BiGGViz：用于可视化基因组尺度 BiGG 代谢网络的 MATLAB 应用
BiGGViz: A MATLAB App for Visualization of Genome-Scale BiGG-Based Metabolic Networks
BiGGViz 是一个基于 MATLAB 的应用，用于交互式可视化与探索 COBRA 兼容的 BiGG 代谢模型。它自动构建反应-反应和代谢物-代谢物图，支持在反应中心与代谢物中心视图间切换、自定义节点外观、基于拓扑的过滤、局部邻域查看、按跳数扩展高亮通路，并可导出可视化结果或网络结构用于下游分析。可选注释表可叠加用户自定义属性与 COBRA 分析结果，包括通量平衡分析（FBA）结果，从而实现通量感知的探索。
来源：Bioinformatics Advances · doi.org
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.