A standardized workflow for kinetic metabolic model curation and dissemination
Fig 4
Strategies for effective visualization of data from kinetic models.
(A) Choosing a graphical representation of a kinetic model which follows community standards enables users and collaborators to more easily draw conclusions and observe trends. SBMLNetwork is able to accept predefined coordinates, from KEGG, for example, and map the corresponding species in the kinetic model onto those positions. (B) Color-coding species nodes and reaction curves is an effective way to distinguish reaction groups and highlight important parts of a model. The example shown includes pyruvate metabolism & Acetyl-CoA formation (orange), glycolysis/gluconeogenesis (purple), amino acid metabolism (blue), redox and energy metabolism (red), and the TCA cycle (green). (C) SBMLNetwork and other visualization tools allow integration of quantitative data such as reaction fluxes and species concentrations. Reaction fluxes and species concentrations are both displayed on a logarithmic scale, using a yellow to red colorbar and node size, respectively.