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S N O O P Y

latest update: January 29, 2024, at 10:16 PM

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Please use the following reference to give credits to Snoopy:
M Heiner, M Herajy, F Liu, C Rohr and M Schwarick:
Snoopy – a unifying Petri net tool;
In Proc. PETRI NETS 2012, Hamburg, Springer, LNCS, volume 7347, pp. 398–407, June 2012 (e-link).

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• News
• Downloads
• General Description
• Imports and Exports
• Video clips, Manuals, Tutorials NEW!
• Snoopy's Steering and Simulation Server (S4)
• Web Animation
• Related Software
• Known Issues
• Bug Reports
• Mailing List
• Snoopy's bibliography
• FAQ

News

• 2023-08-17 stable version for Windows (Linux and MACOSX come soon) supporting High-level stochastic simulator for the colored stochastic Petri nets with a prototype implementation.
• 2022-08-27 stable version release for Windows/Linux/MAC supporting Fuzzy coloured stochastic/continuous/hybrid Petri nets, harmonizing the concept of constants in coloured Petri nets as in uncoloured counterparts, new colour operations for coloured Petri nets, supporting obeservers for coloured quantitative Petri nets, the possibility to specify the seed value for stochastic simulation, and fixing many bugs
• 2019-04-24 beta version release for Windows supporting fuzzy stochastic/continuous/hybrid Petri nets; Mac OS X and Linux versions in preparation
• 2017-12-13 bugfix release; among others, bug in rate functions fixed
• 2017-06-19 added PNML import for P/T nets and High-Level Petri nets, added observers to SPN, CPN and HPN, many bugfixes
• 2017-04-18 added attribute fixed to discrete Petri net classes, improved hybrid simulation algorithms, many bugfixes
• 2017-04-03 comprehensive Manual for Coloured Hybrid Petri Nets in Snoopy published
• 2017-01-19 new improved hybrid simulation algorithm, many bugfixes
• 2016-09-30 bugfix release, e.g. andl import, layout generation, error messages
• 2016-07-03 bugfix release
• 2016-06-19 new approximate stochastic simulation method: delta-leaping
• 2016-04-26 update to wxWidgets 3.1, many bugfixes
• 2016-01-15 bugfix release
• 2015-12-21 handling of larger nets (1000+ nodes, 1000+ edges) optimized, new export snoopy2latex, new simulation GUI, source code refactoring, many bugfixes, 64bit versions only
• 2014-04-01 bugfix release
• 2014-01-27 Snoopy’s Steering and Simulation Server (S4) goes online
• 2013-07-30 bugfix release
• 2013-06-20 new constant implementation and several bug fixes
• 2012-04-27 loading of exported simulation data in simulation dialog and several bug fixes
• 2012-01-30 export and import of Colored Abstract Net Description Language (CANDL) and simulation of colored hybrid Petri nets is now available
• 2011-12-02 new netclass colored hybrid Petri nets (simulation is not available yet) and many improvements for colored Petri nets
• 2011-05-19 improvements of handling larger colored Petri nets and several bug fixes again
• 2011-02-18 new net class hybrid (continuous / stochastic) Petri nets
• 2010-12-17 animation of Snoopy files in a web browser now available
• 2010-09-28 new net classes: colored Petri nets, colored stochastic and continuous Petri nets
• 2009-12-02 new net class Freestyle net
• 2009-07-06 new export of stochastic attributes lists to csv
• 2009-06-10 some bugfixes in the stochastic simulation
• 2009-05-26 New stable version of Snoopy
• 2009-03-27 New Export from stochastic Petri nets to PRISM
• 2009-03-06 New PRNG (Mersenne-Twister) for stochastic Simulation
• 2009-02-04 Many bugfixes and small changes regarding the stability of snoopy
• 2008-11-18 Snoopy is now Unicode capable, many bugfixes
• 2008-10-09 New net class MusicNets available, again many bugfixes

Downloads

• Windows version (64bit)
  • snoopy-stable-windows-2023-08-17.msi (PN2024 conference)
  • after download finished double click on the *.msi and the installation starts
  • start snoopy, e.g. by double click on the icon on your desktop
  • if you get an error message about missing msvcp140.dll, please download and install the visual C++ redistributable for visual studio 2015 here
  • if you get an error message about corrupt or invalid signature on snoopy installation file (*.msi), please relate to this.
• Linux version
  • Mint, Arch distributions 20.2 or higher (64bit): snoopy-stable-linux-Mint64-2022-08-27.tgz
  • other linux distributions available on request
  • after download, extract the archive with "tar xzfv snoopy-stable-linux*.tgz"
  • change into the directory "cd snoopy2/bin" and start snoopy by calling "./snoopy2.sh"
• Mac OS X version (10.11+, Intel only, 64bit)
  • snoopy-stable-macosx-intel-2022-08-27.dmg
  • open the dmg and drag Snoopy to your favorite location
  • start Snoopy, e.g. by double click on the name
  • macOS Catalina, error fix for App can’t be opened because it is from an unidentified developer - youTube

For our faithful long-term friends, who want to transfer their PED-files, we provide here a ped2snoopy converter, and some useful hints to use it.

