Cofactor integration of the KGML-based model generation


One option of the KGML-based model reconstruction is the visualization of cofactors according to the processed reactions of a particular pathway. The molecule symbols for cofactores can be added automatically close to its reaction. Their localization is estimated depending on the location of the basic reaction molecules, which are already determined by the KGML information. In the following, this option was used to improve the reconstruction of the glycolysis of Xanthomonas campestris pv. campestris B100 (Figure 2).

De novo basic figure

Figure 2: KGML-based glycolysis reconstruction of X.campestris pv. campestris B100 using the option for cofactor integration (-c T).

Download XanthomonasB100_cofactorDownload SBML file of X. campestris with integrated cofactors.