Selected References - Papers

2010    2009    2008    2007    2006    2005    2004    2003    2002    2001    2000    1999    1998    1997    1996    1995    1994    1992    Index

  2010

S Soliman, M Heiner:
A Unique Transformation from Ordinary Differential Equations to Reaction Networks;
PLoS ONE 5(12): e14284, December 2010.

F Liu, M Heiner:
Computation of Enabled Transition Instances for Colored Petri Nets;
Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), volume 643 of CEUR Workshop Proceedings, CEUR-WS.org, pp. 51-65, October 2010.

M Herajy, M Heiner:
Hybrid Petri Nets for Modelling of Hybrid Biochemical Interactions;
Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), volume 643 of CEUR Workshop Proceedings, CEUR-WS.org, pp. 66-79, October 2010.

M Schwarick:
IDD-MC - a model checker for bounded stochastic Petri nets;
Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), volume 643 of CEUR Workshop Proceedings, CEUR-WS.org, pp. 80-87, October 2010.

C Rohr:
Simulative CSL model checking of Stochastic Petri nets in IDD-MC;
Proc. 17th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2010), volume 643 of CEUR Workshop Proceedings, CEUR-WS.org, pp. 88-93, October 2010.

M Heiner, C Rohr, M Schwarick, S Streif:
A Comparative Study of Stochastic Analysis Techniques;
Proc. 8th International Conference on Computational Methods in Systems Biology (CMSB 2010), Trento, ACM digital library, pp. 96-106, September 2010.

M Schwarick, A Tovchigrechko:
IDD-based model validation of biochemical networks;
Theoretical Computer Sience, doi:10.1016/j.tcs.2010.06.030, Juli 2010.

M Heiner, C Mahulea, M Silva:
On the Importance of the Deadlock Trap Property for Monotonic Liveness;
Int. Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2010, Braga, Portugal, pp. 39-54, June 21 2010.

F Liu, M Heiner:
Colored Petri nets to model and simulate biological systems;
Int. Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2010, Braga, Portugal, pp, 70-84, June 21 2010.

C Rohr, W Marwan, M Heiner:
Snoopy - a unifying Petri net framework to investigate biomolecular networks;
Bioinformatics 2010 26(7): 974-975 (Advanced Access published February 7, 2010).

R Breitling, RA Donaldson, DR Gilbert, M Heiner:
Biomodel Engineering - From Structure to Behavior (position paper);
Trans. on Computational Systems Biology XII, Special Issue on Modeling Methodologies, Springer LNCS/LNBI 5945, pp. 1-12, 2010.

M Heiner, K Sriram:
Structural Analysis to Determine the Core of Hypoxia Response Network;
PLoS ONE 5(1): e8600, January 2010.

  2009

M Heiner, S Lehrack, D Gilbert, W Marwan:
Extended Stochastic Petri Nets for Model-based Design of Wetlab Experiments;
Trans. on Computational Systems Biology XI, Springer LNCS/LNBI 5750, pp. 138-163, 2009.

M Schwarick, M Heiner:
CSL model checking of biochemical networks with Interval Decision Diagrams;
Proc. 7th International Conference on Computational Methods in Systems Biology (CMSB 2009), Bologna, September 2009, Springer LNCS/LNBI 5688, pp. 296-312.

M Heiner, M Schwarick, A Tovchigrechko:
DSSZ-MC - A Tool for Symbolic Analysis of Extended Petri Nets;
Proc. PETRI NETS 2009, Paris, June 2009, Springer LNCS 5606, pp. 323-332.

D Gilbert, R Breitling, M Heiner, R Donaldson:
An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways;
Proc. 9th International Workshop on Membrane Computing (WMC 2008), Springer LNCS 5391, pp. 13-28, 2009.

  2008

M Schwarick:
Transient Analysis of Stochastic Petri Nets With Interval Decision Diagrams;
Proc. 15th German Workshop on Algorithms and Tools for Petri Nets (AWPN 2008), volume 380 of CEUR Workshop Proceedings, pp. 43-48. CEUR-WS.org, September 2008.

