**KEGG**'.

- 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 ...

**Creator: **Sebastian Curth

**Submitter**: Sebastian Curth

**Investigations:** Modular Model Building

**Studies:** Automated Model Building

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 ...

**Creator: **Sebastian Curth

**Submitter**: Sebastian Curth

**Investigations:** Modular Model Building

**Studies:** Reactome Analysis

**Assays:** Graph Analysis, KEGG Data Mining

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 ...

**Creator: **Sebastian Curth

**Submitter**: Sebastian Curth

**Investigations:** Modular Model Building

**Studies:** Reactome Analysis

**Assays:** Graph Analysis, KEGG Data Mining

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

**Creator: **Sebastian Curth

**Submitter**: Sebastian Curth