Frequently Asked Questions

General

Help! Where can I ask questions?

Send an email to our discussion mailing list. For more information, see MailingLists

Can I run PathVisio when I'm offline?

Certainly. The first time you download PathVisio, normally a desktop icon is created. But even if you chose not to create this desktop icon, you can still run PathVisio offline. See RunPathvisioOffline for details.

What is the relation between PathVisio and GenMAPP?

PathVisio has grown out of a need to extend  GenMAPP. GenMAPP has many good features but has hit limits in terms of its flexibility to adapt to new needs. We cooperate closely with the GenMAPP group to share code and ideas. PathVisio borrows heavily from the good aspects of GenMAPP, such as its simplicity and usability, but tries to improve on other aspects, such as flexibility and expansion to other platforms (linux and Mac OS X).

What is the relation between PathVisio and Cytoscape?

PathVisio and Cytoscape are very different programs. But after you install the [Cytoscape_plugin GPML plugin for Cytoscape], you will be able to open in Cytyoscapes pathways created in PathVisio. The Cytoscape plugin can be installed from the plugin manager menu within cytoscape.

What is the relation between PathVisio and WikiPathways

PathVisio and WikiPathways? are compatible. Pathways created in PathVisio can be shared on WikiPathways, and pathways downloaded from WikiPathways can be opened in PathVisio. Also, some of the program code of PathVisio is embedded in WikiPathways, as a Java applet.

How do I cite PathVisio?

See HowToCite

Trouble-shooting

The download link doesn't work

Try clearing the Java webstart cache, you can find instructions here:  http://www.ngs.ac.uk/clearwebstartcache. If that doesn't help, please contact our mailinglist (see: MailingLists).

Pathway Diagrams

What is the meaning of each graphical symbol in pathways?

See Pathway Styles

Does PathVisio support dynamic layouts of pathways?

No, PathVisio sees pathways as drawings, not as graphs. This makes the program less complex to use, but if you are more interested in graph-oriented features, we recommend you to take a look at  Cytoscape

Does PathVisio support SBML? How About BioPAX?

At the moment PathVisio only supports our custom GPML format and GenMAPP MAPP format. BioPAX import / export is currently in Beta (See BiopaxPluginHelp) Support for SBML is planned but will not be ready in the near future.

Gene expression / omics data

Which microarrays are supported by PathVisio

Out of the box, common affymetrix, illumina and agilent microarrays are supported

Can I use PathVisio for metabolomics data?

Yes, you can use PathVisio for many types of large datasets, including metabolomics. PathVisio supports all types of data that can be linked to identifiers on your pathways.