Database analysis of simulated and recorded electrophysiological datasets with PANDORA's toolbox

Neuroinformatics

Volumn 7, Issue 2, 2009, Pages 93-111

  Günay, Cengiz ^a   Edgerton, Jeremy R ^a   Li, Su ^b   Sangrey, Thomas ^c   Prinz, Astrid A ^a   Jaeger, Dieter ^a  

^a EMORY UNIVERSITY   (United States)

^b EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY GRADUATE UNIVERSITY   (Japan)

Author keywords

Automated analysis; Data visualization; Database; Electrophysiology; Large datasets; Matlab; Neural model; Open source; Pandora; Simulation; SQL

Indexed keywords

ACTION POTENTIAL; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CELL MEMBRANE POTENTIAL; COMPUTER PROGRAM; COMPUTER SIMULATION; DATA BASE; DRUG EFFECT; ELECTROPHYSIOLOGY; ELECTROSTIMULATION; FACTUAL DATABASE; GANGLION; GLOBUS PALLIDUS; MULTIVARIATE ANALYSIS; NEPHROPIDAE; NERVE CELL; PATCH CLAMP; PHYSIOLOGY; RAT; TIME;

ACTION POTENTIALS; ANIMALS; COMPUTER SIMULATION; DATABASE MANAGEMENT SYSTEMS; DATABASES, FACTUAL; ELECTRIC STIMULATION; ELECTROPHYSIOLOGICAL PHENOMENA; GANGLIA, INVERTEBRATE; GLOBUS PALLIDUS; MEMBRANE POTENTIALS; MODELS, NEUROLOGICAL; MULTIVARIATE ANALYSIS; NEPHROPIDAE; NEURONS; PATCH-CLAMP TECHNIQUES; RATS; SOFTWARE; TIME FACTORS;

EID: 67651229652     PISSN: 15392791     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12021-009-9048-z     Document Type: Article

References (52)

