Institut NeuroPSI - UMR9197
CNRS Université Paris-Saclay
Gif-Sur-Yvette
France

Dr. Andrew DAVISON

Chargé de Recherche
Neuroinformatics, Neuroinformatique

andrew . davison(At)cnrs . fr
+33(0) 1 69 82 34 51
ORCID : 0000-0002-4793-7541

Activités de recherche

I am a senior research scientist in the ICN department, where I lead the Neuroinformatics group. You might also be interested in my personal homepage or my Twitter feed.

See my ORCID account

See my personal homepage

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.

Article dans une revue

2020

ref_biblio
Sharon Crook, Andrew P. Davison, Robert Mcdougal, Hans Ekkehard Plesser. Editorial: Reproducibility and Rigour in Computational Neuroscience. Frontiers in Neuroinformatics, Frontiers, 2020, 14, pp.23. ⟨10.3389/fninf.2020.00023⟩. ⟨hal-02913122⟩
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https://hal.archives-ouvertes.fr/hal-02913122/file/fninf-14-00023.pdf BibTex
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Kael Dai, Juan Hernando, Yazan Billeh, Sergey Gratiy, Judit Planas, et al.. The SONATA data format for efficient description of large-scale network models. PLoS Computational Biology, Public Library of Science, 2020, 16 (2), pp.e1007696. ⟨10.1371/journal.pcbi.1007696⟩. ⟨hal-02913116⟩
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https://hal.archives-ouvertes.fr/hal-02913116/file/journal.pcbi.1007696%20%281%29.pdf BibTex
ref_biblio
Andrew P. Davison. [Rp] Dendrodendritic inhibition and simulated odor responses in a detailed olfactory bulb network model. ReScience C, 2020, ⟨10.5281/zenodo.3972130⟩. ⟨hal-03046451⟩
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https://hal.archives-ouvertes.fr/hal-03046451/file/article-7.pdf BibTex

2019

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Padraig Gleeson, Matteo Cantarelli, Boris Marin, Adrian Quintana, Matt Earnshaw, et al.. Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. Neuron, Elsevier, 2019, 103 (3), pp.395. ⟨10.1016/j.neuron.2019.05.019⟩. ⟨hal-02193259⟩
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https://hal.archives-ouvertes.fr/hal-02193259/file/PIIS0896627319304441.pdf BibTex

2018

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Ján Antolík, Andrew P. Davison. Arkheia: Data Management and Communication for Open Computational Neuroscience. Frontiers in Neuroinformatics, Frontiers, 2018, 12, pp.6. ⟨10.3389/fninf.2018.00006⟩. ⟨hal-01737956⟩
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https://hal.sorbonne-universite.fr/hal-01737956/file/fninf-12-00006.pdf BibTex
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Inga Blundell, Romain Brette, Thomas Cleland, Thomas Close, Daniel Coca, et al.. Code Generation in Computational Neuroscience: A Review of Tools and Techniques. Frontiers in Neuroinformatics, Frontiers, 2018, 12, pp.68. ⟨10.3389/fninf.2018.00068⟩. ⟨hal-01996352⟩
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https://hal.sorbonne-universite.fr/hal-01996352/file/fninf-12-00068.pdf BibTex

2017

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Stephen Eglen, Ben Marwick, Yaroslav Halchenko, Michael Hanke, Shoaib Sufi, et al.. Toward standard practices for sharing computer code and programs in neuroscience. Nature Neuroscience, Nature Publishing Group, 2017, 20 (6), pp.770-773. ⟨10.1038/nn.4550⟩. ⟨hal-02064847⟩
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Stephen Eglen, Ben Marwick, Yaroslav Halchenko, Michael Hanke, Shoaib Sufi, et al.. Toward standard practices for sharing computer code and programs in neuroscience. Nature Neuroscience, Nature Publishing Group, 2017, 20 (6), pp.770-773. ⟨10.1038/nn.4550⟩. ⟨hal-02332234⟩
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Padraig Gleeson, Andrew P. Davison, R Angus Silver, Giorgio Ascoli. A Commitment to Open Source in Neuroscience. Neuron, Elsevier, 2017, 96 (5), pp.964-965. ⟨10.1016/j.neuron.2017.10.013⟩. ⟨hal-02064834⟩
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Nicolas Rougier, Konrad Hinsen, Frédéric Alexandre, Thomas Arildsen, Lorena Barba, et al.. Sustainable computational science: the ReScience initiative. PeerJ Computer Science, PeerJ, 2017, 3, pp.e142. ⟨10.7717/peerj-cs.142⟩. ⟨hal-01592078⟩
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https://arxiv.org/pdf/1707.04393 BibTex
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Leonid L. Rubchinsky, Sungwoo Ahn, Wouter Klijn, Ben Cumming, Stuart Yates, et al.. 26th Annual Computational Neuroscience Meeting (CNS*2017): Part 2. BMC Neuroscience, BioMed Central, 2017, 18 (Suppl 1), pp.59. ⟨10.1186/s12868-017-0371-2⟩. ⟨hal-01580190⟩
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https://hal.inria.fr/hal-01580190/file/12868_2017_Article_371.pdf BibTex

