Example Features

Genome Scale Modeling

The image series shows the intermediate drawing steps to a genome-scale metabolic network. The diagram was created by stepwise importing single pathways from the KEGG databases and combining them to a consistent diagram. The model consists of 826 metabolites, 846 reactions and 59 pathways. In total, the diagram contains 3560 graphical items and 3651 connections.

The drawing process has taken eight days. This includes collecting network data, parametrization of the model (i.e. atom mappings, constraints etc.) and proofreading of the complete model against literature information. Considering the costs of drawing such a diagram with a common graphics software tool and/or creating a model in textual manner (e.g. SBML) eight days are a significant improvement. Having the high reusability of networks built with Omix in mind, eight days are quite less compared with the time effort of separate drawing, modeling and visualization tasks.