A hierarchical parallel scheme for global parameter estimation in systems biology

Proceedings - International Parallel and Distributed Processing Symposium, IPDPS 2004 (Abstracts and CD-ROM)

Volumn 18, Issue , 2004, Pages 571-579

  He, J ^a   Sosonkina, M ^c   Shaffer, C A ^a   Tyson, J J ^b   Watson, L T ^a   Zwolak, J W ^a  

^a State University   (United States)

^b VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

^c IOWA STATE UNIVERSITY   (United States)

Author keywords

DIRECT (DIviding RECTangles) algorithm; Global optimization; GPSHMEM (generalized portable shared memory); Load balancing strategy; Multidisciplinary design optimization; Parallel and distributed data structures; Parameter estimation; Systems biology

Indexed keywords

DIRECT (DIVIDING RECTANGLES) ALGORITHM; GPSHMEM (GENERALIZED PORTABLE SHARED MEMORY); LOAD BALANCING STRATEGY; MULTIDISCIPLINARY DESIGN OPTIMIZATION; PARALLEL AND DISTRIBUTED DATA STRUCTURES; SYSTEMS BIOLOGY;

BIOLOGY; COMPUTATIONAL METHODS; COMPUTER PROGRAMMING; DATA STORAGE EQUIPMENT; DATA STRUCTURES; GLOBAL OPTIMIZATION; PARALLEL ALGORITHMS; PARAMETER ESTIMATION; PROBLEM SOLVING;

PARALLEL PROCESSING SYSTEMS;

EID: 12444255195     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (21)

1. N. A. Allen, C. A. Shaffer, M. T. Vass, N. Ramakrishnan, and L. T. Watson, "Improving the development process for Eukaryotic cell cycle models with a modeling support environment", in Winter Simulation Conference, to appear, December, 2003.
2. C. A. Baker, L. T. Watson, B. Grossman, R. T. Haftka, and W. H. Mason, "Parallel global aircraft configuration design space exploration", in High Performance Computing Symposium 2000, A. Tentner (Ed.), Soc. for Computer Simulation Internat, San Diego, CA, 2000, pp. 101-106.
3. M. C. Bartholomew-Biggs, S. C. Parkhurst, and S. P. Wilson, "Using DIRECT to solve an aircraft routing problem", Computational Optimization and Applications, vol. 21, no. 3, pp. 311-323, 2002.
4. W. R. Esposito and C. A. Floudas, "Global optimization in parameter estimation of nonlinear algebraic models via the Error-In-Variables approach", Ind Eng. Chemistry and Research, vol. 37, pp. 1841-1858, 1998.
5. J. M. Gablonsky, "Modifications of the DIRECT algorithm", PhD thesis, Department of Mathematics, North Carolina State University, Raleigh, NC, 2001.
6. C. Gau and M. A. Stadtherr, "Nonlinear parameter estimation using interval analysis", in AIchE Symposium, vol. 94, no. 320, pp 445-450, 1999.
7. A. Grama, A. Gupta, G. Karypis, and V. Kumar, Introduction to Parallel Computing, Pearson Education Limited, 2nd Edition, 2003.
8. W. Gropp, E. Lusk, and R. Thakur, Using MPI-2: Advanced features of the message-passing interface, The MIT Press, Cambridge, Massachusetts, London, England, 1999.
9. J. He, A. Verstak, L. T. Watson, T. S. Rappaport, C. R. Anderson, N. Ramakrishnan, C. A. Shaffer, W. H. Tranter, K. Bae, and J. Jiang, "Global optimization of transmitter placement in wireless communication systems", in Proc. High Performance Computing Symposium 2002, A. Tentner (ed.), Soc. for Modeling and Simulation International, San Diego, CA, pp. 328-333, 2002.
10. J. He, L. T. Watson, N. Ramakrishnan, C. A. Shaffer, A. Verstak, J. Jiang, K. Bae, and W. H. Tranter, "Dynamic data structures for a direct search algorithm", Computational Optimization and Applications, vol. 23, pp. 5-25, 2002.
11. D. R. Jones, C. D. Perttunen, and B. E. Stuckman, "Lipschitzian optimization without the Lipschitz constant", J. Optim. Theory Appl., vol. 79, no. 1, pp. 157-181, 1993.
12. D. J. Marriplis, "Parallel performance investigation of an unstructured mesh Naiver-Stokes solver", Internat. J. High Performance Computing Appl., vol. 16, no. 4, pp. 395-407, 2002.
13. V. Kumar, A. Y. Crama, and N. R. Vempaty, "Scalable load balancing techniques for parallel computers", J. Parallel Distributed Computing, vol. 22, pp. 60-79, 1994.
14. C. G. Moles, P. Mendes, and J. R. Banga, "Parameter estimation in biochemical pathways: a comparison of global optimization methods", Genome Res., vol. 13, pp. 2467-2474, 2003.
15. J. Moore, "Private Communication", Aug., 1997.
16. K. Parzyszek, J. Nieplocha, and R. A. Kendall, "A generalized portable SHMEM library for high performance computing", in 12th IASTED International Conference Parallel and Distributed Computing and Systems (PDCS), pp. 401-406, 2000.
17. R. Rabenseifner, and G. Wellein, "Communication and optimization aspects of parallel programming models on hybrid architectures", Internat. J. High Performance Computing Appl., vol. 17, no. 1, pp. 49-62, 2003.
18. M. Ruiz, O. Lopera, and C. de la Plata, "Component-based derivation of a parallel stiff ODE solver", Internat. J. Parallel Programming, vol. 30, no. 2, pp. 99-148, 2002.
19. Z. Tang, T. R. Coleman, and W. G. Dunphy, "Two distinct mechanisms for negative regulation of the Weel protein kinase", EMBO J., vol. 12, no. 9, pp. 3427-36, 1993.
20. L. T. Watson and C. A. Baker, "A fully-distributed parallel global search algorithm", Engineering Computations, vol. 18, no. 1/2, pp. 155-169, 2001.
21. J. W. Zwolak, J. J. Tyson, and L. T. Watson, "Parameter estimation in a cell cycle model for frog egg extracts", in High Performance Computing Symposium 2002, A. Tentner (ed.), Soc. for Modeling and Simulation Internat., San Diego, CA, pp. 67-74 2002.