PathRings

PathRings is a cutting-edge web-based software tool that has been designed to help biologists explore and interpret biological pathways in a comprehensive and interactive manner. With the advent of high-throughput methods generating biological data on a vast scale, genomic, transcriptomic, and proteomic data must be interpreted in the context of signaling and metabolic pathways to yield testable hypotheses. PathRings has been specifically developed to address the limitations of current visualization tools, which provide limited viewing and manipulation capabilities to address complex data analysis problems.

PathRings integrates metabolic and signaling pathways from Reactome in a single compound graph visualization, which uses color to highlight genes and pathways affected by input data. This feature allows biologists to interpret data in an exploratory and comprehensive manner, providing an overview of the impact of gene expression data on all pathways to facilitate pattern finding. Additionally, PathRings offers detailed pathway information and a dynamic multi-view bubbles interface designed to support analytical tasks.

The tool permits an overview of the impact of gene expression data on all pathways to facilitate visual pattern finding. Detailed pathways information can be opened in new visualizations while maintaining the overview, which forms a visual exploration provenance. The dynamic multi-view bubbles interface is designed to support biologists' analytical tasks by letting users construct incremental views that further reflect biologists' analytical processes. This approach decomposes complex tasks into simpler ones and automates multi-view management.

PathRings can effectively support comparative tasks over substantially larger collections than existing tools.