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.

Examples: PubMed ID (e.g. '17590932'); Organism (e.g. 'Clostridium acetobutylicum'); EntryID (e.g. 'EntryID41')


To order by any of the first five columns, click the table header.

Data
EntryID
Organism Strain Data type Project name Access Associated models All metadata
30 Escherichia coli K-12 W3110 time-series data of metabolites Visto4 [yes]|[more] ["Institute of Biochemical Engineering, University of Stuttgart", "---\n- enzymatic\n- HPLC/HIC\n", "application/pdf", "Chassagnole_2002.pdf", 255701, Tue, 23 Apr 2013 17:30:11 UTC +00:00, "Christophe Chassagnole, Naruemol Noisommit-Rizzi, Joachim W. Schmid, Klaus Mauch, Matthias Reuss", "8.7", "glucose", "17234", "aerobic", "mM", nil, "0.1", nil, nil, nil, "---\n- perchloric acid\n", "chemostat", 30, false, true, "Biotechnology and Bioengineering", "dynamic model, Escherichia coli, intracellular metabolites, transient conditions, control and stability analysis", "Dynamic modeling of the central carbon metabolism of Escherichia coli.", "--- []\n", "Escherichia coli", "KIMODATAID30_v1.xlsx", "7.0", "--- []\n", "", "17590932", "liquid nitrogen (-196 ºC) and perchloric acid", nil, "manually every 3 seconds with vacuum-sealed, precooled glass tubes containing the quenching solution", "K-12 W3110", "35.0", "--- []\n", "2", "1.5", 2002] Administrator KiMoSys Data AccessID30 / EntryID30 ["Institute of Biochemical Engineering, University of Stuttgart ", nil, "Christophe Chassagnole, Naruemol Noisommit-Rizzi, Joachim W. Schmid, Klaus Mauch, Matthias Reuss", "BIOMD0000000051", "Metabolism", "application/omex+xml", "COMBINE_KIMOMODELID13.omex", 249522, Mon, 30 Jun 2014 17:38:01 UTC +00:00, "Original model source: in BioModels database.", Wed, 19 Mar 2014 14:31:21 UTC +00:00, Wed, 06 Mar 2013 19:18:54 UTC +00:00, "0.1", 13, "Biotechnology and Bioengineering", "dynamic model, Escherichia coli, parameter fitting, flux control coefficients", "Escherichia coli", "Dynamic modeling of the central carbon metabolism of Escherichia coli.", "Chassagnole2002_Carbon_Metabolism", "ordinary differential equations", 30, "", "17590932", nil, "Chassagnole_2002.pdf", "", "---\n- Model building\n- Model validation\n", 2002] Administrator KiMoSys Model AccessID13 / EntryID13
35 Escherichia coli WT K-12 BW25113 and mutants flux measurements Visto4 [yes]|[more] ["Institute for Advanced Biosciences, Keio University", "--- []\n", nil, nil, nil, nil, "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", "See Supplementary files of the original article (Tabel S3).", "glucose", "CHEBI:17234", "aerobic", "(mmol/gDW/h)", nil, "0.1, 0.2, 0.4, 0.5 and 0.7", nil, nil, nil, "--- []\n", "chemostat", 35, false, true, "Science", "Escherichia coli, perturbations response, chemostat, single knockouts", "Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations.", "--- []\n", "Escherichia coli", "KIMODATAID35_v3.xlsx", "7.0", "---\n- GC-MS\n", "", "17379776", "", nil, "", "WT K-12 BW25113 and mutants", "37.0", "---\n- 13C constrained MFA\n", "3", "1.0", 2007] Administrator KiMoSys Data AccessID35 / EntryID35 ["Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA", nil, "Ali Khodayari, Ali R. Zomorrodi, James C.Liao, Costas D. Maranas", "", "Metabolism", nil, nil, nil, nil, "", nil, Tue, 04 Nov 2014 23:47:28 UTC +00:00, "", 36, "Metabolic Engineering", "ensemble modeling, kinetic modeling, metabolic network", "Escherichia coli", "A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data.", "Kinetic model of Escherichia coli core metabolism", "ordinary differential equations", nil, "", "24928774", nil, "Khodayari_2014.pdf", "http://www.matlab.com (MATLAB)", "---\n- Model building\n- Model validation\n", 2014] Administrator KiMoSys Model AccessID36 / EntryID36 ["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680‑4 Kawazu, Iizuka, Fukuoka 820‑8502, Japan", nil, "Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto and Hiroyuki Kurata", "", "Metabolism", "application/octet-stream", "COMBINE_KIMOMODELID38.omex", 6603649, Mon, 23 Jul 2018 21:38:00 UTC +00:00, "MATLAB version of the model is available at http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html. ", Fri, 20 Jul 2018 16:47:46 UTC +00:00, Thu, 12 Jul 2018 12:32:20 UTC +00:00, "0.2, 0.4, 0.5 and 0.7", 38, "Microbial Cell Factories", "Systems biology, Rational design, Dynamic model, Enzyme kinetics, Transcription factor, Signal transduction, Allosteric enzyme", "Escherichia coli", "Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli", "E. coli Central Carbon Metabolism", "ordinary differential equations", nil, "", "27329289", nil, "Jahan_2016.pdf", "MATLAB2007 or higher", "---\n- Model building\n- Model validation\n", 2016] Administrator KiMoSys Model AccessID38 / EntryID38 ["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan", nil, "Hiroyuki Kurata and Yurie Sugimoto", "", "Metabolism", nil, nil, nil, nil, "Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.", Tue, 24 Jul 2018 15:46:04 UTC +00:00, Fri, 20 Jul 2018 16:54:23 UTC +00:00, "0.2, 0.4, 0.5 and 0.7", 41, "Journal of Bioscience and Bioengineering", "Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli", "Escherichia coli", "Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures", "Continuous kinetic model of Escherichia coli", "ordinary differential equations", nil, "", "29054464", nil, "Kurata_2018.pdf", "MATLAB (MathWorks)", "---\n- Model building\n- Model validation\n", 2018] Administrator KiMoSys Model AccessID41 / EntryID41 ["Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, United Kingdom ", nil, "Ahmad A. Mannan, Yoshihiro Toya, Kazuyuki Shimizu, Johnjoe McFadden, Andrzej M. Kierzek , Andrea Rocco", "", "Metabolism", nil, nil, nil, nil, "For the analysis and evaluation of the kinetic model, the solver ode15s was used.", nil, Sun, 22 Jul 2018 12:01:48 UTC +00:00, "0.2", 42, "Plos One", "E. coli, Bistability, Central Metabolism", "Escherichia coli", "Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.", "kinetic model of the central carbon metabolism of E. coli ", "ordinary differential equations", nil, "", "26469081", nil, "Mannan_2015.PDF", "MATLAB® R2007b (version 7.5.0)", "---\n- Model building\n", 2015] Administrator KiMoSys Model AccessID42 / EntryID42
37 Lactococcus lactis MG1363 time-series data of metabolites PneumoSyS Visto4 [yes]|[more] ["Instituto de Teconcologia Química e Biológica, Universidade Nova de Lisboa and Instituto de Biologia Experimental e Tecnológico, Oeiras, Portugal", "---\n- NMR\n", "application/pdf", "Neves_2002.pdf", 662982, Tue, 30 Apr 2013 18:51:58 UTC +00:00, "Ana Rute Neves, Rita Ventura, Nahla Mansour, Claire Shearman, Michael J. Gasson, Christopher Maycock, Ana Ramos and Helena Santos", "", "glucose", "CHEBI:17234", "anaerobic", "", nil, "", nil, nil, nil, "---\n- boiling ethanol\n", "batch", 37, false, true, "The Journal of Biological Chemistry", "Lactococcus lactis, metabolism of glucose, NMR, in vivo", "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.", "--- []\n", "Lactococcus lactis", "KIMODATAID37_v1.xlsx", "6.5", "--- []\n", "PneumoSyS", "12011086", "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.", nil, " Cells were harvested in logarithmic growth phase (A 600 = 2.2)", "MG1363", "30.0", "--- []\n", "2", "0.050", 2002] Administrator KiMoSys Data AccessID37 / EntryID37 ["Department of Modeling of Biological Processes, COS Heidelberg ⁄ BIOQUANT, University of Heidelberg, Germany", nil, "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", "levering1", "Metabolism", "application/omex+xml", "COMBINE_KIMOMODELID23.omex", 1068365, Mon, 30 Jun 2014 17:53:53 UTC +00:00, "Original model source: in JWS online database.", Mon, 10 Mar 2014 11:18:15 UTC +00:00, Mon, 06 May 2013 15:37:33 UTC +00:00, "", 23, "FEBS Journal", "Lactococcus lactis, metabolism of glucose, NMR, in vivo", "Lactococcus lactis", "Role of phosphate in the central metabolism of two lactic acid bacteria - a comparative systems biology approach.", "glycolysis Lactococcus lactis", "ordinary differential equations", 37, "", "22325620", nil, "Levering_2012.pdf", "http://www.copasi.org (COPASI)", "---\n- Model building\n- Model validation\n", 2012] Administrator KiMoSys Model AccessID23 / EntryID23 ["Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID)", nil, "Susana Vinga, Ana R. Neves, Helena Santos, B. W. Brandt and S. A. L. M. Kooijman", "", "Metabolism", nil, nil, nil, nil, "Archive containing all files to run and plot simulations. Requires MATLAB.", Thu, 15 May 2014 09:26:26 UTC +00:00, Mon, 06 May 2013 18:05:17 UTC +00:00, "", 24, "Philosophical transactions of the royal society B", "Lactococcus lactis, metabolism of glucose, NMR, in vivo", "Lactococcus lactis", "Subcellular metabolic organization in the context of dynamic energy budget and biochemical systems theories", "DEB L. lactis model", "ordinary differential equations", 37, "", "20921043", nil, "Vinga_2010.pdf", "http://www.matlab.com (MATLAB)", "---\n- Model building\n", 2010] Administrator KiMoSys Model AccessID24 / EntryID24 ["Instituto de Engenharia de Sistemas e Computadores, Investigacão e Desenvolvimento (INESC-ID), R Alves Redol 9, 1000-029 Lisboa, Portugal.", nil, "Rafael S. Costa, Andras Hartmann, Paula Gaspar, Ana R. Neves and Susana Vinga", "", "Metabolism", nil, nil, nil, nil, " Copasi model file used to produce manuscript figures.", Mon, 21 Jul 2014 10:18:41 UTC +00:00, Mon, 21 Jul 2014 10:15:55 UTC +00:00, "—", 35, "Molecular BioSystems", "L. lactis, extended model, mannitol and 2,3-butanediol production, control analysis", "Lactococcus lactis", "An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production", "glycolysis Lactococcus lactis for mannitol and 2,3-butanediol production", "ordinary differential equations", nil, "PneumoSyS", "24413179", nil, "Costa_2014.pdf", "http://www.copasi.org (COPASI)", "---\n- Model building\n- Model validation\n", 2014] Rafael Costa Model AccessID35 / EntryID35 ["", nil, "Costa, R.S.", nil, "Metabolism", nil, nil, nil, nil, "", nil, Sun, 12 Apr 2015 16:04:40 UTC +00:00, "", 37, "", "flavonoid pathway, L. lactis, Naringenin", "Lactococcus lactis", "Modeling Lactococcus lactis for synthetic biology", "flavonoid biosynthetic pathway in L. lactis", "ordinary differential equations", nil, "", "", nil, nil, "", "---\n- Model building\n", nil] Rafael Costa Model AccessID37 / EntryID37
38 Escherichia coli K-12 BW25113 and ppc, pyk mutants time-series data of metabolites Visto4 [yes]|[more] ["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Japan ", "---\n- enzymatic\n", "application/pdf", "Kadir_2010.pdf", 2038907, Wed, 24 Apr 2013 14:40:24 UTC +00:00, "Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu", "", "glucose", "CHEBI:17234", "aerobic", "g/L", nil, "—", nil, nil, nil, "---\n- enzymatic\n- perchloric acid\n", "batch", 38, false, true, "Microbial Cell Factories", "Specific Growth Rate, Flux Balance Analysis, Oxidative Pentose Phosphate Pathway, Main Metabolic Pathway, Isotopomer Distribution", "Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.", "--- []\n", "Escherichia coli ", "KIMODATAID38_v1.xlsx", "7.0", "--- []\n", "", "21092096", "15ml of 60% (v/v) aqueous methanol containing 70mM HEPES at -80ºC", nil, "5ml from the culture broth", "K-12 BW25113 and ppc, pyk mutants", "37.0", "--- []\n", "2", "1.0", 2010] Administrator KiMoSys Data AccessID38 / EntryID38 ["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", nil, "Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu", "", "Metabolism", nil, nil, nil, nil, "", Sat, 21 Jul 2018 20:34:09 UTC +00:00, Wed, 24 Apr 2013 15:07:11 UTC +00:00, "—", 16, "Microbial Cell Factories", "Escherichia coli, single-gene knockouts, main central metabolism and TCA", "Escherichia coli", "Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.", "glycolysis Escherichia coli model", "ordinary differential equations", 38, "", "21092096", nil, "Kadir_2010.pdf", "http://www.matlab.com (MATLAB)", "---\n- Model validation\n", 2010] Administrator KiMoSys Model AccessID16 / EntryID16 ["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680‑4 Kawazu, Iizuka, Fukuoka 820‑8502, Japan", nil, "Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto and Hiroyuki Kurata", "", "Metabolism", "application/octet-stream", "COMBINE_KIMOMODELID38.omex", 6603649, Mon, 23 Jul 2018 21:38:00 UTC +00:00, "MATLAB version of the model is available at http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html. ", Fri, 20 Jul 2018 16:47:46 UTC +00:00, Thu, 12 Jul 2018 12:32:20 UTC +00:00, "0.2, 0.4, 0.5 and 0.7", 38, "Microbial Cell Factories", "Systems biology, Rational design, Dynamic model, Enzyme kinetics, Transcription factor, Signal transduction, Allosteric enzyme", "Escherichia coli", "Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli", "E. coli Central Carbon Metabolism", "ordinary differential equations", nil, "", "27329289", nil, "Jahan_2016.pdf", "MATLAB2007 or higher", "---\n- Model building\n- Model validation\n", 2016] Administrator KiMoSys Model AccessID38 / EntryID38 ["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan", nil, "Hiroyuki Kurata and Yurie Sugimoto", "", "Metabolism", nil, nil, nil, nil, "Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.", nil, Tue, 24 Jul 2018 16:03:02 UTC +00:00, "—", 45, "Journal of Bioscience and Bioengineering", "Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli", "Escherichia coli", "Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures", "Batch kinetic model of Escherichia coli", "ordinary differential equations", nil, "", "29054464", nil, "Kurata_2018.pdf", "MATLAB (MathWorks)", "---\n- Model building\n", 2018] Administrator KiMoSys Model AccessID45 / EntryID45
