Data files

GEO format data

Phosphorylation site of the HPr protein detected ba mass spectromety

Describes the assumptions made, how to integrate the new reactions to the rest of the glycolysis model, the parameters needed and the preliminary parameter values collected from the litterature.

call ConvertStdModel2SBTtest('Conti_Ferm_Std', 'CD_Transcriptomic.csv', 'glucose.csv', 'OD.csv',0)

transcriptome, glucose, biomass data inside

acetic acid pulse 100mM acetic acid step 50mM, 70mM

• automated integration of transcriptomic and reactome data to differential equations
• structure of the paths is maintained
• continuous fermentation model in standard format for data integration, two component model (cell and fermenter)

call >> Kegg2SBToolbox2('model_map.txt', 'reactions_compounds_final.csv','extracellular.txt','testmodel.txt') for an example

where model_map is the desired mapping of species, reaction_compounds_final.csv is the entire network, extracellular.txt is a manual ...

acetic acid addition

step experiment: 50mM, 70mM, 100mM, 120mM

pulse 200mM

pulse acetic acid: 70mM (2x), 80mM, shift to 4.5, pulse acetic acid: 70mM

acetic acid addition 70mM

Basic Graph statistics

RCM: Reaction-Compound Mapping, an edge between nodes means reaction contains metabolite MMM: Metabolite-Metabolite Mapping, an edge between nodes means these metabolites are reaction partners

_comp: entire network after removal of duplicated edges _del: taken from the entire network the largest connected subgraph after deletion of a set of nodes

betw: betweeness of nodes clos: closeness of nodes neigh: neighbours node_degree: number of edges per node path: shortest paths ...

RCM: Reaction-Compound Mapping, an edge between nodes means reaction contains metabolite MMM: Metabolite-Metabolite Mapping, an edge between nodes means these metabolites are reaction partners

_comp: entire network after removal of duplicated edges _del: taken from the entire network the largest connected subgraph after deletion of a set of nodes _upload: entire network before removal of duplicated edges

X_depthY: subgraphs where X is a chosen central component and Y is the Yth of neighbour to ...

Out

Columnwise datamatrix of reactions, gene identifiers, substrates and products. The direction of reactions is not given.

WT (Cy3) vs. trxB (Cy5)_exp. growth phase

WT (Cy5) vs. trxB (Cy3)_stationary growth phase_DyeFlip

WT (Cy3) vs. trxB (Cy5)_stationary growth phase