Pathway Logic is a powerful computational science software system for researchers. Pathway Logic tools facilitate the understanding of complex biological systems and accelerate the design of experiments to test hypotheses about their functions in vivo.
Pathway Logic exemplifies how formal modeling techniques can be used to develop the new science of symbolic systems biology. The system is based on a simple but powerful logic (called rewriting logic) and its implementation in Maude, a rewriting logic language co-developed by SRI.
The system models and analyzes signal transduction—the metabolic and protease networks in both mammalian and microbial cells. Pathways leading from different initial conditions can be generated automatically from collections of network elements. In silico experiments can then be performed to study the effects of perturbations of these networks.
The Pathway Logic Assistant (PLA) provides an interactive graphical interface to browse and query Pathway Logic network models. Using PLA, a biologist can
- Define initial conditions
- Display and navigate the model network restricted to these conditions
- Compute and display subnets and execution paths with given endpoints
- Perturb the network by knocking out network elements
- Compare two networks
- Incrementally explore network connections
PLA and several network models are available for download and use at no charge. An extensive collection of Pathway Logic publications is available, as is an online demonstration of the Pathway Logic assistant. Guided tours of each of the models and documentation for using the Pathway Logic assistant are also available.