41 Escherichia coli WT K-12 BW25113 and mutants metabolites at steady-state Visto4 [yes]|[more] ["Institute for Advanced Biosciences, Keio University", "---\n- CE-MS\n", nil, nil, nil, nil, "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", "See Supplementary files of the original article (Tabel S3).", "glucose", "CHEBI:17234", "aerobic", "mM", nil, "0.1, 0.2, 0.4, 0.5 and 0.7", nil, nil, nil, "---\n- chloroform\n", "chemostat", 41, false, true, "Science", "Escheirchia coli, perturbations response, chemostat, single knockouts", "Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations.", "--- []\n", "Escherichia coli", "KIMODATAID41_v1.xlsx", "7.0", "--- []\n", "", "17379776", "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", nil, "Aliquots of 10 mL were withdrawn at OD600 0.85", "WT K-12 BW25113 and mutants", "37.0", "--- []\n", "1", "1.0", 2007] Administrator KiMoSys Data AccessID41 / EntryID41 ["Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, United Kingdom ", nil, "Ahmad A. Mannan, Yoshihiro Toya, Kazuyuki Shimizu, Johnjoe McFadden, Andrzej M. Kierzek , Andrea Rocco", "", "Metabolism", nil, nil, nil, nil, "For the analysis and evaluation of the kinetic model, the solver ode15s was used.", nil, Sun, 22 Jul 2018 12:01:48 UTC +00:00, "0.2", 42, "Plos One", "E. coli, Bistability, Central Metabolism", "Escherichia coli", "Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.", "kinetic model of the central carbon metabolism of E. coli ", "ordinary differential equations", nil, "", "26469081", nil, "Mannan_2015.PDF", "MATLAB® R2007b (version 7.5.0)", "---\n- Model building\n", 2015] Administrator KiMoSys Model AccessID42 / EntryID42
42 Clostridium acetobutylicum ATCC824 time-series data of metabolites Visto4 [yes]|[more] ["University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics", "---\n- GC-MS\n", "application/pdf", "Haus_2011.pdf", 588418, Fri, 11 Apr 2014 17:19:41 UTC +00:00, "Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer", "", "glucose", "CHEBI:17234", "anaerobic", "mM", nil, "0.1", nil, nil, nil, "---\n- not used\n", "chemostat", 42, false, true, "BMC Systems Biology", "Clostridium acetobutylicum, continuous culture, effect of pH, solvent production", "A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.", "--- []\n", "Clostridium acetobutylicum", "KIMODATAID42_v0.xlsx", "5.7 and 4.5", "--- []\n", "", "21247470", "—", 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.", "ATCC824", "37.0", "--- []\n", "2", "1.0", 2011] Administrator KiMoSys Data AccessID42 / EntryID42 ["University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics", nil, "Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer", "", "Metabolism", "application/omex+xml", "COMBINE_KIMOMODELID19.omex", 401646, Mon, 30 Jun 2014 20:38:42 UTC +00:00, "", Fri, 11 Apr 2014 17:25:43 UTC +00:00, Fri, 03 May 2013 13:15:51 UTC +00:00, "0.1", 19, "BMC Systems Biology", "Clostridium acetobutylicum, continuous culture, effect of pH, solvent production", "Clostridium acetobutylicum", "A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.", "first forward shift", "ordinary differential equations", 42, "", "21247470", nil, "Haus_2011.pdf", " http://www.sbtoolbox.org (SBToolbox)", "---\n- Model building\n", 2011] Administrator KiMoSys Model AccessID19 / EntryID19 ["University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics", nil, "Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer", "", "Metabolism", "application/omex+xml", "COMBINE_KIMOMODELID20.omex", 401633, Mon, 30 Jun 2014 20:39:10 UTC +00:00, "", Fri, 11 Apr 2014 17:26:19 UTC +00:00, Fri, 03 May 2013 13:24:53 UTC +00:00, "0.1", 20, "BMC Systems Biology", "Clostridium acetobutylicum, continuous culture, effect of pH, solvent production", "Clostridium acetobutylicum", "A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.", "second forward shift", "ordinary differential equations", 42, "", "21247470", nil, "Haus_2011.pdf", "http://www.sbtoolbox.org (SBToolbox)", "---\n- Model building\n", 2011] Administrator KiMoSys Model AccessID20 / EntryID20 ["University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics", nil, "Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer", "", "Metabolism", "application/omex+xml", "COMBINE_KIMOMODELID21.omex", 401643, Mon, 30 Jun 2014 20:39:32 UTC +00:00, "", Fri, 11 Apr 2014 17:24:43 UTC +00:00, Fri, 03 May 2013 13:31:42 UTC +00:00, "0.1", 21, "BMC Systems Biology", "Clostridium acetobutylicum, continuous culture, effect of pH, solvent production", "Clostridium acetobutylicum", "A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.", "third forward shift", "ordinary differential equations", 42, "", "21247470", nil, "Haus_2011.pdf", "http://www.sbtoolbox.org (SBToolbox)", "---\n- Model building\n", 2011] Administrator KiMoSys Model AccessID21 / EntryID21 ["University of Rostock, Institute of Computer Science, Department of Systems Biology & Bioinformatics", nil, "Sylvia Haus, Sara Jabbari, Thomas Millat, Holger Janssen, Ralf-Jörg Fischer, Hubert Bahl, John R King, Olaf Wolkenhauer", "", "Metabolism", "application/omex+xml", "COMBINE_KIMOMODELID22.omex", 401628, Mon, 30 Jun 2014 20:39:48 UTC +00:00, "", Fri, 11 Apr 2014 17:27:26 UTC +00:00, Fri, 03 May 2013 13:40:10 UTC +00:00, "0.1", 22, "BMC Systems Biology", "Clostridium acetobutylicum, continuous culture, effect of pH, solvent production", "Clostridium acetobutylicum", "A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.", "reverse forward shift", "ordinary differential equations", 42, "", "21247470", nil, "Haus_2011.pdf", "http://www.sbtoolbox.org (SBToolbox)", "---\n- Model building\n", 2011] Administrator KiMoSys Model AccessID22 / EntryID22
44 Escherichia coli WT K-12 BW25113 and mutants enzyme/protein concentrations Visto4 [yes]|[more] ["Institute for Advanced Biosciences, Keio University", "--- []\n", nil, nil, nil, nil, "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", "See Supplementary files of the original article (Tabel S3).", "glucose", "CHEBI:17234", "aerobic", "(mg-protein/g-dry cell weight)", nil, "0.1, 0.2, 0.4, 0.5 and 0.7", nil, nil, nil, "--- []\n", "chemostat", 44, false, true, "Science", "Escheirchia coli, perturbations response, chemostat, single knockouts", "Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations.", "---\n- LC-MS/MS\n- 2D gel-MALDI-TOF\n", "Escherichia coli", "KIMODATAID44_v0.xlsx", "7.0", "--- []\n", "", "17379776", "", nil, "", "WT K-12 BW25113 and mutants", "37.0", "--- []\n", "4", "1.0", 2007] Administrator KiMoSys Data AccessID44 / EntryID44 ["Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, United Kingdom ", nil, "Ahmad A. Mannan, Yoshihiro Toya, Kazuyuki Shimizu, Johnjoe McFadden, Andrzej M. Kierzek , Andrea Rocco", "", "Metabolism", nil, nil, nil, nil, "For the analysis and evaluation of the kinetic model, the solver ode15s was used.", nil, Sun, 22 Jul 2018 12:01:48 UTC +00:00, "0.2", 42, "Plos One", "E. coli, Bistability, Central Metabolism", "Escherichia coli", "Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.", "kinetic model of the central carbon metabolism of E. coli ", "ordinary differential equations", nil, "", "26469081", nil, "Mannan_2015.PDF", "MATLAB® R2007b (version 7.5.0)", "---\n- Model building\n", 2015] Administrator KiMoSys Model AccessID42 / EntryID42
51 Escherichia coli K-12 AG1 time-series data of metabolites Visto4 [no] ["Institute for Advanced Biosciences, Keio University, Japan", "---\n- enzymatic\n", "application/pdf", "Ishii_2007.pdf", 142546, Wed, 23 Apr 2014 10:27:14 UTC +00:00, "Nobuyoshi Ishii, Yoshihiro Suga, Akiko Hagiya, Hisami Watanabe, Hirotada Mori, Masataka Yoshino, Masaru Tomita", "", "glucose", "CHEBI:17234", "aerobic", "mM", nil, "—", nil, nil, nil, "---\n- sonication\n", "batch", 51, false, true, "FEBS Letters", "dynamic simulation, enzyme kinetics, metabolism, glycolysis, in vitro", "Dynamic simulation of an in vitro multi-enzyme system.", "--- []\n", "Escherichia coli", "KIMODATAID51_v0.xlsx", "not specified", "--- []\n", "", "17239859", "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)].", nil, "Samples were obtained 2 h after addition of 0.1 mM isopropyl-b-D-thiogalactopyranoside (IPTG)", "K-12 AG1", "37.0", "--- []\n", "2", "0.2", 2007] Administrator KiMoSys Data AccessID51 / EntryID51
52 Escherichia coli K-12 DSM 498 metabolites at steady-state Visto4 [no] ["Institut fuer Bioverfahrenstechnik, Technische Universitaet Braunschweig, Gausstrasse 17, 38106 Braunschwieg, Germany", "---\n- enzymatic\n- LC-MS\n", nil, nil, nil, nil, "Julia Hiller, Ezequiel Franco-Lara, Dirk Weuster-Botz", "", "glucose", "CHEBI:17234", "aerobic", "mM", nil, "0.125", nil, nil, nil, "---\n- freezing-thawing in methanol\n", "chemostat", 52, false, true, "Biotechnology Letters", "extraction methods, metabolic profiling and multi-substrate", "Metabolic profiling of Escherichia coli cultivations: evaluation of extraction and metabolite analysis procedures.", "--- []\n", "Escherichia coli ", "KIMODATAID52_v0.xlsx", "7.0", "--- []\n", "", "17479221", "centrifugation at -19 ºC, 6000g, 3min", nil, "6g cell suspension, 25 g 60% MeOH-H2O 30mM TEA, pH=7.5, T=40ºC", "K-12 DSM 498", "37.0", "--- []\n", "1", "3.0", 2007] Administrator KiMoSys Data AccessID52 / EntryID52
54 Escherichia coli K-12 DSM metabolites at steady-state Visto4 [no] ["Institute of Biotechnology, Research Center Juelich, 52425 Juelich, Germany", "---\n- LC-ESI-MS\n", nil, nil, nil, nil, "Arne Buchholz, Ralf Takors, and Christian Wandrey", "", "glucose", "CHEBI:17234", "aerobic", "mM", nil, "0.125", nil, nil, nil, "---\n- methanol-water\n", "chemostat", 54, false, true, "Analytical Biochemistry", "Escherichia coli, intracellular metabolites, ESI, extraction, LC-MS, quantification", "Quantification of intracellular metabolites in Escherichia coli K12 using liquid chromatographic-electrospray ionization tandem mass spectrometric techniques.", "--- []\n", "Escherichia coli", "KIMODATAID54_v0.xlsx", "not specified", "--- []\n", "", "11488613", "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).", 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.", "K-12 DSM", "not specified", "--- []\n", "1", "0.4", 2001] Administrator KiMoSys Data AccessID54 / EntryID54
55 Pichia pastoris X-33 metabolites at steady-state Visto4 [no] ["Department of Chemical Engineering, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallès, Spain", "---\n- GC-MS\n- LC-MS\n- HPLC-UV/RI\n", "application/pdf", "Jorda_2013.pdf", 779343, Wed, 23 Apr 2014 10:41:24 UTC +00:00, "Joel Jordà, Camilo Suarez, Marc Carnicer, Angela ten Pierick, Joseph J Heijnen, Walter van Gulik, Pau Ferrer, Joan Albiol and Aljoscha Wahl", "4.0", "glucose", "CHEBI:17234", "aerobic", "(µmol/l) and (µmol/gDW)", nil, "0.09", nil, nil, nil, "---\n- boiling ethanol\n", "chemostat", 55, false, true, "BMC Systems Biology", "Pichia pastoris, intracellular, extracellular, glucose, glucose:methanol", "Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary 13C flux analysis.", "--- []\n", "Pichia pastoris", "KIMODATAID55_v0.xlsx", "5.0", "--- []\n", "", "23448228", "Approximately 1 g of broth were rapidly withdrawn and immediately mixed with 5 ml of precooled quenching solution at -40°C. ", nil, " One hour before the switch to the labelled feed using a dedicated rapid-sampling setup.", "X-33", "25.0", "--- []\n", "1", "1.0", 2013] Administrator KiMoSys Data AccessID55 / EntryID55
57 Pichia pastoris X-33 flux measurements Visto4 [no] ["Department of Chemical Engineering, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallès, Spain", "--- []\n", "application/pdf", "Jorda_2013.pdf", 779383, Tue, 15 Apr 2014 10:39:34 UTC +00:00, "Joel Jordà, Camilo Suarez, Marc Carnicer, Angela ten Pierick, Joseph J Heijnen, Walter van Gulik, Pau Ferrer, Joan Albiol and Aljoscha Wahl", "4.0", "glucose", "CHEBI:17234", "aerobic", "(mmol/gDW.h)", nil, "0.09", nil, nil, nil, "--- []\n", "chemostat", 57, false, true, "BMC Systems Biology", "Pichia pastoris, instationary 13C-metabolic flux analysis, GC-MS, LC-MS", "Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics ans instationary 13C flux analysis.", "--- []\n", "Pichia pastoris", "KIMODATAID57_v0.xlsx", "5.0", "---\n- GC-MS\n- LC-MS\n", "", "23448228", "", nil, "", "X-33", "25.0", "---\n- 13C constrained MFA\n", "3", "1.0", 2013] Administrator KiMoSys Data AccessID57 / EntryID57
58 Homo sapiens HepG2 (ATCC number HB-8065) metabolites at steady-state Visto4 [no] ["Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany", "---\n- GC-MS\n- LC-MS\n- HPLC-UV/RI\n", "application/pdf", "Maier_2010.pdf", 1005199, Thu, 06 Jun 2013 13:47:09 UTC +00:00, "Klaus Maier, Ute Hofmann, Mathias Reuss and Klaus Mauch", "not specified", "glucose", "CHEBI:17234", "aerobic", "(mmol/L)", nil, "—", nil, nil, nil, "---\n- hot water\n", "batch", 58, false, true, "BMC Systems Biology", "Hepatoma Cells, in vivo Dynamics, Dynamic Model, Control", "Dynamics and control of the central carbon metabolism in Hepatoma cells.", "--- []\n", "Homo sapiens", "KIMODATAID58_v0.xlsx", "not specified", "--- []\n", "", "20426867", "hot air", nil, "Removal of cell culture medium by suction (5 seconds).", "HepG2 (ATCC number HB-8065)", "37.0", "--- []\n", "1", "not specified", 2010] Administrator KiMoSys Data AccessID58 / EntryID58
