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Snoopy's bibliography - Tool Related Papers

latest update: February 20, 2019, at 03:01 PM

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, 398–407, June 2012

This list contains Snoopy-related papers, authored or co-authored by (current / former) members of Snoopy's development team. The papers explain Snoopy and its special features, some of them by using Snoopy for case studies.

2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008 - 2007 - 2006 -2005 - 2004 - 2003

2014

• [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 ]
• [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 ]
• [LH14]
  F Liu and M Heiner:
  Petri Nets for Modeling and Analyzing Biochemical Reaction Networks;
  In Approaches in Integrative Bioinformatics, (M Chen and R Hofestädt, Eds.), Springer, pages 245–272, 2014. [ url ] [ pdf ] [ doi ] [ BibTeX ]
• [LHY14]
  F Liu, M Heiner and M Yang:
  Modeling and analyzing biological systems using colored hierarchical Petri nets, illustrated by C. elegans vulval development;
  WSPC Journal of Biological Systems, 22(3):463–493, online May 2014. [ doi ] [ BibTeX ]

2013

• [BDR+13]
  MA Blätke, A Dittrich, C Rohr, M Heiner, F Schaper and W Marwan:
  JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology;
  Molecular BioSystems, 9(6):1290-1307, 2013. [ url ] [ doi ] [ BibTeX ]
• [GGH+13]
  Q Gao, D Gilbert, M Heiner, F Liu, D Maccagnola and D Tree:
  Multiscale Modelling and Analysis of Planar Cell Polarity in the Drosophila Wing;
  IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(2):337-351, 2013 (online: August 01, 2012). [ doi ] [ BibTeX ]
• [GHLS13]
  D Gilbert, M Heiner, F Liu and N Saunders:
  Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology;
  In Proc. PETRI NETS 2013, Milano, Springer, LNCS, volume 7927, pages 230–249, June 2013. [ url ] [ doi ] [ BibTeX ]
• [HG13]
  M Heiner and D Gilbert:
  BioModel Engineering for Multiscale Systems Biology;
  Progress in Biophysics and Molecular Biology, 111(2-3):119–128, April 2013 (online: October 12, 2012). [ url ] [ doi ] [ 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 ]
• [HSH13]
  M Herajy, M Schwarick and M Heiner:
  Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle;
  ToPNoC VIII, LNCS 8100, 2013. [ pdf ] [ doi ] [ BibTeX ]
• [LH13a]
  F Liu and M Heiner:
  Modeling membrane systems using colored stochastic Petri nets;
  Nat. Computing, 12(4):617 - 629, 2013. [ url ] [ doi ] [ BibTeX ]
• [LH13b]
  F Liu and M Heiner:
  Multiscale modelling of coupled Ca2+ channels using coloured stochastic Petri nets;
  IET Systems Biology, 7(4):106 - 113, August 2013. [ doi ] [ BibTeX ]
• [LHY13]
  F Liu, M Heiner and M Yang:
  Colored Petri Nets for Multiscale Systems Biology – Current Modeling and Analysis Capabilities in Snoopy;
  In Proc. 7th International Conference on Systems Biology (ISB 2013), Huangshan/China, IEEE, pages 24 - 30, August 2013. [ url ] [ doi ] [ BibTeX ]
• [PGH+13]
  O Parvu, D Gilbert, M Heiner, F Liu and N Saunders:
  Modelling and Analysis of Phase Variation in Bacterial Colony Growth;
  In Proc. CMSB 2013, Vienna, Springer, LNCS/LNBI, volume 8130, pages 78–-91, September 2013. [ doi ] [ BibTeX ]

