Agents & artifacts for systems biology: Toward a framework based on TuCSoN

4th International Industrial Simulation Conference 2006, ISC 2006

Volumn , Issue , 2006, Pages 25-32

  Montagna, Sara ^a   Ricci, Alessandro ^a   Omicini, Andrea ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SYSTEMS; MULTI AGENT SYSTEMS;

AGENT COORDINATION; AGENT-BASED FRAMEWORK; BIOLOGICAL COMPONENTS; BIOLOGICAL NETWORKS; DISTRIBUTED SIMULATIONS; MULTIAGENT SYSTEMS (MASS); SYSTEM LEVELS; SYSTEMS BIOLOGY;

COMPUTER SIMULATION;

EID: 84898461989     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (25)

1. Borghoff, U., P. Bottoni, P. Mussio, and R. Pareschi. 1996, June. A systemic metaphor of multi-agent coordination in living systems. In 10th European Simulation Multiconfer-ence (EMS'96), 245-253. Budapest, Hungary.
2. Cardelli, L. 2005, September. Abstract machines of systems biology. Transactions on Computational Systems Biology. 7/7 3737:145-168.
3. Celada, P., and P. Seiden. 1992. A computer model for cellular interaction in the immune system. Immunology Today 13 (2): 56-62.
4. Chee Meng, T., S. Somani, and P. Dhar. 2004. Modelling and simulation of biological systems with stochasticity. In Silico Biology 3 (4): 293-309.
5. Corradini, E, E. Merelli, and M. Vita. 2005. A multi-agent system for modelling the oxidation of carbohydrate cellular process. In Computational Science and Its Applications - ICCSA 2005 Part II, Volume 3481 of LNCS, 1265-1273. Springer Verlag.
6. Curti, M., P. Degano, C. Priami, and C. T. Baldari. 2004. Modelling biochemical pathways through enhanced pi-calculus. Theoretical Computer Science 325 (1): 111-140.
7. Dhar, P., H. Zhu, and S. Mishra. 2004, September. Computational approach to systems biology: From fraction to integration and beyond. IEEE Transactions on Nanobio-science III (3): 144-152.
8. Epstein, J. M., and R. L. Axtell. 1996, November. Growing artificial societies - social science from the bottom up. The MIT Press.
9. Finkelstein, A., J. Hetherington, L. Li, O. Margominski, P. Saffrey, R. Seymour, and A. Warner. 2004. Computational challenges of systems biology. IEEE Computer 37 (5): 26-33.
10. Fisher, J., D. Harel, E. J. A. Hubbard, N. Piterman, M. J. Stern, and N. Swerdlin. 2005, May. Combining state-based and scenario-based approaches in modeling biological systems. In Computational Methods in Systems Biology: International Conference, ed. V Danos and V Schachter, Volume 3082 of LNBI, 145-168: Springer-Verlag.
11. Gonzalez, P., M. Cardenas, D. Camacho, A. Franyuti, O. Rosas, and J. Otero. 2003, February-March. Cellu-lat: an agent-based intracellular signalling model. BioSystems 68 (2-3): 171-185.
12. Khan, S., R. Makkena, F. McGeary, K. Decker, W. Gillis, and C. Schmidt. 2003, 14-18 July. A multi-agent system for the quantitative simulation of biological networks. In 2nd International Joint Conference on Autonomous Agents and Multiagent Systems (AAMAS 2003), ed. J. S. Rosenschein, T. Sandholm, M. J. Wooldridge, and M. Yokoo, 385-392. New York, USA: ACM Press.
13. Kitano, H. 2002, March. Systems biology: A brief overview. Science 295:1662-1664.
14. Omicini, A., and E. Denti. 2001, November. From tuple spaces to tuple centres. Science of Computer Programming 41 (3): 277-294.
15. Omicini, A., A. Ricci, and M. Viroli. 2006. Agens Faber: Toward a theory of artefacts for MAS. Electronic Notes in Theoretical Computer Sciences. 1st International Workshop "Coordination and Organization," (CoOrg 2005), COORDINATION 2005, Namur, Belgium, 22 April 2005. Post-proceedings.
16. Omicini, A., and F. Zambonelli. 1999, September. Coordination for Internet application development. Autonomous Agents and Multi-Agent Systems 2 (3): 251-269. Special Issue: Coordination Mechanisms for Web Agents.
17. Peleg, M., I. Yeh, and R. Altman. 2002. Modeling biological process using workflow and Petri nets. Bioinfomatics 18 (6): 825-837.
18. Pogson, M., M. Holcomb, and E. Qwarnstrom. 2004. An agent based model of the nf-kb signalling pathways. In The VInternational Conference on Systems Biology (ICSB 2004).
19. Querrec, G., V Rodin, J. F. Abgrall, S. Kerdelo, and J. Tisseau. 2003. Uses of multiagents systems for simulation of MAPK pathway. In 3rd IEEE Symposium on Bioinformat-ics and Bioengineering (BIBE'03), 421-425. IEEE.
20. Regev, A., E. M. Panina, W. Silverman, L. Cardelli, and E. Y Shapiro. 2004. Bioambients: an abstraction for biological compartments. Theor. Comput. Sci. 325 (1): 141-167.
21. Regev, A., W. Silverman, and E. Shapiro. 2001. Representation and simulation of biochemical processes using the pi-calculus process algebra. In Pacific Symposium of Bio-computing (PSB 2001), 459-470.
22. Ricci, A., M. Viroli, and A. Omicini. 2006, March. Programming MAS with artifacts. In Programming Multi-Agent Systems, ed. R. P. Bordini, M. Dastani, J. Dix, and A. El Fallah Seghrouchni, Volume 3862 of LNAI, 206-221. springer. 3rd international workshop (pro-mas 2005), aamas 2005, utrecht, the netherlands, 26 july 2005. revised and invited papers.
23. Shimizu, T. S., and D. Bray. 2001. Computational cell biology - the stochastic approach. Cambridge, MA: The MIT Press.
24. Stepney, S., R. Smith, J. Timmis, A. Tyrrel, M. Neal, and A. Hone. 2005, July. Conceptual frameworks for artificial immune systems. International Journal of Unconventional Computing 1 (3): 315-338.
25. Wooldridge, M. J., and N. R. Jennings. 1995. Intelligent agents: Theory and practice. The Knowledge Engineering Review 10 (2): 115-152.