Optimizing ion channel models using a parallel genetic algorithm on graphical processors

Journal of Neuroscience Methods

Volumn 206, Issue 2, 2012, Pages 183-194

  Ben Shalom, Roy ^a   Aviv, Amit ^a   Razon, Benjamin ^a,b   Korngreen, Alon ^a  

^a BAR ILAN UNIVERSITY   (Israel)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

CUDA; Data fitting; Genetic algorithm; GPGPU; GPU; Graphic card; Neuron; Parallel computation; Voltage gated channels

Indexed keywords

VOLTAGE GATED POTASSIUM CHANNEL;

ARTICLE; COMPUTER SIMULATION; GENETIC ALGORITHM; MEMORY; NEUROPHYSIOLOGY; PRIORITY JOURNAL; PROCESS OPTIMIZATION;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; ION CHANNELS; MODELS, BIOLOGICAL;

EID: 84859062903     PISSN: 01650270     EISSN: 1872678X     Source Type: Journal    
DOI: 10.1016/j.jneumeth.2012.02.024     Document Type: Article

References (37)

1. Colquhoun D., Hawkes A. A Q-matrix cookbook. Single-channel recording 1995, 589-633. Plenum Press, New York. B. Sakmann, E. Neher (Eds.).
2. Colquhoun D., Sigworth F. Fitting and statistical analysis of single-channel records. Single-channel recording 1995, 483-585. Plenum, New York. B. Sakman, E. Neher (Eds.).
3. Eichner H., Klug T., Borst A. Neural simulations on multi-core architectures. Front Neuroinform 2009, 3:21.
4. Gropp W.a.T., Rajeev, Lusk E. Using MPI-2: advanced features of the message passing interface 1999, MIT Press. 2nd ed.
5. Gurkiewicz M., Korngreen A. A numerical approach to ion channel modelling using whole-cell voltage-clamp recordings and a genetic algorithm. PLoS Comput Biol 2007, 3:e169.
6. Gurkiewicz M., Korngreen A. Recording analysis, and function of dendritic voltage-gated channels. Pflugers Arch 2006, 453:283-292.
7. Gurkiewicz M., Korngreen A., Waxman S.G., Lampert A. Kinetic modeling of Nav1.7 provides insight into erythromelalgia-associated F1449V mutation. J Neurophysiol 2011, 105:1546-1557.
8. Hamill O.P., Marty A., Neher E., Sakmann B., Sigworth F.J. Improved patch-clamp techniques for high-resolution current recording from cells and cell-free membrane patches. Pflugers Arch 1981, 391:85-100.
9. Hines M.L., Carnevale N.T. Expanding NEURON's repertoire of mechanisms with NMODL. Neural Comput 2000, 12:995-1007.
10. Hines M.L., Carnevale N.T. The NEURON simulation environment. Neural Comput 1997, 9:1179-1209.
11. Hines M.L., Carnevale N.T. NEURON: a tool for neuroscientists. Neuroscientist 2001, 7:123-135.
12. Hodgkin A.L., Huxley A.F. The components of membrane conductance in the giant axon of Loligo. J Physiol 1952, 116:473-496.
13. Hodgkin A.L., Huxley A.F. Currents carried by sodium and potassium ions through the membrane of the giant axon of Loligo. J Physiol 1952, 116:449-472.
14. Hodgkin A.L., Huxley A.F. The dual effect of membrane potential on sodium conductance in the giant axon of Loligo. J Physiol 1952, 116:497-506.
15. Hodgkin A.L., Huxley A.F. A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 1952, 117:500-544.
16. Hodgkin A.L., Huxley A.F., Katz B. Measurement of current-voltage relations in the membrane of the giant axon of Loligo. J Physiol 1952, 116:424-448.
17. John E.S., Jan S., David J.H., Kirby L.V., Wen-mei W.H., Klaus S. High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs. Proceedings of 2nd workshop on general purpose processing on graphics processing units 2009, ACM, Washington, D.C.
18. Keren N., Bar-Yehuda D., Korngreen A. Experimentally guided modelling of dendritic excitability in rat neocortical pyramidal neurones. J Physiol 2009, 587:1413-1437.
19. Keren N., Peled N., Korngreen A. Constraining compartmental models using multiple voltage recordings and genetic algorithms. J Neurophysiol 2005, 94:3730-3742.
20. Liu Y., Maskell D.L., Schmidt B. CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units. BMC Res Notes 2009, 2:73.
21. Manavski S.A., Valle G. CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. BMC Bioinformatics 2008, 9(Suppl. 2):S10.
22. Mitchell M. An introduction to genetic algorithms 1996, The MIT Press, Cambridge, MA, US.
23. Nageswaran J.M., Dutt N., Krichmar J.L., Nicolau A., Veidenbaum A.V. A configurable simulation environment for the efficient simulation of large-scale spiking neural networks on graphics processors. Neural Networks 2009, 22:791-800.
24. NVIDIA. CUDA C best practices guide; 2011a.
25. NVIDIA. Nsight; 2011b.
26. NVIDIA. NVIDIA CUDA compute unified device architecture programming guide; 2011c.
27. NVIDIA. NVIDIA Fermi compute architecture whitepaper; 2009.
28. NVIDIA. NVIDIA Tesla GPU computing technical brief; 2007.
29. Pinto N., Doukhan D., DiCarlo J.J., Cox D.D. A high-throughput screening approach to discovering good forms of biologically inspired visual representation. PLoS Comput Biol 2009, 5:e1000579.
30. Qin F., Auerbach A., Sachs F. Estimating single-channel kinetic parameters from idealized patch-clamp data containing missed events. Biophys J 1996, 70:264-280.
31. Qin F., Auerbach A., Sachs F. Maximum likelihood estimation of aggregated Markov processes. Proc Biol Sci/R Soc 1997, 264:375-383.
32. Rossant C., Goodman D.F., Fontaine B., Platkiewicz J., Magnusson A.K., Brette R. Fitting neuron models to spike trains. Front Neurosci 2011, 5:9.
33. Sakmann B., Neher E. Single channel recording 1995, Plenum, New York, p. 700.
34. Stone J.E., Phillips J.C., Freddolino P.L., Hardy D.J., Trabuco L.G., Schulten K. Accelerating molecular modeling applications with graphics processors. J Comput Chem 2007, 28:2618-2640.
35. Tobias B., Lothar T. A comparison of selection schemes used in evolutionary algorithms. Evol Comput 1996, 4:361-394.
36. Willms A.R., Baro D.J., Harris-Warrick R.M., Guckenheimer J. An improved parameter estimation method for Hodgkin-Huxley models. J Comput Neurosci 1999, 6:145-168.
37. Won-Ki J., Beyer J., Hadwiger M., Blue R., Law C., Vazquez-Reina A., et al. Analysis tools for large-scale neuroscience data sets. IEEE Comput Graph Appl 2010, 30:58-70.