• ped2snoopy for Windows
• ped2snoopy for Linux

Here are some examples to get used to the tool:

• example directory
• general Petri net examples (zip)
• Petri net examples related to biochemical networks (zip)

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There is no all-covering manual available, but you will hopefully not miss it. Anyway, below you find some useful hints (tricks and tips, undocumented features, scheduled extensions, etc) - not supposed to be exhaustive. Please see also Manuals and FAQ.

General Description

Snoopy is a software tool to design and animate hierarchical graphs, among others Petri nets. The tool has been developed - and is still under development - at the University of Technology in Cottbus, Dep. of Computer Science, "Data Structures and Software Dependability".

The tool is in use for the verification of technical systems, especially software-based systems, as well as for the validation of natural systems, i.e. biochemcial networks as metabolic, signal transduction, gene regulatory networks, compare poster "overview on the research activities of our working group".

Basic Properties

• extensible
• generic design facilitates add on of new graph types
• adaptive
• simultaneous use of several graph types
• GUI adopts dynamically to graph type in active window
• platform independent
• implementation: C++, wxWidgets, Xerces
• supported for Windows, Mac OS X and Linux

Main Features

• hierarchies by subgraphs
• logical (fusion) nodes
• different shapes for net elements
• colouring of graph elements (e.g. paths or invariants)
• automated layout by Graphviz library
• digital signature by md5 hash function
• animation of place/transition Petri nets
• simulation of (fuzzy) stochastic/continuous/hybrid Petri nets
• printing support: eps, Xfig, FrameMaker
• import/export from/to analysis tools, see related software
• SBML L2V4 import/export using LibSBML (rules, events, functions not supported)
• PNML support, except export of QPNc in Snoopy to High-Level Petri Nets in PNML
• support of web-based Petri net animation, see sampler
• generation of Latex documentation
• constants multi-column sorting
• cleaning unused declarations (with dependency check)
• selective import/export features from/to ANDL/CANDL formats
• Snoopy command-line feature with a few available commands so far

Available Graph Classes

• place/transition Petri net - QPN
• extended Petri net (read / inhibitor / equal / reset / marking-dependent arcs) - XPN
• time(d) Petri net - TPN
• (extended) stochastic Petri net - XSPN
• continuous Petri net - CPN
• hybrid (continuous & stochastic) Petri nets - HPN
• fuzzy stochastic / continuous / hybrid Petri nets - FSPN / FCPN / FHPN
• coloured fuzzy stochastic / continuous / hybrid Petri nets - FSPNC / FCPNC / FHPNC
• colored qualitative / stochastic / continuous / hybrid Petri nets - QPNc / XSPNc / CPNc / HPNc
• modulo Petri net - MPN
• "music" Petri net
• reachability graph - RG
• MTBDD/MTIDD
• fault tree - FT
• extended fault tree - XFT
• freestyle net
• EDL signature net
• < your favourite graph class ? >

Upcoming

• coloured Petri net classes (as already supported in uncoloured classes)
  • value sets for constants and merging of constants with parameters;
  • general functions
  • marking-dependent arcs;
  • general observers
  • acyclic colour sets
  • export of QPNc to High-Level Petri Nets in PNML

Imports and Exports

All imports and exports to non Snoopy file formats are listed here.

Imports

• ANDL ⇒ QPN, XPN, CPN, XSPN, HPN
• CANDL ⇒ QPNc, XPNc, CPNc, XSPNc, HPNc
• APNN ⇒ QPN, XPN, XSPN
• SBML ⇒ QPN, CPN, XSPN
• PED ⇒ QPN
• PNML ⇒ QPN, QPNc
• TINA ⇒ QPN
• CSV (colored Declarations) ⇒ QPNc, XPNc, CPNc, XSPNc, HPNc
• CSV (Markings, Functions, Parameters) ⇒ XSPN
• DNF ⇒ FT, XFT
• Simulation results in CSV ⇒ CPN, XSPN, HPN, CPNc, XSPNc, HPNc