D Gilbert, M Heiner, S Rosser, R Fulton, X Gu, M Trybilo:
A Case Study in Model-driven Synthetic Biology;
IFIP WCC 2008, 2nd IFIP Conference on Biologically Inspired Collaborative Computing (BICC 2008),  Milano, Sept. 2008, Springer Boston, IFIP, Vol . 268, pp. 163-175, 2008.

R Breitling, D Gilbert, M Heiner, R Orton:
A structured approach for the engineering of biochemical network models, illustrated for signalling pathways;
Briefings in Bioinformatics, September 2008; 9: 404 - 421.

M Heiner, R Richter, C Rohr, M Schwarick:
Snoopy - A Tool to Design and Execute Graph-Based Formalisms. [Extended Version]
Petri Net Newsletter 74 (April 2008) ISSN 0931-1084, pp. 8-22.
This paper is an extended version of Proc. PNTAP 2008 (associated to SIMUTools 2008), Marseille, ACM digital library, ISBN 978-963-9799-20-2, March 2008.

M Heiner, R Richter, M Schwarick:
Snoopy - A Tool to Design and Animate/Simulate Graph-Based Formalisms;
Proc. International Workshop on Petri Nets Tools and APplications (PNTAP 2008, associated to SIMUTools 2008), Marseille, ACM digital library, ISBN 978-963-9799-20-2, March 2008.  abstract

E Grafahrend-Belau, F Schreiber, M Heiner, A Sackmann, BH Junker, S Grunwald, A Speer, K Winder, I Koch:
Modularization of biochemical networks based on classification of Petri net T-invariants;
BMC Bioinformatics 2008, 9:90.

  2007

M Heiner, R Richter, M Schwarick:
Snoopy - A Tool to Design and Animate/Simulate Graph-Based Formalisms;
Proc. AWPN Workshop, Koblenz, pp. 8-13, September 2007.

L Popova, M Heiner:
Quantitative Evaluation of Time Petri Nets and Applications to Technical and Biochemical Networks;
Proc. International Workshop on Concurrency, Specification and Programming (CS&P 2007), Lagów, September 2007, vol. 2, pp. 473-484.  abstract

D Gilbert, M Heiner, S Lehrack:
A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets;
Proc. 5th International Conference on Computational Methods in Systems Biology (CMSB 2007), Edinburgh, September, Springer LNCS/LNBI 4695, pp. 200-216.
This paper is a short version of  Techn. Report I-02/2007, BTU Cottbus, July 2007. abstract

  2006

A Sackmann, M Heiner,  I Koch:
Application of Petri net based analysis techniques to signal transduction pathways;
BMC Bioinformatics 2006, 7:482. abstract

D Gilbert, M Heiner:
From Petri Nets to Differential Equations - an Integrative Approach for Biochemical Network Analysis;
Proc. ICATPN 2006, Turku, June, Springer LNCS 4024, pp. 181-200.
This paper is a short version of  Techn. Report I-04/2005, BTU Cottbus, July 2007 abstract

  2005

L Popova-Zeugmann, M Heiner, I Koch:
Time Petri Nets for Modelling and Analysis of Biochemical Networks;
Fundamenta Informaticae 67 (2005) 149–162. abstract

I Koch, BH Junker, 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 (Advance Access published November 16, 2004). abstract

  2004

I Koch, M Schüler, M Heiner:
STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks;
In Silico Biology 5, 0014 (2004). abstract

T Runge:
Application of Coloured Petri Nets in Systems Biology;
Proc. 5th Workshop CPN, Univ. of Aarhus, October 2004, pp. 77–95. abstract

M Heiner, I Koch:
Petri Net Based System Validation in Systems Biology;
Proc. ICATPN 2004, Bologna, June, Springer LNCS 3099, pp. 216 - 237. abstract

M Heiner, I Koch, J Will:
Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis;
BioSystems 2004, Vol 75/1-3, pp. 15-28. abstract

  2003

K Voss, M Heiner, I Koch:
Steady State Analysis of Metabolic Pathways Using Petri Nets;
In Silico Biology 3, 0031 (2003) abstract

M Heiner, I Koch, J Will:
Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis;
Proc. First Int. Workshop on Computational Methods in Systems Biology (CMSB 2003), Rovereto, Febr. 2003, Springer LNCS 2602, p. 173.

