Lecture 17: Compartments in BioPEPA

Working through the following paper:

  • Federica Ciocchetta and Maria Luisa Guerriero. Modelling Biological Compartments in Bio-PEPA, in MeCBIC 2008: Proceedings of the Second International Meeting on Membrane Computing and Biologically Inspired Process Calculi. Electronic Notes in Theoretical Computer Science 227:77–95, January 2009.

Adding compartments to BioPEPA: syntax; compositional operational semantics; structured locations including compartments, membranes, and the boundaries between them; appropriate kinetics; sample model of intracellular calcium oscillations.

Homework

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