Snoopy: a tool to design and animate/simulate graph-based formalisms

Abstract

We sketch the fundamental properties and features of Snoopy, a tool to model and execute (animate, simulate) hierarchical graph-based system descriptions. The tool comes along with several pre-fabricated graph classes, especially some kind of Petri nets and other related graphs, and facilitates a comfortable integration of further graph classes due to its generic design.To support an aspect-oriented model engineering, different graph classes may be used simultaneously. Snoopy provides some features (hierarchical nodes, logical nodes), which are particularly useful for larger models, or models with an higher connectivity degree.There are several Petri net classes available, among them the purely qualitative place/transition nets in its standard definition and in a version enhanced by four special arcs as well as two quantitative extensions of it -stochastic Petri nets and continuous Petri nets. Each of these classes enjoys dedicated animation or simulation features.Our tool runs on Windows and Linux operating systems, and it is available free of charge for non-commercial use. Categories and Subject Descriptors D.2.2 [Software Engineering]: Design Tools and Techniques-State diagrams, Petri nets General Terms Model Creation and ExecutionKeywords editor, animator, simulator, numerical integration algorithms, qualitative and quantitative Petri nets.Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. International Workshop on Petri Nets Tools and APplications PRELIMINARIESThe support by tools is a necessary condition for the acceptance of a formalism. The perspective from various abstraction levels by several models of different expressive strength is a crucial point for a sophisticated evaluation of a system under investigation, technical or natural ones.In this paper, we present Snoopy [35], a generic and adaptive tool for modelling and animating/simulating hierarchical graph-based formalisms. While concentrating our development as far on several kinds of Petri nets and related graph classes, the generic design of Snoopy facilitates also a comfortable extension by new graph classes.The simultaneous use of several graph classes is supported by the dynamic adaptation of the graphical user interface to the active one. So it is possible to treat qualitative and quantitative models of the system under investigation side by side.For example you can start with a qualitative Petri net model and increase first your confidence in the net behaviour by animating it, i.e. playing the token game, before checking some essential properties using external analysis tools. Later you can easily move on to related quantitative models, deterministically timed, stochastic or co...

Understanding Network Behavior by Structured Representations of Transition Invariants

“…The case studies have been done using Snoopy [18,45]-a tool to design and animate or simulate hierarchical graphs, among them the qualitative Petri nets as used in this paper. Snoopy provides export to various analysis tools as well as import and export of the Systems Biology Markup Language (SBML) [13].…”

DSSZ-MC – A Tool for Symbolic Analysis of Extended Petri Nets

“…APNN has been adapted to allow the specification of the non-standard arc types. The input format can be generated, e.g., by the export feature of our hierarchical Petri net editor Snoopy [HRS08] which supports standard place/transition Petri nets as well as the extended Petri net class. All analyses supported by DSSZ-MC involve the construction of the state space, so the models have to be bounded.…”

Design and development of software tools for Bio-PEPA

“…However, they also do not support direct state-space based CTMC analyses and for ODE analyses they have to reduce rule-based models to the level of Bio-PEPA models, where all different types of molecules are explicitly known at the beginning of the simulation. The Stochastic Pi Machine (Phillips 2009), BIOCHAM (Fages and Soliman 2008) and the Petri-net based tool Snoopy (Heiner et al 2008) are other related simulation environments for biochemical systems that differ in their syntax, semantics and specific model analysis capabilities. SPiM is a process algebra that supports the dynamic opening of new "communication channels" between molecules (the basic property that makes rule-based modelling possible and direct ODE analysis impossible), BIOCHAM is another rule-based reaction-style modelling language and Snoopy relies on the graphical representation of Petri-nets to describe models (as opposed to the textual representations of process algebras).…”