Andrew Davison

I am a senior research scientist in the UNIC lab (Unité de Neuroscience, Information et Complexité) of the CNRS, where I lead the Neuroinformatics group. You might also be interested in my personal homepage or my Twitter feed. My ORCID ID is 0000-0002-4793-7541.

My main research interests are in large-scale, data-constrained, biologically-detailed modelling of neuronal networks. My work at the moment has several strands:

  • development of tools to facilitate collaborative modelling, model sharing, and the use of novel hardware (GPU, neuromorphic) for neuronal simulations, notably PyNN, NineML and NeuroML.
  • promoting reproducible research in computational neuroscience and neuroinformatics, both through trying to spread best practices and through tool development (see the Sumatra project).
  • promoting neurophysiology data sharing, by participation in international standardisation efforts, by development of tools to harmonize the handling of electrophysiology data in Python (see the Neo project), and by development of a framework to simplify databasing of neurophysiology data in small labs (see the Helmholtz project).
  • development of models of the early visual system, from retina to primary visual cortex, in close collaboration with experimentalists.

For more information, and a possibly more up-to-date list of publications, see my personal homepage

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Books and Thesis (1)

2001

Andrew Davison, Mathematical modelling of information processing in the olfactory bulb, In: () Ph.D. thesis, University of Cambridge , (2001)

Articles (19)

2015

Eric Muller, James Bednar, Markus Diesmann, M-O Gewaltig, Michael L. Hines and Andrew Davison, Python in Neuroscience, Frontiers in Neuroinformatics 9: doi:10.3389/fninf.2015.00011, (2015)

C Pouzat, Andrew Davison and K Hinsen, La recherche reproductible : une communication scientifique explicite, Statistique et société 3: 35-38, (2015)

2012

Sharon Crook, James Bednar, Sandra Berger, Robert C. Cannon, Andrew Davison, Mikael Djurfeldt, Jochen Eppler, Birgit Kriener, Steve Furber, Bruce Graham, Hans Plesser, Lars Schwabe, Leslie Smith, Volker Steuber and Sacha van Albada, Creating, documenting and sharing network models, Network: Computation in Neural Systems : , (2012) [pdf] [abstract]

Andrew Davison, Collaborative modelling: The future of computational neuroscience?, Network: Computation in Neural Systems : , (2012) [pdf] [abstract]

Andrew Davison, Automated capture of experiment context for easier reproducibility in computational research, Computing in Science and Engineering 14: 48-56, (2012) [pdf] [abstract]

2011

Daniel Brüderle, MA Petrovici, Bernhard Vogginger, Matthias Ehrlich, Thomas Pfeil, Sebastian Milner, A Grubl, K Wendt, Eric Muller, M-O Schwartz, D Husmann de Oliveira , S Jeltsch, J Fieres, M Schilling , P Muller, O Breitwieser, V Petkov, L Muller, Andrew Davison, P Krishnamurthy , Jens Kremkow, M Lundqvist, Eilif Muller, J Partzsch, S Scholze, H Zühl, C MAYR, Alain Destexhe, Markus Diesmann, TC Potjans , Anders Lansner, R Schüffny , Johannes Schemmel and Karlheinz Meier, A comprehensive workflow for general-purpose neural modeling with highly configurable neuromorphic hardware systems. , Biological Cybernetics 104: 263-296, (2011) [pdf]

2010

Padraig Gleeson, Sharon Crook, Robert C. Cannon, Michael L. Hines, Guy O. Billings, Matteo Farinella, Thomas M. Morse, Andrew Davison, Subhasis Ray, Upinder S. Bhalla, Simon R. Barnes, Yoana D. Dimitrova and R. Angus Silver, NeuroML: A language for describing data driven models of neurons and networks with a high degree of biological detail., PLoS Computational Biology 6: e1000815, (2010) [pdf] [abstract]

2009

Olivier Marre, Pierre Yger, Andrew Davison and Yves Frégnac, Reliable recall of spontaneous activity patterns in chaotic cortical networks., The Journal of Neuroscience 29(46): 14596-14606, (2009)

Andrew Davison, Michael L. Hines and Eric Muller, Trends in programming languages for neuroscience simulations, Frontiers in Neuroscience 3: 374-380, (2009) [pdf] [abstract]

Daniel Brüderle, Eric Muller, Andrew Davison, Eric Muller, Johannes Schemmel and Karlheinz Meier, Establishing a novel modeling tool: a python-based interface for a neuromorphic hardware system, Frontiers in Neuroinformatics 3: 17.1-17.4, (2009) [pdf] [abstract]

Michael L. Hines, Andrew Davison and Eilif Muller, NEURON and Python, Frontiers in NeuroInformatics 2: doi:10.3389/neuro.11.001.2009, (2009) [pdf] [abstract]

