Lecture 17: Compartments in BioPEPA

18 March 2010

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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PEPA Club

11 March 2010

Complementary Approaches to Understanding the Plant Circadian Clock

Maria Luisa Guerriero
Centre for Systems Biology at Edinburgh
11am Friday, 12 March, 2010
Room 3.02, Informatics Forum

Links: Seminar abstract; About PEPA Club.

This talk describes a BioPEPA model for the circadian clock in the green alga Ostreococcus tauri, demonstrating in particular the use of BioPEPA to drive many different kinds of analysis of the same model.

Dr Guerriero is a researcher at CSBE working on formal verification of process algebra models for systems biology. This talk is a rehearsal for a presentation at the FTBC 2010 workshop From Biology To Concurrency and Back in Cyprus later this month.

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Posted by Ian Stark