Publications

Neuron

Please cite the following paper when discussing NeuroML v2.0 or LEMS.

Cannon RC, Gleeson P, Crook S, Ganapathy G, Marin B, Piasini E and Silver RA (2014) LEMS: A language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2, Frontiers in Neuroinformatics 8: 79.

Vella M, Cannon RC, Crook S, Davison AP, Ganapathy G, Robinson HP, Silver RA and Gleeson P (2014) libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience. Frontiers in Neuroinformatics 8: 38.

Please cite the following paper when discussing NeuroML in general or models in v1.8.1.

Gleeson, P., S. Crook, R. C. Cannon, M. L. Hines, G. O. Billings, et al. (2010) NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail. PLoS Computational Biology 6(6): e1000815.

Günay, C. et al. (2008) Computational intelligence in electrophysiology: Trends and open problems. In Smolinski, Milanova and Hassanien, eds. Applications of Computational Intelligence in Biology. Springer, Berlin/Heidelberg.

Gleeson, P., V. Steuber, and R. A. Silver (2007) neuroConstruct: A Tool for Modeling Networks of Neurons in 3D Space. Neuron. 54(2):219-235.

Cannon R. C., M. O. Gewaltig, P. Gleeson, U. S. Bhalla, H. Cornelis, M. L. Hines, F. W. Howell, E. Muller, J. R. Stiles, S. Wils, E. De Schutter (2007) Interoperability of Neuroscience Modeling Software: Current Status and Future Directions. Neuroinformatics Volume 5, 127-138.

Crook, S., P. Gleeson, F. Howell, J. Svitak and R.A. Silver (2007) MorphML: Level 1 of the NeuroML standards for neuronal morphology data and model specification. Neuroinformatics. 5(2):96-104.

Brette, R. et al. (2007) Simulations of networks of spiking neurons: A review of tools and strategies. Journal of Computational Neuroscience. 23:349-398.

Crook, S. and F. Howell (2007) XML for data representation and model specification in neuroscience. In Methods in Molecular Biology Book Series: Neuroinformatics. ed. C. Crasto, Humana Press.

Crook, S., D. Beeman, P. Gleeson and F. Howell (2005) XML for model specification in neuroscience: An introduction and workshop summary. Brains, Minds, and Media. 1:bmm228 (urn:nbn:de:0009-3-2282).

Qi, W. and S. Crook (2004) Tools for neuroinformatic data exchange: An XML application for neuronal morphology data. Neurocomputing. 58-60C:1091-1095.

Goddard, N., M. Hucka, F. Howell, H. Cornelis, K. Shankar and D. Beeman (2001) Towards NeuroML: Model description methods for collaborative modeling in neuroscience. Philosophical Transactions of the Royal Society B. 356:1209-1228.


Book Chapters

Crook, SM, HE Plesser, AP Davison (2013) Lessons from the past: approaches for reproducibility in computational neuroscience. In JM Bower, ed. 20 Years of Computational Neuroscience, Springer.

Gleeson, P, V Steuber, RA Silver and S Crook (2012) NeuroML. In Le Novere, ed. Computational Systems Biology, Springer.


Abstracts

Cannon, R, P Gleeson, S Crook, RA Silver (2012) A declarative model specification system allowing NeuroML to be extended with user-defined component types. BMC Neuroscience. 13(Suppl 1): P42.

Gleeson P, S Crook, A Silver, R Cannon (2011) Development of NeuroML version 2.0: Greater extensibility, support for abstract neuronal models and interaction with Systems Biology languages. BMC Neuroscience. 12:P29.

Gleeson, P., S. Crook, S. Barnes and R.A. Silver (2008) Interoperable model components for biologically realistic single neuron and network models implemented in NeuroML. Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics 2008. doi: 10.3389/conf.neuro.11.2008.01.135.

Larson, S. and M. Martone (2008) A spatial framework for multi-scale computational neuroanatomy. Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics 2008. doi: 10.3389/conf.neuro.11.2008.01.134.

Crook, S., P. Gleeson and R.A. Silver (2007) NetworkML: Level 3 of the NeuroML standards for multiscale model specification and exchange. Society for Neuroscience Abstracts. 102.28.

Gleeson, P., S. Crook, V. Steuber and R.A. Silver (2007) Using NeuroML and neuroConstruct to build neuronal network models for multiple simulators. BMC Neuroscience. 8(2):P101.

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