1. P Achard ED Schutter 2006 Complex parameter landscape for a complex neuron model PLoS Computers in Biology 2 7 e94 10.1371/journal.pcbi.0020094 10.1371/journal.pcbi.0020094 (Pubitemid 44147389)
2. SM Baxter SW Day JS Fetrow SJ Reisinger 2006 Scientific software development is not an oxymoron PLoS Computers in Biology 2 975 978 1:CAS:528:DC%2BD28XhtVCgtL3N
3. BP Bean 2007 The action potential in mammalian central neurons Nature Reviews. Neuroscience 8 6 451 465 10.1038/nrn2148 17514198 10.1038/nrn2148 1:CAS:528:DC%2BD2sXlsVSktb0%3D (Pubitemid 46789230)
4. J Bjaalie 2008 Understanding the brain through neuroinformatics Front Neuroscience 2 1 19 21 10.3389/neuro.01.022.2008 10.3389/neuro.01.022.2008
5. JG Bjaalie S Grillner 2007 Global neuroinformatics: The international neuroinformatics coordinating facility Journal of Neuroscience 27 14 3613 3615 10.1523/jneurosci.0558-07.2007 17409224 10.1523/JNEUROSCI.0558-07.2007 1:CAS:528:DC%2BD2sXksFSlu7o%3D (Pubitemid 46557656)
6. H Bokil O Tchernichovski PP Mitra 2006 Dynamic phenotypes: Time series analysis techniques for characterizing neuronal and behavioral dynamics Neuroinformatics 4 1 119 128 16595862 10.1385/NI:4:1:119 (Pubitemid 43780282)
7. Bower, J. M., & Beeman, D. (1998). The book of GENESIS (2nd ed.). New York: Springer.
8. EN Brown RE Kass PP Mitra 2004 Multiple neural spike train data analysis: State-of-the-art and future challenges Nature Neuroscience 7 5 456 461 15114358 10.1038/nn1228 1:CAS:528:DC%2BD2cXjsFKltrg%3D (Pubitemid 38552378)
9. RJ Calin-Jageman MJ Tunstall BD Mensh PS Katz WN Frost 2007 Parameter space analysis suggests multi-site plasticity contributes to motor pattern initiation in Tritonia Journal of Neurophysiology 98 4 2382 2398 10.1152/jn.00572.2007 17652417 10.1152/jn.00572.2007 (Pubitemid 47584420)
10. RC Cannon MO Gewaltig P Gleeson US Bhalla H Cornelis ML Hines, et al. 2007 Interoperability of neuroscience modeling software: Current status and future directions Neuroinformatics 5 2 127 138 10.1007/s12021-007-0004-5 17873374 10.1007/s12021-007-0004-5 (Pubitemid 351359821)
11. Carnevale, N., & Hines, M. (2006). The NEURON book. Cambridge: Cambridge University Press.
12. Chamberlin, D. D., & Boyce, R. F. (1974). SEQUEL: A structured English query language. In International conference on management of data, proceedings of the 1974 ACM SIGFIDET (now SIGMOD) workshop on data description, access and control (pp. 249-264). Ann Arbor, Michigan.
13. E Codd 1970 A relational model of data for large shared data banks Communications of the ACM 13 6 377 387 10.1145/362384.362685
14. J Cui L Xu SL Bressler M Ding H Liang 2008 BSMART: A MATLAB/C toolbox for analysis of multichannel neural time series Neural Networks 21 8, Sp. Iss. SI 1094 1104 10.1016/j.neunet.2008.05.007 18599267 10.1016/j.neunet.2008.05.007
15. Eaton, J. W. (2002). GNU Octave. A numerical engineering software package. http://www.che.wisc.edu/octave.
16. Elmasri, R., & Navathe, S. B. (1994). Fundamentals of database systems (2nd ed.). Reading: Addison-Wesley.
17. Fonseca, C. M., & Fleming, P. J. (1993). Genetic algorithms for multiobjective optimization: Formulation, discussion and generalization. In Genetic algorithms: Proceedings of the fifth international conference (pp. 416-423). San Francisco: Morgan Kaufmann.
18. D Gardner A Toga G Ascoli J Beatty J Brinkley A Dale, et al. 2003 Towards effective and rewarding data sharing Neuroinformatics 1 3 289 295 15046250 10.1385/NI:1:3:289 (Pubitemid 36988728)
19. D Gardner H Akil GA Ascoli DM Bowden W Bug DE Donohue, et al. 2008 The neuroscience information framework: A data and knowledge environment for neuroscience Neuroinformatics 6 3 149 160 10.1007/s12021-008-9024-z 18946742 10.1007/s12021-008-9024-z
20. P Gleeson V Steuber RA Silver 2007 neuroConstruct: A tool for modeling networks of neurons in 3D space Neuron 54 2 219 235 10.1016/j.neuron.2007.03.025 17442244 10.1016/j.neuron.2007.03.025 1:CAS:528:DC%2BD2sXltF2nsb8%3D (Pubitemid 46561205)
21. Günay, C. (2007). Plotting and analysis for neural database-oriented research applications (PANDORA) toolbox. http://userwww.service.emory.edu/ ~cgunay/pandora.
22. Günay, C. (2008a). PANDORA neural analysis toolbox. In Intenational Neuroinformatics coordinating facility (INCF) software center. http://software.incf.org/software/44/view/PANDORA.
23. Günay, C. (2008b). PANDORA neural analysis toolbox. SimToolDB. http://senselab.med.yale.edu/SimToolDB.
24. C Günay JR Edgerton D Jaeger 2008 Channel density distributions explain spiking variability in the globus pallidus: A combined physiology and computer simulation database approach Journal of Neuroscience 28 30 7476 7491 10.1523/jneurosci.4198-07.2008 18650326 10.1523/JNEUROSCI.4198-07.2008
25. C Günay RM Hooper KR Hammett AA Prinz 2008 Calcium sensor properties for activity-dependent homeostatic regulation of pyloric network rhythms in the lobster stomatogastric ganglion BMC Neuroscience 9 Suppl 1 P42 10.1186/1471-2202-9-S1-P42
26. Günay, C., Smolinski, T., Lytton, W., et al. (2008c). Computational intelligence in electrophysiology: Trends and open problems. In T. Smolinski, M. Milanova, & A. E. Hassanien (Eds.), Applications of computational intelligence in biology: Current trends and open problems (chap. XIV, pp. 325-359). New York: Springer.
27. AV Herz R Meier MP Nawrot W Schiegel T Zito 2008 G-Node: An integrated tool-sharing platform to support cellular and systems neurophysiology in the age of global neuroinformatics Neural Networks 21 8 1070 1075 10.1016/j.neunet. 2008.05.011 18653312 10.1016/j.neunet.2008.05.011 (Special Issue on Neuroinformatics)
