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PathVisio
by PathVisio
What PathVisio is
PathVisio is free, open-source desktop software for drawing, editing, and analyzing biological pathways. It runs on Linux, macOS, and Windows, and can operate offline after installation. The program works with gene-expression and metabolomics datasets when measurements can be linked to pathway identifiers, and common Affymetrix, Illumina, and Agilent microarrays are supported out of the box. PathVisio is the pathway editor for WikiPathways, a community-curated database that supports collaborative pathway editing. Because it is developed in Java, plugins can extend it; the repository lists BioPAX, BridgeDb, GSEA, PathSBML, and WikiPathways options. Files use GPML or GenMAPP MAPP formats, with BioPAX import and export available through a plugin. Pathways can open in Cytoscape after installing the WikiPathways App. Version 3.x requires Java 8. PathVisio treats pathways as drawings rather than graphs, so dynamic layouts are unavailable. Its plugin manager needs internet access.
Who it suits
PathVisio suits researchers and analysts working with pathway diagrams, gene-expression, metabolomics, or microarray data. It is also relevant to WikiPathways contributors and users who need plugin-based extension.
What it does well
- Free open-source desktop software
- Runs on Linux, macOS, and Windows
- Supports several common microarray types
- Plugin repository extends Java application
- Works offline after installation
What to know first
- Version 3.x requires Java 8
- Dynamic pathway layouts are not supported
- Plugin manager requires an internet connection
- WikiPathways uploads are currently not working
Plans
| Plan | Billed and limits | Price |
|---|---|---|
| PathVisio | Free open-source pathway analysis and drawing software | Free |
As pathvisio.org lists them, read 12 Oct 2026. The maker's own page has the final word.
Verdict
PathVisio provides cross-platform pathway drawing and analysis with broad dataset and plugin support at no cost. Users should account for its drawing-based model, Java 8 requirement, and current WikiPathways upload issue.
Facts from PathVisio's own pages
- Available plugins
- The plugin repository lists plugins including BioPAX, BridgeDb, GSEA, PathSBML, and WikiPathways. · pathvisio.org, 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, 12 Oct 2026
- Cytoscape
- The FAQ says pathways created in PathVisio can be opened in Cytoscape after installing the WikiPathways App. · pathvisio.org, 12 Oct 2026
- Data analysis
- PathVisio supports large datasets, including metabolomics, when their data can be linked to identifiers on pathways. · pathvisio.org, 12 Oct 2026
- Data sources
- Gene-expression datasets; metabolomics; Affymetrix microarrays; Illumina microarrays; Agilent microarrays; genes; proteins; genetic variants; metabolites; metabolic reactions; WikiPathways; BridgeDb · pathvisio.org, 20 Sept 2026
- Diagram limitation
- PathVisio treats pathways as drawings rather than graphs and does not support dynamic pathway layouts. · pathvisio.org, 12 Oct 2026
- Extensible
- PathVisio is developed in Java and can be extended with plugins. · pathvisio.org, 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, 12 Oct 2026
- Free plan
- Yes · pathvisio.org, 20 Sept 2026
- Headquarters
- Maastricht, Netherlands · pathvisio.org, 28 Sept 2026
- Microarrays
- Common Affymetrix, Illumina, and Agilent microarrays are supported out of the box. · pathvisio.org, 12 Oct 2026
- Offline use
- PathVisio can run offline, but its plugin manager requires an internet connection. · pathvisio.org, 12 Oct 2026
- Pathway curation
- PathVisio is the pathway editor for WikiPathways, a community-curated pathway database that enables collaborative pathway editing. · pathvisio.org, 12 Oct 2026
- Platform
- desktop · pathvisio.org, 20 Sept 2026
- Platforms
- The download page provides installers for Windows, macOS, and Linux. · pathvisio.org, 12 Oct 2026
- Purpose
- PathVisio is software for drawing, editing, and analyzing biological pathways. · pathvisio.org, 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, 12 Oct 2026
- System requirement
- PathVisio version 3.x requires Java 8 and cannot work with other Java versions. · pathvisio.org, 12 Oct 2026
Where PathVisio stands on Freedom251
- Data Visualization Software#43 of 98