Java Security Settings


When starting PathVisio, you might see an error like this:

In the latest Java update the security settings for self-signed applications have been adapted (Java 7 Update 51). Self-Signed applications, like Pathvisio, are blocked on high security level.

PathVisio is still safe to run. We also are in the progress of registering a certificate which will allow users to also run PathVisio on high security level. Until then, you can either use the binary installation of PathVisio or lower the Java security settings. Instructions on how to set your security settings can be found here.


General questions


1. Help! Where can I ask questions?

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

2. 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.

3. 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).

4. 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 with a plugin. Also, some of the program code of PathVisio is embedded in WikiPathways, as a Java applet.

5. What is the relation between PathVisio and Cytoscape?

PathVisio (and pathway drawing and editing tool) and Cytoscape (a network tool) are very different programs. You can use the pathways drawn in PathVisio in Cytoscape, by installing the WikiPathways App. With this application you will be able to open pathways created in PathVisio and uploaded to WikiPathways as either pathway diagrams or networks.

6. How do I cite PathVisio?

See HowToCite

7. Which databases are supported for pathway elements?

Check out the list of supported systems codes here.


Pathway Diagrams


1. What is the meaning of each graphical symbol in pathways?

Since there is a close collaboration with WikiPathways, elaborate documentation can be found here.

2. 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.

3. Does PathVisio support other standards, such as BioPax, SBGN and SBML?

All pathways drawn in PathVisio are modeled with our custom GPML format; this format is machine readable, easy to learn by novel users and extendable for experienced users. BioPAX import / export is currently supported through the Biopax3 plugin. SBGN models on all three levels (activity flow, process description and entity relationships) is accessible through the SBGN plugin. Pathways drawn in SBML can be opened in PathVisio as well with the pathSBML plugin, allowing for pathway analysis and converting to GPML format.


Gene expression / omics data


1. Which microarrays are supported by PathVisio?

Out of the box, common affymetrix, illumina and agilent microarrays are supported. Find the full list of supported data(base) identifiers here.

2. Can I use PathVisio for proteomics, metabolomics data?

Yes, you can use PathVisio for many types of large datasets (aka OMICS), including proteomics and metabolomics. PathVisio supports all types of data that can be linked to identifiers on your pathways. Please annotate your dataset with one of the supported database identifiers.

3. Are my dataset and visualization settings saved?

Yes, PathVisio creates several files in the directory of the dataset you imported.

  • The .pgex file contains the dataset itself.
  • The .pgex.xml file contains all the visualizations that you created for this dataset.
  • The pgex.ex.txt contains possible warnings/errors that occurred when you imported the dataset (also related to identifier mapping).

If you want to reopen your dataset including the visualizations, just go to ‘Data’ -> ‘Select expression dataset’ and select the .pgex file.


Plugin installation


1. Errors when installing/updating a plugin

As a first step, you could try to remove the original (old) plugin from within PathVisio. Click on “Plugins/Plugin Manager” to see which plugins are currently Available, Installed, if there are any Errors, and what the Status is of the plugin repository you are connected to. In the Installed tab, you can uninstall individual plugins, and then try to reinstall them from the Available tab.

2. Errors when installing a plugin: full clean up

As a second step you can try to clean the PathVisio bundle directory to make sure there are no old libraries that are causing problems (be aware this will delete all installed plugins and you will need to re-install all of them!).

  1. Close PathVisio
  2. Go to your local PathVisio directory:
    • Windows: in your home directory, go into the hidden directory “AppData”- “Roaming” – “PathVisio”
    • MacOS / Linux: in your home directory, go into the hidden directory “.PathVisio”
  3. Remove the .bundles directory
  4. Restart PathVisio
3. Can’t connect to repository

If you are online but can’t connect to the repository, maybe due to proxy settings, follow the steps below to install a plugin. This is a lot more complex than using the plugin manager, so only use it if the plugin manager really doesn’t work.

  1. Go to http://repository.pathvisio.org/plugins/
  2. Go into the directory of the plugin you want to install, then in the version you want to use and then download the jar file
  3. Please be aware that you need to download all additional dependencies of the plugin as well. The plugin manager makes sure all dependencies are installed, but when installing it locally you will need to download them manually.
  4. Save all jars in one directory.
  5. Start PathVisio and go to “Plugins -> Install local plugins”. Select the directory that contains all jar files.
  6. Select the plugin you want to start.
  7. Then the plugin should be installed in PathVisio.

Troubleshooting


1. The download (link) doesn’t work

Try clearing the Java webstart cache, you can find instructions here: http://www.ngs.ac.uk/ukca/certificates/certwizard/clearwebstartcache.

Also be sure to use the binary installation of PathVisio (not the webstart one, this version is only meant for training purposes!). Installation on Windows, Linux and Mac is supported. However for Mac/Apple users you need to locate the PathVisio folder in your own download folder (which is different compared to installing programs through the App Store).

If that doesn’t help, please contact our mailing list (see: MailingLists).

2. Where can I find the log file?

You can find your pathvisio.log file in the local PathVisio directory:

  • Windows: in your home directory, go into the hidden directory “AppData”- “Roaming” – “PathVisio”
  • MacOS / Linux: in your home directory, go into the hidden directory “.PathVisio”