59 Rattus not specified time-series data of metabolites Visto4 [no] ["Department of Computational Biology, Graduate School of Frontier Sciencies, The University of Tokyo, Kashiwa, Chiba, Japan", "---\n- enzymatic\n- CE-MS\n", "application/pdf", "Rei_2013.pdf", 918733, Fri, 07 Jun 2013 13:36:43 UTC +00:00, "Rei Noguchi, Hiroyuki Kubota, Katsuyuki Yugi, Yu Toyoshima, Yasunori Komori, Tomoyoshi Soga, Shinya Kuroda", "not specified", "glucose", "CHEBI:17234", "aerobic", "µM", nil, "—", nil, nil, nil, "---\n- chloroform-methanol\n", "batch", 59, false, true, "Molecular Sytems Biology", "glucose metabolism, insulin, computational model, network motif, temporal coding", "The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns.", "--- []\n", "Rattus", "KIMODATAID59_v0.xlsx", "not specified", "--- []\n", "", "23670537", "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).", nil, "collected manually", "not specified", "not specified", "--- []\n", "2", "not specified", 2013] Administrator KiMoSys Data AccessID59 / EntryID59
61 Saccharomyces cerevisiae FY4 time-series data of metabolites Visto4 [no] ["ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland", "---\n- HPLC-UV/RI\n", "application/pdf", "Zampar_2013.pdf", 2754858, Tue, 15 Apr 2014 11:42:39 UTC +00:00, "Guillermo G Zampar, Anne Kümmel, Jennifer Ewald, Stefan Jol, Bastian Niebel, Paola Picotti, Ruedi Aebersold, Uwe Sauer, Nicola Zamboni and Matthias Heinemann", "correlation of OD with biomass: 0.486 gDW/L OD", "glucose", "CHEBI:17234", "aerobic", "(mM) and (gDW/L)", nil, "—", nil, nil, nil, "---\n- not used\n", "batch", 61, false, true, "Molecular Systems Biology", "diauxic shift, metabolome, S. cerevisiae, extracelullar", "Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast.", "--- []\n", "Saccharomyces cerevisiae", "KIMODATAID61_v0.xlsx", "5.0", "--- []\n", "", "23549479", "—", nil, "1 ml samples and centrifuged for 4 min at 4000, r.p.m at 4 ºC", "FY4", "30.0", "--- []\n", "2", "2.0", 2013] Administrator KiMoSys Data AccessID61 / EntryID61
62 Saccharomyces cerevisiae FY4 time-series data of metabolites Visto4 [no] ["ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland", "---\n- LC-MS\n- GC-TOF\n", "application/pdf", "Zampar_2013.pdf", 2754858, Tue, 15 Apr 2014 12:42:25 UTC +00:00, "Guillermo G Zampar, Anne Kümmel, Jennifer Ewald, Stefan Jol, Bastian Niebel, Paola Picotti, Ruedi Aebersold, Uwe Sauer, Nicola Zamboni and Matthias Heinemann", "correlation of OD with biomass: 0.486 gDW/L OD", "glucose", "CHEBI:17234", "aerobic", "(mmol/L) of total cell volume", nil, "—", nil, nil, nil, "---\n- hot ethanol\n", "batch", 62, false, true, "Molecular Systems Biology", "diauxic shift, metabolome, S. cerevisiae, intracellular", "Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast.", "--- []\n", "Saccharomyces cerevisiae", "KIMODATAID62_v0.xlsx", "5.0", "--- []\n", "", "23549479", "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.", nil, "withdrawn from the culture at specific time points.", "FY4", "30.0", "--- []\n", "2", "2.0", 2013] Administrator KiMoSys Data AccessID62 / EntryID62
63 Escherichia coli NCM 3722 and mutants time-series data of metabolites Visto4 [yes]|[more] ["Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA and Department of Chemistry, Princeton University, Princeton, NJ, USA", "---\n- LC-ESI-MS\n", "application/pdf", "Yuan_2009.pdf", 742006, Fri, 11 Apr 2014 17:39:37 UTC +00:00, "Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen and Joshua D Rabinowitz", "", "glucose", "CHEBI:17234", "anaerobic", "mM", nil, "—", nil, nil, nil, "---\n- methanol\n", "batch", 63, false, true, "Molecular Systems Biology", "E. coli, ammonia assimilation, nitrogen upshift", "Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.", "--- []\n", "Escherichia coli", "KIMODATAID63_v0.xlsx", "≈ 7.0", "--- []\n", "", "19690571", "filters were submerged directly into -75 ºC methanol or -20 ºC 40:40:20 acetonitrile:methanol:water with 0.1 % formic acid.", nil, "filter cultures were prepared by passing 5 ml of exponentially growing liquid batch culture through membrane filters.", "NCM 3722 and mutants", "37.0", "--- []\n", "2", "", 2009] Administrator KiMoSys Data AccessID63 / EntryID63 ["Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA and Department of Chemistry, Princeton University, Princeton, NJ, USA", nil, "Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen and Joshua D Rabinowitz", "", "Metabolism", "application/omex+xml", "COMBINE_KIMOMODELID25.omex", 645413, Mon, 30 Jun 2014 17:56:44 UTC +00:00, "", Fri, 11 Apr 2014 17:38:32 UTC +00:00, Wed, 12 Jun 2013 13:43:10 UTC +00:00, "—", 25, "Molecular Systems Biology", "E. coli, ammonia assimilation, nitrogen upshift, differential equations, sensitivity analysis", "Escherichia coli", "Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli.", "Nitrogen assimilation model", "ordinary differential equations", 63, "", "19690571", nil, "Yuan_2009.pdf", "written in C++", "---\n- Model building\n- Model validation\n", 2009] Administrator KiMoSys Model AccessID25 / EntryID25
64 Escherichia coli BW25113 and mutants flux measurements Visto4 [no] ["Institute of Biotechnology, ETH, Zurich, Switzerland", "--- []\n", "application/pdf", "Perrenoud_2005.pdf", 390295, Tue, 15 Apr 2014 13:57:52 UTC +00:00, "Annik Perrenoud and Uwe Sauer", "not specified", "glucose", "CHEBI:17234", "aerobic", "(mmol/g.h)", nil, "—", nil, nil, nil, "--- []\n", "batch", 64, false, true, "Journal of Bacteriology", "Escherichia coli, aerobic glucose catabolism", "Impact of global transcriptional regulation by arcA, arcB, cra, crp, cya, fnr, and mlc on glucose catabolism in Escherichia coli.", "--- []\n", "Escherichia coli", "KIMODATAID64_v0.xlsx", "not specified", "---\n- GC-MS\n", "", "15838044", "", nil, "", "BW25113 and mutants ", "37.0", "---\n- 13C constrained MFA\n", "3", "0.030-0.050", 2005] Administrator KiMoSys Data AccessID64 / EntryID64
65 Escherichia coli MG1655 flux measurements Visto4 [no] ["Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland", "--- []\n", "application/pdf", "Nanchen_2006.pdf", 453495, Wed, 12 Jun 2013 15:55:08 UTC +00:00, "Annik Nanchen, Alexander Schicker and Uwe Sauer", "0.2-0.5", "glucose", "CHEBI:17234", "aerobic", "(mmol/gDW.h)", nil, "several dilution rates", nil, nil, nil, "--- []\n", "chemostat", 65, false, true, "Applied and Environmental Microbiology", "Escherichia coli, continuous culture, intracellular fluxes", "Nonlinear dependency of intracellular fluxes on growth rate in miniaturized continuous cultures of Escherichia coli.", "--- []\n", "Escherichia coli", "KIMODATAID65_v0.xlsx", "7.0", "---\n- GC-MS\n", "", "16461663", "", nil, "", "MG1655", "37.0", "---\n- 13C constrained MFA\n", "3", "0.010", 2006] Administrator KiMoSys Data AccessID65 / EntryID65
66 Shewanella oneidensis MR-1 flux measurements Visto4 [no] ["Dept. of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO63130 and Dept. of Chemical Engineering, University of California, Berkeley, CA", "--- []\n", nil, nil, nil, nil, "Yinjie J. Tang, Hector Garcia Martin, Adam Deutchbauer, Xueyang Feng, Rick Huang, Xavier Llora, Adam Arkin, Jay D. Keasling", "0.1 - 1.0", "lactate", "CHEBI:24996", "aerobic", "% of substrate uptake", nil, "—", nil, nil, nil, "--- []\n", "batch", 66, false, true, "Biotechnology Progress", "Shewanella oneidensis, 13C-based, secondary metabolism", "Invariability of central metabolic flux distribution in Shewanella oneidensis MR-1 under environmental or genetic perturbations.", "--- []\n", "Shewanella oneidensis", "KIMODATAID66_v0.xlsx", "7.0", "---\n- GC-MS\n", "", "19610125", "", nil, "", "MR-1", "30.0", "---\n- 13C constrained MFA\n", "3", "0.012", 2009] Administrator KiMoSys Data AccessID66 / EntryID66
67 Escherichia coli MG1655 flux measurements Visto4 [no] ["Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, USA and Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA", "--- []\n", "application/pdf", "Ranganathan_2012.pdf", 3485823, Thu, 20 Jun 2013 16:59:55 UTC +00:00, "Sridhar Ranganathan, Ting Wei Teeb, Anupam Chowdhuryc, Ali R. Zomorrodic, Jong Moon Yoon, Yanfen Fu, Jacqueline V. Shanksb, Costas D. Maranas", "0.36 (gDW/L) = 1 OD550 ", "glucose", "CHEBI:17234", "aerobic", "% substrate uptake", nil, "—", nil, nil, nil, "--- []\n", "batch", 67, false, true, "Metabolic Engineering", "Metabolic flux analysis, E. coli, fatty acids overproduction, MG1655", "An integrated computational and experimental study for overproducing fatty acids in Escherichia coli.", "--- []\n", "Escherichia coli", "KIMODATAID67_v0.xlsx", "7.0", "---\n- NMR\n", "", "23036703", "", nil, "", "MG1655", "37.0", "---\n- 13C constrained MFA\n", "3", "0.4", 2012] Administrator KiMoSys Data AccessID67 / EntryID67
68 Escherichia coli ML103 flux measurements Visto4 [no] ["Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, USA and Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA", "--- []\n", "application/pdf", "Ranganathan_2012.pdf", 3485823, Thu, 20 Jun 2013 17:42:27 UTC +00:00, "Sridhar Ranganathan, Ting Wei Teeb, Anupam Chowdhuryc, Ali R. Zomorrodic, Jong Moon Yoon, Yanfen Fu, Jacqueline V. Shanksb, Costas D. Maranas", "0.36 (gDW/L) = 1 OD550", "glucose", "CHEBI:17234", "aerobic", "mmol/gDW.h", nil, "—", nil, nil, nil, "--- []\n", "batch", 68, false, true, "Metabolic Engineering", "Metabolic flux analysis, E. Coli, fatty acids overproduction, ML103", "An integrated computational and experimental study for overproducing fatty acids in Escherichia coli.", "--- []\n", "Escherichia coli", "KIMODATAID68_v1.xlsx", "7.0", "---\n- NMR\n", "", "23036703", "", nil, "", "ML103", "30.0", "---\n- 13C constrained MFA\n", "3", "0.4", 2012] Administrator KiMoSys Data AccessID68 / EntryID68
69 Saccharomyces cerevisiae CEN.PK2-1C (W.T.), HXT1, HXT7 and TM6 time-series data of metabolites Visto4 [yes]|[more] ["Molecular Biotechnology and Chemical reaction Engineering, Department of Chemical and Biological Engineering, Chalmers University of Technology, Goeteborg, Sweden", "---\n- enzymatic\n", "application/pdf", "Bosch_2008.pdf", 426078, Thu, 21 Nov 2013 18:09:15 UTC +00:00, "Daniel Bosch, Mikael Johansson, Cecilia Ferndahl, Carl Johan Franzén, Christer Larsson and Lena Gustafsson", "correlation of OD with biomass: 0.486 gDW/L OD", "ethanol", "CHEBI:16236", "aerobic", "(mM)", nil, "0.1", nil, nil, nil, "---\n- not used\n", "chemostat", 69, false, true, "FEMS Yeast Research", "Saccharomyces cerevisiae, extracellular, metabolites, glucose and fructose pulse", "Characterization of glucose transport mutants of Saccharomyces cerevisiae during a nutritional upshift reveals a correlation between metabolite levels and glycolytic flux.", "--- []\n", "Saccharomyces cerevisiae", "KIMODATAID69_v1.xlsx", "5.0", "--- []\n", "", "18042231", "—", nil, "duplicate samples of 1ml each were steril filtered (0.22 µm), frozen in liquid N2 and stored at \u0002-20 ºC.", "CEN.PK2-1C (W.T.), HXT1, HXT7 and TM6", "30.0", "--- []\n", "2", "2.0", 2008] Administrator KiMoSys Data AccessID69 / EntryID69 ["Molecular Biotechnology and Chemical reaction Engineering, Department of Chemical and Biological Engineering, Chalmers University of Technology, Goeteborg, Sweden", nil, "Daniel Bosch, Mikael Johansson, Cecilia Ferndahl, Carl Johan Franzén, Christer Larsson and Lena Gustafsson", "", "Metabolism", nil, nil, nil, nil, "", Fri, 11 Apr 2014 17:42:47 UTC +00:00, Thu, 27 Jun 2013 09:17:15 UTC +00:00, "—", 28, "FEMS Yeast Research", "fitting, glucose pulse, Saccharomyce cerevisae, respiro-fermentative growth on glucose,", "Saccharomyces cerevisiae", "Characterization of glucose transport mutants of Saccharomyces cerevisiae during a nutritional upshift reveals a correlation between metabolite levels and glycolytic flux.", "Model for respiro-fermentative growth on glucose", "ordinary differential equations", 69, "", "18042231", nil, "Bosch_2008.pdf", "http://www.matlab.com (MATLAB)", "---\n- Model building\n", 2008] Administrator KiMoSys Model AccessID28 / EntryID28
70 Saccharomyces cerevisiae CEN.PK2-1C (W.T.), HXT1, HXT7 and TM6 time-series data of metabolites Visto4 [yes]|[more] ["Molecular Biotechnology and Chemical reaction Engineering, Department of Chemical and Biological Engineering, Chalmers University of Technology, Goeteborg, Sweden", "---\n- enzymatic\n", "application/pdf", "Bosch_2008.pdf", 426078, Thu, 21 Nov 2013 18:09:41 UTC +00:00, "Daniel Bosch, Mikael Johansson, Cecilia Ferndahl, Carl Johan Franzén, Christer Larsson and Lena Gustafsson", "correlation of OD with biomass: 0.486 gDW/L OD", "ethanol", "CHEBI:16236", "aerobic", "(mM)", nil, "0.1", nil, nil, nil, "---\n- methanol\n", "chemostat", 70, false, true, "FEMS Yeast Research", "Saccharomyces cerevisiae, intracellular, metabolites, glucose and fructose pulse", "Characterization of glucose transport mutants of Saccharomyces cerevisiae during a nutritional upshift reveals a correlation between metabolite levels and glycolytic flux.", "--- []\n", "Saccharomyces cerevisiae", "KIMODATAID70_v1.xlsx", "5.0", "--- []\n", "", "18042231", "samples were directly transferred into tubes with 10mL of methanol maintained at -48ºC; the final concentration of methanol (v/v) was about 75%.", nil, "for all metabolites, except ATP, six samples of 3 mL each", "CEN.PK2-1C (W.T.), HXT1, HXT7 and TM6", "30.0", "--- []\n", "2", "2.0", 2008] Administrator KiMoSys Data AccessID70 / EntryID70 ["Molecular Biotechnology and Chemical reaction Engineering, Department of Chemical and Biological Engineering, Chalmers University of Technology, Goeteborg, Sweden", nil, "Daniel Bosch, Mikael Johansson, Cecilia Ferndahl, Carl Johan Franzén, Christer Larsson and Lena Gustafsson", "", "Metabolism", nil, nil, nil, nil, "", Fri, 11 Apr 2014 17:42:47 UTC +00:00, Thu, 27 Jun 2013 09:17:15 UTC +00:00, "—", 28, "FEMS Yeast Research", "fitting, glucose pulse, Saccharomyce cerevisae, respiro-fermentative growth on glucose,", "Saccharomyces cerevisiae", "Characterization of glucose transport mutants of Saccharomyces cerevisiae during a nutritional upshift reveals a correlation between metabolite levels and glycolytic flux.", "Model for respiro-fermentative growth on glucose", "ordinary differential equations", 69, "", "18042231", nil, "Bosch_2008.pdf", "http://www.matlab.com (MATLAB)", "---\n- Model building\n", 2008] Administrator KiMoSys Model AccessID28 / EntryID28
