Petri net models for the semi-automatic construction of large scale biological networks

Natural Computing

Volumn 10, Issue 3, 2011, Pages 1077-1097

  Chen, Ming ^a   Hariharaputran, Sridhar ^b   Hofestädt, Ralf ^b   Kormeier, Benjamin ^b   Spangardt, Sarah ^b  

^a ZHEJIANG UNIVERSITY   (China)

^b BIELEFELD UNIVERSITY   (Germany)

Author keywords

Cardio disease network; Data integration; Functional Petri net; Model construction; MoVisPP

Indexed keywords

ANALYTIC METHOD; ARTICLE; BIOCHEMISTRY; CATALYSIS; CELL COMMUNICATION; CELL SURFACE; COMPUTER SIMULATION; DATA BASE; ENZYME MECHANISM; GENE CONTROL; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION; INFORMATION PROCESSING; INFORMATION SYSTEM; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MICHAELIS MENTEN KINETICS; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; OPERON; PETRI NET; PROMOTER REGION; QUALITATIVE ANALYSIS; SIGNAL TRANSDUCTION;

EID: 80054983310     PISSN: 15677818     EISSN: 15729796     Source Type: Journal    
DOI: 10.1007/s11047-009-9151-y     Document Type: Article

References (63)

1. Alla H, David R (1998) Continuous and hybrid Petri nets. J Circuits Syst Comput 8(1):159-188 (Pubitemid 128540252)
2. Bairoch A (2000) The ENZYME database in 2000. Nucleic Acids Res 28:304-305 (Pubitemid 30047788)
3. Berman HM, Westbrook J, Feng Z et al (2000) The Protein Data Bank. Nucleic Acids Res 28:235-242 (Pubitemid 30047768)
4. Chaouiya C, Remy E, Ruet P et al (2004) Qualitative modeling of genetic networks: from logical regulatory graphs to standard Petri nets. Lect Notes Comput Sci 3099:137-156
5. Chatr-aryamontri A, Ceol A, Montechi Palazzi L et al (2007) MINT: the Molecular INTeraction database. Nucleic Acids Res 35:D572-D574 (Pubitemid 46056272)
6. Chen M (2002) Modelling and simulation of metabolic networks: Petri nets approach and perspective. In: Proceeding of ''ESM 2002, 16th European Simulation Multiconference'', June 3-5, Darmstadt, Germany, pp 441-444
7. Chen M, Hofestädt R (2003) Quantitative Petri net model of gene regulated metabolic networks in the cell. In Silico Biol 3(3):347-365 (Pubitemid 37493056)
8. Chen M, Freier A, Hofestädt R (2005) Bioinformatics approaches for metabolic pathways. In: Sensen CW (ed) Handbook of genome research. WILEY-VCH Verlag GmbH & Co., Weinheim, pp 461-490
9. Comet J, Klaudel H, Liauzu S (2005) Modeling multi-valued genetic regulatory networks using high-level Petri nets. Lect Notes Comput Sci 3536:208-227 (Pubitemid 41422013)
10. Costanza R, Voinov A (2001) Modelling ecological and economic systems with STELLA: part III. Ecol Model 143(1-2):1-7 (Pubitemid 32964971)
11. David R, Alla H (1992) Petri nets and Grafcet-tools for modeling discrete event systems. Prentice Hall, Upper Saddle River
12. Doi A, Drath R, Nagasaki M et al (1999) Protein dynamics observations of lambda phage by hybrid Petri net. Genome Inform 10:217-218
13. Doi A, Nagasaki M, Matsuno H et al (2006) Simulation-based validation of the p53 transcriptional activity with hybrid functional Petri net. In Silico Biol 6:0001
14. Drath R (1998) Hybrid object nets: an object oriented concept for modeling complex hybrid systems. In: Proc. Hybrid dynamical systems, 3rd international conference on automation of mixed processes, ADPM'98, pp 437-442
15. Funahashi A, Tanimura N, Morohashi M et al (2003) Cell Designer: a process diagram editor for generegulatory and biochemical networks. Biosilico 1:159-162
16. Garvey TD, Lincoln P, Pedersen CJ et al (2003) BioSPICE: access to the most current computational tools for biologists. OMICS 7:411-420 (Pubitemid 38018646)