2012

• [BDH+12]
  MA Blätke, A Dittrich, M Heiner, F Schaper and W Marwan:
  JAK-STAT Signalling as Example for a Database-Supported Modular Modelling Concept;
  In Proc. 10th International Conference on Computational Methods in Systems Biology (CMSB 2012), London, Springer, LNCS/LNBI, volume 7605, pages 362–365, 2012. [ url ] [ doi ] [ BibTeX ]
• [BHM12]
  MA Blätke, M Heiner and W Marwan:
  Predicting Phenotype from Genotype Through Automatically Composed Petri Nets;
  In Proc. 10th International Conference on Computational Methods in Systems Biology (CMSB 2012), London, Springer, LNCS/LNBI, volume 7605, pages 87–106, 2012. [ url ] [ doi ] [ 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 ]
• [HH12.csp]
  M Herajy and M Heiner:
  Towards a Computational Steering and Petri Nets Framework for the Modelling of Biochemical Reaction Networks;
  In Proc. International Workshop on Concurrency, Specification, and Programming (CSP 2012), CEUR-WS.org, CEUR Workshop Proceedings, volume 928, pages 147–159, September 2012. [ url ] [ pdf ] [ BibTeX ]
• [HH+12]
  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, 398–407, June 2012. [ url ] [ doi ] [ BibTeX ]
• [HS12]
  M Herajy and M Schwarick:
  A Hybrid Petri Net Model of the Eukaryotic Cell Cycle;
  In Proc. of the 3rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2012, CEUR-WS.org, CEUR Workshop Proceedings, volume 852, pages 29-43, June 2012. [ url ] [ 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 ]
• [LHY12]
  F Liu, M Heiner and M Yang:
  An efficient method for unfolding colored Petri nets;
  In Proceedings of the 2012 Winter Simulation Conference (WSC 2012), Berlin, IEEE, 978-1-4673-4781-5/12, 2012. [ url ] [ pdf ] [ BibTeX ]
• [Liu12]
  Fei Liu:
  Colored Petri Nets for Systems Biology;
  PhD thesis, BTU Cottbus, Dep. of CS, January 2012. [ pdf ] [ 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 ]

2011

• [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 ]
• [GLG+11]
  Q Gao, F Liu, D Gilbert, M Heiner and D Tree:
  A Multiscale Approach to Modelling Planar Cell Polarity in Drosophila Wing using Hierarchically Coloured Petri Nets;
  In Proc. 9th International Conference on Computational Methods in Systems Biology (CMSB 2011), Paris, ACM digital library, pages 209–218, September 2011. [ url ] [ pdf ] [ BibTeX ]
• [HH11]
  M Herajy and M Heiner:
  Hybrid Representation and Simulation of Stiff Biochemical Networks through Generalised Hybrid Petri Nets;
  Technical report 02-11, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2011. [ pdf ] [ BibTeX ]
• [LH11]
  F Liu and M Heiner:
  Manual for Colored Petri Nets in Snoopy;
  Technical report, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2011. [ pdf ] [ BibTeX ]
• [SRH11]
  M Schwarick , C Rohr and M Heiner:
  MARCIE - Model checking And Reachability analysis done effiCIEntly;
  In Proc. 8th International Conference on Quantitative Evaluation of SysTems (QEST 2011), Aachen, Germany, IEEE CS Press, pages 91–100, September 2011. [ url ] [ pdf ] [ BibTeX ]
• [HRS11]
  M Heiner, C Rohr and M Schwarick:
  Petri net based system analysis;
  Poster, 2011. [ pdf ] [ BibTeX ]

