Psomopoulos Fotis E, Vitsios Dimitrios M, Baichoo Shakuntala, Ouzounis Christos A
Computational Genomics Unit, Institute of Applied Biosciences, Center for Research & Technology Hellas (CERTH), GR-57001 Thessalonica, Greece.
The European Bioinformatics Institute, EMBL Cambridge Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Bioinformatics. 2017 May 1;33(9):1418-1420. doi: 10.1093/bioinformatics/btw813.
BioPAXViz is a Cytoscape (version 3) application, providing a comprehensive framework for metabolic pathway visualization. Beyond the basic parsing, viewing and browsing roles, the main novel function that BioPAXViz provides is a visual comparative analysis of metabolic pathway topologies across pre-computed pathway phylogenomic profiles given a species phylogeny. Furthermore, BioPAXViz supports the display of hierarchical trees that allow efficient navigation through sets of variants of a single reference pathway. Thus, BioPAXViz can significantly facilitate, and contribute to, the study of metabolic pathway evolution and engineering.
BioPAXViz has been developed as a Cytoscape app and is available at: https://github.com/CGU-CERTH/BioPAX.Viz. The software is distributed under the MIT License and is accompanied by example files and data. Additional documentation is available at the aforementioned GitHub repository.
BioPAXViz是一款适用于Cytoscape（版本3）的应用程序，为代谢途径可视化提供了一个全面的框架。除了基本的解析、查看和浏览功能外，BioPAXViz提供的主要新颖功能是，在给定物种系统发育的情况下，对预先计算的途径系统发育概况中的代谢途径拓扑结构进行可视化比较分析。此外，BioPAXViz支持显示层次树，从而能够在单个参考途径的变体集中进行高效导航。因此，BioPAXViz可以显著促进代谢途径进化和工程研究，并为其做出贡献。
BioPAXViz已被开发为一款Cytoscape应用程序，可从以下网址获取：https://github.com/CGU-CERTH/BioPAX.Viz。该软件根据麻省理工学院许可协议进行分发，并附带示例文件和数据。更多文档可在上述GitHub代码库中获取。