Exports

• EPS, Latex, MIF, XFig ⇒ all graph classes
• ANDL ⇒ QPN, XPN, CPN, XSPN, HPN
• CANDL ⇒ QPNc, XPNc, CPNc, XSPNc, HPNc
• APNN ⇒ QPN, XPN, XSPN, QPNc, XPNc, CPNc, XSPNc, HPNc
• SBML ⇒ QPN, XPN, CPN, XSPN
• ODEs to Text ⇒ CPN, HPN
• METATOOL ⇒ QPN, XPN, CPN, XSPN
• Modelica ⇒ CPN, XSPN, HPN
• CPNTool ⇒ QPNc, XPNc, XSPNc
• CSV (colored Declarations) ⇒ QPNc, XPNc, CPNc, XSPNc, HPNc
• CSV (Markings, Functions, Parameters) ⇒ XSPN
• SMART ⇒ QPN, XSPN
• INA ⇒ QPN
• LoLA ⇒ QPN
• Maria ⇒ QPN
• PEP ⇒ QPN
• PNML ⇒ QPN
• Prod ⇒ QPN
• TINA ⇒ QPN
• PRISM ⇒ XSPN
• Simulation results in CSV ⇒ CPN, XSPN, HPN, CPNc, XSPNc, HPNc

Video clips, Manuals, Tutorials

Video clips

• Repressilator - fuzzy bands and membership functions over time (wmv) (4.3 MB) (July 15, 2020)
• Tutorial - coloured fuzzy Petri nets in Snoopy (youtube) (July 15, 2020)
• Tutorial - fuzzy Petri nets in Snoopy (mov) (146 MB) (April 30, 2019)

Manuals

• User's manual for coloured fuzzy Petri nets in Snoopy (pdf) (July 15, 2020)
• Mini manual for fuzzy Petri nets in Snoopy (txt) (April 24, 2019)
• [HLRH17.manual]
  M Herajy, F Liu, C Rohr and M Heiner:
  (Coloured Hybrid Petri Nets in Snoopy - User Manual;
  Technical report 01-17, Brandenburg University of Technology Cottbus, Department of Computer Science, March 2017. [ url ] [ BibTeX ] pn sources
• [S15]
  A Sharma:
  Snoopy Report Generator Snoopy2LATEX (Internship report);
  Technical report, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2015. [ pdf ] [ BibTeX ]
• [HH13.manual]
  M Herajy and M Heiner:
  Snoopy Computational Steering Framework – User Manual Version 1.0;
  Technical report 02-13, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2013. [ pdf ] [ BibTeX ]
• [LHR12.manual]
  F Liu, M Heiner and C Rohr:
  Manual for Colored Petri Nets in Snoopy;
  Technical report 02-12, Brandenburg University of Technology Cottbus, Department of Computer Science, March 2012. [ pdf ] [ BibTeX ] pn sources

Tutorials (selection)

• [BHM15]
  MA Blätke, M Heiner and W Marwan:
  BioModel Engineering with Petri Nets;
  In Algebraic and Discrete Mathematical Methods for Modern Biology, (R Robeva, Ed.), Elsevier Inc., pages 141–193, March 2015. [ url ] [ doi ] [ BibTeX ]
• [MRH12]
  W Marwan, C Rohr and M Heiner:
  Petri nets in Snoopy: A unifying framework for the graphical display, computational modelling, and simulation of bacterial regulatory networks;
  In Methods in Molecular Biology – Bacterial Molecular Networks, (Jv Helden, A Toussaint and D Thieffry, Eds.), Humana Press, pages 409–437, 2012. [ pdf ] [ doi ] [ BibTeX ]
• [BHM11]
  MA Blätke, M Heiner, and W Marwan:
  Tutorial - Petri Nets in Systems Biology;
  Technical report, Otto von Guericke University Magdeburg, Magdeburg Centre for Systems Biology, August 2011. [ pdf ] [ BibTeX ]
• for more, see Snoopy's bibliography

Snoopy’s Steering and Simulation Server (S4)

S4 is an extension of Snoopy, which permits to remotely simulate and interactively steer quantitative Petri net models during a running simulation. Users can share models and collaborate by controlling the execution of a model remotely from different machines (clients). S4 is shipped with an application programming interface (API) which enables user-defined extensions of the core functionalities. Stochastic, continuous and hybrid Petri nets are supported, both as low-level and coloured ones. S4 is platform-independent and distributed free of charge for academic use.

