Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Designing of a simulation tool to analyse the dining philosopher's problem by petri net analysis

Concurrent Systems are those where time is shared by each smaller module. Concurrency is the major problem in many of the real world system. It generally arises due to synchronization problem or improper scheduling between the modules. Such kind of sophisticated and large system is modelled for their analysis and study. Petri Nets is a graphical and mathematical tool which helps in modelling these systems that are concurrent, distributed, parallel, nondeterministic, asynchronous and stochastic. The Dining Philosopher’s Problem is a classic Synchronization problem of the multi-processor systems. The project primarily includes the simulation of an example of multiprocessor system and designing and creation of a special simulation tool for Dining philosopher’s Problem by Petri Net. The tool is created in JAVA. The tool analyses the graph dynamically drawn consisting of places which represents the philosopher can think or eat and availability of the chopsticks and the transition represents whether a philosopher can pick up or return the stick. The prime focus is given to the User-Define Time constraint for a particular philosopher. The simulation tool guides the user at each and every step and the solutions given by the tool ensure a freedom of deadlock and in process coordination