  2002

J Will, M Heiner:
Petri Nets in Biology, Chemistry, and Medicine - Bibliography;
Computer Science Reports 04/02, BTU Cottbus, ISSN 1437-7969, Nov. 2002, 36 p. abstract

T Rottke, D Hatebur, M Heisel, M Heiner:
A Problem-Oriented Approach to Common Criteria Certification;
Proc. SafeComp ’02, Catania, Sept. 2002, Springer LNCS 2434, pp. 334 - 346. abstract

  2001

M Heiner, I Koch, K Voss:
Analysis and Simulation of Steady States in Metabolic Pathways with Petri Nets;
Proc. Third Workshop CPN, Univ. of Aarhus, Aug. 2001, pp. 15 - 34.
improved version in Voss, K.; Heiner, M.; Koch, I. (2003).

P Deussen:
Partial Order Verification of Programmable Logic Controllers;
Proc. 22nd International Conference, ICATPN 2001, Newcastle upon Tyne, Juni 2001, Springer LNCS 2075,  pp. 144 - 163.

M Heiner, T Mertke, P Deussen:
A Safety-Oriented Technical Language for the Requirement Specification in Control Engineering (in German, Eine Sicherheitsfachsprache zur Formulierung steuerungstechnischer Anforderungen);
Computer Science Reports 09/01, BTU Cottbus, Mai 2001, 65 p.

T Mertke, P Deussen, M Heiner:
Eine anwenderorientierte Sicherheitsfachsprache zur Verifikation von Steuerungsprogrammen;
Proc. EKA 2001, 7. Fachtagung, TU Braunschweig, April 2001, pp. 297 - 309.

  2000

M Heiner, T Menzel:
Time-related Modelling of PLC Systems with Time-less Petri Nets;
in Boel, R.; Stremerch, G. (eds.): Discrete Event Systems, Analysis and Control; Kluwer Academic Publishers 2000, pp. 275 - 282. abstract

M Heiner, I Koch, S. Schuster:
Using Time-dependent Petri Nets for the Analysis of Metabolic Networks;
Proc. DFG-Workshop Modelling and Simulation of Metabolic Networks, May 2000, Otto von Guericke Univ. Magdeburg, pp. 15-21.

  1999

M Heiner, M Heisel:
Modelling Safety-Critical Systems with Z and Petri Nets;
Proc. SafeComp '99, Toulouse 1999, Springer LNCS 1698, pp. 361 - 374. abstract

M Heiner, T Menzel:
Modellierung und Analyse von SPS-Anwenderprogrammen mit Petri-Netzen;
Proc. EKA '99, 6. Fachtagung, Braunschweig, May 1999, pp. 247-265. abstract

M Heiner, P Deussen, S Spranger:
A Case Study in Design and Verification of Manufacturing Systems with Hierarchical Petri Nets;
The International Journal of Advanced Manufacturing Technology (1999), 15, pp. 139-152. abstract

  1998

J Spranger:
Combining structural properties and symbolic representation for efficient analysis of Petri nets;
in H.-D. Burkhard, L. Czaja, P. Starke (eds.): Proc. Workshop on Concurrency, Specification &Programming 1998, Berlin, Sept. 1998, Informatik-Bericht Nr. 110, Humbolt Univ. at Berlin, pp. 236-244. abstract

P Deussen:
Algorithmic Aspects of Concurrent Automata;
in H.-D. Burkhard, L. Czaja, P. Starke (eds.): Proc. Workshop on Concurrency, Specification &Programming 1998, Berlin, Sept. 1998, Informatik-Bericht Nr. 110, Humbolt Univ. at Berlin, pp. 39-70. abstract

M Heiner:
Petri Net Based System Analysis without State Explosion;
Proc. Hight Performance Computing '98, Boston, April 1998, SCS Int. San Diego 1998, pp. 394-403. abstract

M Heiner, T Menzel:
A Petri Net Semantics for the PLC Language Instruction List;
Proc. IEE Workshop on Discrete Event Systems (WODES '98), Cagliari, August 1998, pp. 161-165. abstract

M Heiner, T Menzel:
Instruction List Verification Using a Petri Net Semantics;
Proc. IEEE Int. Conf. on Systems, Man, and Cybernetics, San Diego, October 1998, pp. 716-721. abstract

  1997

J Spranger:
FUNlite - A Parallel Petri Net Simulator;
Proc. 42. IWK Ilmenau, September 1997, 6 p. abstract

H König, A Ulrich, M Heiner:
Design for Testability: A Step-wise Approach to Protocol Testing;
in Kim, M.; Kang, S.; Hong, K. (eds.): Proc. 10th Int. Workshop on Testing of Communicating Systems (IWTCS '97), Seoul, Sept. 1997, Chapman &Hall, pp. 125-140.