2016

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Christophe Pouzat, Andrew P. Davison, Konrad Hinsen. La recherche reproductible : une communication scientifique explicite. Statistique et Société, Société française de statistique, 2016, Deux débats sur les données, 3 (1). ⟨hal-01478360⟩
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2015

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Eilif Muller, James A Bednar, Markus Diesmann, Marc-Oliver Gewaltig, Michael Hines, et al.. Python in neuroscience.. Frontiers in Neuroinformatics, Frontiers, 2015, 9, pp.11. ⟨10.3389/fninf.2015.00011⟩. ⟨hal-01159440⟩
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2014

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Mikael Djurfeldt, Andrew P. Davison, Jochen M Eppler. Efficient generation of connectivity in neuronal networks from simulator-independent descriptions.. Front Neuroinform, 2014, 8, pp.43. ⟨10.3389/fninf.2014.00043⟩. ⟨hal-01055563⟩
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Samuel Garcia, Domenico Guarino, Florent Jaillet, Todd Jennings, Robert Pröpper, et al.. Neo: an object model for handling electrophysiology data in multiple formats.. Front Neuroinform, 2014, 8, pp.10. ⟨10.3389/fninf.2014.00010⟩. ⟨hal-01055571⟩
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Michael Vella, Robert C Cannon, Sharon M. Crook, Andrew P. Davison, Gautham Ganapathy, et al.. libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience.. Front Neuroinform, 2014, 8, pp.38. ⟨10.3389/fninf.2014.00038⟩. ⟨hal-01055565⟩
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2013

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Ján Antolík, Andrew P. Davison. Integrated workflows for spiking neuronal network simulations.. Front Neuroinform, 2013, 7, pp.34. ⟨10.3389/fninf.2013.00034⟩. ⟨hal-01055572⟩
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2012

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Sharon M. Crook, James A Bednar, Sandra Berger, Robert Cannon, Andrew P. Davison, et al.. Creating, documenting and sharing network models.. Network: Computation in Neural Systems, Taylor & Francis, 2012, 23 (4), pp.131-49. ⟨10.3109/0954898X.2012.722743⟩. ⟨hal-01055577⟩
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Andrew P. Davison. Automated Capture of Experiment Context for Easier Reproducibility in Computational Research. Computing in Science and Engineering, Institute of Electrical and Electronics Engineers, 2012, 14 (4), pp.48-56. ⟨10.1109/MCSE.2012.41⟩. ⟨hal-01055702⟩
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Andrew P. Davison. Collaborative modelling: the future of computational neuroscience?. Network: Computation in Neural Systems, Taylor & Francis, 2012, 23 (4), pp.157-66. ⟨10.3109/0954898X.2012.718482⟩. ⟨hal-01055579⟩
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2011

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Daniel Brüderle, Mihai A Petrovici, Bernhard Vogginger, Matthias Ehrlich, Thomas Pfeil, et al.. A comprehensive workflow for general-purpose neural modeling with highly configurable neuromorphic hardware systems.. Biological Cybernetics (Modeling), Springer Verlag, 2011, 104 (4-5), pp.263-96. ⟨10.1007/s00422-011-0435-9⟩. ⟨hal-00635967⟩
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2010

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Padraig Gleeson, Sharon M. Crook, Robert C Cannon, Michael L Hines, Guy O Billings, et al.. NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail.. PLoS Computational Biology, Public Library of Science, 2010, 6 (6), pp.e1000815. ⟨10.1371/journal.pcbi.1000815⟩. ⟨hal-00586776⟩
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2009

