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Abstract. This paper gives an overview of the Maude 2.0 system. We emphasize the full generality with which rewriting logic and membership equational logic are supported, operational semantics issues, the new built-in modules, the more general Full Maude module algebra, the new META-LEVEL module, the LTL model checker, and new implementation techniques yielding substantial performance improvements in rewriting modulo. We also comment on Maude's formal tool environment and on applications.

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The genomic sequencing of hundreds of organisms including homo sapiens, and the exponential growth in gene expression and proteomic data for many species has revolutionized research in biology. However, the computational analysis of these burgeoning datasets has been hampered by the sparse successes in combinations of data sources, representations, and algorithms. Here we propose the application of symbolic toolsets from the formal methods community to problems of biological interest, particularly signaling pathways, and more specifically mammalian mitogenic and stress responsive pathways. The results of formal symbolic analysis with extremely efficient representations of biological networks provide insights with potential biological impact. In particular, novel hypotheses may be generated which could lead to wet lab validation of new signaling possibilities. We demonstrate the graphic representation of the results of formal analysis of pathways, including navigational abilities, and describe the logical underpinnings of the approach. In summary, we propose and provide an initial description of an algebra and logic of signaling pathways and biologically plausible abstractions that provide the foundation for the application of highpowered tools such as model checkers to problems of biological interest.

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