Abstract
Inspired by recent works in computational systems biology and existing literature proposing nature-inspired approaches for the coordination of today complex distributed systems, this paper proposes a mechanism to leverage exact computational modelling of chemical reactions for achieving self-organisation in system coordination.
We conceive the notion of biochemical tuple spaces. In this model: a tuple resembles a chemical substance, a notion of activity/pertinency value for tuples is used to model chemical concentration, coordination rules are structured as chemical reactions evolving tuple concentration over time, a tuple space resembles a single-compartment solution, and finally a network of tuple spaces resembles a tissue-like biological system.
The proposed model is formalised as a process algebra with stochastic semantics, and several examples are described up to an ecology-inspired scenario of system coordination, which emphasises the self-organisation features of the proposed model.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Babaoglu, O., Canright, G., Deutsch, A., Caro, G.A.D., Ducatelle, F., Gambardella, L.M., Ganguly, N., Jelasity, M., Montemanni, R., Montresor, A., Urnes, T.: Design patterns from biology for distributed computing. ACM Trans. Auton. Adapt. Syst. 1(1), 26–66 (2006)
Bandara, A., Payne, T.R., Roure, D.D., Gibbins, N., Lewis, T.: A pragmatic approach for the semantic description and matching of pervasive resources. In: Wu, S., Yang, L.T., Xu, T.L. (eds.) GPC 2008. LNCS, vol. 5036, pp. 434–446. Springer, Heidelberg (2008)
Berry, G., Boudol, G.: The chemical abstract machine. Theoretical Computer Science 96(1), 217–248 (1992)
Berryman, A.A.: The origins and evolution of predator-prey theory. Ecology 73(5), 1530–1535 (1992)
Bonâtre, J.-P., Le Métayer, D.: Gamma and the chemical reaction model: Ten years after. In: Coordination Programming, pp. 3–41. Imperial College Press, London (1996)
Bravetti, M.: Stochastic and real time in process algebra: A conceptual overview. Electr. Notes Theor. Comput. Sci. 162, 113–119 (2006)
Bravetti, M., Gorrieri, R., Lucchi, R., Zavattaro, G.: Quantitative information in the tuple space coordination model. Theor. Comput. Sci. 346(1), 28–57 (2005)
Cardelli, L.: Artificial biochemistry. Technical Report TR-08-2006, University of Trento Centre for Computational and Systems Biology (2006)
Cardelli, L., Gordon, A.D.: Mobile ambients. Theoretical Computer Science 240(1), 177–213 (2000)
Cardelli, L., Zavattaro, G.: On the computational power of biochemistry. In: Horimoto, K., Regensburger, G., Rosenkranz, M., Yoshida, H. (eds.) AB 2008. LNCS, vol. 5147, pp. 65–80. Springer, Heidelberg (2008)
Casadei, M., Menezes, R., Viroli, M., Tolksdorf, R.: Using ant’s brood sorting to increase fault tolerance in Linda’s tuple distribution mechanism. In: Klusch, M., Hindriks, K.V., Papazoglou, M.P., Sterling, L. (eds.) CIA 2007. LNCS, vol. 4676, pp. 255–269. Springer, Heidelberg (2007)
Casadei, M., Viroli, M., Gardelli, L.: On the collective sort problem for distributed tuple spaces. Science of Computer Programming (2009) (in press), doi:10.1016/j.scico.2008.09.018
Credi, A., Garavelli, M., Laneve, C., Pradalier, S., Silvi, S., Zavattaro, G.: nanok: A calculus for the modeling and simulation of nano devices. Theor. Comput. Sci. 408(1), 17–30 (2008)
Cunningham, H.C., Roman, G.-C.: A unity-style programming logic for shared dataspace programs. IEEE Trans. Parallel Distrib. Syst. 1(3), 365–376 (1990)
Fisher, J., Henzinger, T.A.: Executable cell biology. Nature Biotechnology 25, 1239–1249 (2007)
Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry 81(25), 2340–2361 (1977)
Giunchiglia, F., Yatskevich, M., Shvaiko, P.: Semantic matching: Algorithms and implementation. J. Data Semantics 4601, 1–38 (2007)
Madhavan, J., Bernstein, P.A., Rahm, E.: Generic schema matching with cupid. In: VLDB, pp. 49–58. Morgan Kaufmann, San Francisco (2001)
Mamei, M., Zambonelli, F.: Programming pervasive and mobile computing applications with the TOTA middleware. In: Pervasive Computing and Communications, March 2004, pp. 263–273. IEEE, Los Alamitos (2004)
Menezes, R., Tolksdorf, R.: Adaptiveness in linda-based coordination models. In: Di Marzo Serugendo, G., Karageorgos, A., Rana, O.F., Zambonelli, F. (eds.) ESOA 2003. LNCS (LNAI), vol. 2977, pp. 212–232. Springer, Heidelberg (2004)
Omicini, A., Zambonelli, F.: Coordination for Internet application development. Autonomous Agents and Multi-Agent Systems 2(3), 251–269 (1999)
Paolucci, M., Kawamura, T., Payne, T.R., Sycara, K.P.: Semantic matching of web services capabilities. In: Horrocks, I., Hendler, J. (eds.) ISWC 2002. LNCS, vol. 2342, pp. 333–347. Springer, Heidelberg (2002)
Paun, G.: Membrane Computing: An Introduction. Springer, New York (2002)
Pierro, A.D., Hankin, C., Wiklicky, H.: Continuous-time probabilistic klaim. Electr. Notes Theor. Comput. Sci. 128(5), 27–38 (2005)
Priami, C.: Stochastic pi-calculus. The Computer Journal 38(7), 578–589 (1995)
Ricci, A., Omicini, A., Viroli, M.: Extending ReSpecT for multiple coordination flows. In: Arabnia, H.R. (ed.) International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2002), Las Vegas, NV, USA, July 2002, vol. III, pp. 1407–1413. CSREA Press (2002)
Tolksdorf, R., Nixon, L.J.B., Simperl, E.P.B.: Towards a tuplespace-based middleware for the Semantic Web. Web Intelligence and Agent Systems 6(3), 235–251 (2008)
Viroli, M., Casadei, M., Omicini, A.: A framework for modelling and implementing self-organising coordination. In: 24th Annual ACM Symposium on Applied Computing (SAC 2009), March 8-12, vol. III, pp. 1353–1360. ACM, New York (2009)
Viroli, M., Omicini, A.: Coordination as a service. Fundamenta Informaticae 73(4), 507–534 (2006)
Zambonelli, F., Viroli, M.: Architecture and metaphors for eternally adaptive service ecosystems. In: IDC 2008, September 2008. Studies in Computational Intelligence, vol. 162, pp. 23–32. Springer, Heidelberg (2008)
Zavattaro, G.: Reachability analysis in bioambients. Electr. Notes Theor. Comput. Sci. 227, 179–193 (2009)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 IFIP International Federation for Information Processing
About this paper
Cite this paper
Viroli, M., Casadei, M. (2009). Biochemical Tuple Spaces for Self-organising Coordination. In: Field, J., Vasconcelos, V.T. (eds) Coordination Models and Languages. COORDINATION 2009. Lecture Notes in Computer Science, vol 5521. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02053-7_8
Download citation
DOI: https://doi.org/10.1007/978-3-642-02053-7_8
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-02052-0
Online ISBN: 978-3-642-02053-7
eBook Packages: Computer ScienceComputer Science (R0)