Andrew Davison

Hi, welcome to my personal homepage. I am a research scientist in the UNIC lab (Unité de Neurosciences Intégratives et Computationnelles) of the CNRS. You might also be interested in my lab homepage.

My main research interests are in large-scale, data-constrained, biologically-detailed modelling of neuronal networks. Most of my work at the moment is in the context of the FACETS project, developing models of the early visual system, from retina to primary visual cortex, and developing tools to facilitate collaborative modelling and reproducible simulations, notably PyNN. For more information on this, see the links under “Projects” below.

I did my PhD in computational neuroscience with Dr Jianfeng Feng at the Babraham Institute (Cambridge), then a postdoc in the laboratory of Prof. Gordon Shepherd at Yale University School of Medicine, researching the encoding and processing of olfactory information in the olfactory epithelium and olfactory bulb, and working on the ModelDB database of neuronal models, then a postdoc at UNIC, working on the SenseMaker project.

Publications

Bruederle D., Muller E., Davison A., Muller E., Schemmel, J. and Meier, K. (2009) Establishing a Novel Modeling Tool: A Python-based Interface for a Neuromorphic Hardware System. Frontiers in Neuroinformatics 3:17: doi:10.3389/neuro.11.017.2009. [Abstract] [Frontiers]

Davison A.P., Brüderle D., Eppler J.M., Kremkow, J., Muller E., Pecevski D.A., Perrinet L. and Yger P. (2009) PyNN: a common interface for neuronal network simulators. Frontiers in Neuroinformatics 2:11: doi:10.3389/neuro.11.011.2008. [Abstract] [Frontiers]

Hines M.L., Davison A.P. and Muller E. (2009) NEURON and Python. Frontiers in Neuroinformatics 3:1: doi:10.3389/neuro.11.001.2009. [Abstract] [Frontiers]

Frégnac Y., Rudolph M., Davison A.P. and Destexhe A. (2007) Complexity in Neuronal Networks. In: Biological Networks, edited by François Képès, World Scientific: Singapore, pp. 291-338. [Google Book Search]

R. Brette and 21 others (2007) Simulation of networks of spiking neurons: A review of tools and strategies. Journal of Computational Neuroscience 23: 349-398. [Abstract] [Preprint from arXiv] [get the models from ModelDB] [PubMed]

more ...

Notes

Modelling single cells in NEURON with the Python interpreter

Installation of NEURON with Python

Accessing hoc from Python

Modelling STDP in the NEURON simulator

Projects

PyNN: a Python package for simulator-independent specification of spiking neuronal network models. In other words, you can write the code for a model once, using the PyNN API, and then run it without modification on any simulator that PyNN supports. more ...
NeuroTools: Python tools to simplify the life of a computational neuroscientist, including simulation setup and instrumentation, data storage, analysis and visualisation. more ...
NeuralEnsemble: An initiative to promote and foster collaborative software development and good software development practices in neuroscience, with an emphasis on use of the Python programming language. Includes Subversion hosting for open-source neuroscience software, the NeuralEnsemble Google Group, and the FACETS CodeJam meetings. more ...