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.
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