- 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 ...
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 ...