Multiple Representations of Biological Processes

  • Carolyn Talcott
  • David L. Dill
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4220)


This paper describes representations of biological processes based on Rewriting Logic and Petri net formalisms and mappings between these representations used in the Pathway Logic Assistant. The mappings are shown to preserve properties of interest. In addition a relevant subnet transformation is defined, that specializes a Petri net model to a specific query to reduce the number of transitions that must be considered when answering the query. The transformation is shown to preserve the query in the sense that no answers are lost.


Signal transduction biological process Pathway Logic Rewriting Logic Petri Net 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Carolyn Talcott
    • 1
  • David L. Dill
    • 2
  1. 1.SRI International 
  2. 2.Stanford University 

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