A Logic Computational Framework to Query Dynamics on Complex Biological Pathways

  • Gustavo Santos-García
  • Javier De Las Rivas
  • Carolyn Talcott
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 294)


Biological pathways define complex interaction networks where multiple molecular elements work in a series of reactions to produce a response to different biomolecular signals. These biological systems are dynamic and we need mathematical methods that can analyze symbolic elements and complex interactions between them to produce adequate readouts of such systems. Rewriting logic procedures are adequate tools to handle dynamic systems which are applied to the study of specific biological pathways behaviour. Pathway Logic is a rewriting logic development applied to symbolic systems biology. Rewriting logic language Maude allows us to define transition rules and to set up queries about the flow in the biological system. In this paper we describe the use of Pathway Logic to model and analyze the dynamics in a well-known signaling transduction pathway: epidermal growth factor (EGF) pathway. We also use Pathway Logic Assistant (PLA) tool to browse and query this system.


signal transduction symbolic systems biology epidermal growth factor signaling Pathway Logic rewriting logic Maude Petri net executable model 


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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Gustavo Santos-García
    • 1
  • Javier De Las Rivas
    • 2
  • Carolyn Talcott
    • 3
  1. 1.Computing CenterUniversidad de SalamancaSalamancaSpain
  2. 2.Bioinformatics and Functional Genomics Research GroupCancer Research Center (CiC-IBMCC, CSIC/USAL)SalamancaSpain
  3. 3.Computer Science LaboratorySRI InternationalMenlo ParkUSA

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