Abstract
Understanding biochemical pathways is one of the big challenges of the field of molecular biology nowadays. Computer science can contribute in this area in a variety of ways. One of them is providing formalisms and tools to simulate and check properties of pathways. One formalism that is well known and suited for modeling concurrent and distributed systems is Milner’s Calculus of Communicating Systems (CCS). CCS is a process algebra and there are many tools that support modeling and automatic verification of properties of systems modeled in terms of CCS processes. This paper describes the regulation of the lactose operon using CCS. We validate our formal model by automatic checking a series of properties that are known for the regulation of the lactose. Thus, we show the viability of using process algebras to model and reason about biochemical networks.
Project partially supported by CNPq (grant 550042).
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References
Voit, E.O.: Computational analysis of biochemical systems. Cambridge University Press, United Kingdom (2000)
Jong, H.D.: Modeling and Simulation of Genetic Regulatory Systems: a literature review. Journal of Computational Biology 9(1), 67–103 (2002)
Antoniotti, M., Policriti, A., Ugel, N., Mishra, B.: Model Building and Model Checking for Biochemical Processes. Cell Biochem. Biophys. 38, 271–286 (2003)
Reddy, V.N.: Modeling Biochemical Pathways: a discrete event systems approach. Master’s thesis, University of Maryland (1994)
Lemke, N., Herédia, F., Barcellos, C.K., Reis, A.N., Mombach, J.C.M.: Essentiality and Damage in Metabolic Networks. Bioinformatics 20(1), 115–119 (2004)
Nelson, D.L., Cox, M.M.: Lehninger Principles of Biochemistry, 4th edn. W. H. Freeman and Co., New York (2004)
Jacob, F., Monod, J.: Genetic Regulatory Mechanisms in the Synthesis of Proteins. Journal of Molecular Biology 3, 318–389 (1961)
Regev, A., Silverman, W., Shapiro, E.: Representation and Simulation of Biochemical Processes using the π-Calculus Process Algebra. In: Pacific Symposium on Biocomputing, vol. 6, pp. 459–470 (2001)
Ciobanu, G., Ciubotariu, V., Tanasă, B.: A π-Calculus Model of the Na Pump. Genome Informatics 13, 469–471 (2002)
Yildirim, N., Mackey, M.C.: Feedback Regulation in the Lactose Operon: a mathematical modeling study and comparison with experimental data. Biophysical Journal 84, 2841–2851 (2003)
Chabrier-Rivier, N., Chiaverini, M., Danos, V., Fages, F., Schächter, V.: Modeling and Querying Biomolecular Interaction Networks. Theoretical Computer Science 325, 25–44 (2004)
Milner, R.: Communication and Concurrency. Prentice Hall, New York (1989)
Lewin, B.: Genes VIII. Pearson Prentice Hall, USA (2004)
The CWB-NC website, http://www.cs.sunysb.edu/~cwb/
Clarke, E.M., Emerson, E.A., Sistla, A.P.: Automatic Verification of Finite-State Concurrent Systems Using Temporal Logic Specifications. ACM Transactions on Programming Languages and Systems 8(2), 244–263 (1986)
The MONET website, http://www.inf.unisinos.br/~lbbc/monet
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Pinto, M.C., Foss, L., Mombach, J.C.M., Ribeiro, L. (2005). Modeling and Property Verification of Lactose Operon Regulation. In: Setubal, J.C., Verjovski-Almeida, S. (eds) Advances in Bioinformatics and Computational Biology. BSB 2005. Lecture Notes in Computer Science(), vol 3594. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11532323_11
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DOI: https://doi.org/10.1007/11532323_11
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-28008-8
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