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Translating SBML Models into the Stochastic π-Calculus for Stochastic Simulation

  • Claudio Eccher
  • Paola Lecca
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4230)

Abstract

This paper addresses the translation of Systems Biology Mark-Up Language (SBML) Level 2 models of network of biochemical reactions into the Biochemical Stochastic π-calculus (SPI). SBML is XML-based formalism for systems biology, while SPI can describe the concurrency of the different interactions occurring in a network of biochemical stochastic reactions. SPI models can be used for simulation by available computer packages. We present the approach followed in designing a software tool for working biologists that parses an SBML model and performs the unsupervised translation into the process algebra model. To test the correctness of the translation process we present the results obtained by performing simulations of a translated simplified circadian clock model, comparing our results with that obtained with the original differential equation model.

Keywords

System Biology Order Reaction Process Algebra Second Order Reaction System Biology Markup Language 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Claudio Eccher
    • 1
    • 2
  • Paola Lecca
    • 1
  1. 1.Dept. of Information and Communication TechnologiesUniversity of TrentoItaly
  2. 2.ITC-irst Center for Scientific and Technological ResearchPovo (Trento)Italy

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