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
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 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", "Escherichia coli, single-gene knockouts, main central metabolism and TCA", "Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.", "--- []\n", "Escherichia coli ", "KIMODATAID38_v0.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 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, "", Fri, 11 Apr 2014 17:30:07 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 building\n", 2010] Administrator KiMoSys Model AccessID16 / EntryID16
41 Escherichia coli WT K-12 BW25113 and mutants metabolites at steady-state Visto4 [no] ["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
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, "", "21092096", 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, "", "21092096", 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, "", "21092096", 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 [no] ["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
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_v0.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_v0.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", "", "(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_v0.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



Contribute to Database

Want to submit data?

You can submit data using the following:


Web platform submission

- By embedding your data into our database. Download a copy and complete the Excel template form. See instructions in the form.

Add Electronic Data-Submission


- Suggest a dataset (in any format) to be added to the database.

Add Quick Submit


Paper submission form

- Submit the data file via email to be added to the database.
Fill out the Excel template and email to kimosys@kdbio.inesc-id.pt.



Questions? If you need assistance in submitting your data, please contact KiMoSys curators or consult FAQ.



Top