Andrew Davison, Daniel Brüderle, Jochen Eppler, Jens Kremkow, Eilif Muller, Dejan Pecevski, Laurent Perrinet and Pierre Yger, PyNN: a common interface for neuronal network simulators, Frontiers in NeuroInformatics 2: doi:10.3389/neuro.11.011.2008, (2009) [pdf] [abstract]

2007

Romain Brette, Michelle Rudolph, Ted Carnevale, Michael L. Hines, David Beeman, James M. Bower, Markus Diesmann, Abigail Morrison, Philip H. Goodman, Frederick C. Harris Jr, Milind Zirpe, Thomas Natschläger, Dejan Pecevski, Bard Ermentrout, Mikael Djurfeldt, Anders Lansner, Olivier Rochel, Thierry Vieville, Eric Muller, Andrew Davison, Sami El Boustani and Alain Destexhe, Simulation of networks of spiking neurons: a review of tools and strategies, J Comput Neurosci 23: 349-98, (2007) [pdf] [abstract]

2006

Andrew Davison and Yves Frégnac, Learning cross-modal spatial transformations through spike timing-dependent plasticity, J Neurosci 26: 5604-15, (2006) [pdf] [abstract]

Mathilde Badoual, Quan Zou, Andrew Davison, Michelle Rudolph, Thierry Bal, Yves Frégnac and Alain Destexhe, Biophysical and phenomenological models of multiple spike interactions in spike-timing dependent plasticity, Int J Neural Syst 16: 79-97, (2006) [pdf] [abstract]

2004

Andrew Davison, Thomas M. Morse, Michele Migliore, Gordon M. Shepherd and Michael L. Hines, Semi-automated population of an online database of neuronal models (ModelDB) with citation information, using PubMed for validation, Neuroinformatics 2: 327-32, (2004) [pdf] [abstract]

2003

Michele Migliore, Thomas M. Morse, Andrew Davison, Luis Marenco, Gordon M. Shepherd and Michael L. Hines, ModelDB: making models publicly accessible to support computational neuroscience, Neuroinformatics 1: 135-9, (2003) [pdf]

Andrew Davison, Jianfeng Feng and David Brown, Dendrodendritic inhibition and simulated odor responses in a detailed olfactory bulb network model, J Neurophysiol 90: 1921-35, (2003) [pdf] [abstract] [ModelDB]

2000

Andrew Davison, Jianfeng Feng and David Brown, A reduced compartmental model of the mitral cell for use in network models of the olfactory bulb, Brain Res Bull 51: 393-9, (2000) [abstract] [ModelDB]

Presentations (27)

2010

Andrew Davison, Integration: a collaborative software tool-chain for neuromorphic computation, Poster At: Frontiers in Neuromorphic Computation, (Paris (France)) (2010)

Andrew Davison, Automated tracking of computational experiments using Sumatra, Poster At: EuroSciPy 2010, (Paris (France)) (2010)

Andrew Davison, Challenges and solutions in replicability and provenance tracking, Poster At: CNS*2010, (San Antonio (Texas)) (2010)

Andrew Davison, Thierry Brizzi, Olivier Manette, Cyril Monier and Yves Frégnac, Helmholtz: a modular tool for neuroscience databases, Poster At: Front. Neurosci. Conference Abstract Neuroinformatics, (Kobe (Japan)) (2010)

2009

Pierre Yger, Sami El Boustani, Olivier Marre, Andrew Davison, Alain Destexhe and Yves Frégnac, Spatial organization of evoked neuronal dynamics in 2D recurrent networks, with or without structured stimulation, Poster At: BMC Neuroscience 10 , (Berlin (Germany)) (2009)

Pierre Yger, Sami El Boustani, Olivier Marre, Andrew Davison, Alain Destexhe and Yves Frégnac, Spatial organization of evoked neuronal dynamics in 2D recurrent networks, with or without structured stimulation, Poster At: Eighteenth Annual Computational Neuroscience Meeting, (Berlin (Germany)) (2009)

2008

Pierre Yger, Abigail Morrison, Markus Diesmann, Andrew Davison and Yves Frégnac, STDP in topogra-phical neuronal networks, Poster At: RIKEN BSI Workshop, (Wako (Japan)) (2008)

Pierre Yger, Andrew Davison and Yves Frégnac, PyNN: a common Python interface for network simulators. , Poster At: 17th Annual Computational Neuroscience Meeting , (Portland (USA)) (2008)

Pierre Yger, Olivier Marre, Andrew Davison and Yves Frégnac, Reliable recall of spontaneous activity patterns in chaotic cortical networks, Poster At: NeuroComp, (Marseille) (2008) [pdf] [abstract]

2007

Andrew Davison, Pierre Yger, Jens Kremkow, Laurent Perrinet and Eilif Muller, PyNN: Towards a universal neural simulator API in Python, Poster At: CNS, (Toronto) (2007) [abstract]