71 Penicillium chrysogenum DS12975 time-series data of metabolites Visto4 [no] ["Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, Netherlands", "---\n- HPLC-UV/RI\n- LC-ESI-MS\n", "application/pdf", "Nasution_2006.pdf", 292170, Fri, 21 Jun 2013 17:04:51 UTC +00:00, "U. Nasution, W.M. Van Gulik, A. Proell, W.A. van Winden, J.J. Heijnen", "6.21 ± 0.16", "glucose", "CHEBI:17234", "aerobic", "(µmol/gDW)", nil, "0.05", nil, nil, nil, "---\n- hot ethanol\n", "chemostat", 71, false, true, "Metabolic Engineering", "glucose pulse, in vivo kinetics, metabolome, Penicillium chrysogenum", "Generating short-term kinetic responses of primary metabolism of Penicillium chrysogenum through glucose perturbation in the bioscope mini reactor.", "--- []\n", "Penicillium chrysogenum", "KIMODATAID71_v0.xlsx", "6.5", "--- []\n", "", "16807032", "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).", 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.", "DS12975", "25.0", "--- []\n", "2", "4.0", 2006] Administrator KiMoSys Data AccessID71 / EntryID71
72 Aspergillus niger SKANip8 (W.T.) and SKAn1015 flux measurements Visto4 [no] ["Institute of Biochemical Engineering, Technische Universitat Braunschweig, Gaussstrasse 17, Braunschweig, Germany", "--- []\n", "application/pdf", "Driouch_2012.pdf", 1268569, Sat, 22 Jun 2013 14:35:53 UTC +00:00, "Habib Driouch, Guido Melzer, Christoph Wittmann", "", "glucose", "CHEBI:17234", "aerobic", "(mmol/gh)", nil, "—", nil, nil, nil, "--- []\n", "batch", 72, false, true, "Metabolic Engineering", "Aspergillus niger, 13C metabolic flux, fructofuranosidase", "Integration of in vivo and in silico metabolic fluxes for improvement of recombinant protein production.", "--- []\n", "Aspergillus niger", "KIMODATAID72_v0.xlsx", "5.0", "---\n- GC-MS\n", "", "22115737", "", nil, "", "SKANip8 (W.T.) and SKAn1015", "37.0", "---\n- 13C constrained MFA\n", "3", "0.025", 2012] Administrator KiMoSys Data AccessID72 / EntryID72
73 Aspergillus niger N402 (W.T.) and icl overexpression flux measurements Visto4 [no] ["Department for Systems Biology, Center for Microbial Biotechnology, Building 223, Technical University of Denmark, Lyngby, Denmark.", "--- []\n", "application/pdf", "Meijer_2009.pdf", 793540, Sun, 23 Jun 2013 12:31:56 UTC +00:00, "S. Meijer, J Otero, R. Olivares, M.R. Andersen, L. Olsson, J. Nielsen", "2.0-4.0", "glucose", "CHEBI:17234", "aerobic", "% substrate uptake", nil, "", nil, nil, nil, "--- []\n", "batch", 73, false, true, "Metabolic Engineering", "Aspergillus niger, isocitrate lyase over-expression, glyoxylate bypass", "Overexpression of isocitrate lyase-glyoxylate bypass influence on metabolism in Aspergillus niger.", "--- []\n", "Aspergillus niger", "KIMODATAID73_v0.xlsx", "2.5", "---\n- GC-MS\n", "", "19271267", "", nil, "", "N402 (W.T.) and icl overexpression", "30.0", "---\n- 13C constrained MFA\n", "3", "2.0", 2009] Administrator KiMoSys Data AccessID73 / EntryID73
74 Escherichia coli K-12 MG1655 metabolites at steady-state Visto4 [no] ["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", "---\n- LC-ESI-MS\n", "application/pdf", "DeMey_2010.pdf", 1348974, Tue, 25 Jun 2013 14:31:11 UTC +00:00, "Marjan De Mey, Hilal Taymaz-Nikerel, Gino Baart, Hendrik Waegeman, Jo Maertens, Joseph J. Heijnen, Walter M. Van Gulik", "8.4 (Experiment 1) and 8.02 (Experiment 2)", "glucose", "CHEBI:17234", "aerobic", "(µmol/gDW)", nil, "0.1", nil, nil, nil, "---\n- boiling ethanol\n", "chemostat", 74, false, true, "Metabolic Engineering", "Escherichia coli, glucose pulse, BioScope, chemostat", "Catching prompt metabolite dynamics in Escherichia coli with the BioScope at oxygen rich conditions.", "--- []\n", "Escherichia coli", "KIMODATAID74_v0.xlsx", "5.0", "--- []\n", "", "20447466", "tubes containing 5ml of 60% aqueous methanol, pre-cooled at -40 ºC and immediately mixed after sampling by vortexing.", nil, "1ml of broth rapidly withdrawn from the bioreactor.", "K-12 MG1655", "37.0", "--- []\n", "1", "4.0", 2010] Administrator KiMoSys Data AccessID74 / EntryID74
75 Escherichia coli K-12 MG1655 time-series data of metabolites Visto4 [no] ["Department of Biotechnoloy, Delft University of Technology, Kluyver Center for Genomics of Industrial Fermentation Julianalaan 67, 2628 BC Delft, The Netherlands", "---\n- enzymatic\n- GC-MS\n- LC-MS\n- HPLC-UV/RI\n", "application/pdf", "Nikerel_2013.pdf", 2224811, Tue, 25 Jun 2013 15:06:47 UTC +00:00, "Hilal Taymaz-Nikerel, Marjan De Mey, Gino Baart, Jo Maertens, Joseph J. Heijnen, Walter M. Van Gulik", "8.36 (Experiment 1) and 8.02 (Experiment 2)", "glucose", "CHEBI:17234", "aerobic", "(µmol/gDW)", nil, "0.1", nil, nil, nil, "---\n- boiling ethanol\n", "chemostat", 75, false, true, "Metabolic Engineering", "Escherichia coli, intracellular metabolites, stimulus response", "Changes in substrate availability in Escherichia coli lead to rapid metabolite, flux and growth rate responses.", "--- []\n", "Escherichia coli", "KIMODATAID75_v1.xlsx", "7.0", "--- []\n", "", "23370343", "not specified", nil, "differential method", "K-12 MG1655", "37.0", "--- []\n", "2", "4.0", 2013] Administrator KiMoSys Data AccessID75 / EntryID75
76 Streptomyces coelicolor M145 (W.T.) and phoP mutant (INB201) time-series data of metabolites Visto4 [no] ["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 ", "---\n- GC-MS\n- LC-MS\n", "application/pdf", "Wentzel_2012.pdf", 1290587, Fri, 28 Jun 2013 14:43:07 UTC +00:00, "Alexander Wentzel, Harvard Sletta, Stream Consortium, Trond E. Ellingsen and Per Bruheim", "see worksheets", "glucose", "CHEBI:17234", "aerobic", "µM", nil, "—", nil, nil, nil, "---\n- methanol\n", "batch", 76, false, true, "Metabolites", "Streptomyces coelicolor, transition phase, metabolic switching metabolite profiling", "Intracellular metabolite pool changes in response to nutrient depletion induced metabolic switching in Streptomyces coelicolor.", "--- []\n", "Streptomyces coelicolor", "KIMODATAID76_v0.xlsx", "not specified", "--- []\n", "", "", "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. ", nil, " Samples for metabolite profiling were withdrawn from the cultivations in 1–2 h time intervals.", "M145 (W.T.) and phoP mutant (INB201)", "30.0", "--- []\n", "2", "1.8", 2012] Administrator KiMoSys Data AccessID76 / EntryID76
77 Shewanella oneidensis MR-1 (ATCC 70050) time-series data of metabolites Visto4 [yes]|[more] ["Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, Missouri, United States of America", "---\n- enzymatic\n", "application/pdf", "Feng_2012.pdf", 1271214, Wed, 03 Jul 2013 16:40:55 UTC +00:00, "Xueyang Feng, You Xu, Yixin Chen, Yinjie J. Tang", "≈ 0.3 - 0.5", "lactate", "CHEBI:24996", "aerobic", "(g/L) and (mM)", nil, "—", nil, nil, nil, "---\n- not used\n", "batch", 77, false, true, "PLOS Computational Biology", "Shewanella oneidensis, dynamic metabolism, extracellular", "Integrating flux balance analysis into kinetic models to decipher the dynamic metabolism of Shewanella oneidensis.", "--- []\n", "Shewanella oneidensis", "KIMODATAID77_v0.xlsx", "not specified", "--- []\n", "", "22319437", "—", nil, "manually at different time", "MR-1 (ATCC 70050)", "30.0", "--- []\n", "2", "0.1", 2012] Administrator KiMoSys Data AccessID77 / EntryID77 ["", nil, "Xueyang Feng, You Xu, Yixin Chen, Yinjie J. Tang", "", "Metabolism", nil, nil, nil, nil, "", Fri, 11 Apr 2014 17:54:44 UTC +00:00, Wed, 03 Jul 2013 16:54:30 UTC +00:00, "—", 30, "PLOS Computational Biology", "DFBA, kinetic model", "Shewanella oneidensis", "Integrating flux balance analysis into kinetic models to decipher the dynamic metabolism of Shewanella oneidensis MR-1.", "Kinetic model of Shewanella oneidensis MR-1 ", "ordinary differential equations", 77, "", "22319437", nil, "Feng_2012.pdf", "http://www.matlab.com (MATLAB)", "---\n- Model building\n- Model validation\n", 2012] Administrator KiMoSys Model AccessID30 / EntryID30
78 Escherichia coli K-12 overproduce 1,3-propanediol time-series data of metabolites Visto4 [no] ["Department of Chemical Engineering, Bioinformatics and Metabolic Engineering Laboratory, Massachusetts Institute of Technology, Cambridge", "---\n- HPLC-UV/RI\n", "application/pdf", "Antoniewicz_2007.pdf", 1081894, Fri, 05 Jul 2013 14:28:29 UTC +00:00, "Maciek R. Antoniewicz, David F. Kraynie, Lisa A. Laffend, Joanna González-Lergier, Joanne K. Kelleher and Gregory Stephanopoulos", "3.0 ", "glucose", "CHEBI:17234", "aerobic", "mM", nil, "—", nil, nil, nil, "---\n- not used\n", "fed-batch", 78, false, true, "Metabolic Engineering", "E. coli, extracelullar metabolites, HPLC", "Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol.", "--- []\n", "Escherichia coli", "KIMODATAID78_v0.xlsx", "6.8 ± 0.04", "--- []\n", "", "17400499", "—", nil, "Periodically taken during the fed-batch ", "K-12 overproduce 1,3-propanediol", "34.0", "--- []\n", "2", "1.0", 2007] Administrator KiMoSys Data AccessID78 / EntryID78
79 Escherichia coli BW25113 and arcA mutant metabolites at steady-state Visto4 [no] ["Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan", "---\n- CE-TOF-MS\n", nil, nil, nil, nil, "Yoshihiro Toya, Kenji Nakahigashi, Masaru Tomita and Kazuyuki Shimizu", "", "glucose", "CHEBI:17234", "aerobic and anaerobic", "(µM)", nil, "0.2", nil, nil, nil, "---\n- chloroform\n- sonication\n", "chemostat", 79, false, true, "Molecular BioSystems", "Escherichia coli, intracelullar metabolites", "Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data.", "--- []\n", "Escherichia coli", "KIMODATAID79_v0.xlsx", "7.0", "--- []\n", "", "22790675", "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.", nil, "5 mg of cells were passed through a 0.45 mm pore filter (Millipore) filled with saline.", "BW25113 and arcA mutant", "37.0", "--- []\n", "1", "1.0", 2012] Administrator KiMoSys Data AccessID79 / EntryID79
80 Escherichia coli BW25113 and arcA mutant flux measurements Visto4 [no] ["Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan", "--- []\n", nil, nil, nil, nil, "Yoshihiro Toya, Kenji Nakahigashi, Masaru Tomita and Kazuyuki Shimizu", "", "glucose", "CHEBI:17234", "aerobic and anaerobic", "(mmol/gDW.h)", nil, "0.2", nil, nil, nil, "--- []\n", "chemostat", 80, false, true, "Molecular BioSystems", "Escherichia coli, metabolic flux distributions", "Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data.", "--- []\n", "Escherichia coli", "KIMODATAID80_v0.xlsx", "7.0", "---\n- MALDI-TOF\n", "", "22790675", "", nil, "", "BW25113 and arcA mutant", "37.0", "---\n- 13C constrained MFA\n", "3", "1.0", 2012] Administrator KiMoSys Data AccessID80 / EntryID80
81 Mus musculus E13.5 Balb/c enzyme/protein concentrations Visto4 [yes]|[more] ["Division of Systems Biology of Signal Transduction, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany", "--- []\n", "application/pdf", "Bachmann_2011.pdf", 1464156, Wed, 23 Apr 2014 17:40:13 UTC +00:00, "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", "4.0×10^7 (cells/L)", "", "", "", "(a.u.)", nil, "—", nil, nil, nil, "--- []\n", "batch", 81, false, true, "Molecular Systems Biology", "apoptosis, erythropoietin, mathematical modeling, negative feedback, SOCS, simulation and data analysis, signal transduction", "Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range.", "---\n- immunoblotting\n", "Mus musculus", "KIMODATAID81_v0.xlsx", "not specified", "--- []\n", "", "21772264", "", nil, "", "E13.5 Balb/c", "37.0", "--- []\n", "4", "", 2011] Administrator KiMoSys Data AccessID81 / EntryID81 ["Division of Systems Biology of Signal Transduction, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany", nil, "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", "", "Signal", "application/omex+xml", "COMBINE_KIMOMODELID31.omex", 1445888, Mon, 30 Jun 2014 17:59:26 UTC +00:00, "", nil, Wed, 23 Apr 2014 17:30:03 UTC +00:00, "", 31, "Molecular Systems Biology", "apoptosis, erythropoietin, mathematical modeling, negative feedback, SOCS, simulation and data analysis, signal transduction", "Mouse", "Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range.", "transcriptional model of JAK2/STAT5 signaling", "ordinary differential equations", nil, "", "21772264", nil, "Bachmann_2011.pdf", "http://www.matlab.com (MATLAB)", "---\n- Model building\n", 2011] Administrator KiMoSys Model AccessID31 / EntryID31
82 Homo sapiens colorectal cancer cell lines SW480, SW403, HCT116, RKO, LIM1215 and HT29 enzyme/protein concentrations Visto4 [no] ["Laboratory of Molecular Tumour Pathology, Institute of Pathology, Charité - Universitatsmedizin Berlin, Berlin, Germany, and Institute for Theoretical Biology, Humboldt University Berlin, Berlin, Germany", "--- []\n", "application/pdf", "Klinger_2013.pdf", 402404, Wed, 23 Apr 2014 17:56:27 UTC +00:00, "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", "", "", "", "aerobic", "(a.u.)", nil, "—", nil, nil, nil, "--- []\n", "batch", 82, false, true, "Molecular Systems Biology", "cancer, EGFR signaling, modular response analysis, signal transduction", "Network quantification of EGFR signaling unveils potential for targeted combination therapy.", "---\n- immunoblotting\n", "Homo sapiens", "KIMODATAID82_v0.xlsx", "not specified", "--- []\n", "", "23752269", "", nil, "", "colorectal cancer cell lines SW480, SW403, HCT116, RKO, LIM1215 and HT29", "37.0", "--- []\n", "4", "", 2013] Administrator KiMoSys Data AccessID82 / EntryID82
