Important security information about running Cytoscape via Java Web Start
When you click on a Java Web Start link, you are downloading the program and running it on your own machine. This is somewhat similar to a Java applet that runs on your local machine, with some important differences.
Most importantly, Cytoscape differs from most web-deployed applications in that we configure the application to run with FULL PERMISSIONS. This is primarily because Cytoscape was written to run from the command line and thus expects access to the local machine, like the ability to open and save network files. This means that running Cytoscape via Java Web Start has the same security implications as downloading, installing, and running the application on your local computer. If security is a concern for you, you should consider whether this is what you want to do. By running Cytoscape you agree to the terms of the license agreement, including the standard disclaimer regarding limitation of liability. You can view a copy of the license here.
When you first click on a Web Start link, Java Web Start will provide a warning message informing you of the security risks before starting the application.
Click "Start" if you want to continue, or "Exit" to abort. If you run the application by clicking "Start", Java Web Start will not present this dialog on future requests to run the same application, unless you remove it from your local archive (see below).
Cytoscape allows externally developed plugin modules to be loaded by a user once Cytoscape has started. These plugins inherit all of the permissions granted to the core platform, including the ability to read and write from/to the local disk. Each plugin module has its own license agreement. The Cytoscape team cannot under any circumstances be responsible for or make any guarantees regarding the safety or functionality of any plugin modules that are not distributed with the core platform.
Java Web Start will usually store the application on your local machine (in a Web Start archive) so that it can be run later without having to download the application again. You can manage your downloaded applications by running the Java Web Start executable itself; this is usually called javaws and should be in your Java or Java Web Start application folder. Java Web Start will also automatically check for and download any updates to the web-available Cytoscape application. Cytoscape Web Start applications may not work properly if a connection to the internet is not available.
In the course of a normal Cytoscape session, the application may save certain files to your local disk for the purposes of saving configuration information. In particular, Cytoscape may attempt to place a vizmap.props file in your home directory to save visual mapping specifications. Such files may be written without prompting the user. These files may be safely deleted without affecting the ability of Cytoscape to function properly.