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 or my Twitter feed.

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

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 Computational Biology 6: e1000815. [Abstract] [PLoS]

Davison A.P., Hines M. and Muller E. (2009) Trends in programming languages for neuroscience simulations. Frontiers in Neuroscience 3:3: doi:10.3389/neuro.01.036.2009. [Abstract] [Full text]

Marre O., Yger P., Davison A.P. and Frégnac Y. (2009) Reliable recall of spontaneous activity patterns in cortical networks. The Journal of Neuroscience 29: 14596-14606. [Abstract]

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]

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]

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

News

Sumatra 0.2 released: 10/7/2010 more ...
Tracking computational experiments with Sumatra: 6/4/2010 more ...
PyNN 0.6.0 released: 14/2/2010 more ...
3rd INCF Congress of Neuroinformatics: 4/2/2010 more ...

$3rd INCF Congress of Neuroin\ formatics, Kobe, Japan, Aug 30-Sept 1$

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 ...
Sumatra: Automated tracking of numerical experiments. more ...