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Fig. 7 | BMC Systems Biology

Fig. 7

From: Modelling with ANIMO: between fuzzy logic and differential equations

Fig. 7

Abstraction of a biochemical reaction to a Timed Automata model. a Classical depiction of a well-studied intracellular signal transduction reaction: protein MAPK-ERK kinase (MEK) activates downstream protein extracellular-regulated kinase (ERK). b A Timed Automaton model of ERK, consisting of two locations (circles), inactive_ERK and active_ERK, and one transition (edge) between the locations. This transition will take place when it is possible to synchronize with the corresponding action activate_ERK! in the MEK automaton. c A Timed Automaton model of active MEK, consisting of one location and one transition. t<20 is called an invariant on the location, allowing residence in this location as long as clock time t is smaller than 20 units. t>18 is called a guard on the transition, allowing the transition to take place when clock t is greater than 18 units. Together, the invariant and guard in this example ensure that the transition must take place in the (continuous) time interval 18<t<20. When the transition takes place, the action activate_Erk! is performed (thus allowing the ERK automaton to reach the active_ERK location) and the local clock coupled to this automaton is reset, t:=0

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