| kegg | create kegg repository arguments |
| geneKO.maps | create a list that map gene id to KO id. |
| assembling.genome | create genome framework for the virtual cell model |
| assembling.metabolic | add metabolism network information for the virtual cell model |
| assembling.TRN | add transcription regulation network information for the virtual cell model |
| vcell.markup | Save the virtual cell data model in XML file format. |
| compile.biocyc |