Data files

Protein copy number estimates, Mean and SD based on multiple proteomics experiments. Compatible with internal and external metabolite measurements for Growth curve A. Used as training data for the model

Contains the absolute copy number per locus tag during growth between 0.25 and 96hours of growth Growth in batch, cells attached to the bottom of the flask, non-aerated, non-stirred

Symmetric mean absolute percentage error per sample graph for the 40 independent samples

Contains training data and model with addition of the NoxE reaction 6h, 24h and 48h metabolite concentration data as well as calculated oxygen concentrations assuming no diffusion limit through the biofilm layer

Contains relative metabolite concentrations for 40 samples based on technical triplicates. Medium and SD values were calculated and used for 1000 sampled simmulations (sampling from the measurement distribution per metabolite) per sample. Also contains annotion to link metabolite concentrations and protein fold change measurements for OE and KO mutants to the model as well as external glucose, acetate and lactate concentrations. A SBtab like format was used to easily load the MEAN and SD metabolite ...

Contains the estimated oxygen concentration and metabolite concentrations as wel as the model with addition of an oxygen inhibition parameter. Results: Addition of the oxygen inhibition term does not improve the modell with the current parameter set

Contains the FC metabolite concentration values data and a R script to perform PCA, generate hetamaps and a correlation network.

Violin plot of the metabolic control of model parameters on the flux through PFK (as a proxy for flux through glycolysis) based on a 100.000 Latin Hypercube samples from the parameter space (range 0.001-100 for Km values and 0.001-1000 for Vmax values).

Shows the correlation in metabolic control between parameters. The plot shows central carbon metabolis basically consist of a few control hubs of reactions of which the parameters are correlated. In other words, just the reaction network combined with allosteric control and equilibrium constants impose some constrains on possible parameter value combinations that lead to certain behaviour (such as the flux and concentrations measured in vivo/vitro).

Contains the raw output of the global sensitivity analysis, can be used as input for plotting using the R script "plotLocalGlobalSensitivity1.5.R" associated to the same asset

Data file for PLaSMo accesssion ID PLM_7, version 2

Data file for PLaSMo accesssion ID PLM_89, version 2

Data file for PLaSMo accesssion ID PLM_5, version 1

Data file for PLaSMo accesssion ID PLM_89, version 1

Data file for PLaSMo accesssion ID PLM_91, version 1

Data file for PLaSMo accesssion ID PLM_90, version 1

Data file for PLaSMo accesssion ID PLM_87, version 1

Data file for PLaSMo accesssion ID PLM_92, version 1

Data file for PLaSMo accesssion ID PLM_85, version 1

Data file for PLaSMo accesssion ID PLM_88, version 1

Data file for PLaSMo accesssion ID PLM_86, version 1

Data file for PLaSMo accesssion ID PLM_83, version 1

Data file for PLaSMo accesssion ID PLM_84, version 1

Data file for PLaSMo accesssion ID PLM_24, version 1

Data file for PLaSMo accesssion ID PLM_24, version 1

Data file for PLaSMo accesssion ID PLM_24, version 1

Data file for PLaSMo accesssion ID PLM_24, version 1

Data file for PLaSMo accesssion ID PLM_24, version 1

Data file for PLaSMo accesssion ID PLM_52, version 1

Data file for PLaSMo accesssion ID PLM_52, version 1