Fuzzy Matching in Symbolic Systems Biology
Symbolic systems biology aims to explore biological processes as whole systems instead of small and independent elements. The goal is to define formal models that capture biologists intuitions and reasoning. Pathway Logic is a system for developing executable formal models of biomolecular processes. Using the Maude system, these models of dynamic processes can be represented and analyzed. The Pathway Logic Assistant uses forwards and backwards collection to assemble a connected set of rules from a rule knowledge base to model a system specified by an initial state (experimental setup). For this to succeed the rules must represent component states at the same level of detail, while we would like the knowledge base to capture as much detail as possible. In this paper, we propose a different way to perform matching in the process of rewriting in the high-performance rewriting language Maude. The basic concept is that of ‘‘fuzzy match’’ or ‘‘fuzzy instantiates to’’. It will be used to check requirements imposed by controls in forward collection, and with some elaboration to check whether the change part of a rule applies forwards or backwards.
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