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Stefan Leye, Corrado Priami, and Adelinde Uhrmacher (2007)

A Parallel Beta-binders Simulator

The Microsoft Research - University of Trento Centre for Computational and Systems Biology.

Beta-binders is a comparatively new modeling formalism introduced for systems biology. To execute Beta-binders models, suitable simulators are required which translate the operational semantics of Beta-binders into a sound and efficient execution. Efficiency can be reached by parallel and distributed simulation and by a proper representation of models to ensure a fast manipulation. Both possibilities are considered in the implementation of the described hierarchical Beta-binders simulator. The description includes a tree structure which reflects the PI-calculus and Beta-binders processes and the algorithm of the simulator which enables a distributed and optimistic, parallel execution.

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