Abstract
CBS is a Calculus of Biochemical Systems intended to allow the modelling of metabolic, signalling and regulatory networks in a natural and modular manner. In this paper we extend CBS with features directed towards practical, large-scale applications, thus yielding LBS: a Language for Biochemical Systems. The two main extensions are expressions for modifying large complexes in a step-wise manner and parameterised modules with a notion of subtyping; LBS also has nested declarations of species and compartments. The extensions are demonstrated with examples from the yeast pheromone pathway. A formal specification of LBS is then given through an abstract syntax, static semantics and a translation to a variant of coloured Petri nets. Translation to other formalisms such as ordinary differential equations and continuous time Markov chains is also possible.
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References
Regev, A., et al.: Representation and simulation of biochemical processes using the pi-calculus process algebra. In: Pacific Symposium on Biocomputing, pp. 459–470 (2001)
Calder, M., et al.: Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA. In: Priami, C., Ingólfsdóttir, A., Mishra, B., Riis Nielson, H. (eds.) Transactions on Computational Systems Biology VII. LNCS (LNBI), vol. 4230, pp. 1–23. Springer, Heidelberg (2006)
Reddy, V.N., et al.: Petri net representation in metabolic pathways. In: Proc. Int. Conf. Intell. Syst. Mol. Biol., pp. 328–336 (1993)
Paun, G., Rozenberg, G.: A guide to membrane computing. Theor. Comput. Sci. 287(1), 73–100 (2002)
Danos, V., et al.: Rule-based modelling of cellular signalling. In: Caires, L., Vasconcelos, V.T. (eds.) CONCUR 2007. LNCS, vol. 4703, pp. 17–41. Springer, Heidelberg (2007)
Faeder, J.R., et al.: Graphical rule-based representation of signal-transduction networks. In: Liebrock, L.M. (ed.) Proc. 2005 ACM Symp. Appl. Computing, pp. 133–140. ACM Press, New York (2005)
Chabrier-Rivier, N., et al.: The biochemical abstract machine BIOCHAM. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 172–191. Springer, Heidelberg (2005)
Regev, A., et al.: BioAmbients: an abstraction for biological compartments. Theor. Comput. Sci. 325(1), 141–167 (2004)
Priami, C., Quaglia, P.: Beta binders for biological interactions. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 20–33. Springer, Heidelberg (2005)
Guerriero, M.L., et al.: An automated translation from a narrative language for biological modelling into process algebra. In: Calder, M., Gilmore, S. (eds.) CMSB 2007. LNCS (LNBI), vol. 4695, pp. 136–151. Springer, Heidelberg (2007)
Mjolsness, E., Yosiphon, G.: Stochastic process semantics for dynamical grammars. Ann. Math. Artif. Intell. 47(3-4), 329–395 (2006)
Kwiatkowski, M., Stark, I.: The continuous pi-calculus: a process algebra for biochemical modelling. In: Heiner, M., Uhrmacher, A.M. (eds.) Proc. CMSB. LNCS. Springer, Heidelberg (2008)
Plotkin, G.: A calculus of biochemical systems (in preparation)
Heiner, M., et al.: Petri nets for systems and synthetic biology. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol. 5016, pp. 215–264. Springer, Heidelberg (2008)
Pedersen, M., Plotkin, G.: A language for biochemical systems. Technical report, University of Edinburgh (2008), http://www.inf.ed.ac.uk/publications/report/1270.html
Hucka, M., et al.: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4), 524–531 (2003)
Hoops, S., et al.: COPASI – a COmplex PAthway SImulator. Bioinformatics 22(24), 3067–3074 (2006)
Kofahl, B., Klipp, E.: Modelling the dynamics of the yeast pheromone pathway. Yeast 21(10), 831–850 (2004)
Murata, T.: Petri nets: properties, analysis and applications. Proc. IEEE 77(4), 541–580 (1989)
Garrington, T.P., Johnson, G.L.: Organization and regulation of mitogen-activated protein kinase signaling pathways. Current Opinion in Cell Biology 11, 211–218 (1999)
Pierce, B.C.: Types and Programming Languages. MIT Press, Cambridge (2002)
Jensen, K.: Coloured Petri Nets: Basic Concepts, Analysis Methods and Practical Use, vol. 1. Springer, Heidelberg (1992)
Bergmann, F., Sauro, H.: Human-readable model definition language (first draft, revision 2). Technical report, Keck Graduate Institute (2006)
Kitano, H., et al.: Using process diagrams for the graphical representation of biological networks. Nat. Biotechnol. 23(8), 961–966 (2005)
Moodie, S.L., et al.: A graphical notation to describe the logical interactions of biological pathways. Journal of Integrative Bioinformatics 3(2) (2006)
Oda, K., et al.: A comprehensive pathway map of epidermal growth factor receptor signaling. Molecular Systems Biology (2005)
Pedersen, M.: Compositional definitions of minimal flows in Petri nets. In: Heiner, M., Uhrmacher, A.M. (eds.) Proc. CMSB. LNCS. Springer, Heidelberg (2008)
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Pedersen, M., Plotkin, G. (2008). A Language for Biochemical Systems. In: Heiner, M., Uhrmacher, A.M. (eds) Computational Methods in Systems Biology. CMSB 2008. Lecture Notes in Computer Science(), vol 5307. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88562-7_9
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DOI: https://doi.org/10.1007/978-3-540-88562-7_9
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