PathVisio

Plans and prices

Every plan, in full

On the record

Available plugins

The plugin repository lists plugins including BioPAX, BridgeDb, GSEA, PathSBML, and WikiPathways.pathvisio.org · read 12 Oct 2026

Current service notice

The site says WikiPathways uploads are currently not working and asks curators to contact the maintainers for help updating pathways.pathvisio.org · read 12 Oct 2026

Cytoscape

The FAQ says pathways created in PathVisio can be opened in Cytoscape after installing the WikiPathways App.pathvisio.org · read 12 Oct 2026

Data analysis

PathVisio supports large datasets, including metabolomics, when their data can be linked to identifiers on pathways.pathvisio.org · read 12 Oct 2026

Data sources

Gene-expression datasets; metabolomics; Affymetrix microarrays; Illumina microarrays; Agilent microarrays; genes; proteins; genetic variants; metabolites; metabolic reactions; WikiPathways; BridgeDbpathvisio.org · read 20 Sep 2026

Diagram limitation

PathVisio treats pathways as drawings rather than graphs and does not support dynamic pathway layouts.pathvisio.org · read 12 Oct 2026

Extensible

PathVisio is developed in Java and can be extended with plugins.pathvisio.org · read 12 Oct 2026

File formats

PathVisio supports its custom GPML format and GenMAPP MAPP format; BioPAX import and export is supported through a plugin, while SBML support is described as planned.pathvisio.org · read 12 Oct 2026

Microarrays

Common Affymetrix, Illumina, and Agilent microarrays are supported out of the box.pathvisio.org · read 12 Oct 2026

Offline use

PathVisio can run offline, but its plugin manager requires an internet connection.pathvisio.org · read 12 Oct 2026

Pathway curation

PathVisio is the pathway editor for WikiPathways, a community-curated pathway database that enables collaborative pathway editing.pathvisio.org · read 12 Oct 2026

Platform

desktoppathvisio.org · read 20 Sep 2026

Purpose

PathVisio is software for drawing, editing, and analyzing biological pathways.pathvisio.org · read 12 Oct 2026

Support

The contact page directs installation help and bug reports to GitHub issues, and analysis questions to a Google group.pathvisio.org · read 12 Oct 2026

System requirement

PathVisio version 3.x requires Java 8 and cannot work with other Java versions.pathvisio.org · read 12 Oct 2026

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