Grohar: Automated Visualization of Genome-Scale Metabolic Models and Their Pathways

Genome-scale metabolic models (GEMs) have become a powerful tool for the investigation of the entire metabolism of the organism in silico. These models are, however, often extremely hard to reconstruct and also difficult to apply to the selected problem. Visualization of the GEM allows us to easier comprehend the model, to perform its graphical analysis, to find and correct the faulty relations, to identify the parts of the system with a designated function, etc. Even though several approaches for the automatic visualization of GEMs have been proposed, metabolic maps are still manually drawn or at least require large amount of manual curation. We present Grohar, a computational tool for automatic identification and visualization of GEM (sub)networks and their metabolic fluxes. These (sub)networks can be specified directly by listing the metabolites of interest or indirectly by providing reference metabolic pathways from different sources, such as KEGG, SBML, or Matlab file. These pathways are identified within the GEM using three different pathway alignment algorithms. Grohar also supports the visualization of the model adjustments (e.g., activation or inhibition of metabolic reactions) after perturbations are induced.