2010

• [GHBO10]
  D Gilbert, M Heiner, R Breitling and R Orton:
  Computation modelling of kinase signalling cascades;
  In MAP Kinase Signaling Protocols, (R Seger, Ed.) Pages 369–384, 2010. [ url ] [ doi ] [ BibTeX ]
• [HDG10]
  M Heiner, R Donaldson and D Gilbert:
  Petri Nets for Systems Biology;
  In Symbolic Systems Biology: Theory and Methods, (MS Iyengar, Ed.), Jones & Bartlett Learning, LCC, pages 61–97, 2010. [ url ] [ pdf ] [ BibTeX ]
• [HH10]
  M Herajy and M Heiner:
  Hybrid Petri Nets for Modelling of Hybrid Biochemical Interactions;
  In Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), CEUR-WS.org, CEUR Workshop Proceedings, volume 643, pages 66–79, October 2010. [ pdf ] [ BibTeX ]
• [HMS10]
  M Heiner, C Mahulea and M Silva:
  On the Importance of the Deadlock Trap Property for Monotonic Liveness;
  In Int. Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2010, Braga, Portugal, pages 39-54, June 2010. [ pdf ] [ BibTeX ]
• [HRSS10]
  M Heiner, C Rohr, M Schwarick and S Streif:
  A Comparative Study of Stochastic Analysis Techniques;
  In Proc. 8th International Conference on Computational Methods in Systems Biology (CMSB 2010), Trento, ACM digital library, pages 96–106, September 2010. [ pdf ] [ doi ] [ BibTeX ]
• [HS10]
  M Heiner and K Sriram:
  Structural Analysis to Determine the Core of Hypoxia Response Network;
  PLoS ONE, 5(1):e8600, 2010. [ doi ] [ BibTeX ]
• [LH10]
  F Liu and M Heiner:
  Colored Petri nets to model and simulate biological systems;
  In Int. Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2010, Braga, Portugal, pages 70-84, June 2010. [ pdf ] [ BibTeX ]
• [LH10b]
  F Liu and M Heiner:
  Computation of Enabled Transition Instances for Colored Petri Nets;
  In Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), CEUR-WS.org, CEUR Workshop Proceedings, volume 643, pages 51–65, October 2010. [ pdf ] [ BibTeX ]
• [RMH10]
  C Rohr, W Marwan and M Heiner:
  Snoopy - a unifying Petri net framework to investigate biomolecular networks;
  Bioinformatics, 26(7):974–975, 2010 ((Advanced Access: February 7, 2010)). [ url ] [ doi ] [ BibTeX ]
• [Rohr10]
  C Rohr:
  Simulative CSL model checking of Stochastic Petri nets in IDD-MC;
  In Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), CEUR-WS.org, CEUR Workshop Proceedings, volume 643, pages 88–93, October 2010. [ pdf ] [ BibTeX ]

2009

• [H09]
  M Heiner:
  Understanding Network Behaviour by Structured Representations of Transition Invariants – A Petri Net Perspective on Systems and Synthetic Biology;
  In Algorithmic Bioprocesses, (A Condon, D Harel, JN Kok, A Salomaa and E Winfree, Eds.), Springer, pages 367–389, 2009. [ url ] [ pdf ] [ doi ] [ BibTeX ]
• [HLGM09]
  M Heiner, S Lehrack, D Gilbert and W Marwan:
  Extended Stochastic Petri Nets for Model-based Design of Wetlab Experiments;
  Transactions on Computational Systems Biology XI, 5750:138–163, 2009. [ url ] [ pdf ] [ doi ] [ BibTeX ]
• [HST09]
  M Heiner, M Schwarick and A Tovchigrechko:
  DSSZ-MC – A Tool for Symbolic Analysis of Extended Petri Nets;
  In Proc. PETRI NETS 2009, Paris, Springer, LNCS, volume 5606, pages 323–332, June 2009. [ url ] [ pdf ] [ doi ] [ BibTeX ]
• [Liu09.manual]
  F Liu:
  Manual for Snoopy2Prism Export;
  Technical report, Brandenburg University of Technology Cottbus, Department of Computer Science, March 2009. [ pdf ] [ BibTeX ]
• [Schw09]
  Marcel Schwarze:
  Web-based Petri net animation (in German);
  Diploma thesis, FH Lausitz, Dep. of CS, November 2009. [ BibTeX ]
• [SH09]
  M Schwarick and M Heiner:
  CSL model checking of biochemical networks with Interval Decision Diagrams;
  In Proc. 7th International Conference on Computational Methods in Systems Biology (CMSB 2009), Bologna, Italy, Springer, LNCS/LNBI, volume 5688, pages 296–312, September 2009. [ url ] [ pdf ] [ doi ] [ BibTeX ]

