**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