86 Escherichia coli K-12 MG1655 flux measurements Visto4 [no] ["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", "--- []\n", "application/pdf", "Millard_2014.pdf", 1574738, Mon, 20 Apr 2015 14:43:51 UTC +00:00, "Pierre Millard, Stéphane Massou, Christoph wittmann, Jean-Charles Portais, Fabien Létisse", "", "glucose", "17234", "aerobic", "% substrate uptake", nil, "—", nil, nil, nil, "--- []\n", "batch", 86, false, true, "Analytical Biochemistry", "(13)C-labeling experiments, Isotopes, Isotopologue, Mass isotopomer, Metabolism, Sampling procedures", "Sampling of intracellular metabolites for stationary and non-stationary 13C metabolic flux analysis in Escherichia coli", "--- []\n", "Escherichia coli", "KIMODATAID86_v2.xlsx", "7.0", "---\n- NMR\n- GC-MS\n- LC-MS\n", "", "25102204", "", nil, "", "K-12 MG1655", "37.0", "---\n- 13C constrained MFA\n", "3", "0.150", 2014] Administrator KiMoSys Data AccessID86 / EntryID86
87 Escherichia coli K-12 MG1655 metabolites at steady-state Visto4 [no] ["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", "---\n- NMR\n- GC-MS\n- LC-MS\n", "application/pdf", "Millard_2014.pdf", 1574738, Fri, 01 May 2015 11:55:03 UTC +00:00, "Pierre Millard, Stéphane Massou, Christoph wittmann, Jean-Charles Portais, Fabien Létisse", "—", "glucose", "17234", "aerobic", "mM", nil, "—", nil, nil, nil, "---\n- hot ethanol\n", "batch", 87, false, true, "Analytical Biochemistry", "Quantitative metabolomics, Metabolism, Sampling procedures", "Sampling of intracellular metabolites for stationary and non-stationary 13C metabolic flux analysis in Escherichia coli", "--- []\n", "Escherichia coli", "KIMODATAID87_v0.xlsx", "7.0", "--- []\n", "", "25102204", "different methods (see Figure 1).", nil, "different methods (see Figure 1).", "K-12 MG1655", "37.0", "--- []\n", "1", "0.150", 2014] Administrator KiMoSys Data AccessID87 / EntryID87
88 Bacillus subtilis BSB168 metabolites at steady-state Visto4 [no] ["Institute of Molecular System Biology, ETH Zurich, Zurich, Switzerland.", "---\n- HPLC-MS\n", "application/pdf", "Chubukov_2013.pdf", 559480, Tue, 05 May 2015 16:47:23 UTC +00:00, "Victor Chubukov, Markus Uhr, Ludovic Le Chat, Roelco J Kleijn, Matthieu Jules, Hannes Link, Stephane Aymerich, Joerg Stelling and Uwe Sauer", "3.0 g cells/OD600", "glucose, fructose, gluconate, succinate+glutamate, glycerol, malate, malate, malate+glucose, pyruvate", "", "aerobic", "mMol/L cell volume", nil, "—", nil, nil, nil, "---\n- hot ethanol\n", "batch", 88, false, true, "Molecular Systems Biology", "central carbon metabolism, metabolic flux, transcriptional regulation", "Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis", "--- []\n", "Bacillus subtilis", "KIMODATAID88_v3.xlsx", "—", "--- []\n", "", "24281055", "—", 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.", "BSB168", "37.0", "--- []\n", "1", "0.03", 2013] Administrator KiMoSys Data AccessID88 / EntryID88
89 Bacillus subtilis BSB168 flux measurements Visto4 [no] ["Institute of Molecular System Biology, ETH Zurich, Zurich, Switzerland.", "--- []\n", "application/pdf", "Chubukov_2013.pdf", 559480, Tue, 12 May 2015 15:24:47 UTC +00:00, "Victor Chubukov, Markus Uhr, Ludovic Le Chat, Roelco J Kleijn, Matthieu Jules, Hannes Link, Stephane Aymerich, Joerg Stelling and Uwe Sauer", "3.0 g cells/OD600", "glucose, fructose, gluconate, succinate+glutamate, glycerol, malate, malate, malate+glucose, pyruvate", "", "aerobic", "mmol/g/h", nil, "—", nil, nil, nil, "--- []\n", "batch", 89, false, true, "Molecular Systems Biology", "central carbon metabolism, metabolic flux, transcriptional regulation", "Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis.", "--- []\n", "Bacillus subtilis", "KIMODATAID89_v0.xlsx", "—", "---\n- GC-MS\n", "", "24281055", "", nil, "", "BSB168", "37.0", "---\n- 13C constrained MFA\n", "3", "0.03", 2013] Administrator KiMoSys Data AccessID89 / EntryID89
90 Thermus thermophilus HB8 (ATCC 27634) flux measurements Visto4 [no] ["Department of Chemical & Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark DE 19716, USA", "--- []\n", "application/pdf", "Swarup_2014.pdf", 1039072, Tue, 22 Sep 2015 12:48:07 UTC +00:00, "Aditi Swarup, Jimg Lu, Kathleen C. DeWoody, Maciek R. Antoniewicz", "0.39 (g/L)/OD600 cell dry weight and 25.3 g/C-mol for the molecular weight of dry biomass", "glucose", "17234", "aerobic", "% substrate uptake", nil, "—", nil, nil, nil, "--- []\n", "batch", 90, false, true, "Metabolic Engineering", "Extremophile, Thermophilic bacterium, Optimal growth, Metabolic network model, Isotopic labeling", "Metabolic network reconstruction, growth characterization and 13C-metabolic flux analysis of the extremophile Thermus thermophilus HB8", "--- []\n", "Thermus thermophilus", "KIMODATAID90_v0.xlsx", "7.9", "---\n- GC-MS\n", "", "24909362", "", nil, "", "HB8 (ATCC 27634)", "70", "---\n- 13C constrained MFA\n", "3", "0.01", 2014] Administrator KiMoSys Data AccessID90 / EntryID90
91 Rattus C57BLKS/J-m+/+db and mutants metabolites at steady-state Visto4 [no] ["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.", "---\n- NMR\n", "application/pdf", "Zheng_2016.pdf", 3790994, Tue, 26 Apr 2016 15:38:14 UTC +00:00, "Yongquan Zheng, Yunjun Yang, Baijun Dong, Hong Zheng, Xiaodong Lin, Du Yao, Xiaokun Li, Liangcai Zhao, Hongchang Gao", "", "glucose", "17234", "aerobic", "unitless", nil, "", nil, nil, nil, "---\n- chloroform\n", "batch", 91, false, true, "Molecular brain", "Diabetes-associated cognition decline, Nuclear magnetic resonance, Metabonomics, Glutamate-glutamine cycle", "Metabonomic profiles delineate potential role of glutamate-glutamine cycle in db/db mice with diabetes-associated cognitive decline", "--- []\n", "Rattus", "KIMODATAID91_v2.xlsx", "7", "--- []\n", "", "", "specimens of hippocampus were dissected immediately, snap-frozen in liquid nitrogen and stored at -80 °C until use.", nil, " The mice were sacrificed by decapitation at 17-wk of age, and specimens of hippocampus were collected manually.", "C57BLKS/J-m+/+db and mutants", "25", "--- []\n", "1", "0.0005", 2016] Administrator KiMoSys Data AccessID91 / EntryID91
92 Escherichia coli WT K-12 strain NCM3722 of E. coli metabolites at steady-state Visto4 [no] ["Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton", "---\n- NMR\n- LC-ESI-MS\n", nil, nil, nil, nil, "Bryson D Bennett, Elizabeth H Kimball, Melissa Gao, Robin Osterhout, Stephen J Van Dien, and Joshua D Rabinowitz", "Cultures were grown to OD650 of 0.35.", "glucose, glycerol, acetate", "", "aerobic", "mM", nil, "-", nil, nil, nil, "---\n- acidic acetonitrile-methanol\n", "batch", 92, false, true, "Nature Chemical Biology", "", "Absolute Metabolite Concentrations and Implied Enzyme Active Site Occupancy in Escherichia coli.", "--- []\n", "Escherichia coli", "KIMODATAID92_v2.xlsx", "not specified", "--- []\n", "", "19561621", "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.", 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.", "WT K-12 strain NCM3722 of E. coli", "37", "--- []\n", "1", "0.05", 2009] Administrator KiMoSys Data AccessID92 / EntryID92
93 Saccharomyces cerevisiae CEN.PK 113-7D, CEN.PK/JT4, FY4 metabolites at steady-state Visto4 [no] ["Institute of Molecular Systems Biology, ETH Zurich", "---\n- LC-MS\n- GC-TOF\n", "application/pdf", "Kummel_2010.pdf", 260572, Sat, 07 Jul 2018 21:16:38 UTC +00:00, "Anne Kümmel, Jennifer Christina Ewald, Sarah‐Maria Fendt, Stefan Jasper Jol, Paola Picotti, Ruedi Aebersold, Uwe Sauer, Nicola Zamboni, Matthias Heinemann", "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.", "glucose", "17234", "aerobic", "mM", nil, "-", nil, nil, nil, "---\n- hot ethanol\n", "batch", 93, false, true, "FEMS Yeast Research", "glucose repression; hexokinase 2; FY4; CEN.PK; PKA; metabolomics", "Differential glucose repression in common yeast strains in response to HXK2 deletion.", "--- []\n", "Saccharomyces cerevisiae", "KIMODATAID93_v1.xlsx", "5.0", "--- []\n", "", "20199578", "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.", 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.", "CEN.PK 113-7D, CEN.PK/JT4, FY4 ", "30", "--- []\n", "1", "not specified", 2010] Administrator KiMoSys Data AccessID93 / EntryID93
94 Bacillus subtilis Wild-type BSB168 trp+ metabolites at steady-state Visto4 [no] ["Institute of Molecular System Biology, ETH Zurich, CH-8093 Zurich, Switzerland", "---\n- LC-MS\n- GC-TOF\n", "application/pdf", "Kleijn_2010.pdf", 1325603, Mon, 09 Jul 2018 20:51:51 UTC +00:00, "Roelco J. Kleijn, Joerg M. Buescher, Ludovic Le Chat, Matthieu Jules, Stephane Aymerich and Uwe Sauer", "0.5", "glucose, glucose + malate, malate", "", "aerobic", "mM", nil, "-", nil, nil, nil, "---\n- hot ethanol\n", "batch", 94, false, true, "The Journal of Biological Chemistry", "Metabolism, Metabolism/Gluconeogenesis, Metabolism/Intermediary, Metabolism/Regulation, Metabolism/Tricarboxylic Acid Cycle, Methods/Mass Spectrometry, flux analysis, metabolomics", "Metabolic Fluxes during Strong Carbon Catabolite Repression by Malate in Bacillus subtilis.", "--- []\n", "Bacillus subtilis", "KIMODATAID94_v2.xlsx", "not specified", "--- []\n", "", "19917605", "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.", 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", "Wild-type BSB168 trp+", "37", "--- []\n", "1", "0.03", 2009] Administrator KiMoSys Data AccessID94 / EntryID94
95 Bacillus subtilis Wild-type BSB168 trp+ flux measurements Visto4 [no] ["Institute of Molecular System Biology, ETH Zurich, CH-8093 Zurich, Switzerland", "--- []\n", "application/pdf", "Kleijn_2010.pdf", 1325603, Wed, 11 Jul 2018 22:06:12 UTC +00:00, "Roelco J. Kleijn, Joerg M. Buescher, Ludovic Le Chat, Matthieu Jules, Stephane Aymerich and Uwe Sauer", "dry weight was inferred from a predetermined conversion factor of 0.48 g of cells/A600", "glucose, glucose + malate, malate", "", "aerobic", "", nil, "-", nil, nil, nil, "--- []\n", "batch", 95, false, true, "The Journal of Biological Chemistry", "Metabolism, Metabolism/Gluconeogenesis, Metabolism/Intermediary, Metabolism/Regulation, Metabolism/Tricarboxylic Acid Cycle, Methods/Mass Spectrometry, flux analysis, metabolomics", "Metabolic Fluxes during Strong Carbon Catabolite Repression by Malate in Bacillus subtilis.", "--- []\n", "Bacillus subtilis", "KIMODATAID95_v4.xlsx", "not specified", "---\n- GC-MS\n", "", "19917605", "", nil, "", "Wild-type BSB168 trp+", "37", "---\n- 13C constrained MFA\n", "3", "0.03", 2010] Administrator KiMoSys Data AccessID95 / EntryID95
96 Escherichia coli Wild‐type E. coli BW25113, Pyk and Pgi mutants time-series data of metabolites Visto4 [yes]|[more] ["Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan", "---\n- CE-TOF-MS\n", "application/pdf", "Toya_2010.pdf", 1380598, Fri, 13 Jul 2018 11:15:07 UTC +00:00, "Yoshihiro Toya, Nobuyoshi Ishii, Kenji Nakahigashi, Takashi Hirasawa, Tomoyoshi Soga, Masaru Tomita, Kazuyuki Shimizu", "1 OD600 = 0.3 g/L", "glucose", "17234", "aerobic", "g/L and mM", nil, "—", nil, nil, nil, "---\n- chloroform-methanol\n", "batch", 96, false, true, "Biotechnology Progress", "13C-metabolic flux analysis, batch culture, Escherichia coli, Pyk mutant, Pgi", "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.", "--- []\n", "Escherichia coli", "KIMODATAID96_v1.xlsx", "7.0", "--- []\n", "", "20730757", "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.", nil, "An aliquot of culture broth containing 0.015 g of cells was passed through a 0.45‐μm pore size filter.", "Wild‐type E. coli BW25113, Pyk and Pgi mutants", "37", "--- []\n", "2", "1.2", 2010] Administrator KiMoSys Data AccessID96 / EntryID96 ["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680‑4 Kawazu, Iizuka, Fukuoka 820‑8502, Japan", nil, "Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto and Hiroyuki Kurata", "", "Metabolism", "application/octet-stream", "COMBINE_KIMOMODELID38.omex", 6603649, Mon, 23 Jul 2018 21:38:00 UTC +00:00, "MATLAB version of the model is available at http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html. ", Fri, 20 Jul 2018 16:47:46 UTC +00:00, Thu, 12 Jul 2018 12:32:20 UTC +00:00, "0.2, 0.4, 0.5 and 0.7", 38, "Microbial Cell Factories", "Systems biology, Rational design, Dynamic model, Enzyme kinetics, Transcription factor, Signal transduction, Allosteric enzyme", "Escherichia coli", "Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli", "E. coli Central Carbon Metabolism", "ordinary differential equations", nil, "", "27329289", nil, "Jahan_2016.pdf", "MATLAB2007 or higher", "---\n- Model building\n- Model validation\n", 2016] Administrator KiMoSys Model AccessID38 / EntryID38 [" Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan", nil, "Yu Matsuoka and Hiroyuki Kurata", "", "Metabolism", nil, nil, nil, nil, "Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.", Fri, 20 Jul 2018 16:25:00 UTC +00:00, Thu, 19 Jul 2018 15:05:36 UTC +00:00, "—", 40, "Biotechnology for Biofuels", "Kinetic modeling, Fermentation, Dissolved oxygen limitation, Redox regulation, ArcA, Fnr, Respiratory chain, NADH/NAD+ ratio, Escherichia coli ", "Escherichia coli", "Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations.", "E. coli redox regulation model", "ordinary differential equations", nil, "", "28725263", nil, "Matsuoka_2017.pdf", "MATLAB (MathWorks) was used for all simulations.", "---\n- Model building\n- Model validation\n", 2017] Administrator KiMoSys Model AccessID40 / EntryID40 ["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan", nil, "Hiroyuki Kurata and Yurie Sugimoto", "", "Metabolism", nil, nil, nil, nil, "Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.", nil, Tue, 24 Jul 2018 16:03:02 UTC +00:00, "—", 45, "Journal of Bioscience and Bioengineering", "Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli", "Escherichia coli", "Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures", "Batch kinetic model of Escherichia coli", "ordinary differential equations", nil, "", "29054464", nil, "Kurata_2018.pdf", "MATLAB (MathWorks)", "---\n- Model building\n", 2018] Administrator KiMoSys Model AccessID45 / EntryID45
