Using Pathway Logic to Integrate Signal Transduction and Gene Expression Data 1 SRI International (original) (raw)
The qualitative and quantitative study of biological processes as integrated systems not just isolated parts. Goals: • Model causal networks of biomolecular processes and interactions in a logical framework • Develop formal models that are as close as possible to domain expert’s mental models • Compute with and analyze these networks • Abstract and refine logical models • Simulate or use deduction to check properties • Make predictions, experiment, update model 3 Pathway Logic Pathway Logic (PL) is an approach to modeling biological entities and processes based on rewriting logic. Signal transduction processes are modeled at different levels of abstraction in the PL knowledge base. The resulting signaling networks can be queried using formal methods tools. For example, given an initial state: • execute--show me some signaling pathway • search--show me all pathways leading to a specified final condition • model-check--is there a pathway with certain given properties? 4 The Pathway Lo...
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