Recent Progress in Visualizing Constraint-Based Flux-Balance Models in Cytoscape

Abstract

The last several years have seen an explosion in the quality and quantity of genome-scale data. From metabolism to transcription and translation, the “-omics” revolution has given systems biologists the ability to develop increasingly comprehensive models of biochemical reaction networks. But as the size and scope of systems-level models has increased, it has become more difficult to understand and communicate their behavior in an intuitive manner. We believe that a robust set of tools designed to aid in the visualization of systems-level models can offer a way forward in this regard. We will report on recent advances in the development of several plugins for the popular Cytoscape network visualization software platform. These plugins are designed to represent large constraint-based models in an immediately understandable way. Several plugins are under development, including functionalities for importing and updating hand-curated maps from the BiGG database, and mapping flux distributions throughout reaction networks, but the centerpiece will be a unique algorithmic approach to network lay-out that will create highly-readable maps with little or no hand-curation necessary.