الفهرس 
Simulation of Coloured Hybrid Petri NetsOnly 14 pages are availabe for public view
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Abstract
With the progress of biological modeling, the size as well as the scales of constructing biological models have been considerably increased. In addition to, these models can combine the deterministic and stochastic processes at the same time. Therefore, hybrid simulation is highly required for the construction and the execution of these systems.
Nevertheless, the current hybrid simulation algorithm still take considerable time and may not be very suitable to execute all kinds of models. The main reasons for such limitation is the model size and the repetition of components in the model. To deal with theses challenges, coloured hybrid Petri nets provide a great opportunity to construct multi scale models, since they provide a tool to fold simulator subnets into a single one.
Moreover, coloured hybrid Petri nets support the hybrid (stochastic/ deterministic) execution of same model, as well as hybrid modelling of complex biological systems using a parametrised language and abstract high-level notations permitting various timing features. However, the current approach of simulating coloured hybrid Petri nets involves unfolding the coloured nets into low level counterpart. Unfortunately, this step is time consuming process.
In thesis, we investigate the direct execution of coloured hybrid Petri nets on the coloures level. Therefore, we drive an algorithm to calculate the rate of change in the marking of each coloured continuous place based on our approach which generate the direct semantic of coloured continuous Petri nets. Moreover, calculating the rate of change in the marking of each coloured stochastic place based on our approach which generate the direct semantics of coloured stochastic Petri nets.
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Furthermore, we model the dynamics of intracellular calcium which is intricate and requires the interplay of stochastic and deterministic processes as there are multiple spatial and temporal scales involved with coloured hybrid Petri nets in two and three dimensional space. we have applied our approach on the simulation of calcium modelling that captures completely the calcium behavior over the time.