Snoopy is a software tool that allows users to create and simulate Petri net models of bacterial regulatory networks. Petri nets combine graphical models with mathematical representations of dynamic systems. Snoopy allows researchers to visually design Petri nets using places, transitions, arcs, and tokens to represent biological components and processes. It then enables simulations of these models to study bacterial behavior computationally. Snoopy provides a common platform for experimentalists and theorists to collaborate on modeling biochemical networks.
Nanoparticles for the Treatment of Alzheimer’s Disease_102718.pptx
SNOOPY.pptx
1. Snoopy for Petri Nets
Presented by: Hajra Qayyum
Reg. No: 432849
Course: Integrative System Biology
Atta-Ur-Rehman School of Applied Biosciences
National University of Science and Technology, Islamabad
3. Introduction
• Petri nets combine mathematical theory with graphical representation
of the dynamic behavior of systems.
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Figure 1: Aspects of petri nets
4. Components
• Particular kind of bipartite directed graphs populated by four types of
objects:
1. Places: state of the system being modelled
2. Transitions: event causing change in the system
3. Directed arcs: connection between a transition and a place
4. Tokens: object being processed or resource being consumed or
produced by the system.
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6. Types of Petri Nets
• Place/Transition (P/T) Nets
• Colored Petri Nets
• Timed Petri Nets
• Stochastic Petri Nets
• Fuzzy Petri Nets
• Any many more…….
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7. 1: Simple P/T Nets
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Figure 3: Petri-Net representation of a enzyme-catalyzed process
(glucose into glucose-6-phosphate).
8. 2: Colored Petri Nets
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Figure 4: Petri-Net representation repressilator system
14. Advantages
• Common communication platform (modelling language) for
experimentalists and theoreticians.
• Unifying framework for the graphical display, computational
modelling, simulation, and bioinformatic annotation of biochemical
networks, such as bacterial regulatory networks.
• In other words, a graphical representation of a Petri net drawn in
Snoopy can be executed, i.e. simulations can be run with a mouse
click; no special additional encoding is required.
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Colored Petri nets extend P/T nets by adding colors to tokens, which can represent different properties or attributes. They are often used to model complex systems with multiple resources or entities
Colored Petri nets extend P/T nets by adding colors to tokens, which can represent different properties or attributes. They are often used to model complex systems with multiple resources or entities
Timed Petri nets add time intervals to transitions, which can represent the duration of a process or the delay between events. They are often used to model real-time systems.
Stochastic Petri nets add probabilities to transitions, which can represent the likelihood of a process or event occurring. They are often used to model systems with uncertain or random behavior.
P/T nets are the simplest and most widely used type of Petri net. They consist of places, transitions, and arcs, and are often used to model concurrent processes.
