Channelpedia: An integrative and interactive database for ion channels

Frontiers in Neuroinformatics

Volumn 5, Issue , 2011, Pages

  Ranjan, Rajnish ^a   Khazen, Georges ^a   Gambazzi, Luca ^a   Ramaswamy, Srikanth ^a   Hill, Sean L ^a   Sch�rmann, Felix ^a   Markram, Henry ^a  

^a EPFL   (Switzerland)

Author keywords

Database; Hodgkin Huxley model; Information management; Ion channel; Kinetics; Structured wiki

Indexed keywords

ION CHANNEL; VOLTAGE GATED POTASSIUM CHANNEL;

ARTICLE; COMPUTER ANALYSIS; DATA SYNTHESIS; HODGKIN HUXLEY EQUATION; INFORMATION PROCESSING; INFORMATION SYSTEM; MATHEMATICAL PARAMETERS; NERVE CELL EXCITABILITY; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PUBLICATION;

EID: 84994056664     PISSN: None     EISSN: 16625196     Source Type: Journal    
DOI: 10.3389/fninf.2011.00036     Document Type: Article

References (22)

1. Aranda, B., Achuthan, P., Alam-Faruque, Y., Armean, I., Bridge, A., Derow, C., Feuermann, M., Ghanbarian, A. T., Kerrien, S., Khadake, J., Kerssemakers, J., Leroy, C., Menden, M., Michaut, M., Montecchi-Palazzi, L., Neuhauser, S. N., Orchard, S., Perreau, V., Roechert, B., Van Eijk, K., and Hermjakob, H. (2010). The IntAct molecular interaction database in 2010. Nucleic Acids Res. 38, D525-D531.
2. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., and Sherlock, G. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29.
3. Baranauskas, G., Tkatch, T., and Surmeier, D. J. (1999). Delayed rectifier currents in rat globus pallidus neurons are attributable to Kv2.1 and Kv3.1/3.2 K(+) channels. J. Neurosci. 19, 6394-6404.
4. Beeman, D., and Bower, J. M. (2004). Simulator-independent representation of ionic conductance models with channeldb. Neurocomputing 1085-1090.
5. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000). The protein data bank. Nucleic Acids Res. 28, 235-242.
6. Brammar, E. C. C. A. W. J. (1998). Ion Channel Facts Book Voltage-Gated Channels. San Diego: Academic Press.
7. Chan, C. S., Guzman, J. N., Ilijic, E., Mercer, J. N., Rick, C., Tkatch, T., Meredith, G. E., and Surmeier, D. J. (2007). “Rejuvenation” protects neurons in mouse models of Parkinson’s disease. Nature 447, 1081-1086.
8. Contributors, W. (2004). “Ion Channel” Wikipedia, the Free Encyclopedia. Available at: http://en.wikipedia.org/wiki/Ion_channel [accessed February 10, 2011].
9. Dhaka, A., Viswanath, V., and Patapoutian, A. (2006). Trp ion channels and temperature sensation. Annu. Rev. Neurosci. 29, 135-161.
10. Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gordon, L., Hendrix, M., Hourlier, T., Johnson, N., Kahari, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Kulesha, E., Larsson, P., Longden, I., Mclaren, W., Overduin, B., Pritchard, B., Riat, H. S., Rios, D., Ritchie, G. R., Ruffier, M., Schuster, M., Sobral, D., Spudich, G., Tang, Y. A., Trevanion, S., Vandrovcova, J., Vilella, A. J., White, S., Wilder, S. P., Zadissa, A., Zamora, J., Aken, B. L., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernandez-Suarez, X. M., Herrero, J., Hubbard, T. J., Parker, A., Proctor, G., Vogel, J., and Searle, S. M. (2011). Ensembl 2011. Nucleic Acids Res. 39, D800-D806.
11. Gleeson, P., Crook, S., Cannon, R. C., Hines, M. L., Billings, G. O., Farinella, M., Morse, T. M., Davison, A. P., Ray, S., Bhalla, U. S., Barnes, S. R., Dimitrova, Y. D., and Silver, R. A. (2010). NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Comput. Biol. 6, e1000815. doi:10.1371/journal.pcbi.1000815
12. Harmar, A. J., Hills, R. A., Rosser, E. M., Jones, M., Buneman, O. P., Dunbar, D. R., Greenhill, S. D., Hale, V. A., Sharman, J. L., Bonner, T. I., Catterall, W. A., Davenport, A. P., Delagrange, P., Dollery, C. T., Foord, S. M., Gutman, G. A., Laudet, V., Neubig, R. R., Ohlstein, E. H., Olsen, R. W., Peters, J., Pin, J. P., Ruffolo, R. R., Searls, D. B., Wright, M. W., and Spedding, M. (2009). IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels. Nucleic Acids Res. 37, D680-D685.
13. Hille, B. (2001). Ion Channels of Excitable Membranes. Sunderland, MA: Sinauer.
14. Hines, M. L., and Carnevale, N. T. (2000). Expanding neuron’s repertoire of mechanisms with NMODL. Neural Comput. 12, 995-1007.
15. Hines, M. L., and Carnevale, N. T. (2001). NEURON: a tool for neuroscientists. Neuroscientist 7, 123-135.
16. Hines, M. L., Morse, T., Migliore, M., Carnevale, N. T., and Shepherd, G. M. (2004). ModelDB: a database to support computational neuroscience. J. Comput. Neurosci. 17, 7-11.
17. Hodgkin, A. L., and Huxley, A. F. (1952). A quantitative description of membrane current and its application to conduction and excitation in nerve. J. Physiol. (Lond.) 117, 500-544.
18. Jain, E., Bairoch, A., Duvaud, S., Phan, I., Redaschi, N., Suzek, B. E., Martin, M. J., Mcgarvey, P., and Gasteiger, E. (2009). Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics 10, 136. doi:10.1186/1471-2105-10-136
19. Johnson, M. D., and Mcintyre, C. C. (2008). Quantifying the neural elements activated and inhibited by globus pallidus deep brain stimulation. J. Neurophysiol. 100, 2549-2563.
20. Li, B., and Gallin, W. J. (2004). VKCDB: voltage-gated potassium channel database. BMC Bioinformatics 5, 3. doi:10.1186/1471-2105-5-3
21. Matsumoto, Y. M. (2011). Ruby A Programmer’s Best Friend. Available at: http://www.ruby-lang.org/en/
22. Twigger, S. N., Shimoyama, M., Bromberg, S., Kwitek, A. E., and Jacob, H. J. (2007). The Rat Genome Database, update 2007-easing the path from disease to data and back again. Nucleic Acids Res. 35, D658-D662.