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Items: 1 to 20 of 177

1.

Simulation of P systems with active membranes on CUDA.

Cecilia JM, García JM, Guerrero GD, Martínez-del-Amor MA, Pérez-Hurtado I, Pérez-Jiménez MJ.

Brief Bioinform. 2010 May;11(3):313-22. doi: 10.1093/bib/bbp064. Epub 2009 Dec 28.

PMID:
20038568
2.

High-performance analysis of biological systems dynamics with the DiVinE model checker.

Barnat J, Brim L, Safránek D.

Brief Bioinform. 2010 May;11(3):301-12. doi: 10.1093/bib/bbp074. Epub 2010 Apr 28.

PMID:
20478855
3.

GPU computing for systems biology.

Dematté L, Prandi D.

Brief Bioinform. 2010 May;11(3):323-33. doi: 10.1093/bib/bbq006. Epub 2010 Mar 7. Review.

PMID:
20211843
4.

Flexible experimentation in the modeling and simulation framework JAMES II--implications for computational systems biology.

Ewald R, Himmelspach J, Jeschke M, Leye S, Uhrmacher AM.

Brief Bioinform. 2010 May;11(3):290-300. doi: 10.1093/bib/bbp067. Epub 2010 Jan 28.

PMID:
20118105
5.

Comparison of GPU- and CPU-implementations of mean-firing rate neural networks on parallel hardware.

Dinkelbach HÜ, Vitay J, Beuth F, Hamker FH.

Network. 2012;23(4):212-36. doi: 10.3109/0954898X.2012.739292. Epub 2012 Nov 9.

PMID:
23140422
6.

The Beta Workbench: a computational tool to study the dynamics of biological systems.

Dematté L, Priami C, Romanel A.

Brief Bioinform. 2008 Sep;9(5):437-49. doi: 10.1093/bib/bbn023. Epub 2008 May 7.

PMID:
18463130
7.

GPU accelerated biochemical network simulation.

Zhou Y, Liepe J, Sheng X, Stumpf MP, Barnes C.

Bioinformatics. 2011 Mar 15;27(6):874-6. doi: 10.1093/bioinformatics/btr015. Epub 2011 Jan 11.

8.

High performance cellular level agent-based simulation with FLAME for the GPU.

Richmond P, Walker D, Coakley S, Romano D.

Brief Bioinform. 2010 May;11(3):334-47. doi: 10.1093/bib/bbp073. Epub 2010 Feb 1.

PMID:
20123941
9.

Parallelized computation for computer simulation of electrocardiograms using personal computers with multi-core CPU and general-purpose GPU.

Shen W, Wei D, Xu W, Zhu X, Yuan S.

Comput Methods Programs Biomed. 2010 Oct;100(1):87-96. doi: 10.1016/j.cmpb.2010.06.015. Epub 2010 Jul 31.

PMID:
20674066
10.

Implementation and performance evaluation of reconstruction algorithms on graphics processors.

Castaño Díez D, Mueller H, Frangakis AS.

J Struct Biol. 2007 Jan;157(1):288-95. Epub 2006 Sep 1.

PMID:
17029985
11.

Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology.

Schmidt H, Jirstrand M.

Bioinformatics. 2006 Feb 15;22(4):514-5. Epub 2005 Nov 29.

PMID:
16317076
12.

Taming the complexity of biological pathways through parallel computing.

Ballarini P, Guido R, Mazza T, Prandi D.

Brief Bioinform. 2009 May;10(3):278-88. doi: 10.1093/bib/bbp020. Epub 2009 Apr 1.

PMID:
19339382
13.

A configurable simulation environment for the efficient simulation of large-scale spiking neural networks on graphics processors.

Nageswaran JM, Dutt N, Krichmar JL, Nicolau A, Veidenbaum AV.

Neural Netw. 2009 Jul-Aug;22(5-6):791-800. doi: 10.1016/j.neunet.2009.06.028. Epub 2009 Jul 2.

PMID:
19615853
14.

UML as a cell and biochemistry modeling language.

Webb K, White T.

Biosystems. 2005 Jun;80(3):283-302. Epub 2005 Feb 17.

PMID:
15888343
15.

A system for compartmental modelling and simulation.

Leaning MS, Boroujerdi MA.

Comput Methods Programs Biomed. 1991 Jun;35(2):71-92.

PMID:
1914454
16.

Streaming parallel GPU acceleration of large-scale filter-based spiking neural networks.

Slażyński L, Bohte S.

Network. 2012;23(4):183-211. doi: 10.3109/0954898X.2012.733842. Epub 2012 Oct 25.

PMID:
23098420
17.

Nexa: a scalable neural simulator with integrated analysis.

Benjaminsson S, Lansner A.

Network. 2012;23(4):254-71. doi: 10.3109/0954898X.2012.737087. Epub 2012 Nov 1.

PMID:
23116128
18.

Resources, standards and tools for systems biology.

Wierling C, Herwig R, Lehrach H.

Brief Funct Genomic Proteomic. 2007 Sep;6(3):240-51. Epub 2007 Oct 17.

PMID:
17942476
19.

On the hybridization of memetic algorithms with branch-and-bound techniques.

Gallardo JE, Cotta C, Fernández AJ.

IEEE Trans Syst Man Cybern B Cybern. 2007 Feb;37(1):77-83.

PMID:
17278561
20.

Integration of the Gene Ontology into an object-oriented architecture.

Shegogue D, Zheng WJ.

BMC Bioinformatics. 2005 May 10;6:113.

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