BiGGViz: A MATLAB App for Visualization of Genome-Scale BiGG-Based Metabolic Networks
Shu-Liang Yu, Rachael Hageman BlairAbstract
Motivation
Genome-scale metabolic reconstructions have become essential tools in systems biology for studying cellular metabolism and supporting in silico experimentation. The Biochemical, Genetic, and Genomic (BiGG) knowledge base provides standardized, open-source metabolic models in multiple formats, including Systems Biology Markup Language (SBML) and MATLAB MAT files, facilitating model reuse and integration with computational frameworks such as the COBRA Toolbox. However, visualizing and exploring large-scale metabolic networks remains challenging, particularly for users without extensive programming expertise. Accessible and interactive visualization tools are needed to improve the interpretation, communication, and exploration of dense reaction and metabolite networks.
Results
We developed BiGGViz, a MATLAB-based application for interactive visualization and exploration of COBRA-compatible BiGG metabolic models. BiGGViz automatically constructs reaction-reaction and metabolite-metabolite graphs and provides an interactive graphical interface for network exploration. Users can switch between reaction- and metabolite-centric views, customize node appearance, apply topology-based filtering, inspect local neighborhoods, highlight pathways with configurable hop-based expansion, and export visualizations or network structures for downstream analyses. Optional annotation tables support overlay of user-defined attributes and COBRA-derived analyses, including flux balance analysis (FBA) results, enabling flux-aware exploration of genome-scale metabolic networks. BiGGViz supports exploratory systems biology analyses, result communication, educational applications, and integration with downstream Cytoscape-based workflows. A scriptable wrapper, exportBiGGViz, is also provided to support reproducible, code-driven analysis pipelines.
Availability and Implementation
BiGGViz is implemented in MATLAB and is freely available at https://github.com/mogystats/BiGGViz. Browser-based documentation and a detailed Getting Started tutorial are available at https://mogystats.github.io/BiGGViz/GettingStarted.html.