Chemical-oriented simulation of computational systems with ALCHEMIST

Journal of Simulation

Volumn 7, Issue 3, 2013, Pages 202-215

  Pianini, D ^a   Montagna, S ^a   Viroli, M ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

Bio inspiration; Distribution; Pervasive systems; Simulation

Indexed keywords

AUTONOMOUS AGENTS; COMPUTATIONAL CHEMISTRY; COMPUTATIONAL METHODS; INFORMATION SERVICES; MOBILE AGENTS; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

BIO-INSPIRATION; DISTRIBUTION; PERVASIVE COMPUTING APPLICATIONS; PERVASIVE COMPUTING SYSTEMS; PERVASIVE SYSTEMS; SIMULATION; SIMULATION FRAMEWORK; STOCHASTIC SIMULATION ALGORITHMS;

UBIQUITOUS COMPUTING;

EID: 84880894483     PISSN: 17477778     EISSN: 17477786     Source Type: Journal    
DOI: 10.1057/jos.2012.27     Document Type: Article

References (60)

1. Alves R, Antunes F and Salvador A (2006). Tools for kinetic modeling of biochemical networks. Nature Biotechnology 24(6) pp 667-672. (Pubitemid 43884436)
2. Autili M, Benedetto P and Inverardi P (2009). Context-aware adaptive services: The plastic approach. In: FASE'09 Proceedings. Springer-Verlag, Berlin, Heidelberg, pp 124-139.
3. Babaoglu Öet al (2006). Design patterns from biology for distributed computing. TAAS 1(1): 26-66. (Pubitemid 44373717)
4. Babulak E and Wang M (2008). Discrete event simulation: State of the art. iJOE 4(2): 60-63.
5. Banâtre J-P, Fradet P and Métayer DL (2001). Gamma and the chemical reaction model: Fifteen years after. In: Proceedings of the Workshop on Multiset Processing: Multiset Processing, Mathematical, Computer Science, and Molecular Computing Points of View, ser. WMP'00. Springer-Verlag, London, UK, pp 17-44.
6. Banâtre J-P and Métayer DL (1993). Programming by multiset transformation. Communications of the ACM 36(1): 98-111.
7. Bandini S, Manzoni S and Vizzari G (2009a). Agent based modeling and simulation: An informatics perspective. Journal of Artificial Societies and Social Simulation 12(4): 4.
8. Bandini S, Manzoni S and Vizzari G (2009b). Crowd behavior modeling: From cellular automata to multi-agent systems. In: Uhrmacher AM and Weyns D (eds). Multi-agent Systems: Simulation and Applications ser. Computational Analysis, Synthesis, and Design of Dynamic Systems, CRC Press, Taylor Francis Group, Boca Raton, FL 33487-2742, pp 389-418.
9. Bandini S and Vizzari G (2007). Regulation function of the environment in agent-based simulation. In: Proceedings of the 3rd International Conference on Environments for Multi-agent Systems III, ser. E4MAS'06, Springer-Verlag, Berlin, Heidelberg, 2007, pp 157-169.
10. Bergstra JA and Bethke I (2002). Molecular dynamics. Journal of Logic and Algebraic Programming 51(2): 193-214. (Pubitemid 34544918)
11. Berry G and Boudol G (1992). The chemical abstract machine. Theoretical Computer Science 96(1): 217-248.
12. Brijder R, Ehrenfeucht A, Main MG and Rozenberg G (2011). A tour of reaction systems. International Journal of Foundations of Computer Science 22(7): 1499-1517.
13. Bull JM et al (2003). Benchmarking Java against C and Fortran for scientific applications. Concurrency and Computation: Practice and Experience 15(3-5): 417-430.
14. Cardelli L and Gordon AD (2000). Mobile ambients. Theoretical Computer Science 240(1): 177-213.
15. Cowan R (2000). Stochastic models for DNA replication. In: Shanbhag DN and Rao CR (eds). Stochastic Processes: Modelling and Simulation, Vol. 21. Handbook of Statistics. Elsevier, pp 137-166.
16. Credi A et al (2007). Modelization and simulation of nano devices in {nano k} calculus. In: Computational Methods in Systems Biology, International Conference, CMSB 2007, Edinburgh, Scotland, 20-21 September, Proceedings, ser. Lecture Notes in Computer Science, Vol. 4695. Springer, pp 168-183.
17. Ewald R, Maus C, Rolfs A and Uhrmacher AM (2007). Discrete event modeling and simulation in systems biology. Journal of Simulation 1(2): 81-96.
18. Fernandez-Marquez JL et al (2012). Description and composition of bio-inspired design patterns: A complete overview. Natural Computing, doi: 10.1007/s11047-012-9324-y, online First, pp 1-25.
19. Fok C-L, Roman G-C and Lu C (2009). Enhanced coordination in sensor networks through flexible service provisioning. In: Field, J and Vasconcelos, VT (eds). Proceedings of COORDINATION 2009 ser. LNCS, Vol. 5521, Springer-Verlag, Lisbon, Portugal.
20. Gardelli L, ViroliMand Omicini A (2007). Design patterns for selforganising systems. In: Verbrugge, R and Varga, LZ (eds). Proceedings of the Multi-agent Systems and Applications V, ser, LNAI, Burkhard, H-D. Springer, September, Vol. 4696, pp 123-132, 5th International Central and Eastern European Conference on Multi-agent Systems (CEEMAS'07), Leipzig, Germany, 25-27 September.
21. Gibson MA and Bruck J (2000). Efficient exact stochastic simulation of chemical systems with many species and many channels. Journal of Physical Chemistry A 104(9): 1876-1889.
22. Gillespie DT (1977). Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry 81(25): 2340-2361.
23. Harel D (1987). Statecharts: A visual formalism for complex systems. Science of Computer Programming 8(3): 231-274. (Pubitemid 17617706)
24. Helleboogh A, Vizzari G, Uhrmacher A and Michel F (2007). Modeling dynamic environments in multi-agent simulation. Autonomous Agents and Multi-agent Systems 14(1): 87-116.
25. Hoschek W (2004). The Colt Distribution: Open Source Libraries for High Performance Scientific and Technical Computing in Java. CERN, Geneva: http://acs.lbl.gov/software/colt/.
26. Lecca P, Ihekwaba AEC, Dematté L and Priami C (2010). Stochastic simulation of the spatio-temporal dynamics of reaction-diffusion systems: The case for the bicoid gradient. Journal of Integrative Bioinformatics 7(1): 1-32.
27. Luke S et al (2005). Mason: A multiagent simulation environment. Simulation 81(7): 517-527. (Pubitemid 41448648)
28. Macal CM and North MJ (2010). Tutorial on agent-based modelling and simulation. Journal of Simulation 4(3): 151-162.
29. Mallavarapu A, Thomson M, Ullian B and Gunawardena J (2009). Programming with models: Modularity and abstraction provide powerful capabilities for systems biology. Journal of the Royal Society, Interface/the Royal Society 6(32): 257-270.
30. Mamei M and Zambonelli F (2009). Programming pervasive and mobile computing applications: The TOTA approach. ACM Transactions on Software Engineering and Methodology 18(4): 1-56.
31. Matsumoto M and Nishimura T (1998). Mersenne twister: A 623- dimensionally equidistributed uniform pseudo-random number generator. ACM Transactions on Modelling and Computer Simulation 8(1): 3-30.
32. Minar N, Burkhart R, Langton C and Askenazi M (1996). The {S}warm simulation system: A toolkit for building multi-agent simulations. Working Paper 96-06-042, Santa Fe, CA.
33. Molesini A, CasadeiM, Omicini A and ViroliM(2011). Simulation in agent-oriented software engineering: The SODA case study. Science of Computer Programming, August 2011, Special Issue on Agent-oriented Design methods and Programming Techniques for Distributed Computing in Dynamic and Complex Environments. [Online]: http://www.sciencedirect.com/science/article/pii/ S0167642311001778.
34. Molesini A, Omicini A and Viroli M (2009). Environment in agentoriented software engineering methodologies. Multiagent and Grid Systems 5(1): 37-57, Special Issue 'Engineering Environments in Multi-agent Systems'.
35. Montagna S, Pianini D and Viroli M (2012). A model for Drosophila melanogaster development from a single cell to stripe pattern formation. In: 27th Annual ACM Symposium on Applied Computing (SAC 2012), Riva del Garda (Trento), Italy, 26-30 March, to appear.
36. Murata T (1989). Petri nets: Properties, analysis and applications. Proceedings of the IEEE, Vol. 77, pp 541-580.
37. Murphy AL, Picco GP and Roman G-C (2006). Lime: A model and middleware supporting mobility of hosts and agents. ACM Transactions on Software Engineering and Methodology 15(3): 279-328. (Pubitemid 44371449)
38. North MJ, Howe TR, Collier NT and Vos JR (2007). A declarative model assembly infrastructure for verification and validation. In: Takahashi S, Sallach D and Rouchier J (eds). Advancing Social Simulation: The First World Congress. Springer: Japan, pp 129-140.