M Heiner, L Popova-Zeugmann:
On Integration of Qualitative and Quantitative Analysis of Manufacturing Systems Using Petri Nets;
Proc. 42. Int. wissenschaftliches Kolloquium (IWK '97), Ilmenau, September 1997, TU Ilmenau, Vol. 1, pp. 557-562. abstract

M Heiner:
Verification and Optimization of Control Programs by Petri Nets without State Explosion;
Proc. 2nd Int. Workshop on Manufacturing and Petri Nets held at Int. Conf. on Application and Theory of Petri Nets (ICATPN '97), Toulouse, June 1997, pp. 69-84. abstract

L Popova-Zeugmann, M Heiner:
Worst-case Analysis of Concurrent Systems with Duration Interval Petri Nets;
in Schnieder, E.; Abel, D. (eds.): Entwurf komplexer Automatisierungssysteme `97, Proc. 5. Fachtagung EKA '97, Braunschweig, May 1997, IfRA 1997, pp. 162-179,
improved version: Humboldt-Universität zu Berlin, Informatik-Bericht Nr. 83, May 1997, 18 p. abstract

M Heiner:
On Exploiting the Analysis Power of Petri nets for the Validation of Discrete Event Systems;
Proc. 2nd IMACS Symposium on Mathematical Modelling (MATHMOD VIENNA '97), Wien, February 1997, ARGESIM Report No. 11, pp. 171-176. abstract

  1996

M Heiner, P Deussen, J Spranger:
A Case Study in Developing Control Software of Manufacturing Systems with Hierarchical Petri Nets;
Proc. 1st Int. Workshop on Manufacturing and Petri Nets held at Int. Conf. on Application and Theory of Petri Nets (ICATPN `96), Osaka, June 1996, 20 p. abstract

G Lindner, M Heiner, T Kobienia:
Deadlock Detection in a Distributed Implementation of a Visualization System for Medical Measurement Signals;
Proc. IEEE Int. Conf. on Systems, Man and Cybernetics, Beijing, Oct. 1996, IEEE Press, Vol. 3, pp. 2299-2304. abstract

M Heiner, P Deussen:
Petri Net Based Design and Analysis of Reactive Systems;
Proc. Int. Workshop on Discrete Event Systems (WODES '96), Edingburgh, August 1996, 6 p. abstract

M Heiner, P Deussen:
A Case Study in Design and Validation of Reactive Systems by Means of Petri Nets;
Proc. IMACS Multiconference on Computational Engineering in Systems Applications (CESA `96), Symposium "Discrete Events and Manufacturing Systems", Lille, July 1996, 6 p. abstract

  1995

D Wikarski, M Heiner:
On the Application of Markovian Object Nets to Integrated Qualitative and Quantitative Software Analysis;
Fraunhofer ISST, Berlin, ISST-Reports No. 29/95, Oct. 1995, 33p.

M Heiner:
Petri Net Based Software Dependability Engineering;
Proc. 9th Symposium on Quality and Reliability in Electronics (RELECTRONIC '95), Budapest, Oct. 1995, pp. 181- 186. abstract

  1994

M Heiner, G Ventre, D Wikarski:
A Petri Net Based Methodology to Integrate Qualitative and Quantitative Analysis;
Information and Software Technology 36(94)7, 435-441. abstract

  1992

M Heiner:
Petri Net Based Software Validation - Prospects and Limitations;
ICSI Berkeley, Techn. Report TR-92-022, March 1992, 64p.

 . . .  t h e  e n d  . . .

Any comments or questions are welcome. Please direct them to: