Using Petri Net tools to study properties and dynamics of biological systems

Journal of the American Medical Informatics Association

Volumn 12, Issue 2, 2005, Pages 181-199

  Peleg, Mor ^a   Rubin, Daniel ^b   Altman, Russ B ^c  

^a UNIVERSITY OF HAIFA   (Israel)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGY; COMPUTER PROGRAM; PROCESS MODEL; QUALITATIVE ANALYSIS; SIMULATION;

EID: 14544306029     PISSN: 10675027     EISSN: None     Source Type: Journal    
DOI: 10.1197/jamia.M1637     Document Type: Article

References (37)

1. J.L. Peterson Petri Net Theory and the Modeling of Systems 1981 Prentice-Hall Englewood Cliffs, NJ
2. V.N. Reddy, M.N. Liebman, and M.L. Mavrovouniotis Qualitative analysis of biochemical reaction systems Comput Biol Med 26 1996 9 24
3. Zevedei-Oancea I, Schuster S. Topological analysis of metabolic networks based on Petri Net theory. In Silico Biol. 2003;3 (special Issue: Petri Nets for Metabolic Networks). Available at: http://www.bioinfo.de/isb/2003/03/0029/. Accessed January 4, 2005.
4. R. Kuffner, R. Zimmer, and T. Lengauer Pathway analysis in metabolic databases via differential metabolic display (DMD) Bioinformatics 16 2000 825 836
5. J.S. Oliveira, C.G. Bailey, J.B. Jones-Oliveira, D.A. Dixon, D.W. Gull, and M.L. Chandler A computational model for the identification of biochemical pathways in the Krebs cycle J Comput Biol 10 2003 57 82
6. A.A. Sharov Self-reproducing systems: structure, niche relations and evolution Biosystems 25 1991 237 249
7. J.H. Moore, and L.W. Hahn Petri Net modeling of high-order genetic systems using grammatical evolution Biosystems 72 2003 177 186
8. M. Peleg, I. Yeh, and R.B. Altman Modeling biological processes using Workflow and Petri Net models Bioinformatics 18 2002 825 837
9. K. Voss, M. Heiner, and I. Koch Steady state analysis of metabolic pathways using Petri Nets In Silico Biol 3 3 2003 367 387
10. M. Chen, and R. Hofestaedt Quantitative Petri Net model of gene regulated metabolic networks in the cell In Silico Biol 3 3 2003 347 365
11. H. Matsuno, Y. Tanaka, H. Aoshima, A. Doi, M. Matsui, and S. Miyano Biopathways representation and simulation on hybrid functional Petri Net In Silico Biol 3 3 2003 389 404
12. K. Jensen Coloured Petri Nets: Basic Concepts, Analysis Methods and Practical Use 1995 Springer-Verlag New York
13. M. Peleg, I.S. Gabashvili, and R.B. Altman Qualitative models of molecular function: linking genetic polymorphisms of tRNA to their functional sequelae Proc IEEE 90 2002 1875 1886
14. Matsuno H, Doi A. Hybrid Petri Net Representation of Gene Regulatory Network. Available at: http://helix-web.stanford.edu/psb00/matsuno.pdf. Accessed January 5, 2005.
15. A. Doi, S. Fujita, H. Matsuno, M. Nagasaki, and S. Miyano Constructing biological pathway models with hybrid functional Petri Net In Silico Biol 4 2 2004 0023.Epub 2005 January 5
16. P.J. Haas Stochastic Petri Nets 2002 Springer New York
17. N. Bahi-Jaber, and D. Pontier Modeling transmission of directly transmitted infectious diseases using colored stochastic Petri Nets Math Biosci 185 2003 1 13
18. D. Tsavachidou, and M.N. Liebman Modeling and simulation of pathways in menopause J Am Med Inform Assoc 9 2002 461 471
19. W.M. Mounts, and M.N. Liebman Qualitative modeling of normal blood coagulation and its pathological states using stochastic activity networks Int J Biol Macromol 20 1997 265 281
20. W.M. Mounts, and M.N. Liebman Application of Petri Nets and stochastic activity nets to modeling biological pathways and processes Int J Biol Macromol 20 1997 265 281
21. Workgroup Management Coalition. Interface 1: Process Definition Interchange; 1999. Report no. TC-1016 (O, P, X). Available at http://www.wfmc.org/standards/docs. Accessed January 5, 2005.
22. W.M.P. van der Aalst The application of Petri Nets to workflow management J Circuits Syst Comput 8 1998 21 66
23. K. Takahashi, K. Yugi, K. Hashimoto, Y. Yamada, C.J.F. Pickett, and M. Tomita Computational challenges in cell simulation: a software engineering approach IEEE Intelligent Syst 17 2002 64 71
24. H. de Jong Modeling and simulation of genetic regulatory systems: a literature review J Comput Biol 9 1 2002 67 103
25. J.W. Barnwell, and M.R. Galinski Invasion of vertebrae cells: erythrocytes I.W. Sherman Malaria: Parasite Biology, Pathogenesis, and Protection 1998 ASM Press Washington DC 93 122
26. D.D. Deavours, G. Clark, and T. Courtney The Mobius framework and its implementation IEEE Trans Software Eng 28 2003 956 969
27. R. German, C. Kelling, A. Zimmermann, and G. Hommel TimeNET - a toolkit for evaluating non-Markovian stochastic Petri Nets Performance Eval 24 1995 69 87
28. K. Jensen Coloured Petri Nets. Basic Concepts, Analysis Methods and Practical Use. Volume 1, Basic Concepts. Monographs in Theoretical Computer Science 1992 Springer-Verlag New York
29. H.M.W. Verbeek, T. Basten, and WMP van der Aalst Diagnosing workflow processes using Woflan Comput J 44 2001 246 279
30. J.D. Ullman Elements of ML Programming 1993 Prentice-Hall Englewood Cliffs, NJ
31. J. Esparza, and M. Nielsen Decibility issues for Petri Nets - a survey J Inf Process Cybernet 30 1994 143 160
32. W.P.M. van der Aalst, and B. Basten Inheritance of Workflows: An Approach to Tackling Problems Related to Change. Computing Science Report no. 99/06 1999 Eindhoven University of Technology Eindhoven, the Netherlands
33. J. Gennari, M.A. Musen, and R.W. Fergerson The evolution of Protege: an environment for knowledge-based systems development Int J Hum Comput Interact 58 2002 89 123
34. M. Peleg, S. Tu, A. Mahindroo, and R. Altman Modeling and analyzing biomedical processes using Workflow/Petri Net models and tools MedInfo 2004 2004 74 78
35. D. Tsavachidou, and M.N. Liebman Modeling and simulation of pathways in menopause J Am Med Inform Assoc 9 2002 461 471
36. P.J. Goss, and J. Peccoud Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri Nets Proc Natl Acad Sci U S A 95 1998 6750 6755
37. T.E. Turner, S. Schnell, and K. Burrage Stochastic approaches for modelling in vivo reactions Comput Biol Chem 28 2004 165 178