39. Oancea B, Rosca IG, Andrei T and Iacob AI (2011). Evaluating Java performance for linear algebra numerical computations. Procedia Computer Science 3: 474-478.
40. Omicini A, Ricci A and Viroli M (2008). Artifacts in the A&A meta-model for multi-agent systems. Autonomous Agents and Multi-agent Systems 17(3): 432-456 December, Special Issue on Foundations, Advanced Topics and Industrial Perspectives of Multi-agent Systems.
41. Omicini A and Zambonelli F (1999). Coordination for internet application development. Autonomous Agents and Multi-agent Systems 2(3): 251-269.
42. Paun G (2002). Membrane Computing: An Introduction. Springer- Verlag, New York: Secaucus, NJ.
43. Pollacia LF (1989). A survey of discrete event simulation and stateof- the-art discrete event languages. SIGSIM Simulation Digest 20(3): 8-25.
44. Priami C (1995). Stochastic pi-calculus. The Computer Journal 38(7): 578-589.
45. Ricci A, Piunti M and Viroli M (2011). Environment programming in multiagent systems - An artifact-based perspective. Autonomous Agents and Multi-agent Systems 23(2): 158-192.
46. Roy PV et al (2008). Self-management for large-scale distributed systems: An overview of the selfman project. In: Bonsangue MM, Graf S and de Roever W-P (eds). Formal Methods for Components and Objects, LNCS No. 5382. Springer Verlag, pp 153-178.
47. Schumacher M, Grangier L and Jurca R (2007). Governing environments for agent-based traffic simulations. In: Proceedings of the 5th international Central and Eastern European conference on Multi-agent Systems and Applications V, ser. CEEMAS'07. Springer-Verlag, Berlin, Heidelberg pp 163-172.
48. Sklar E (2007). Netlogo, a multi-agent simulation environment. Artificial Life 13(3): 303-311.
49. Slepoy A, Thompson AP and Plimpton SJ (2008). A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks. The Journal of Chemical Physics 128(20): 205101.
50. Uhrmacher AM and Priami C (2005). Discrete event systems specification in systems biology - A discussion of stochastic pi calculus and devs. In: Proceedings of the 37th Conference on Winter Simulation, ser. WSC'05. Winter Simulation Conference, pp 317-326. (Pubitemid 46187721)
51. Viroli M and Casadei M (2009). Biochemical tuple spaces for selforganising coordination. In: Field LJ and Vasconcelos VT (eds). Proceedings of the Coordination Languages and Models, ser., Lisbon, Portugal: Springer, June, Vol. 5521, pp 143-162, Proceedings of the 11th International Conference (COORDINATION 2009).
52. Viroli M, Casadei M, Montagna S and Zambonelli F (2011). Spatial coordination of pervasive services through chemicalinspired tuple spaces. ACM Transactions on Autonomous and Adaptive Systems 6(2): 14:1-14:24.
53. Viroli M et al (2007). Infrastructures for the environment of multiagent systems. Autonomous Agents and Multi-agent Systems 14(1): 49-60. (Pubitemid 44601223)
54. Viroli M et al (2011). A coordination approach to adaptive pervasive service ecosystems. In: 1st Awareness Workshop 'Challenges in Achieving Self-awareness in Autonomous Systems' (AWARE 2011), SASO 2011, Ann Arbor, MI, 7 October.
55. Viroli M and Zambonelli F (2010). A biochemical approach to adaptive service ecosystems. Information Sciences 180(10): 1876-1892.
56. Weyns D, Boucké N and Holvoet T (2006). Gradient field-based task assignment in an AGV transportation system. In: Proceedings of the Fifth International Joint Conference on Autonomous Agents and Multiagent Systems, ser. AAMAS'06, ACM, New York, NY, pp 842-849. (Pubitemid 46609564)
57. Zambonelli F et al (2011). Self-aware pervasive service ecosystems. Procedia Computer Science 7: 197-199, Proceedings of the 2nd European Future Technologies Conference and Exhibition 2011 (FET 11).
58. Zambonelli F and Viroli M (2011). A survey on nature-inspired metaphors for pervasive service ecosystems. International Journal of Pervasive Computing and Communications 7(3): 186-204.
59. Zeigler B (1984). Multifaceted Modelling and Discrete Event Simulation. Academic Press.
60. Zeigler BP (1976). Theory of Modeling and Simulation. John Wiley.