbml_file_name":"Kurata_2018.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"29054464","dilution_rate":"0.2, 0.4, 0.5 and 0.7","name_of_model":"Continuous kinetic model of Escherichia coli","manuscript_title":"Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures","authors":"Hiroyuki Kurata and Yurie Sugimoto","journal":"Journal of Bioscience and Bioengineering","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan","project_name":"","biomodels_id":"","keywords":"Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli","software":"MATLAB (MathWorks)","control":"2018-07-24T15:46:04.831Z","main_organism":"Escherichia coli","year":2018,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 106 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 16 | glycolysis Escherichia coli model | Metabolism | ordinary differential equations | Model validation | |
{"id":16,"organism_id":38,"comments":"","sbml_file_name":"Kadir_2010.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"21092096","dilution_rate":"—","name_of_model":"glycolysis Escherichia coli model","manuscript_title":"Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.","authors":"Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu","journal":"Microbial Cell Factories","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan","project_name":"","biomodels_id":"","keywords":"Escherichia coli, single-gene knockouts, main central metabolism and TCA","software":"http://www.matlab.com (MATLAB)","control":"2018-07-21T20:34:09.507Z","main_organism":"Escherichia coli","year":2010,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 107 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 16 | glycolysis Escherichia coli model | Metabolism | ordinary differential equations | Model validation | |
{"id":16,"organism_id":38,"comments":"","sbml_file_name":"Kadir_2010.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"21092096","dilution_rate":"—","name_of_model":"glycolysis Escherichia coli model","manuscript_title":"Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.","authors":"Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu","journal":"Microbial Cell Factories","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan","project_name":"","biomodels_id":"","keywords":"Escherichia coli, single-gene knockouts, main central metabolism and TCA","software":"http://www.matlab.com (MATLAB)","control":"2018-07-21T20:34:09.507Z","main_organism":"Escherichia coli","year":2010,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 108 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 43 | Singh2006_TCA_Ecoli_acetate | Metabolism | ordinary differential equations | Model validation | |
{"id":43,"organism_id":null,"comments":"Original model source: in BioModels database.","sbml_file_name":"Singh_2006.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"16887020","dilution_rate":"","name_of_model":"Singh2006_TCA_Ecoli_acetate","manuscript_title":"Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets","authors":"Vivek Kumar Singh and Indira Ghosh","journal":"Theoretical Biology and Medical Modelling","affiliation":"Bioinformatics Centre, University of Pune, India","project_name":"","biomodels_id":"BIOMD0000000221","keywords":"Tuberculosis, Steady State Flux, Glyoxylate Bypass, Metabolic Control Analysis, Experimental Flux","software":"Jarnac 2.14 (http://jdesigner.sourceforge.net/Site/Jarnac.html)","control":null,"main_organism":"Escherichia coli","year":2006,"combine_archive_file_name":"COMBINE_KIMOMODELID43.omex","combine_archive_content_type":"application/octet-stream","combine_archive_file_size":253672,"combine_archive_updated_at":"2018-07-27T10:28:17.660Z","review_journal_id":null,"doi":null} Administrator KiMoSys |
| 44 | Singh2006_TCA_Ecoli_glucose | Metabolism | ordinary differential equations | Model validation | |
{"id":44,"organism_id":null,"comments":"Original model source: in BioModels database.","sbml_file_name":"Singh_2006.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"16887020","dilution_rate":"","name_of_model":"Singh2006_TCA_Ecoli_glucose","manuscript_title":"Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets","authors":"Vivek Kumar Singh and Indira Ghosh","journal":"Theoretical Biology and Medical Modelling","affiliation":"Bioinformatics Centre, University of Pune, India","project_name":"","biomodels_id":"BIOMD0000000222","keywords":"Tuberculosis, Steady State Flux, Glyoxylate Bypass, Metabolic Control Analysis, Experimental Flux","software":"Jarnac 2.14 (http://jdesigner.sourceforge.net/Site/Jarnac.html)","control":null,"main_organism":"Escherichia coli","year":2006,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
DataEntryID 111 Associated Models
| Model EntryID |
Model name | Category | Model Type | Data used for | Access | Json |
|---|---|---|---|---|---|---|
| 46 | vanEunen2012 - Yeast Glycolysis (glucose upshift) | Metabolism | ordinary differential equations | Model building and Model validation | |
{"id":46,"organism_id":null,"comments":"Original model source: in BioModels database.","sbml_file_name":"vanEunen_2012.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"22570597","dilution_rate":"","name_of_model":"vanEunen2012 - Yeast Glycolysis (glucose upshift)","manuscript_title":"Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics","authors":"Karen van Eunen, José A. L. Kiewiet, Hans V. Westerhoff, Barbara M. Bakker","journal":"PLoS Computational Biology","affiliation":"Department of Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands","project_name":"","biomodels_id":"BIOMD1403250001","keywords":"yeast glycolysis, In Vivo and in Vitro Enzyme Kinetics, computational model","software":"MATLAB (MathWorks)","control":null,"main_organism":"Saccharomyces cerevisiae","year":2012,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys |
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