17. Gene Ontology Consortium (2006) The Gene Ontology (GO) project in 2006. Nucleic Acids Res 34:D322-D326
18. Genrich H, Kueffner R, Voss K (2001) Executable Petri net models for the analysis of metabolic pathways. Int J STTT 3(4):394-404
19. Gilbert D, Heiner M, Rosser S, Fulton R, Gu X, Trybilo M (2008) A case study in model-driven synthetic biology. In: IFIP WCC 2008, 2nd IFIP conference on biologically inspired collaborative computing (BICC 2008), vol 268, Milano, September 2008. Springer, Boston, IFIP, pp 163-175
20. Goryanin I, Hodgman TC, Selkov E (1999) Mathematical simulation and analysis of cellular metabolism and regulation. Bioinformatics 15:749-758 (Pubitemid 29484337)
21. Goss PJE, Peccoud J (1998) Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. Proc Natl Acad Sci USA 95:6750-6755 (Pubitemid 28278052)
22. Goss PJE, Peccoud J (1999) Analysis of the stabilizing effect of Rom on the genetic network controlling ColE1 plasmid replication. In: Pacific symposium on biocomputing'99, pp 65-76
23. Gronewold A, Sonnenschein M (1997) Asynchronous layered cellular automata for the structured modeling of ecological systems. In: 9th European simulation symposium (ESS'97), SCS, pp 286-290
24. Gronewold A, Sonnenschein M (1998) Event-based modeling of ecological systems with asynchronous cellular automata. Ecol Model 108:37-52 (Pubitemid 28253469)
25. Hamosh A, Scott AF, Amberger JS et al (2005) Online Inheritance in Man (OMIM), a knowledgebase of human gene and genetic disorders. Nucleic Acid Res 33:D514-D517 (Pubitemid 40207927)
26. Heiner M, Koch I, Will J (2004) Model validation of biological pathways using Petri nets-demonstrated for apoptosis. Biosystems 75:15-28 (Pubitemid 38887549)
27. Heiner M, Richter R, Schwarick M, Rohr C (2008a) Snoopy-a tool to design and execute graph-based formalisms. Petri Net Newsl 74:8-22
28. Heiner M, Gilbert D, Donaldson R (2008b) Petri nets for systems and synthetic biology. In: Bernardo M, Degano P, Zavattaro G (eds) SFM 2008, LNCS, vol 5016. Springer, Heidelberg, pp 215-264
29. Hofestädt R (1994) A Petri net application to model metabolic processes. SAMS 16:113-122
30. Hofestädt R, Thelen S (1998) Quantitative modeling of biochemical networks. In Silico Biol 1:39-53
31. Hoops S, Sahle S, Gauges R et al (2006) COPASI-a COmplex PAthway SImulator. Bioinformatics 22:3067-3074 (Pubitemid 44884083)
32. Hu ZJ, Mellor J, Wu J et al (2004) VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinform 5:17
33. Huang H, Barker WC, Chen Y et al (2003) iProClass: an integrated database of protein family, function and structure information. Nucleic Acids Res 31(1):390-392 (Pubitemid 36150409)
34. Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318-356
35. Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acid Res 28(1): 27-30 (Pubitemid 30047706)
36. Kauffman S (1969) Metabolic stability and epigenesis in randomly connected nets. J Theor Biol 11:326-356
37. Kitano H, Funahashi A, Matsuoka Y et al (2005) Using process diagram for the graphical representation of biological networks. Nat Biotechnol 23(8):961-966 (Pubitemid 41114029)
38. Koh G, Teong H, Clément V et al (2006) A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathway and their crosstalk. Bioinformatics 2:271-280
39. Kueffner R, Zimmer R, Lengauer T (2000) Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics 16(9):825-836
40. Lee D, Zimmer R, Lee S et al (2006) Colored Petri net modeling and simulation of signal transduction pathways. Metab Eng 8:112-122 (Pubitemid 43356394)
