PathVisio

Spec sheet

Purpose

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

Platforms

The download page provides installers for Windows, macOS, and Linux.Read 12 Oct 2026 · pathvisio.org

Free plan

YesRead 20 Sep 2026 · pathvisio.org

Support

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

Headquarters

Maastricht, NetherlandsRead 28 Sep 2026 · pathvisio.org

Available plugins

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

Current service notice

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

Cytoscape

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

Data analysis

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

Data sources

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

Diagram limitation

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

Extensible

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

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.Read 12 Oct 2026 · pathvisio.org

Microarrays

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

Offline use

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

Pathway curation

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

Platform

desktopRead 20 Sep 2026 · pathvisio.org

System requirement

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

Plans and prices

Every PathVisio plan and price →

Where Specifiction places it

• Data Visualization Software#60 of 987.8