Data files

Data file for PLaSMo accesssion ID PLM_64, version 1

Data file for PLaSMo accesssion ID PLM_64, version 1

Data file for PLaSMo accesssion ID PLM_64, version 1

Data file for PLaSMo accesssion ID PLM_64, version 1

Data file for PLaSMo accesssion ID PLM_64, version 1

Data file for PLaSMo accesssion ID PLM_71, version 2

Data file for PLaSMo accesssion ID PLM_71, version 2

Data file for PLaSMo accesssion ID PLM_1045, version 1

Data file for PLaSMo accesssion ID PLM_1045, version 1

Data file for PLaSMo accesssion ID PLM_1045, version 1

Comparison of Kcat values model and values from literature. Model values are based on Vmax enzyme parameters (maximum activity per enzyme molecule). Literature values are largely based on whole cell enzyme extract assays and do not take into account allosteric control. In addition activity is measured at varying time points and varying conditions. The error based on differences in enzyme concentrations at different time points and the error in protein copy number measurements is taken into account ...

Contains relative mutant (OE, KO) perturbation and time series samples metabolite concentrations and enzyme fold change of targeted enzymes used for model validation. Measured are the relative fold change, Mean and SD of log2 fold change values are based on multiple measurements per sample (minimum of three). Contains input data for Automated Model simulations pipeline to load and update the models metabolite concentrations and enzyme parameters to simulate all sample using a custom python script ...

Master file, aggregates metabolite concentrations inside and outside the cell, protein copy number and flux estimates for metabolites in the core model. Based on all internal metabolite concentrations, external metabolite concentrations from growth curve data, flux of glucose, lactate and acetate based on growth curve data and protein copy number data for enzyme concentrations. Combines absolute and relative measurements and metabolomics measurements from different experiment to get an as complete ...

Contains growth curve data such as Glucose uptake rate, lactate and acetate production at different time points. Growth curve A was used train the model with external glucose concentration as well as external lactate, acetate concentration and estimated glucose acetate and lactate flux

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