Pierre Yger, Olivier Marre, Sami El Boustani, Pierre Baudot, Cyril Monier, Manuel Levy, Andrew Davison and Yves Frégnac, Chaos control: Reliable signal propagation and pattern completion in chaotic neuronal networks, Poster At: SFN, (San Diego) (2007) [pdf] [abstract]

2006

Andrew Davison, NModLib: a database of components for neuroscience models. , Invited Talk At: World Association of Modeling - Biologically Accurate Modeling Meeting, (San Antonio, Texas (USA)) (2006)

Andrew Davison, Simulator-independent network modelling with Python and XML. , Invited Talk At: Modeling the Brain's Labyrinth, (Fodele, Crete (Greece)) (2006)

Andrew Davison, NModLib: a database of components for neuroscience models, Poster At: World Association of Modeling - Biologically Accurate Modeling Meeting, (San Antonio, Texas) (2006) [abstract]

Andrew Davison, Pierre Yger, Jason Chan, Fiona Newell and Yves Frégnac, A combined psychophysical-modelling study of the mechanisms of tactile picture perception, Poster At: CNS*2006, (Edinburgh, UK) (2006) [abstract]

Andrew Davison, Simulator-independent network modelling with Python and XML, Talk At: Modeling the Brain's Labyrinth, (Fodele, Crete, Greece) (2006) [abstract]

2005

Andrew Davison, Ammar Belatreche, Johannes Fieres, Jason Chan, Fiona Newell and Yves Frégnac, The Two-Ring paradigm: a computational approach to multisensory code binding. , Poster At: International SenseMaker Workshop on Life-Like Perception Systems, (Derry (U.K)) (2005)

Andrew Davison and Yves Frégnac, The Two-ring paradigm: a computational approach of multisensory code binding. , Invited Talk At: International SenseMaker Workshop, (School of computing Intelligence, University of Ulster, Derry (Northern Ireland)) (2005)

Andrew Davison, Ammar Belatreche, Johannes Fieres, Jason Chan, Fiona Newell and Yves Frégnac, The Two-Ring paradigm: a computational approach to multisensory code binding, Talk At: International SenseMaker Workshop on Life-Like Perception Systems, (Derry, UK) (2005) [abstract]

2004

Andrew Davison, Learning simple computations in spiking basis function networks using spike time-dependent plasticity, Poster At: FENS, (Lisbon, Portugal) (2004) [abstract]

Andrew Davison and Yves Frégnac, Training a network of spiking neurons to perform coordinate transformations, Poster At: SfN, ( San Diego, California) (2004)

2002

Andrew Davison, Michael L. Hines and Gordon M. Shepherd, Membrane bistability and sub-threshold oscillations in an olfactory bulb mitral cell model, Poster At: AChemS XXIV, (Sarasota, Florida) (2002)

2001

Andrew Davison and Jianfeng Feng, A model of network interactions in the olfactory bulb, Poster At: AChemS XXIII, (Sarasota, Florida) (2001) [abstract]

Andrew Davison, Zhishang Zhou, Michael L. Hines and Gordon M. Shepherd, Simulating sodium and potassium currents in an olfactory mitral cell model, Talk At: SfN, (San Diego, California) (2001) [abstract]

2000

Andrew Davison, Jianfeng Feng and David Brown, Spike synchronization in a biophysically-detailed model of the olfactory bulb, Poster At: CNS*00, (Brugge, Belgium) (2000) [abstract]

1999

Andrew Davison, Jianfeng Feng and David Brown, Structure of lateral inhibition in an olfactory bulb model, Talk At: IWANN'99, (Alicante, Spain) (1999) [abstract]

1997

Andrew Davison, Tanya Miller, Ian Belton, S Bolton and David Bonnett, An assessment of image registration in the treatment planning of tumours of the brain, Talk At: Radiology 1997 - Imaging, Science and Oncology, (Birmingham, U.K) (1997)

Book Chapters (4)

2006

Yves Frégnac, Michelle Rudolph, Andrew Davison and Alain Destexhe, Complexity in Neuronal Networks, In: Biological Networks (François Képès) World Scientific 291-338, (2006) [pdf]

2004

Andrew Davison, Biologically-detailed network modelling, In: Computational Neuroscience: A Comprehensive Approach (J. Feng) Chapman and Hall/CRC Press 287-304, (2004)

2002

Andrew Davison, Thomas M. Morse, Michele Migliore, Luis Marenco, Gordon M. Shepherd and Michael L. Hines, ModelDB: A Resource for Neuronal and Network Modeling, In: Neuroscience Databases: A Practical Guide (R. Kötter) Kluwer Academic Publishers 99-109, (2002) [abstract]

Andrew Davison and Gordon M. Shepherd, Olfactory Bulb, In: The Handbook of Brain Theory and Neural Networks, 2nd Edn (M. Arbib) The MIT Press , (2002)