SBML Importer Plugin for PathVisio

Biological models are abstract representations of biological processes. Models can be diagrammatic, e.g pathways, serving as frameworks to visualize and integrate experimental measurements of genes and gene products. Models can also be mathematical, describing the biological process by means of various equations. Computational biologists use mathematical models to predict how a process might be affected by environmental or internal stimuli. SBML is a standard format widely accepted for storing and exchanging such mathematical models. PathVisio (pathvisio.org) is an open source pathway creating, editing, visualization, and analysis tool. It uses GPML to store and exchange pathways. The new SBML importer plugin for PathVisio facilitates model curation and extension by providing modelers with an up-to-date graphical (SBGN-PD) representation of their model. This representation can then be compared to existing pathways for the same process, which will facilitate both pathway improvement and critical assessment of model implementation aspects like lumping of reaction steps and reduction of parallel routes. Existing PathVisio functionality enables model outcomes to be graphically visualized on the model representation to ease comprehension. The plugin also enables model validation and direct import of SBML models from Biomodels. Furthermore, imported models can then be shared with the community for distribution and further curation through WikiPathways (wikipathways.org), which also uses GPML as its native format.