Bor-Yuh Evan Chang and Manu Sridharan

EECS Department, University of California, Berkeley

Technical Report No. UCB/CSD-03-1251

2003

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.

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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},
    Year= {2003},
    Month= {Jun},
    Url= {http://www2.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://www2.eecs.berkeley.edu/Pubs/TechRpts/2003/5547.html
%F Chang:CSD-03-1251