2008

• [Bayer08]
  Denny Bayer:
  Testing with Music (in German);
  Bachelor thesis, BTU Cottbus, Dep. of CS, September 2008. [ pdf ] [ BibTeX ]
• [BGHO08]
  R Breitling, D Gilbert, M Heiner and R Orton:
  A structured approach for the engineering of biochemical network models, illustrated for signalling pathways;
  Briefings in Bioinformatics, 9(5):404–421, September 2008. [ doi ] [ BibTeX ]
• [GHR+08]
  D Gilbert, M Heiner, S Rosser, R Fulton, X Gu and M Trybio:
  A Case Study in Model-driven Synthetic Biology;
  In IFIP WCC 2008, 2nd IFIP Conference on Biologically Inspired Collaborative Computing (BICC 2008), Milano, Springer, IFIP, volume 268, pages 163–175, September 2008. [ url ] [ pdf ] [ BibTeX ]
• [GSH+08]
  E Grafahrend-Belau, F Schreiber, M Heiner, A Sackmann, BH Junker, S Grunwald, A Speer, K Winder and I Koch:
  Modularization of biochemical networks based on classification of Petri net T-invariants;
  BMC Bioinformatics, 9:90, 2008. [ doi ] [ BibTeX ]
• [HGD08]
  M Heiner, D Gilbert and R Donaldson:
  Petri Nets for Systems and Synthetic Biology;
  In SFM 2008, (M Bernardo, P Degano and G Zavattaro, Eds.), Springer, pages 215–264, 2008. [ pdf ] [ doi ] [ BibTeX ]
• [HRRS08]
  M Heiner, R Richter, C Rohr and M Schwarick:
  Snoopy – A Tool to Design and Animate/Simulate Graph-Based Formalisms;
  In Petri Net Newsletter, GI, pages 8–22, April 2008 (This paper is an extended version of Proc. PNTAP 2008). [ pdf ] [ BibTeX ]
• [KH08]
  I Koch and M Heiner:
  Petri Nets;
  In Biological Network Analysis, (BH Junker and F Schreiber, Eds.), John Wiley & Sons, pages 139–179, 2008 (Series Eds. Yi Pan, Albert Y. Zomaya). [ url ] [ BibTeX ]
• [HRS08]
  M Heiner, R Richter and M Schwarick:
  Snoopy - A Tool to Design and Animate/Simulate Graph-Based Formalisms;
  In Proc. International Workshop on Petri Nets Tools and APplications (PNTAP 2008, associated to SIMUTools 2008), ACM digital library, 2008. [ url ] [ pdf ] [ 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 ]

2007

• [Dube07]
  Matthias Dube:
  Development and Realisation of a General Concept for Interactions between two Net Classes in Snoopy (in German);
  Diploma thesis, BTU Cottbus, Dep. of CS, February 2007. [ BibTeX ]
• [HRS07]
  M Heiner, R Richter and M Schwarick:
  Snoopy - A Tool to Design and Animate/Simulate Graph-Based Formalisms;
  In Proc. AWPN Workshop, Koblenz, Sept. 2007, pages 8-13, 2007. [ url ] [ pdf ] [ BibTeX ]
• [Kurth07]
  Anja Kurth:
  Fault trees in Snoopy (in German);
  Diploma thesis, BTU Cottbus, Dep. of CS, January 2007. [ BibTeX ]
• [Lehr07]
  Sebastian Lehrack:
  A Modelling and Simulation Tool for Stochastic Petri Nets Models of Biochemical Networks (in German);
  Diploma thesis, BTU Cottbus, Dep. of CS, November 2007. [ pdf ] [ BibTeX ]

