StochKit-FF: Efficient systems biology on multicore architectures

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 6586 LNCS, Issue , 2011, Pages 167-175

  Aldinucci, Marco ^a   Bracciali, Andrea ^b   Liò, Pietro ^c   Sorathiya, Anil ^c   Torquati, Massimo ^d  

^a UNIVERSITY OF TURIN   (Italy)

^b CNR   (Italy)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d UNIVERSITY OF PISA   (Italy)

Author keywords

multicore; simulation; Stochastic biological models

Indexed keywords

BIOLOGICAL MODELS; EFFICIENT SYSTEMS; EXTRACTING INFORMATION; HIV INFECTION; MULTI CORE; MULTI-CORES; MULTICORE ARCHITECTURES; NOVEL CONCEPT; PARALLEL VERSION; PROGRAMMING TOOLKITS; SIMULATION; STOCHASTIC MODELLING; STOCHASTIC SIMULATIONS; STRUCTURED DATA;

BIOLOGICAL SYSTEMS; DIFFERENTIAL EQUATIONS; EXPERIMENTS; PARALLEL ARCHITECTURES; SOFTWARE ARCHITECTURE; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

MULTICORE PROGRAMMING;

EID: 80051706079     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-21878-1_21     Document Type: Conference Paper

References (13)

1. Petzold, L.: StochKit web page, http://engineering.ucsb.edu/~cse/StochKit
2. Perelson, A., Neumann, A., Markowitz, M., Leonard, J., Ho, D.: HIV-1 dynamics in vivo: Virion clearance rate, infected cell life-span, and viral generation time. Science 271, 1582-1586 (1996) (Pubitemid 26097216)
3. Sguanci, L., Bagnoli, F., Liò, P.: Modeling HIV quasispecies evolutionary dynamics. BMC Evolutionary Biology 7(2), S5 (2007)
4. Gillespie, D.: Exact stochastic simulation of Coupled Chemical Reactions. The Journal of Physical Chemistry 81(25), 2340-2361 (1977)
5. Chao, L., Davenport, M., Forrest, S., Perelson, A.: A stochastic model of cytotoxic t cell responses. Journal Theoretical Biology 228, 227-240 (2004) (Pubitemid 38496284)
6. Wilkinson, D.: A stochastic model of cytotoxic T cell responses. CRC press, Boca Raton (2006)
7. Sorathiya, A., Liò, P., Bracciali, A.: Formal reasoning on qualitative models of coinfection of HIV and Tuberculosis and HAART therapy. BMC Bioinformatics 11(1) (2010); Asia Pacific Bioinformatics Conference
8. Cole, M.: Algorithmic Skeletons: Structured Management of Parallel Computations. Research Monographs in Parallel and Distributed Computing. Pitman (1989)
9. Intel Threading Building Blocks, http://software.intel.com/en-us/intel- tbb
10. Asanovic, K., Bodik, R., Demmel, J., Keaveny, T., Keutzer, K., Kubiatowicz, J., Morgan, N., Patterson, D., Sen, K., Wawrzynek, J., Wessel, D., Yelick, K.: A view of the parallel computing landscape. CACM 52(10), 56-67 (2009)
11. Fastflow project (2009), http://mc-fastflow.sourceforge.net
12. Aldinucci, M., Meneghin, M., Torquati, M.: Efficient smith-waterman on multi-core with FastFlow. In: Proc. of Intl. Euromicro PDP 2010: Parallel Distributed and Network-Based Processing, Pisa, Italy, pp. 195-199. IEEE, Los Alamitos (February 2010)
13. Aldinucci, M., Gorlatch, S., Lengauer, C., Pelagatti, S.: Towards parallel programming by transformation: The FAN skeleton framework. Parallel Algorithms and Applications 16(2-3), 87-121 (2001)