Downloads

• S4 (Windows)
• S4 (Mac OS X)

User guides

• quick start and installation note
• product sheet
• manual

References

• [HH14b]
  M Herajy and M Heiner:
  A Steering Server for Collaborative Simulation of Quantitative Petri Nets;
  In Proc. PETRI NETS 2014, Tunis, Springer, LNCS, volume 8489, pages 374–384, June 2014. [ url ] [ doi ] [ BibTeX ]
• [HH14a]
  M Herajy and M Heiner:
  Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks;
  Fundamenta Informaticae, 129(1-2):49-67, 2014. [ url ] [ doi ] [ BibTeX ]
• [Herajy13]
  Mostafa Herajy:
  Computational Steering of Multi-Scale Biochemical Networks;
  PhD thesis, BTU Cottbus, Dep. of CS, January 2013. [ pdf ] [ BibTeX ]
• [HH12]
  M Herajy and M Heiner:
  Hybrid Representation and Simulation of Stiff Biochemical Networks;
  J. Nonlinear Analysis: Hybrid Systems, 6(4):942–959, November 2012. [ url ] [ doi ] [ BibTeX ]

Web Animation

We support web browser animation of Snoopy files (extended Petri nets only). Therefor we use XSL transformation to SVG and JavaScript for animation. Download: patty.zip

Installation notes:

• Unpack patty.zip into the root folder of your web server.
• Copy your Snoopy files on your web server.
• Add the Snoopy files to the type text/xml, e.a. add the line "AddType text/xml spept spped" to your .htaccess file.
• If that is not possible rename the files from "filename.spped" to "filename.xml".
• Now you can open your Snoopy files in your browser basicStructures.pn.

Attention: Web browsers are constantly evolving and often differ in some subtle details. It is hardly possible to master this vast variety at the current state of technology. For known bugs see sampler.

This feature is based on:

• [Schw09]
  Marcel Schwarze:
  Web-based Petri net animation (in German);
  Diploma thesis, FH Lausitz, Dep. of CS, November 2009. [ BibTeX ]
• [Schu08]
  Krispin Schulz:
  An Extension of the Snoopy Software to Process and Manage Petri Net Animations (in German);
  Bachelor thesis, BTU Cottbus, Dep. of CS, November 2008. [ pdf ] [ BibTeX ]

Related Software

• Abstract Petri Net Notation (APNN)
• ADAM - Analysis of Dynamic Algebraic Models, see [HBG+11]
• Charlie
• INA - Integrated Net Analyzer
• LoLA - Low Level Petri net Analyzer
• Marcie - Model checking And Reachability analysis done effiCIEntly
• Maria - The Modular Reachability Analyzer
• MC2(PLTLc) - a Monte Carlo Model Checker for PLTLc
• McKit - The Model-Checking Kit
• METATOOL
• PEP - Programming Environment based on Petri Nets (export of low level nets without layout)
• PInA
• PRISM - probabilistic symbolic model checker
• PROD - An Advanced Tool for Efficient Reachability Analysis
• SBML Level 2 Version 3
• SBML Software Matrix
• TINA - TIme petri Net Analyzer

Known Issues

• The following three issues are caused by (current state of) the wxWidgets library
  • Mac OS: the key shortcut 'cmd-C' is used twice: for copy in text fields and as accelerator for the cancel button, with cancel button overwriting the former functionality. intermediate solution: use cmd-X followed by cmd-V instead.
  • Linux: shortcuts to select net elements (such as P, T, A, S) don't work;
  • Retina display: support is buggy, that’s why it’s in Snoopy disabled;
• PNML: Snoopy does not support acyclic colour sets (sorts), ie all colour sets (sorts) are cyclic in Snoopy. Please check your imported High-Level Petri Nets.
• The colour operator "--" is only supported by the Generic and Gecode unfolders, but not by the IDD unfolder.
• The colour operator 'numOf' is only supported by Snoopy. However, unfolding colour expressions involving this operator is not appropriately implemented. Snoopy Animator gives a the expected behaviour, but the unfolded net is not correct.
• Unfolding sophisticated arc colour expressions involving the operator "++" using the IDD unfolder may result in unexpected results due to a bug in the implementation of the IDD unfolder, so please use the Genereic/Gecode unfolders in this case.
• Unfolding colour expressions involving nested colour functions (for coloured Petri nets) is only supported by the Geneeric/Gecode unfolders, but not by the IDD unfolder.
• Unfolding sophisticated tuple colour expressions involving the pre-define function "all()" is only supported by the Generic/Gecode unfolders, so please do not use the IDD unfolder.

Bug Reports

Submit your bug reports and comments about Snoopy HERE.

• Please check, if your problem still exists in the latest available version of Snoopy
• Please include the information about your platform (Windows, Linux) and Snoopy build details (available in the Help->About window)

Mailing List

You can join our mailing list if you want to kept posted of Snoopy's development: snoopy [period] informatik [snail] lists [period] b-tu [period] de

This mailing list is for discussion of new features, bug reports, and for announcements of new Snoopy versions.

For joining our mailing list write an email to snoopy [period] informatik-join [snail] lists [period] b-tu [period] de (both the Subject: header and body of such a message are ignored).

For leaving our mailing list you may send an email to snoopy [period] informatik-leave [snail] lists [period] b-tu [period] de (as with the -join address, the Subject: header and body of the message is ignored).

Another way you can subscribe to or unsubscribe from the list is through the web interface.