2006

• [GH06]
  Gilbert, D. and Heiner, M.:
  From Petri nets to differential equations - an integrative approach for biochemical network analysis;
  In Proc. ICATPN 2006, LNCS 4024, Springer, pages 181–200, 2006. [ url ] [ pdf ] [ BibTeX ]
• [Lehr06]
  S Lehrack:
  Three Petri net approaches for Biochemical Network Analysis;
  Technical report I-01/2006, Brandenburg University of Technology Cottbus, Department of Computer Science, July 2006. [ pdf ] [ BibTeX ]
• [Sche06]
  Daniel Scheibler:
  A Tool to Design and Simulate continuous Petri Nets (in German);
  Diploma thesis, BTU Cottbus, Dep. of CS, January 2006. [ pdf ] [ BibTeX ]
• [SHK06]
  A Sackmann, M Heiner and I Koch:
  Application of Petri net based analysis techniques to signal transduction pathways;
  BMC Bioinformatics 2006, 7:482, 2006. [ url ] [ doi ] [ BibTeX ]
• [Wind06]
  Katja Winder:
  Invariant-supported Petri Net Structuring (in German);
  Diploma thesis, BTU Cottbus, Dep. of CS, January 2006. [ pdf ] [ BibTeX ]

2005

• [Dube05]
  Matthias Dube:
  Signing and Verifying SNOOPY-files;
  Student thesis, BTU Cottbus, Dep. of CS, March 2005. [ pdf ] [ BibTeX ]
• [GH05]
  D Gilbert and M Heiner:
  From Petri Nets to Differential Equations - an Integrative Approach for Biochemical Network Analysis;
  Technical report I-04/2005, Brandenburg University of Technology Cottbus, Department of Computer Science, December 2005. [ pdf ] [ BibTeX ]
• [KJH05]
  I Koch, BH Junker and M Heiner:
  Application of Petri Net Theory for Modelling and Validation of the Sucrose Breakdown Pathway in the Potato Tuber;
  Bioinformatics, April 2005, 21:1219 - 1226, 2005. [ doi ] [ BibTeX ]
• [PHK05]
  L Popova-Zeugmann, M Heiner and I Koch:
  Time Petri Nets for Modelling and Analysis of Biochemical Networks);
  Fundamenta Informaticae, 67:149–162, 2005. [ url ] [ pdf ] [ BibTeX ]
• [SHK05]
  A Sackmann, M Heiner and I Koch:
  Modelling signal transduction pathways of yeast with Petri nets, European Conference on Mathematical and Theoretical Biology (ECMTB 2005), Dresden/Germany, July 2005;
  Poster, 2005. [ pdf ] [ BibTeX ]

2004

• [Fieb04]
  Markus Fieber:
  Entwurf und Implementierung eines generischen, adaptiven Werkzeugs zur Arbeit mit Graphen (in German);
  Diploma thesis, BTU Cottbus, Dep. of CS, July 2004. [ pdf ] [ BibTeX ]
• [HK04]
  M Heiner and I Koch:
  Petri Net Based System Validation in Systems Biology;
  In Proc. ICATPN 2004, Bologna, June, Springer, LNCS, volume 3099, pages 216-237, 2004. [ pdf ] [ doi ] [ BibTeX ]
• [HKW04]
  M Heiner, I Koch and J Will:
  Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis;
  BioSystems, 75/1-3:15-28, 2004. [ pdf ] [ doi ] [ BibTeX ]
• [Neum04]
  Gerry Neumann:
  Modelling of Biochemical Processes with Petri Nets; Hemostasis vs. Fibrinolysis vs. Inhibitors (in German);
  Diploma thesis, BTU Cottbus, Dep. of CS, July 2004. [ pdf ] [ BibTeX ]

2003

• [Fieb03]
  Markus Fieber:
  Snoopy: Ein generisches, adaptives Werkzeug für Graphen (in German);
  Study thesis, BTU Cottbus, Dep. of CS, January 2003. [ pdf ] [ BibTeX ]
• [HKW03]
  M Heiner, I Koch and J Will:
  Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis;
  In Proc. First Int. Workshop on Computational Methods in Systems Biology (CMSB 2003), Rovereto, Febr. 2003, Springer, LNCS, volume 2602, page 173, 2003. [ pdf ] [ doi ] [ BibTeX ]
• Pagnoni, Visconti, Russo:
  SIGNET: A Tool for Securing Complex Petri Net Projects; November 2003
• M. Heiner:
  Authenticated Petri Nets - motivation for an integrated security component, March 2003.