Modelling, property verification and behavioural equivalence of lactose operon regulation

Computers in Biology and Medicine

Volumn 37, Issue 2, 2007, Pages 134-148

  Pinto, Marcelo Cezar ^a   Foss, Luciana ^a   Mombach, José Carlos Merino ^b   Ribeiro, Leila ^a  

^a FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^b UNIVERSIDADE DO VALE DO RIO DOS SINOS   (Brazil)

Author keywords

CCS; Model checking; Observational equivalence; Systems biology

Indexed keywords

BIOCHEMICAL ENGINEERING; COMMUNICATION SYSTEMS; COMPUTER SCIENCE; COMPUTER SIMULATION; MOLECULAR BIOLOGY; NEURAL NETWORKS;

CALCULUS OF COMMUNICATING SYSTEMS (CCS); MODEL CHECKING; OBSERVATIONAL EQUIVALENCE; SYSTEMS BIOLOGY;

SUGARS;

LACTOSE;

ARTICLE; AUTOANALYSIS; CALCULUS OF COMMUNICATING SYSTEM; GENE CONTROL; LACTOSE OPERON; MATHEMATICS; MODEL; PRIORITY JOURNAL; REGULATORY MECHANISM; SYSTEMS BIOLOGY; VALIDATION PROCESS;

LACTOSE; MODELS, THEORETICAL; OPERON; SYSTEMS BIOLOGY;

EID: 33845406908     PISSN: 00104825     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiomed.2006.01.006     Document Type: Article

References (35)

1. JigCell Website Glossary. http://jigcell.biol.vt.edu/glossary.html.
2. Voit E.O. Computational Analysis of Biochemical Systems (2000), Cambridge University Press, United Kingdom
3. Jong H.D. Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 9 1 (2002) 67-103
4. Antoniotti M., Policriti A., Ugel N., and Mishra B. Model building and model checking for biochemical processes. Cell Biochem. Biophys. 38 (2003) 271-286
5. V.N. Reddy, Modeling biochemical pathways: a discrete event systems approach, Master's Thesis, University of Maryland, 1994.
6. Lemke N., Herédia F., Barcellos C.K., Reis A.N., and Mombach J.C.M. Essentiality and damage in metabolic networks. Bioinformatics 20 1 (2004) 115-119
7. Milner R. Communication and Concurrency (1989), Prentice-Hall, New York
8. Milner R., and Parrow J. A calculus for mobile processes I. Inf. Comput. 100 (1992) 1-40
9. Milner R., Parrow J., and Walker D. A calculus for mobile processes II. Inf. Comput. 100 (1992) 41-77
10. Regev A., Silverman W., and Shapiro E. Representation and simulation of biochemical processes using the π-calculus process algebra. in: Pacific Symposium on Biocomputing vol. 6 (2001), World Scientific Press, Singapore 459-470
11. Ciobanu G., Ciubotariu V., and Tanasǎ B. A π-calculus model of the Na pump. Genome Inf. 13 (2002) 469-471
12. Yildirim N., and Mackey M.C. Feedback regulation in the lactose operon: a mathematical modelling study and comparison with experimental data. Biophys. J. 84 (2003) 2841-2851
13. Chabrier-Rivier N., Chiaverini M., Danos V., Fages F., and Schächter V. Modeling and querying biomolecular interaction networks. Theor. Comput. Sci. 325 (2004) 25-44
14. Pinto M.C., Foss L., Mombach J.C.M., and Ribeiro L. Modeling and property verification of lactose operon regulation. Lecture Notes in Bioinformatics 3594 (2005) 95-106
15. Nelson D.L., and Cox M.M. Lehninger Principles of Biochemistry. fourth ed. (2004), W. H. Freeman, New York
16. Jacob F., and Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3 (1961) 318-389
17. Wong P., Gladney S., and Keasling J.D. Mathematical model of the lac operon: inducer exclusion, catabolite repression, and diauxic growth on glucose and lactose. Biotechnol. Prog. 13 2 (1997) 132-143
18. Goss P.J.E., and Peccoud J. Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. Proc. Natl. Acad. Sci. USA 95 12 (1998) 6750-6755
19. Lecca P., Priami C., Quaglia P., Rossi B., Laudanna C., and Constantin G. A stochastic process algebra approach to simulation of autoreactive lymphocyte recruitment. Simulation 80 6 (2004) 273-288
20. Lewin B. Genes VIII (2004), Pearson Prentice Hall, USA
21. Keller R. Formal verification of parallel programs. Commun. ACM 19 7 (1976) 371-384
22. Vilar J.M.G., Guet C.C., and Leibler S. Modeling network dynamics: the lac operon, a case study. J. Cell Biol. 161 3 (2003) 471-476
23. The CWB-NC website. http://www.cs.sunysb.edu/∼cwb/.
24. E.A. Emerson, C.-L. Lei, Efficient model checking in fragments of the propositional mu-calculus, in: Symposium on Logic in Computer Science, 1, 1986, Cambridge, Massachusetts, USA, IEEE Computer Society Press, pp. 459-470.
25. Kozen D. Results on the propositional mu-calculus. Theor. Comput. Sci. 27 3 (1983) 333-354
26. Clarke E.M., Emerson E.A., and Sistla A.P. Automatic verification of finite-state concurrent systems using temporal logic specifications. ACM Trans. Programming Languages Syst. 8 2 (1986) 244-263
27. Cleaveland R., Parrow J., and Steffen B. The concurrency workbench: a semantics-based tool for the verification of concurrent systems. ACM Trans. Programming Languages Syst. 15 1 (1993) 36-72
28. Uhrmacher A.M., Degenring D., and Zeigler B.P. Discrete event multi-level models for systems biology. Trans. Comput. Syst. Biol. 1 (2005) 66-89
29. N. Chabrier-Rivier, F. Fages, S. Soliman, The biochemical abstract machine BIOCHAM, in: CMSB 2004-Computational Methods in Systems Biology, Lecture Notes in Computer Science, vol. 3082, Springer, Berlin, pp. 172-191.
30. Calzone L., Chabrier-Rivier N., Fages F., Gentils L., and Soliman S. Machine learning bio-molecular interactions from temporal logic properties. Proceedings of CMSB 2005-Computational Methods in Systems Biology (2005)
31. Mardare R., and Priami C. Logical analysis of biological systems. Fundam. Informaticae 64 (2005) 271-285
32. Kwiatkowska M.Z., Norman G., and Parker D. Probabilistic model checking in practice: case studies with PRISM. SIGMETRICS Perform. Eval. Rev. 32 4 (2005) 16-21
33. Calder M., Vyshemirsky V., Gilbert D., and Orton R. Analysis of signalling pathways using the prism model checker. Proceedings of CMSB 2005-Computational Methods in Systems Biology (2005) 179-190
34. V. Danos, J. Krivine, Reversible communicating systems, CONCUR 2004-Concurrency Theory, Lecture Notes in Computer Science, vol. 3170, Springer, Berlin, 2004, pp. 292-307.
35. Battistella E., Souza J.G.C., Barcellos C.K., Lemke N., and Mombach J.C.M. An integrated model for cellular analysis. Genet. Mole. Res. 4 (2005) 506-513