41. Loew LM, Schaff JC (2001) The virtual cell: a software environment for computational cell biology. Trends Biotechnol 19:401-406 (Pubitemid 32925033)
42. Matsuno H, Doi A, Nagasaki M et al (2000) Hybrid Petri net representation of gene regulatory network. Pac Symp Biocomput 5:338-349
43. Matsuno H, Doi A, Drath R et al (2001) Genomic Object Net: basic architecture for representing and simulating biopathways. In: RECOMB'2001, April 20, Montréal, Canada
44. Matsuno H, Murakami R, Yamane R et al (2003) Boundary formation by notch signaling in Drosophila multicellular systems: experimental observations and a gene network modeling by Genomic Object Net. Pac Symp Biocomput :152-163
45. Mendes P (1993) GEPASI: a software package for modeling the dynamics, steady states and control of biochemical and other systems. Comput Appl Biosci :563-571 (Pubitemid 23309017)
46. Michaelis L, Menten ML (1913) Die Kinetik der Invertinwirkung. Biochem Z 49:333-369
47. Michal G (1982) Biochemical pathways wall chart. Boehringer Mannheim GmbH Biochemica, Mannheim
48. Nagasaki M, Doi A, Matsuno H et al (2003) Genomic Object Net: a platform for modelling and simulating biopathways. Appl Bioinform 2(3):181-184
49. Nagasaki M, Doi A, Matsuno H et al (2004) Integrating biopathway databases for large-scale modeling and simulation. In: The second Asia-Pacific bioinformatics conferences, volume 29 of conferences in research and practice in information technology, Australian Computer Society, pp 43-52
50. Petri CA (1962) Kommunikation mit Automaten. Dissertation, Institut für Instrumentelle Mathematik, Schriften des IIM Nr. 2, Bonn
51. Reddy VN, Mavrovouniotis ML, Liebman MN (1993) Petri Net representation in metabolic pathways. In: Proceedings first international conference on intelligent systems for molecular biology, AAAI Press, Menlo Park, pp 328-336
52. Reisig WA (1982) Primer in Petri Net design. Springer, Berlin
53. Ruth M, Hannon B (1997) Modeling dynamic biological systems. Springer, New York
54. Sackmann A, Heiner M, Koch I (2006) Application of Petri net based analysis techniques to signal transduction pathways. BMC Bioinform 7:482
55. Sauro HM (1993) SCAMP: a general-purpose simulator and metabolic control analysis program. Comput Appl Biosci 9:441-450 (Pubitemid 23233971)
56. Shaw O, Steggles J, Wipat A (2005) Automatic parameterisation of stochastic Petri net models of biological network. Electron Notes Theor Comput Sci (ENTCS) 153:111-129 (Pubitemid 43867456)
57. Siepel A, Farmer A, Tolopko A et al (2001) ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics 17:83-94 (Pubitemid 32178016)
58. Simao E, Remy E, Thieffry D et al (2005) Qualitative Modeling of regulated metabolic pathways: application to the tryptophan biosynthesis in E. coli. Bioinformatics 21:190-196
59. Steggles L, Banks R, Shaw O et al (2007) Qualitatively modeling and analysing genetic regulatory networks: a Petri net approach. Bioinformatics 23:336-343 (Pubitemid 46323156)
60. Tomita M, Hashimoto K, Takahashi K et al (1999) E-CELL: software environment for whole-cell simulation. Bioinformatics 15:72-84 (Pubitemid 29101200)
61. Troncale S, Tahi F, Campard D et al (2006) Modeling and simulation with hybrid functional Petri nets of the role of Interleukin-6 in human early haematopoiesis. Pac Symp Biocomput 11:427-438
62. Valk R (1978) Self-modifying nets: a natural extension of Petri nets. LNCS 62:464-476
63. Voss K, Heiner M, Koch I (2003) Steady state analysis of metabolic pathways using Petri nets. In Silico Biol 3:0031