97 Saccharomyces cerevisiae Y23925 enzyme/protein concentrations Visto4 [yes]|[more] ["Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK", "--- []\n", "application/pdf", "Smallbone_2013.pdf", 755835, Sun, 15 Jul 2018 21:24:27 UTC +00:00, "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", "monitored by measuring the electrical capacitance of the culture.", "glucose", "17234", "aerobic", "molecules/cell", nil, "µmax", nil, nil, nil, "--- []\n", "chemostat", 97, false, true, "FEBS Letters", "Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling", "A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.", "---\n- LC-MS/MS\n", "Saccharomyces cerevisiae", "KIMODATAID97_v4.xlsx", "not specified", "--- []\n", "", "23831062", "", nil, "", "Y23925", "not specified", "--- []\n", "4", "not specified", 2013] Administrator KiMoSys Data AccessID97 / EntryID97 ["Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK", nil, "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.", "smallbone18", "Metabolism", nil, nil, nil, nil, "Original model source: in JWS online database.", nil, Mon, 16 Jul 2018 19:34:20 UTC +00:00, "", 39, "FEBS Letters", "Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling", "Saccharomyces cerevisiae", "A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.", "smallbone18", "ordinary differential equations", nil, "", "23831062", nil, "Smallbone_2013.pdf", "Copasi (www.copasi.org)", "---\n- Model validation\n", 2013] Administrator KiMoSys Model AccessID39 / EntryID39
98 Saccharomyces cerevisiae TAP-tagged strain enzyme/protein concentrations Visto4 [yes]|[more] ["Howard Hughes Medical Institute, University of California–San Francisco, San Francisco, California 94143-2240, USA", "--- []\n", "application/pdf", "Ghaemmaghami_2003.pdf", 873183, Mon, 16 Jul 2018 15:29:11 UTC +00:00, "Sina Ghaemmaghami, Won-Ki Huh, Kiowa Bower, Russell W. Howson, Archana Belle, Noah Dephoure, Erin K. O'Shea & Jonathan S. Weissman", "OD of ~0.7 ", "glucose", "17234", "aerobic", "molecules/cell", nil, "—", nil, nil, nil, "--- []\n", "chemostat", 98, false, true, "Nature", "yeast, protein expression, S. cerevisiae", "Global analysis of protein expression in yeast.", "---\n- LC-MS/MS\n", "Saccharomyces cerevisiae", "KIMODATAID98_v0.xlsx", "not specified", "--- []\n", "", "14562106", "", nil, "", "TAP-tagged strain ", "30", "--- []\n", "4", "0.0017", 2003] Administrator KiMoSys Data AccessID98 / EntryID98 ["Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK", nil, "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.", "smallbone18", "Metabolism", nil, nil, nil, nil, "Original model source: in JWS online database.", nil, Mon, 16 Jul 2018 19:34:20 UTC +00:00, "", 39, "FEBS Letters", "Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling", "Saccharomyces cerevisiae", "A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.", "smallbone18", "ordinary differential equations", nil, "", "23831062", nil, "Smallbone_2013.pdf", "Copasi (www.copasi.org)", "---\n- Model validation\n", 2013] Administrator KiMoSys Model AccessID39 / EntryID39
99 Saccharomyces cerevisiae Y23925 metabolites at steady-state Visto4 [yes]|[more] ["Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK", "---\n- GC-MS\n- LC-MS\n", "application/pdf", "Smallbone_2013.pdf", 755835, Mon, 16 Jul 2018 15:49:58 UTC +00:00, "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", "monitored by measuring the electrical capacitance of the culture.", "glucose", "17234", "aerobic", "molecules/cell", nil, "µmax", nil, nil, nil, "---\n- freezing-thawing in methanol\n- methanol-water\n", "chemostat", 99, false, true, "FEBS Letters", "Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling", "A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.", "--- []\n", "Saccharomyces cerevisiae", "KIMODATAID99_v2.xlsx", "not specified", "--- []\n", "—", "23831062", "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. ", nil, "10 ml of culture.", "Y23925", "not specified", "--- []\n", "1", "not specified", 2013] Administrator KiMoSys Data AccessID99 / EntryID99 ["Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK", nil, "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.", "smallbone18", "Metabolism", nil, nil, nil, nil, "Original model source: in JWS online database.", nil, Mon, 16 Jul 2018 19:34:20 UTC +00:00, "", 39, "FEBS Letters", "Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling", "Saccharomyces cerevisiae", "A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.", "smallbone18", "ordinary differential equations", nil, "", "23831062", nil, "Smallbone_2013.pdf", "Copasi (www.copasi.org)", "---\n- Model validation\n", 2013] Administrator KiMoSys Model AccessID39 / EntryID39
100 Saccharomyces cerevisiae CEN.PK113-1A enzyme/protein concentrations Visto4 [no] ["VTT Technical Research Centre of Finland, Finland", "--- []\n", "application/pdf", "Rintala_2009.pdf", 2927778, Wed, 18 Jul 2018 12:56:46 UTC +00:00, "Eija Rintala, Mervi Toivari, Juha-Pekka Pitkänen, Marilyn G Wiebe, Laura Ruohonen and Merja Penttilä", "not specified", "glucose", "17234", "aerobic and anaerobic", "―", nil, "0.1 ± 0.02", nil, nil, nil, "--- []\n", "chemostat", 100, false, true, "BMC Genomics", "Aerobic Condition, MAPK Signalling, Pathway Central Carbon Metabolism, Filamentous Growth, Ergosterol Biosynthesis", "Low oxygen levels as a trigger for enhancement of respiratory metabolism in Saccharomyces cerevisiae.", "---\n- 2D gel-MALDI-TOF\n", "Saccharomyces cerevisiae", "KIMODATAID100_v1.xlsx", "5", "--- []\n", "", "19804647", "", nil, "", "CEN.PK113-1A", "30", "--- []\n", "4", "2.5", 2009] Administrator KiMoSys Data AccessID100 / EntryID100
101 Escherichia coli BW25113, pflA, pta, ppc, adhE and pykF mutants metabolites at steady-state Visto4 [yes]|[more] ["Department of Biochemical Engineering & Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", "---\n- enzymatic\n", "application/pdf", "Zhu_2005.pdf", 292546, Thu, 19 Jul 2018 14:32:27 UTC +00:00, "Jiangfeng Zhu, Kazuyuki Shimizu", "See worksheet for the different strains. Cell dry weight was determined by measuring the optical density at 600 nm. ", "glucose", "17234", "aerobic", "yield on glucose (g/g)%", nil, "—", nil, nil, nil, "---\n- not used\n", "batch", 101, false, true, "Metabolic Engineering", "Escherichia coli, Enzyme activity, Metabolite concentration, Metabolic flux analysis, Lactate production, Pyruvate metabolism", "Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic condition.", "--- []\n", "Escherichia coli", "KIMODATAID101_v1.xlsx", "7.0", "--- []\n", "", "15781419", "—", nil, " Samples were centrifuged for 10 min at 4 °C and 6000×g to remove the cells for extracellular metabolite analysis. ", "BW25113, pflA, pta, ppc, adhE and pykF mutants", "37", "--- []\n", "1", "1.0", 2005] Administrator KiMoSys Data AccessID101 / EntryID101 [" Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan", nil, "Yu Matsuoka and Hiroyuki Kurata", "", "Metabolism", nil, nil, nil, nil, "Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.", Fri, 20 Jul 2018 16:25:00 UTC +00:00, Thu, 19 Jul 2018 15:05:36 UTC +00:00, "—", 40, "Biotechnology for Biofuels", "Kinetic modeling, Fermentation, Dissolved oxygen limitation, Redox regulation, ArcA, Fnr, Respiratory chain, NADH/NAD+ ratio, Escherichia coli ", "Escherichia coli", "Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations.", "E. coli redox regulation model", "ordinary differential equations", nil, "", "28725263", nil, "Matsuoka_2017.pdf", "MATLAB (MathWorks) was used for all simulations.", "---\n- Model building\n- Model validation\n", 2017] Administrator KiMoSys Model AccessID40 / EntryID40
102 Escherichia coli BW25113, pflA, pta, ppc, adhE and pykF mutants enzyme/protein concentrations Visto4 [no] ["Department of Biochemical Engineering & Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan.", "--- []\n", "application/pdf", "Zhu_2005.pdf", 292546, Fri, 20 Jul 2018 13:04:40 UTC +00:00, "Jiangfeng Zhu, Kazuyuki Shimizu", "Cell dry weight was determined by measuring the optical density at 600 nm. See worksheet.", "glucose", "17234", "aerobic", "mmol/min mg protein", nil, "—", nil, nil, nil, "--- []\n", "batch", 102, false, true, "Metabolic Engineering", "Escherichia coli, Enzyme activity, Metabolite concentration, Metabolic flux analysis, Lactate production, Pyruvate metabolism", "Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic condition.", "---\n- 2D gel-MALDI-TOF\n", "Escherichia coli", "KIMODATAID102_v2.xlsx", "7.0", "--- []\n", "", "15781419", "", nil, "", "BW25113, pflA, pta, ppc, adhE and pykF mutants", "37", "--- []\n", "4", "1.0", 2005] Administrator KiMoSys Data AccessID102 / EntryID102
103 Escherichia coli BW25113, pflA, pta, ppc, adhE and pykF mutants metabolites at steady-state Visto4 [no] ["Department of Biochemical Engineering & Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", "---\n- enzymatic\n", "application/pdf", "Zhu_2005.pdf", 292546, Fri, 20 Jul 2018 14:51:02 UTC +00:00, "Jiangfeng Zhu, Kazuyuki Shimizu", "Cell dry weight was determined by measuring the optical density at 600 nm.", "glucose", "17234", "aerobic", "mM/g DCW", nil, "—", nil, nil, nil, "---\n- perchloric acid\n- boiling ethanol\n", "batch", 103, false, true, "Metabolic Engineering", "Escherichia coli, Enzyme activity, Metabolite concentration, Metabolic flux analysis, Lactate production, Pyruvate metabolism", "Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic condition.", "--- []\n", "Escherichia coli", "KIMODATAID103_v1.xlsx", "7.0", "--- []\n", "", "15781419", "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.", 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. ", "BW25113, pflA, pta, ppc, adhE and pykF mutants", "37", "--- []\n", "1", "1.0", 2005] Administrator KiMoSys Data AccessID103 / EntryID103
104 Escherichia coli K-12 BW25113 and ppc, pck, pyk mutants flux measurements Visto4 [yes]|[more] ["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", "--- []\n", "application/pdf", "Kadir_2010.pdf", 2038907, Sat, 21 Jul 2018 11:27:22 UTC +00:00, "Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu", "not specified", "glucose", "17234", "aerobic", "(mmol/g-dry cell weight/h)", nil, "0.2", nil, nil, nil, "--- []\n", "chemostat", 104, false, true, "Microbial Cell Factories", "Specific Growth Rate, Flux Balance Analysis, Oxidative Pentose Phosphate Pathway, Main Metabolic Pathway, Isotopomer Distribution", "Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.", "--- []\n", "Escherichia coli", "KIMODATAID104_v1.xlsx", "7.0", "---\n- GC-MS\n", "", "21092096", "", nil, "", "K-12 BW25113 and ppc, pck, pyk mutants", "37", "---\n- 13C constrained MFA\n", "3", "1.0", 2010] Administrator KiMoSys Data AccessID104 / EntryID104 ["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan", nil, "Hiroyuki Kurata and Yurie Sugimoto", "", "Metabolism", nil, nil, nil, nil, "Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.", Tue, 24 Jul 2018 15:46:04 UTC +00:00, Fri, 20 Jul 2018 16:54:23 UTC +00:00, "0.2, 0.4, 0.5 and 0.7", 41, "Journal of Bioscience and Bioengineering", "Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli", "Escherichia coli", "Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures", "Continuous kinetic model of Escherichia coli", "ordinary differential equations", nil, "", "29054464", nil, "Kurata_2018.pdf", "MATLAB (MathWorks)", "---\n- Model building\n- Model validation\n", 2018] Administrator KiMoSys Model AccessID41 / EntryID41
105 Escherichia coli BW25113 and ppc mutant flux measurements Visto4 [yes]|[more] ["Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", "--- []\n", "application/pdf", "Peng_2004.pdf", 271660, Sat, 21 Jul 2018 14:36:12 UTC +00:00, "Lifeng Peng, Marcos J. Arauzo-Bravo, Kazuyuki Shimizu", "see worksheet.", "glucose", "17234", "aerobic", "(mmol/g-dry cell weight/h)", nil, "0.2", nil, nil, nil, "--- []\n", "chemostat", 105, false, true, "FEMS Microbiology Letters", "ppc mutant Escherichia coli, 2-Dimensional nuclear magnetic resonance, Gas chromatography-mass spectrometry, Metabolic flux analysis", "Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements.", "--- []\n", "Escherichia coli", "KIMODATAID105_v2.xlsx", "7.0", "---\n- NMR\n- GC-MS\n", "", "15158257", "", nil, "", "BW25113 and ppc mutant", "37", "---\n- 13C constrained MFA\n", "3", "1.0", 2004] Administrator KiMoSys Data AccessID105 / EntryID105 ["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", nil, "Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu", "", "Metabolism", nil, nil, nil, nil, "", Sat, 21 Jul 2018 20:34:09 UTC +00:00, Wed, 24 Apr 2013 15:07:11 UTC +00:00, "—", 16, "Microbial Cell Factories", "Escherichia coli, single-gene knockouts, main central metabolism and TCA", "Escherichia coli", "Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.", "glycolysis Escherichia coli model", "ordinary differential equations", 38, "", "21092096", nil, "Kadir_2010.pdf", "http://www.matlab.com (MATLAB)", "---\n- Model validation\n", 2010] Administrator KiMoSys Model AccessID16 / EntryID16 ["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan", nil, "Hiroyuki Kurata and Yurie Sugimoto", "", "Metabolism", nil, nil, nil, nil, "Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.", Tue, 24 Jul 2018 15:46:04 UTC +00:00, Fri, 20 Jul 2018 16:54:23 UTC +00:00, "0.2, 0.4, 0.5 and 0.7", 41, "Journal of Bioscience and Bioengineering", "Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli", "Escherichia coli", "Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures", "Continuous kinetic model of Escherichia coli", "ordinary differential equations", nil, "", "29054464", nil, "Kurata_2018.pdf", "MATLAB (MathWorks)", "---\n- Model building\n- Model validation\n", 2018] Administrator KiMoSys Model AccessID41 / EntryID41
