A flexible architecture for performance experiments with the pi-Calculus and its extensions

SIMUTools 2010 - 3rd International ICST Conference on Simulation Tools and Techniques

Volumn , Issue , 2010, Pages

  Leye, Stefan ^a   John, Mathias ^a   Uhrmacher, Adelinde M ^a  

^a Institute of Computer Science   (Germany)

Author keywords

Discre event simulation; Pi Calculus; Process algebra; Simulation environment; Software

Indexed keywords

COMPUTER SOFTWARE; EFFICIENCY; SIMULATORS; STOCHASTIC SYSTEMS;

COMPUTATIONAL SYSTEMS BIOLOGY; EVENT SIMULATION; FLEXIBLE ARCHITECTURES; PERFORMANCE EXPERIMENT; PERFORMANCE SIMULATOR; PI CALCULUS; PROCESS ALGEBRAS; SIMULATION ENVIRONMENT;

CALCULATIONS;

EID: 84922927939     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.4108/ICST.SIMUTOOLS2010.8820     Document Type: Conference Paper

References (28)

1. S. Balakirsky and T. R. Kramer. Comparing algorithms: Rules of thumb and an example. In Performance Metrics for Intelligent Systems, 2004.
2. A. Bloch, B. Haagensen, M. K. Høyer, and S. U. Knudsen. The StoPi-calculus and simulator - a stochastic pi-calculus and the implementation of a simulator. Technical report, University of Aalborg, 2003.
3. R. Brown. Calendar queues: a fast o (1) priority queue implementation for the simulation event set problem. Communications of the ACM, 31:1220-1227, 1988.
4. M. B. Elowitz and S. Leibler. A synthetic oscillatory network of transcriptional regulators. Nature, 403:335-338, 2000.
5. R. Ewald, J. Rössel, J. Himmelspach, and A. M. Uhrmacher. A plug-in - based architecture for random number generation in simulation systems. In WSC, 2008.
6. M. Gibson and J. Bruck. Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels. J. Chem. Physics, 104:1876-1889, 2000.
7. D. T. Gillespie. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. The Journal of Physical Chemistry, 22, 1976.
8. D. T. Gillespie. Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry, 81, 1977.
9. R. S. M. Goh and I. L.-J. Thng. Mlist: An efficient pending event set structure for discrete event simulation. International Journal of SIMULATION, 4:66-77, 2003.
10. J. Himmelspach, R. Ewald, and A. M. Uhrmacher. A flexible and scalable experimentation layer for JAMES II. In WSC, pages 827-835, 2008.
11. J. Himmelspach and A. M. Uhrmacher. The event queue problem and pdevs. In Proceedings of the SpringSim'07, DEVS Integrative M&S Symposium, pages 257-264. SCS, 2007.
12. J. Himmelspach and A. M. Uhrmacher. Plug'n simulate. In Proceedings of the 40th Annual Simulation Symposium, pages 137-143. IEEE Computer Society, 2007.
13. M. John, R. Ewald, and A. M. Uhrmacher. A spatial extension to the pi calculus. In Electronic Notes in Theoretical Computer Science, volume 194, pages 133-148, 2008.
14. M. John, C. Lhoussaine, J. Niehren, and A. Uhrmacher. The attributed pi calculus. In CMSB, pages 83-102, 2008.
15. V. Khomenko and R. Meyer. Checking Pi Calculus Structural Congruence is Graph Isomorphism Complete. Technical Report CS-TR: 1100, School of Computing Science, Newcastle University, 2008.
16. S. Leye, J. Himmelspach, M. Jeschke, R. Ewald, and A. M. Uhrmacher. A grid-inspired mechanism for coarse-grained experiment execution. In DSRT, pages 7-16, 2008.
17. S. Leye, M. Jeschke, and M. John. The spacepi simulator, 2007.
18. S. Leye, C. Priami, and A. M. Uhrmacher. A bounded-optimistic, parallel beta-binders simulator. In DSRT, pages 139-148, 2008.
19. C. C. McGeoch. Experimental analysis of algorithms. Notices of the AMS, 48:304-311, 2001.
20. R. Milner, J. Parrow, and D. Walker. A calculus of mobile processes. Inf. Comput., 100(1):1-77, 1992.
21. A. Phillips and L. Cardelli. A correct abstract machine for the stochastic pi-calculus. Electronic Notes in Theoretical Computer Science, 2004.
22. A. Phillips and L. Cardelli. Efficient, correct simulation of biological processes in the stochastic pi-calculus. In CMSB, pages 184-199, 2007.
23. R. Pozo and B. Miller. Java scimark: http://math.nist.gov/scimark2/.
24. C. Priami. Stochastic p-calculus. The Computer Journal, 38/7:578-589, 1995.
25. C. Priami and P. Quaglia. Beta-binders for biological interactions. In CMSB, 2004.
26. C. Priami, A. Regev, E. Shapiro, and W. Silverman. Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Inf. Process. Lett., 80:25-31, 2001.
27. A. Regev, W. Silverman, and E. Shapiro. Representation and simulation of biochimcal processes using the pi-calculus process algebra. In Pacific Symposium on Biocomputing, volume 6, pages 459-470, 2001.
28. Z. Y. Xia, Y. Zhong, and S. Zhang. Analysis for active network security abased on pi-calculus model. Computer Networks and Mobile Computing, 0:366, 2003.