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.

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

2. Objectives of Snoopy
1. Graphical Display
2. Computational Modelling
3. Simulation of bacterial regulatory networks
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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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5. Representations
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Figure 2: Illustrations of components used in modelling a peri network

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

9. 3:Timed Petri Nets
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Figure 5: Generic timed petri-net representation

10. 4: Stochastic Petri Nets
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Figure 6:

11. 5: Fuzzy Petri Nets
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Figure 7: A unifying Petri net framework representing fuzzy petri nets

12. Demonstration
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Figure 8: Snoopy GUI

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3
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Figure 8: Snoopy GUI

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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15. Reference Paper
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