PML: Toward a High-Level Formal Language for Biological Systems
Bor-Yuh Evan Chang and Manu Sridharan
EECS Department
University of California, Berkeley
Technical Report No. UCB/CSD-03-1251
June 2003
http://www.eecs.berkeley.edu/Pubs/TechRpts/2003/CSD-03-1251.pdf
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 computer languages, which have a precise and consistent semantics. While precise, many of these languages may be too low-level to feasibly model 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.
BibTeX citation:
@techreport{Chang:CSD-03-1251,
Author = {Chang, Bor-Yuh Evan and Sridharan, Manu},
Title = {PML: Toward a High-Level Formal Language for Biological Systems},
Institution = {EECS Department, University of California, Berkeley},
Year = {2003},
Month = {Jun},
URL = {http://www.eecs.berkeley.edu/Pubs/TechRpts/2003/5547.html},
Number = {UCB/CSD-03-1251},
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 computer languages, which have a precise and consistent semantics. While precise, many of these languages may be too low-level to feasibly model 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.}
}
EndNote citation:
%0 Report %A Chang, Bor-Yuh Evan %A Sridharan, Manu %T PML: Toward a High-Level Formal Language for Biological Systems %I EECS Department, University of California, Berkeley %D 2003 %@ UCB/CSD-03-1251 %U http://www.eecs.berkeley.edu/Pubs/TechRpts/2003/5547.html %F Chang:CSD-03-1251