106 Escherichia coli W3110 and pck mutant flux measurements Visto4 [yes]|[more] ["Metabolome Unit, Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.", "--- []\n", "application/pdf", "Yang2003.pdf", 372915, Tue, 31 Jul 2018 09:18:03 UTC +00:00, "Yang C, Hua Q, Baba T, Mori H, Shimizu K", "see worksheet.", "glucose", "17234", "aerobic", "(mmol/g-dry cell weight/h)", nil, "0.1, 0.32, 0.55 (WT ) and 0.1 (pck)", nil, nil, nil, "--- []\n", "chemostat", 106, false, true, "Biotechnology and Bioengineering", "Escherichia coli; metabolic flux; 13C labeling; anaplerotic reaction; phosphoenolpyruvate carboxykinase; in vivo regulation", "Analysis of Escherichia coli Anaplerotic Metabolism and Its Regulation Mechanisms From the Metabolic Responses to Altered Dilution Rates and Phosphoenolpyruvate Carboxykinase Knockout.", "--- []\n", "Escherichia coli", "KIMODATAID106_v1.xlsx", "7.0", "---\n- NMR\n", "", "12966569", "", nil, "", "W3110 and pck mutant", "37", "---\n- 13C constrained MFA\n", "3", "1.0", 2003] Administrator KiMoSys Data AccessID106 / EntryID106 ["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", nil, "Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu", "", "Metabolism", nil, nil, nil, nil, "", Sat, 21 Jul 2018 20:34:09 UTC +00:00, Wed, 24 Apr 2013 15:07:11 UTC +00:00, "—", 16, "Microbial Cell Factories", "Escherichia coli, single-gene knockouts, main central metabolism and TCA", "Escherichia coli", "Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.", "glycolysis Escherichia coli model", "ordinary differential equations", 38, "", "21092096", nil, "Kadir_2010.pdf", "http://www.matlab.com (MATLAB)", "---\n- Model validation\n", 2010] Administrator KiMoSys Model AccessID16 / EntryID16
107 Escherichia coli BW25113 and pyk mutant flux measurements Visto4 [yes]|[more] ["Department of Biochemical Engineering and Science, Kyushu Institute of Technology,Iizuka, 820–8502 Fukuoka, Japan", "--- []\n", nil, nil, nil, nil, "Al Zaid Siddiquee K, Arauzo-Bravo MJ, Shimizu K.", "see worksheet.", "glucose", "17234", "aerobic", "(mmol/g-dry cell weight/h)", nil, "0.1", nil, nil, nil, "--- []\n", "chemostat", 107, false, true, "Appl Micriobiol Biotechnology", "Dilution Ratem Intracellular Metabolite, Metabolic Flux Analysis, Oxidative Pentose Phosphate Pathway, Proteinogenic Amino Acid ", "Metabolic flux analysis of pykF gene knockout Escherichia coli based on 13C-labeling experiments together with measurements of enzyme activities and intracellular metabolite concentrations.", "--- []\n", "Escherichia coli", "KIMODATAID107_v1.xlsx", "7.0", "---\n- NMR\n- GC-MS\n", "", "12802531", "", nil, "", "BW25113 and pyk mutant", "37", "---\n- 13C constrained MFA\n", "3", "0.5", 2004] Administrator KiMoSys Data AccessID107 / EntryID107 ["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan", nil, "Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu", "", "Metabolism", nil, nil, nil, nil, "", Sat, 21 Jul 2018 20:34:09 UTC +00:00, Wed, 24 Apr 2013 15:07:11 UTC +00:00, "—", 16, "Microbial Cell Factories", "Escherichia coli, single-gene knockouts, main central metabolism and TCA", "Escherichia coli", "Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.", "glycolysis Escherichia coli model", "ordinary differential equations", 38, "", "21092096", nil, "Kadir_2010.pdf", "http://www.matlab.com (MATLAB)", "---\n- Model validation\n", 2010] Administrator KiMoSys Model AccessID16 / EntryID16
108 Escherichia coli K-12 flux measurements Visto4 [yes]|[more] ["Institute for Advanced Biosciences, Keio University, Yamagata 997-0017, Japan", "--- []\n", nil, nil, nil, nil, "Jiao Zhao, Kazuyuki Shimizu", "", "glucose", "17234", "aerobic", "(mmol/g.h)", nil, "0.11 and 0.22", nil, nil, nil, "--- []\n", "chemostat", 108, false, true, "Journal of Biotechnology", "Mass isotopomer analysis, Metabolic flux analysis, Carbon source, Genetic algorithm, Levenberg-Marquardt algorithm, Escherichia coli K12", "Metabolic flux analysis of Escherichia coli K12 grown on 13C-labeled acetate and glucose using GC-MS and powerful flux calculation method.", "--- []\n", "Escherichia coli", "KIMODATAID108_v1.xlsx", "7.0", "---\n- GC-MS\n", "", "12568740", "", nil, "", "K-12", "37", "---\n- 13C constrained MFA\n", "3", "0.9", 2003] Administrator KiMoSys Data AccessID108 / EntryID108 ["Bioinformatics Centre, University of Pune, India", nil, "Vivek Kumar Singh and Indira Ghosh", "BIOMD0000000221", "Metabolism", "application/octet-stream", "COMBINE_KIMOMODELID43.omex", 253672, Fri, 27 Jul 2018 10:28:17 UTC +00:00, "Original model source: in BioModels database.", nil, Mon, 23 Jul 2018 10:25:20 UTC +00:00, "", 43, "Theoretical Biology and Medical Modelling", "Tuberculosis, Steady State Flux, Glyoxylate Bypass, Metabolic Control Analysis, Experimental Flux", "Escherichia coli", "Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets", "Singh2006_TCA_Ecoli_acetate", "ordinary differential equations", nil, "", "16887020", nil, "Singh_2006.pdf", "Jarnac 2.14 (http://jdesigner.sourceforge.net/Site/Jarnac.html)", "---\n- Model validation\n", 2006] Administrator KiMoSys Model AccessID43 / EntryID43 ["Bioinformatics Centre, University of Pune, India", nil, "Vivek Kumar Singh and Indira Ghosh", "BIOMD0000000222", "Metabolism", nil, nil, nil, nil, "Original model source: in BioModels database.", nil, Mon, 23 Jul 2018 10:39:44 UTC +00:00, "", 44, "Theoretical Biology and Medical Modelling", "Tuberculosis, Steady State Flux, Glyoxylate Bypass, Metabolic Control Analysis, Experimental Flux", "Escherichia coli", "Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets", "Singh2006_TCA_Ecoli_glucose", "ordinary differential equations", nil, "", "16887020", nil, "Singh_2006.pdf", "Jarnac 2.14 (http://jdesigner.sourceforge.net/Site/Jarnac.html)", "---\n- Model validation\n", 2006] Administrator KiMoSys Model AccessID44 / EntryID44
109 Escherichia coli BW25113 and ppc mutant enzyme/protein concentrations Visto4 [no] ["Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan.", "--- []\n", "application/pdf", "Peng_2004.pdf", 271660, Sat, 28 Jul 2018 16:46:57 UTC +00:00, "Lifeng Peng, Marcos J. Arauzo-Bravo, Kazuyuki Shimizu", "Yield of biomass on glucose (g/g): 0,48 (WT) and 0,55 (ppc)", "glucose", "17234", "aerobic", "µmol/min mg(protein)", nil, "0.2", nil, nil, nil, "--- []\n", "chemostat", 109, false, true, "FEMS Microbiology Letters", "ppc mutant Escherichia coli, 2-Dimensional nuclear magnetic resonance, Gas chromatography-mass spectrometry, Metabolic flux analysis", "Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements.", "---\n- 2D gel-MALDI-TOF\n", "Escherichia coli", "KIMODATAID109_v2.xlsx", "7.0", "--- []\n", "", "15158257", "", nil, "", "BW25113 and ppc mutant", "37", "--- []\n", "4", "1.0", 2004] Administrator KiMoSys Data AccessID109 / EntryID109
110 Escherichia coli BW25113 and ppc mutant metabolites at steady-state Visto4 [no] ["Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan.", "---\n- enzymatic\n", nil, nil, nil, nil, "Lifeng Peng, Marcos J. Arauzo-Bravo, Kazuyuki Shimizu", "Yield of biomass on glucose (g/g): 0,48 (WT) and 0,55 (ppc)", "glucose", "17234", "aerobic", "mM", nil, "0.2", nil, nil, nil, "---\n- sonication\n", "chemostat", 110, false, true, "FEMS Microbiology Letters", "ppc mutant Escherichia coli, 2-Dimensional nuclear magnetic resonance, Gas chromatography-mass spectrometry, Metabolic flux analysis", "Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements.", "--- []\n", "Escherichia coli", "KIMODATAID110_v1.xlsx", "7.0", "--- []\n", "", "15158257", "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).", nil, "Cells were harvested by centrifugation at 10,000 g for 10 min.", "BW25113 and ppc mutant", "37", "--- []\n", "1", "1.0", 2004] Administrator KiMoSys Data AccessID110 / EntryID110
111 Saccharomyces cerevisiae CEN.PK113-7D metabolites at steady-state Visto4 [yes]|[more] ["Vrije Universiteit Amsterdam, Department of Molecular Cell Physiology, Amsterdam, The Netherlands.", "---\n- LC-ESI-MS\n", "application/pdf", "vanEunen_2010.pdf", 756037, Mon, 30 Jul 2018 14:53:24 UTC +00:00, "van Eunen K, Dool P, Canelas AB, Kiewiet J, Bouwman J, van Gulik WM, Westerhoff HV, Bakker BM", "Yieldglu,X (g/g) = 0.45 ± 0.02 (D = 0.1h-1) and 0.29 ± 0.01 (D = 0.35h-1)", "glucose", "17234", "aerobic", "mM", nil, "0.1 and 0.35", nil, nil, nil, "---\n- boiling ethanol\n", "chemostat", 111, false, true, "IET Systems Biology", "yeast, glycolysis, glucose-limited chemostat, nitrogen starvation", "Time-dependent regulation of yeast glycolysis upon nitrogen starvation depends on cell history.", "--- []\n", "Saccharomyces cerevisiae", "KIMODATAID111_v1.xlsx", "5.0 ± 0.1", "--- []\n", "", "20232995", "Quenching and washing of the sample was done with 100% and 80% (v/v) methanol/water, respectively, at -40ºC.", nil, "Samples were taken 15 min after the start of the fermentative capacity assay to the protocol described by Canelas et al. [2].", "CEN.PK113-7D", "30", "--- []\n", "1", "1.0", 2010] Administrator KiMoSys Data AccessID111 / EntryID111 ["Department of Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands", nil, "Karen van Eunen, José A. L. Kiewiet, Hans V. Westerhoff, Barbara M. Bakker", "BIOMD1403250001", "Metabolism", nil, nil, nil, nil, "Original model source: in BioModels database.", nil, Mon, 30 Jul 2018 22:00:51 UTC +00:00, "", 46, "PLoS Computational Biology", "yeast glycolysis, In Vivo and in Vitro Enzyme Kinetics, computational model", "Saccharomyces cerevisiae", "Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics", "vanEunen2012 - Yeast Glycolysis (glucose upshift)", "ordinary differential equations", nil, "", "22570597", nil, "vanEunen_2012.pdf", "MATLAB (MathWorks)", "---\n- Model building\n- Model validation\n", 2012] Administrator KiMoSys Model AccessID46 / EntryID46
112 Escherichia coli W3110 and pck mutant metabolites at steady-state Visto4 [no] ["Metabolome Unit, Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.", "---\n- enzymatic\n", "application/pdf", "Yang2003.pdf", 372915, Tue, 31 Jul 2018 15:50:28 UTC +00:00, "Yang C, Hua Q, Baba T, Mori H, Shimizu K", "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", "glucose", "17234", "aerobic", "mM", nil, "0.1, 0.32, 0.55 (WT ) and 0.1 (pck)", nil, nil, nil, "---\n- chloroform\n", "chemostat", 112, false, true, "Biotechnology and Bioengineering", "Escherichia coli; metabolic flux; 13C labeling; anaplerotic reaction; phosphoenolpyruvate carboxykinase; in vivo regulation", "Analysis of Escherichia coli Anaplerotic Metabolism and Its Regulation Mechanisms From the Metabolic Responses to Altered Dilution Rates and Phosphoenolpyruvate Carboxykinase Knockout.", "--- []\n", "Escherichia coli", "KIMODATAID112_v0.xlsx", "7.0", "--- []\n", "", "12966569", "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.", nil, "not described", "W3110 and pck mutant", "37", "--- []\n", "1", "1.0", 2003] Administrator KiMoSys Data AccessID112 / EntryID112
113 Pichia pastoris X-33 metabolites at steady-state Visto4 [no] ["Department of Chemical Engineering, Universitat Autonoma de Barcelona, 08193 Bellaterra (Cerdanyola del Valle`s), Spain", "---\n- GC-MS\n- LC-ESI-MS\n", "application/pdf", "Carnicer_2012.pdf", 986763, Wed, 01 Aug 2018 15:36:45 UTC +00:00, "Marc Carnicer, Andre B. Canelas, Angela ten Pierick, Zhen Zeng, Jan van Dam, Joan Albiol, Pau Ferrer, Joseph J. Heijnen, Walter van Gulik", "≈ 4.5 g/l", "glucose", "17234", "aerobic", "µmol/gDCW", nil, "0.1", nil, nil, nil, "---\n- hot ethanol\n", "chemostat", 113, false, true, "Metabolomics", "Pichia pastoris, Metabolite quantification, Quenching, Chemostat", "Development of quantitative metabolomics for Pichia pastoris.", "--- []\n", "Pichia pastoris", "KIMODATAID113_v0.xlsx", "5.0", "--- []\n", "", "22448155", "approximately, 0.63 ± 0.01 g of broth was rapidly withdrawn and immediately injected in 5 ml of precooled quenching solution.", nil, "samples for intracellular metabolite analysis were taken using a dedicated rapid-sampling setup [2].", "X-33", "25", "--- []\n", "1", "4.0", 2012] Administrator KiMoSys Data AccessID113 / EntryID113
