PML: Toward a High-Level Formal Language for Biological Systems

Authors:
Bor-Yuh Evan Chang;Manu Sridharan
Affiliations:
Computer Science Division, University of California, Berkeley, Berkeley, CA, U.S.A.;Computer Science Division, University of California, Berkeley, Berkeley, CA, U.S.A.
Venue:
Electronic Notes in Theoretical Computer Science (ENTCS)
Year:
2007

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Abstract

Documentation of knowledge about biological pathways is often informal and vague, making it difficult to efficiently synthesize the work of others into a holistic understanding of a system. Several researchers have proposed solving this problem by modeling pathways using formal languages, which have a precise and consistent semantics. While precise, many of these languages may be too low-level to model feasibly complex pathways. We have developed the Pathway Modeling Language (PML), a high-level language for modeling pathways. PML is based on a biological metaphor of molecules with binding sites and has special constructs for handling compartment changes in pathways. Our preliminary work has shown that PML's language constructs serve as a promising basis for modeling complex pathways in a readable and composable manner.