Electrical Engineering
      and Computer Sciences

Electrical Engineering and Computer Sciences

COLLEGE OF ENGINEERING

UC Berkeley

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