114 Pichia pastoris X-33/pGAPaA_Fab and X-33/pGAPaA flux measurements Visto4 [no] ["Department of Chemical Engineering, Autonomous University of Barcelona, Spain", "--- []\n", "application/pdf", "Baumann_2010.pdf", 1396363, Sat, 18 Aug 2018 22:44:26 UTC +00:00, "Kristin Baumann, Marc Carnicer, Martin Dragosits, Alexandra B Graf, Johannes Stadlmann, Paula Jouhten, Hannu Maaheimo, Brigitte Gasser, Joan Albiol, Diethard Mattanovich, Pau Ferrer", "for O2 21% = 0.47 ± 0.02, for O2 11% = 0.45 ± 0.01 and for O2 8% = 0.25 ± 0.01", "glucose", "17234", "aerobic", "(mmol/g.h)", nil, "0.1", nil, nil, nil, "--- []\n", "chemostat", 114, false, true, "BMC Systems Biology", "Hypoxic Condition, Unfold Protein Response, Pentose Phosphate Pathway, Metabolic Flux, Flux Ratio", "A multi-level study of recombinant Pichia pastoris in different oxygen conditions.", "--- []\n", "Pichia pastoris", "KIMODATAID114_v1.xlsx", "5", "---\n- NMR\n", "", "20969759", "", nil, "", "X-33/pGAPaA_Fab and X-33/pGAPaA", "25", "---\n- flux ratio\n- 13C constrained MFA\n", "3", "1.0", 2010] Administrator KiMoSys Data AccessID114 / EntryID114
115 Saccharomyces cerevisiae 59A NADPH-Bdh flux measurements Visto4 [no] ["INRA, UMR1083 SPO, 2 place Viala, F-34060 Montpellier, France", "--- []\n", "application/pdf", "Celton_2012.pdf", 1077632, Sun, 19 Aug 2018 19:03:08 UTC +00:00, "Magalie Celton, Isabelle Sanchez, Anne Goelzer, Vincent Fromion, Carole Camarasa and Sylvie Dequin", "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", "glucose", "17234", "anaerobic", "mmol/100 mmol glucose", nil, "—", nil, nil, nil, "--- []\n", "batch", 115, false, true, "BMC Genomics", "NADPH, Pentose Phosphate Pathway, Acetoin, Intracellular Metabolite, NADPH Oxidation", "A comparative transcriptomic, fluxomic and metabolomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation.", "--- []\n", "Saccharomyces cerevisiae", "KIMODATAID115_v0.xlsx", "5.0", "---\n- GC-MS\n", "", "22805527", "", nil, "", "59A NADPH-Bdh", "28", "---\n- 13C constrained MFA\n", "3", "0.01", 2012] Administrator KiMoSys Data AccessID115 / EntryID115
116 Escherichia coli MG1655 and (pgi, ppc, pta, tpi) mutants flux measurements Visto4 [no] ["Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland", "--- []\n", "application/pdf", "Fong_2006.pdf", 882915, Wed, 22 Aug 2018 22:28:56 UTC +00:00, "Stephen S. Fong, Annik Nanchen, Bernhard O. Palsson and Uwe Sauer", "see spreadsheet", "glucose", "17234", "aerobic", "mmol/gdw h", nil, "—", nil, nil, nil, "--- []\n", "batch", 116, false, true, "Journal of Biological Chemistry", "Escherichia coli, latent pathway activation", "Latent Pathway Activation and Increased Pathway Capacity Enable Escherichia coli Adaptation to Loss of Key Metabolic Enzymes.", "--- []\n", "Escherichia coli", "KIMODATAID116_v2.xlsx", "not specified", "---\n- GC-MS\n", "", "16319065", "", nil, "", "MG1655 and (pgi, ppc, pta, tpi) mutants", "37", "---\n- flux ratio\n- 13C constrained MFA\n", "3", "0.03", 2006] Administrator KiMoSys Data AccessID116 / EntryID116
117 Saccharomyces cerevisiae CEN.PK113-1A flux measurements Visto4 [no] ["VTT Technical Research Centre of Finland, Espoo, Finland", "--- []\n", "application/pdf", "Jouhten_2008.pdf", 756447, Thu, 23 Aug 2018 21:59:13 UTC +00:00, "Paula Jouhten, Eija Rintala, Anne Huuskonen, Anu Tamminen, Mervi Toivari, Marilyn Wiebe, Laura Ruohonen, Merja Penttilä and Hannu Maaheimo", "see spreadsheet", "glucose", "17234", "aerobic and anaerobic", "normalised to the specific glucose uptake rate", nil, "0.1", nil, nil, nil, "--- []\n", "chemostat", 117, false, true, "BMC Systems Biology", "Pentose Phosphate Pathway, Flux Distribution, Flux Ratio, Metabolic Flux Analysis, Central Carbon Metabolism", "Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A", "--- []\n", "Saccharomyces cerevisiae", "KIMODATAID117_v1.xlsx", "5.0", "---\n- NMR\n", "", "18613954", "", nil, "", "CEN.PK113-1A", "30", "---\n- flux ratio\n- 13C constrained MFA\n", "3", "2.5", 2008] Administrator KiMoSys Data AccessID117 / EntryID117
118 Escherichia coli MG1655 and 2 over-expression strains (NOX, ATPase) flux measurements Visto4 [no] ["Department of Systems Biology, Center for Systems Microbiology, Technical University of Denmark, 2800 Denmark", "--- []\n", "application/pdf", "Holm_2010.pdf", 1356725, Fri, 24 Aug 2018 18:15:24 UTC +00:00, "Anders K. Holm, Lars M. Blank, Marco Oldiges, Andreas Schmid, Christian Solem, Peter R. Jensen and Goutham N. Vemuri", "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", "glucose", "17234", "aerobic", "mmol/gdw h", nil, "—", nil, nil, nil, "--- []\n", "batch", 118, false, true, "Journal of Biological Chemistry", "F1Fo ATPase, Glycolysis, Metabolic Regulation, Transcription Regulation, Tricarboxylic Acid (TCA) Cycle, Cofactor Perturbation, Escherichia coli, NADH Oxidase, Soluble ATPase, Systems Biology ", "Metabolic and Transcriptional Response to Cofactor Perturbations in Escherichia coli.", "--- []\n", "Escherichia coli", "KIMODATAID118_v1.xlsx", "not specified", "---\n- GC-MS\n- LC-MS\n", "", "20299454", "", nil, "", "MG1655 and 2 over-expression strains (NOX, ATPase)", "37", "---\n- flux ratio\n", "3", "0.1", 2010] Administrator KiMoSys Data AccessID118 / EntryID118
119 Escherichia coli MG1655 and 2 over-expression strains (NOX, ATPase) metabolites at steady-state Visto4 [no] ["Department of Systems Biology, Center for Systems Microbiology, Technical University of Denmark, 2800 Denmark", "---\n- LC-MS\n", "application/pdf", "Holm_2010.pdf", 1356725, Sat, 25 Aug 2018 15:22:03 UTC +00:00, "Anders K. Holm, Lars M. Blank, Marco Oldiges, Andreas Schmid, Christian Solem, Peter R. Jensen and Goutham N. Vemuri", "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", "glucose", "17234", "aerobic", "μmol/g DCW", nil, "—", nil, nil, nil, "---\n- methanol-water\n", "batch", 119, false, true, "Journal of Biological Chemistry", "F1Fo ATPase, Glycolysis, Metabolic Regulation, Transcription Regulation, Tricarboxylic Acid (TCA) Cycle, Cofactor Perturbation, Escherichia coli, NADH Oxidase, Soluble ATPase, Systems Biology ", "Metabolic and Transcriptional Response to Cofactor Perturbations in Escherichia coli.", "--- []\n", "Escherichia coli", "KIMODATAID119_v0.xlsx", "not specified", "--- []\n", "", "20299454", "quenched in hot phenol (80 °C) and subsequently frozen at −20 °C.", nil, "aliquot of 5 ml of the culture from mid-exponential phase", "MG1655 and 2 over-expression strains (NOX, ATPase)", "37", "--- []\n", "1", "0.1", 2010] Administrator KiMoSys Data AccessID119 / EntryID119
120 Saccharomyces cerevisiae IMS0001 and IMS0002 metabolites at steady-state Visto4 [no] ["Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.", "---\n- GC-MS\n- LC-ESI-MS\n", "application/pdf", "Wisselink_2010.pdf", 1219787, Mon, 27 Aug 2018 21:00:50 UTC +00:00, "H. Wouter Wisselink, Chiara Cipollina, Bart Oud, BarbaraCrimi, Joseph J. Heijnen, Jack T. Pronk, Antonius J.A.van Maris", "Biomass yield (g g−1) = 0.066±0.001 (IMS0001, Glucose), 0.072±0.003 (IMS0002, Glucose) and 0.075±0.001 (IMS0002, Arabinose) ", "glucose and arabinose", "", "anaerobic", "mmol/[gDW]", nil, "0.03", nil, nil, nil, "---\n- boiling ethanol\n", "chemostat", 120, false, true, "Metabolic Engineering", "Saccharomyces cerevisiae, Evolutionary engineering, Arabinose, Transcriptomics, Metabolomics, Metabolic flux ana", "Metabolome, transcriptome and metabolic flux analysis of arabinose fermentation by engineered Saccharomyces cerevisiae", "--- []\n", "Saccharomyces cerevisiae", "KIMODATAID120_v2.xlsx", "5.0", "--- []\n", "", "20816840", "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.", nil, "Sampling and sample preparation for analysis of intracellular metabolite concentrations was carried out as previously described in [1].", "IMS0001 and IMS0002 ", "30", "--- []\n", "1", "1.0", 2010] Administrator KiMoSys Data AccessID120 / EntryID120
121 Saccharomyces cerevisiae IMS0001 and IMS0002 flux measurements Visto4 [no] ["Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.", "--- []\n", "application/pdf", "Wisselink_2010.pdf", 1219787, Tue, 28 Aug 2018 16:39:16 UTC +00:00, "H. Wouter Wisselink, Chiara Cipollina, Bart Oud, BarbaraCrimi, Joseph J. Heijnen, Jack T. Pronk, Antonius J.A.van Maris", "Biomass yield (g g−1) = 0.066±0.001 (IMS0001, Glucose), 0.072±0.003 (IMS0002, Glucose) and 0.075±0.001 (IMS0002, Arabinose) ", "glucose and arabinose", "", "anaerobic", "normalised to the specific glucose uptake rate", nil, "0.03", nil, nil, nil, "--- []\n", "chemostat", 121, false, true, "Metabolic Engineering", "Saccharomyces cerevisiae, Evolutionary engineering, Arabinose, Transcriptomics, Metabolomics, Metabolic flux analysis", "Metabolome, transcriptome and metabolic flux analysis of arabinose fermentation by engineered Saccharomyces cerevisiae.", "--- []\n", "Saccharomyces cerevisiae", "KIMODATAID121_v0.xlsx", "5.0", "---\n- LC-MS\n", "", "20816840", "", nil, "", "IMS0001 and IMS0002 ", "30", "---\n- 13C constrained MFA\n", "3", "1.0", 2010] Administrator KiMoSys Data AccessID121 / EntryID121
122 Saccharomyces cerevisiae WT S288C and gcn4-knockout flux measurements Visto4 [no] ["Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139", "--- []\n", "application/pdf", "Moxley_2009.pdf", 1325393, Wed, 12 Sep 2018 09:46:26 UTC +00:00, "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", "not specified", "glucose", "17234", "aerobic", "", nil, "0.1", nil, nil, nil, "--- []\n", "chemostat", 122, false, true, "Proc Natl Acad Sci USA", "amino acid stress response, fluxomics, gcn4, systems biology", "Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p.", "--- []\n", "Saccharomyces cerevisiae", "KIMODATAID122_v1.xlsx", "5.0", "---\n- GC-MS\n", "", "19346491", "", nil, "", "WT S288C and gcn4-knockout", "30", "---\n- 13C constrained MFA\n", "3", "1.0", 2009] Administrator KiMoSys Data AccessID122 / EntryID122
123 Saccharomyces cerevisiae CEN.PK113-7D ΔLYS1 enzyme/protein concentrations Visto4 [no] ["Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.", "--- []\n", "application/pdf", "Lahtvee_2017.pdf", 2550326, Thu, 20 Sep 2018 17:22:27 UTC +00:00, "Petri-Jaan Lahtvee, Benjamín J. Sánchez, Agata Smialowska, Sergo Kasvandik, Ibrahim E. Elsemman, Francesco Gatto, Jens Nielsen", "see original paper", "glucose", "17234", "aerobic", "pgDW", nil, "0.1", nil, nil, nil, "--- []\n", "chemostat", 123, false, true, "Cell Systems", "integrative data analysis, absolute proteome, absolute transcriptome, protein turnover, protein degradation rates, translation efficiency, genome-scale metabolic modeling, translational control", "Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast.", "---\n- LC-MS/MS\n", "Saccharomyces cerevisiae", "KIMODATAID123_v0.xlsx", "5.5", "--- []\n", "", "28365149", "", nil, "", "CEN.PK113-7D ΔLYS1", "30", "--- []\n", "4", "1", 2017] Administrator KiMoSys Data AccessID123 / EntryID123
124 Saccharomyces cerevisiae CEN.PK113-7D and 38 mutants flux measurements Visto4 [no] ["Institute of Biotechnology, ETH Zürich, 8093 Zürich, Switzerland", "--- []\n", "application/pdf", "Blank_2005.pdf", 318008, Tue, 25 Sep 2018 13:20:17 UTC +00:00, "Lars M Blank, Lars Kuepfer and Uwe Sauer", "see worksheet", "glucose", "17234", "aerobic", "mmol/gh", nil, "—", nil, nil, nil, "--- []\n", "batch", 124, false, true, "BMC Genome Biology", "Pentose Phosphate Pathway, Flux Analysis, Glucose Uptake Rate, Oxidative Pentose Phosphate Pathway", "Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast.", "--- []\n", "Saccharomyces cerevisiae", "KIMODATAID124_v2.xlsx", "5", "---\n- GC-MS\n", "", "15960801", "", nil, "", "CEN.PK113-7D and 38 mutants", "30", "---\n- 13C constrained MFA\n", "3", "0.0012", 2005] Administrator KiMoSys Data AccessID124 / EntryID124
125 Escherichia coli BW25113 flux measurements Visto4 [no] ["Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland; Systems Biology Graduate School, Zurich 8057, Switzerland. ", "--- []\n", "application/pdf", "Gerosa_2015.pdf", 5007487, Tue, 25 Sep 2018 22:34:51 UTC +00:00, "Luca Gerosa, Bart R.B. Haverkorn van Rijsewijk, Dimitris Christodoulou, Karl Kochanowski, Thomas S.B. Schmidt, Elad Noor, Uwe Sauer", "see worksheet", "acetate, fructose, galactose, glucose, glycerol, gluconate, pyruvate, succinate", "", "aerobic", "mmol/gh", nil, "—", nil, nil, nil, "--- []\n", "batch", 125, false, true, "Cell Systems", "computational biology; metabolism; metabolomics; regulation network; transcription factor", "Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data.", "--- []\n", "Escherichia coli", "KIMODATAID125_v2.xlsx", "not specified", "---\n- LC-MS\n", "", "27136056", "", nil, "", "BW25113", "37", "---\n- 13C constrained MFA\n", "3", "0.0035", 2015] Administrator KiMoSys Data AccessID125 / EntryID125
126 Escherichia coli BW25113 metabolites at steady-state Visto4 [no] ["Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland; Systems Biology Graduate School, Zurich 8057, Switzerland. ", "---\n- LC-MS\n", "application/pdf", "Gerosa_2015.pdf", 5007487, Mon, 01 Oct 2018 08:52:44 UTC +00:00, "Luca Gerosa, Bart R.B., Haverkorn van Rijsewijk, Dimitris Christodoulou, Karl Kochanowski, Thomas S.B. Schmidt, Elad Noor, Uwe Sauer", "see worksheet", "acetate, fructose, galactose, glucose, glycerol, gluconate, pyruvate, succinate", "", "aerobic", "µmol * gCDW-1", nil, "—", nil, nil, nil, "---\n- boiling ethanol\n", "batch", 126, false, true, "Cell Systems", "computational biology; metabolism; metabolomics; regulation network; transcription factor", "Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data.", "--- []\n", "Escherichia coli", "KIMODATAID126_v0.xlsx", "not specified", "--- []\n", "", "27136056", "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).", nil, "1 ml aliquots were taken in a 37°C room from exponential phase cultures.", "BW25113", "37", "--- []\n", "1", "0.0035", 2015] Administrator KiMoSys Data AccessID126 / EntryID126



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