CellMC-a multiplatform model compiler for the Cell Broadband Engine and x86

Bioinformatics

Volumn 26, Issue 3, 2009, Pages 426-428

  Caulfield, Emmet ^a   Hellander, Andreas ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77949521942     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp662     Document Type: Article

References (10)

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2. Caulfield, E. (2009) CellMC: An XSLT-based SBML Model Compiler for Cell/BE and IA32. Master's Thesis, Department of Informaion Technology, Uppsala University.
3. Gibson, M.A. and Bruck, J. (2000) Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem., 104, 1876-1889.
4. Gillespie, D.T. (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reacting systems. J. Comput. Phys., 22, 403-434.
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7. Li, H. and Petzold, L. (2009) Efficient parallelization of stochastic simulation algorithm for chemically reacting systems on the graphics processing unit. Int. J. High. Perform. C. DOI: 10.1177/1094342009106066.
8. Mauch, S. and Stalzer, M. (2009) Efficient formulations for exact stochastic simulation of chemical systems. IEEE/ACM Trans. Comput. Biol. Bioinf. IEEE Computer Society Digital Library, IEEE Computer Society. Available at http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.47
9. McCollum, J.M. et al. (2005) The sorting direct method for stochastic simulation of biochemical systems with variying reaction execution behaviour. Comput. Biol. Chem., 30, 39-49.
10. Yoshimi, M. et al. (2008) Practical implementation of a network-based stochastic biochemical simulation system on an FPGA. In FPL 2008 International Conference on Field Programmable Logic and Applications, IEEE. Heidelberg, pp. 663-666.