Data files

35 Data files visible to you, out of a total of 51
No description specified

Creator: Thomas Rimpf

Submitter: Thomas Rimpf

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

transcriptome, glucose, biomass data inside

  • 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

No description specified

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 ...

No description specified
No description specified

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 ...

No description specified

Creator: Sebastian Curth

Submitter: Sebastian Curth

Out

Creator: Sebastian Curth

Submitter: Sebastian Curth

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

Creator: Sebastian Curth

Submitter: Sebastian Curth

No description specified

Creator: Thomas Rimpf

Submitter: Thomas Rimpf

No description specified

Creator: Thomas Rimpf

Submitter: Thomas Rimpf

No description specified

Creator: Thomas Rimpf

Submitter: Thomas Rimpf

No description specified

Creator: Thomas Rimpf

Submitter: Thomas Rimpf

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

Creator: Daniel Hönicke

Submitter: Daniel Hönicke

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

Creator: Daniel Hönicke

Submitter: Daniel Hönicke

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

Creator: Daniel Hönicke

Submitter: Daniel Hönicke

acetic acid puls during acidogenesis shift to solventogensis back-shift to acidogenesis butyric acid puls during acidogenesis

butyric acid pulse during acidogenesis acetic acid pulse during acidogenesis butyric acid pulse during solventogenesis

No description specified

Creators: John Raedts, Wouter Kuit

Submitter: John Raedts

Monitoring of end products ethanol, acetone, butanol, acetate and butyrate during master fermentation of Clostridium acetobutylicum at the steady state pH values 5.5, 5.3, 5.1, 4.9 and 4.7.

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