Mathias John in Lille, France
Hosts: Joachim Niehren, Cédric Lhoussaine
Institution: INRIA Lille Nord Europe, Lille, France
Time: 09/10/2007 - 10/31/2007
My PhD thesis proposes a language for the computational modeling of the spatial dynamics of cell-biological systems. In collaboration with my colleague Roland Ewald and my supervisor Adelinde Uhrmacher in Rostock, I was able to develop a first approach, which is to extend the π-calculus, such that processes can be associated with spacial attributes. During my stay in Lille, this idea could be generalized by introducing reaction constraints to the π-calculus, the fundamental concept of my thesis. Non-deterministic and stochastic semantics and a stochastic simulator were developed. Two subsequent, shorter visits in Lille allowed us to refine the concept, extending it with priority and global variables. Additional expressiveness and modeling studies were worked out in corporation, which show that reaction constraints in the π-calculus form a valuable concept for the spatial modeling of cell-biological systems.
Having a background in computer graphics, I learned a lot about (concurrent) programming languages, in particular about formal semantics, and about formal methods in general during my stay in Lille. Apparently, this was a challenging exercise, but in the end I benefited a lot. Furthermore, I still was able to spare some time to discover the surrounding of Lille, e.g. going to London and Paris.
- John M, Lhoussaine C, Niehren J & Uhrmacher A (2008): The Attributed Pi Calculus. In: Monika Heiner, Adelinde M. Uhrmacher (ed.): Computational Methods in Systems Biology, International Conference CMSB 2008, Vol. 5307, pp. 83-102, Springer Verlag. LNBI.
- John M, Lhoussaine C & Niehren J (2009): Dynamic Compartments in the Imperative Pi-Calculus. In: Pierpaolo Degano and Roberto Gorrieri (ed.): CMSB 2009 - Computational Methods in Systems Biology, Vol. 5688, pp. 235-250, Springer Verlag. LNCS.
- John M, Lhoussaine C, Niehren J & Uhrmacher A (2010): The Attributed Pi-Calculus with Priorities. Transactions on Computational Systems Biology XII, 5945/2010:13-76.