28. M Hines T Morse M Migliore N Carnevale G Shepherd 2004 ModelDB: A database to support computational neuroscience Journal of Computational Neuroscience 17 1 7 11 15218350 10.1023/B:JCNS.0000023869.22017.2e http://senselab.med.yale.edu/ModelDB
29. A Hodgkin A Huxley 1952 A quantitative description of membrane current and its application to conduction and excitation in nerve Journal of Physiology 117 4 500 544 12991237 1:STN:280:DyaG3s%2FhsFGjug%3D%3D
30. QJM Huys MB Ahrens L Paninski 2006 Efficient estimation of detailed single-neuron models Journal of Neurophysiology 96 2 872 890 10.1152/jn.00079.2006 16624998 10.1152/jn.00079.2006 (Pubitemid 44159755)
31. Johnson, D. H., & Sinanović, S. (2001). Symmetrizing the Kullback-Leibler distance. Tech. Rep., Electrical & Computer Engineering Department, MS380 Rice University Houston, Texas 77005-1892. http://www-dsp.rice.edu/~dhj/resistor.pdf.
32. S Kullback R Leibler 1951 On information and sufficiency Annals of Mathematical Statistics 22 1 79 86 10.1214/aoms/1177729694
33. M Lidierth 2009 sigTOOL: A MATLAB-based environment for sharing laboratory-developed software to analyze biological signals Journal of Neuroscience Methods 10.1016/j.jneumeth.2008.11.004 19056423
34. Z Liu J Golowasch E Marder LF Abbott 1998 A model neuron with activity-dependent conductances regulated by multiple calcium sensors Journal of Neuroscience 18 7 309 320
35. WW Lytton 2006 Neural query system-data-mining from within the neuron simulator Neuroinformatics 4 2 163 175 16845167 10.1385/NI:4:2:163 (Pubitemid 44127958)
36. Meier, R., Boven, K., Aertsen, A., & Egert, U. (2007). FIND-finding information in neural data, An open-source analysis toolbox for multiple-neuron recordings and network simulations. In Proc. 7th German Neurosci Meeting (p. 1212).
37. R Meier U Egert A Aertsen MP Nawrot 2008 FIND-A unified framework for neural data analysis Neural Networks 21 8 1085 1093 10.1016/j.neunet.2008.06.019 18692360 10.1016/j.neunet.2008.06.019 (Special Issue on Neuroinformatics)
38. T Morse 2007 Model sharing in computational neuroscience Scholarpedia 2 4 3036 http://www.scholarpedia.org/article/Model-sharing-in-computational- neuroscience
39. M Nicolelis D Dimitrov J Carmena R Crist G Lehew J Kralik, et al. 2003 Chronic, multisite, multielectrode recordings in macaque monkeys Proceedings of the National Academy of Sciences of the United States of America 100 19 11041 11046 12960378 10.1073/pnas.1934665100 1:CAS:528:DC%2BD3sXnslynu78%3D (Pubitemid 37140149)
40. S Pittendrigh G Jacobs 2003 Neurosys: A semistructured laboratory database Neuroinformatics 1 2 167 176 15046239 10.1007/s12021-003-0003-0
41. AA Prinz CP Billimoria E Marder 2003 Alternative to hand-tuning conductance-based models: Construction and analysis of databases of model neurons Journal of Neurophysiology 90 3998 4015 12944532 10.1152/jn.00641.2003 (Pubitemid 37541930)
42. AA Prinz D Bucher E Marder 2004 Similar network activity from disparate circuit parameters Nature Neuroscience 7 12 1345 1352 15558066 10.1038/nn1352 1:CAS:528:DC%2BD2cXhtVCjsLzE (Pubitemid 41057757)
43. M Sekerli C Del Negro R Lee R Butera 2004 Estimating action potential thresholds from neuronal time-series: New metrics and evaluation of methodologies IEEE Transactions on Biomedical Engineering 51 9 1665 1672 10.1109/TBME.2004.827531 15376515 10.1109/TBME.2004.827531 (Pubitemid 39100239)
44. Shepherd, G., Mirsky, J., Healy, M., et al. (1998). The human brain project: Neuroinformatics tools for integrating, searching and modeling multidisciplinary neuroscience data. TINS, 21(11).
45. S Sinanović DH Johnson 2007 Toward a theory of information processing Signal Processing 87 1326 1344 10.1016/j.sigpro.2006.11.005 (Pubitemid 46306208)
46. Smolinski, T. G., Prinz, A. A., & Zurada, J. M. (2008). Hybridization of rough sets and multi-objective evolutionary algorithms for classificatory signal decomposition. In A. E. Hassanien, Z. Suraj, D. Ślezak, & P. Lingras (Eds.), Rough computing: Theories, technologies, and applications (chap. X, pp. 204-227). Hershey: Information Science Reference.
47. AL Taylor TJ Hickey AA Prinz E Marder 2006 Structure and visualization of high-dimensional conductance spaces Journal of Neurophysiology 96 891 905 16687617 10.1152/jn.00367.2006 (Pubitemid 44155224)
48. Van Geit, W., Achard, P., & Schutter, E. D. (2007). Neurofitter: A parameter tuning package for a wide range of electrophysiological neuron models. Frontiers in Neuroinformatics, 1, 1.
49. W Van Geit E De Schutter P Achard 2008 Automated neuron model optimization techniques: A review Biological Cybernetics 99 4-5 241 251 10.1007/s00422-008-0257-6 19011918 10.1007/s00422-008-0257-6
50. MC Vanier JM Bower 1999 A comparative survey of automated parameter-search methods for compartmental neural models Journal of Computational Neuroscience 7 149 171 10515252 10.1023/A:1008972005316 1:STN:280:DyaK1Mvktlaktw%3D%3D (Pubitemid 29433535)
51. C Weaver S Wearne 2006 The role of action potential shape and parameter constraints in optimization of compartment models Neurocomputing 69 10-12 1053 1057 10.1016/j.neucom.2005.12.044 10.1016/j.neucom.2005.12.044 (14th Annual Computational Neuroscience Meeting (CNS 05), Madison, WI, 17-21 July, 2005)
52. R Wood K Gurney C Wilson 2004 A novel parameter optimisation technique for compartmental models applied to a model of a striatal medium spiny neuron Neurocomputing 58 1109 1116 10.1016/j.neucom.2004.01.174 10.1016/j.neucom.2004. 01.174 (Pubitemid 38684370)