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Updated: Mar 3, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution
Fotis E Psomopoulos1, Dimitrios M Vitsios1,2, Shakuntala Baichoo3
1Computational Genomics Unit, Institute of Applied Biosciences, Center for Research & Technology Hellas (CERTH), GR-57001 Thessalonica, Greece.
Summary:
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.
Availability And Implementation:
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.
Contact:
ouzounis@certh.gr.
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