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LFCS Seminar: Jonathan Hayman

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SPO semantics and filtered compression for Kappa

  • LFCS Seminar
When May 23, 2013
from 04:00 PM to 05:00 PM
Where IF 2.33
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Kappa is a language for modelling cellular signalling networks using graph-like structures.  One of the key features of the simulator supporting Kappa, KaSim, is that it is able to produce concise causal accounts for the production of patterns that the user specifies to be of interest, for example producing a causal account for the existence of links between two specified kinds of protein.  In my talk, I'll describe a simple technique that allows the user to tune the level of conciseness of these causal accounts.

I'll begin by giving an overview of recent work studying a semantics for the Kappa language based on the single-pushout approach to graph transformation.  This shall be extended to specify reduction in categories over contact graphs, which are certain kinds of type graph that constrain the forms of link that can exist.  By specifying sub-graphs of the appropriate contact graph for a system, equivalences on morphisms are obtained that restrict attention to the part of the graph that has type in the sub-graph.  It is then shown how the `compression lemma', upon which the production of concise causal accounts depends, can be obtained for any such equivalence.  This provides a uniform way of viewing weak and strong compression as implemented in KaSim, and allows potentially useful forms of compression between them to be obtained.  An example involving (quasi-)processive phosphorylation will be given.

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