Pathway Logic Assistant (PLA)
The Pathway Logic Assistant (PLA) is our software that implements the Pathway Logic vision. The screen shot on the right shows PLA's graphical user interface depicting a signal transduction network as a petri net. In the bipartite graph of the Petri net, round nodes denote places that encode proteins and complexes together with their chemical modification (e.g. an activated Mekk4 is labeled "Mekk4-act"). The transitions between places correspond to rewriting rules in Maude's knowledge base. The places are generally colored in light and dark blue, where the latter indicates that these proteins are part of the starting state used to build the pathways from the Maude knowledge base.
In the top right corner, a thumb nail view of the complete network provides an overview and accepts mouse clicks and drags to move the porthole into the bigger view of the graph on the left. Other features of the GUI are zooming capabilities and context information that appears in another tab on the right when users click on nodes and edges of the graph in the bigger view.
One can select proteins as goals or as to be avoided and then search for paths and subnets that avoid the respective proteins while reaching the specified goals.
You may want to sign up for a Mailing List to receive important announcements about the software.