Welcome to the Pathway Logic Demo.  This demo allows you to explore several Pathway Logic models using the Bionet viewer.  The current viewer is a prototype for a much more functional and interactive interface that will be developed for the Pathway Logic project.

The demo is an applet (i.e. client side) where most of the computation is done on the server side, so the applet's speed is dependent on the client-server internet connection.

The applet requires a recent Java, e.g. 1.4.2, since it uses packages like javax.xml.parser.  However, to hopefully side step this problem we provide two versions of the applet, a light version (127K), which assumes a Java plugin that has everything Bionet needs, and a heavier version (894K) that packages up the XML parsing classes.  We suggest you try the light version  first, then if that doesn't work for you, the heavier one. If you have problems check the FAQ page.

To read about using the demo viewer click here.

The Pathway Logic project at SRI is currently funded by a grant (GM068146) from the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Health.

• Demo 1: Three Ways to Activate Rac1.
  • For a guided tour click here
  • To view this model directly, click on a link: [light]   [heavy]
  • The Maude model is available in Demo1Model
    • Declarations of concepts and operations: theops1.maude
    • Definitions of proteins and other components: components1.maude
    • The transduction rules (network elements): rules1.maude
    • The initial state: qq1.maude
• Demo 2: TNF Signaling Through TNFR1
  • For a guided tour click here
  • To view this model directly, click on a link: [light]   [heavy]
  • The Maude model is available in Demo2Model
    • Declarations of concepts and operations: theops2.maude
    • Definitions of proteins and other components: components2.maude
    • The transduction rules (network elements): rules2.maude
    • The initial state: qq2.maude
• Demo 3: A Model of Signal Transduction from the Epidermal Growth Factor Receptor (EGFR) to the Cyclin D1 Gene
  • For a guided tour click here
  • To view this model directly, click on a link: [light]   [heavy]
  • The Maude model is available in Demo3Model
    • Declarations of concepts and operations: theops3.maude
    • Definitions of proteins and other components: components3.maude
    • The transduction rules (network elements): rules3.maude
    • The initial state: qq3.maude

To try the bionet viewer, click here: [light]   [heavy]

The Bionet Viewer was developed by David Dill and Pamela Gage and adapted for web access by Ian Mason and Carolyn Talcott.  The network image is by GraphicLab.