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Daniel Brüderle, Eric Muller, Andrew Davison, Eilif Muller, Johannes Schemmel, et al.. Establishing a Novel Modeling Tool: A Python-based Interface for a Neuromorphic Hardware System. Frontiers in Neuroinformatics, Frontiers, 2009, 3, pp.17. ⟨10.3389/neuro.11.017.2009⟩. ⟨hal-03047041⟩
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Andrew P. Davison, Daniel Brüderle, Jochen Eppler, Jens Kremkow, Eilif Muller, et al.. PyNN: A Common Interface for Neuronal Network Simulators.. Frontiers in Neuroinformatics, Frontiers, 2009, 2, pp.11. ⟨10.3389/neuro.11.011.2008⟩. ⟨hal-00586786⟩
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https://hal.archives-ouvertes.fr/hal-00586786/file/davison-08.pdf BibTex
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Andrew P. Davison, Michael L Hines, Eilif Muller. Trends in programming languages for neuroscience simulations.. Frontiers in Neuroscience, Frontiers, 2009, 3 (3), pp.374-80. ⟨10.3389/neuro.01.036.2009⟩. ⟨hal-00586787⟩
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Michael L Hines, Andrew P. Davison, Eilif Muller. NEURON and Python.. Front Neuroinformatics, 2009, 3, pp.1. ⟨10.3389/neuro.11.001.2009⟩. ⟨hal-00586782⟩
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Olivier Marre, Pierre Yger, Andrew P. Davison, Yves Frégnac. Reliable recall of spontaneous activity patterns in cortical networks.. Journal of Neuroscience, Society for Neuroscience, 2009, 29 (46), pp.14596-606. ⟨10.1523/JNEUROSCI.0753-09.2009⟩. ⟨hal-00444943⟩
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2007

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Romain Brette, Michael Rudolph, Ted Carnevale, Michael Hines, David Beeman, et al.. Simulation of networks of spiking neurons: A review of tools and strategies.. Journal of Computational Neuroscience, Springer Verlag, 2007, 23 (3), pp.349-98. ⟨10.1007/s10827-007-0038-6⟩. ⟨hal-00180662⟩
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2006

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Mathilde Badoual, Quan Zou, Andrew P. Davison, Michael Rudolph, Thierry Bal, et al.. Biophysical and phenomenological models of multiple spike interactions in spike-timing dependent plasticity.. Int J Neural Syst, 2006, 16 (2), pp.79-97. ⟨hal-00120626⟩
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Andrew P. Davison, Yves Frégnac. Learning cross-modal spatial transformations through spike timing-dependent plasticity.. Journal of Neuroscience, Society for Neuroscience, 2006, 26 (21), pp.5604-15. ⟨10.1523/JNEUROSCI.5263-05.2006⟩. ⟨hal-00120625⟩
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2004

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Andrew P. Davison, Thomas M Morse, Michele Migliore, Gordon M Shepherd, Michael L Hines. Semi-automated population of an online database of neuronal models (ModelDB) with citation information, using PubMed for validation.. Neuroinformatics, Springer, 2004, 2 (3), pp.327-32. ⟨10.1385/NI:2:3:327⟩. ⟨hal-00299855⟩
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2003

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Andrew P. Davison, Jianfeng Feng, David Brown. Dendrodendritic inhibition and simulated odor responses in a detailed olfactory bulb network model.. Journal of Neurophysiology, American Physiological Society, 2003, 90 (3), pp.1921-35. ⟨10.1152/jn.00623.2002⟩. ⟨hal-00299879⟩
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Michele Migliore, Thomas M Morse, Andrew P. Davison, Luis Marenco, Gordon M Shepherd, et al.. ModelDB: making models publicly accessible to support computational neuroscience.. Neuroinformatics, Springer, 2003, 1 (1), pp.135-9. ⟨10.1385/NI:1:1:135⟩. ⟨hal-00586793⟩
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2000

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Andrew P. Davison, J. Feng, D. Brown. A reduced compartmental model of the mitral cell for use in network models of the olfactory bulb.. Brain Research Bulletin, Elsevier, 2000, 51 (5), pp.393-9. ⟨hal-00635986⟩
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Communication dans un congrès

2013

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Andrew P. Davison, Thierry Bal, Domenico Guarino, Olivier Manette, Cyril Monier, et al.. Helmholtz: a customizable framework for neurophysiology data management. Neuroinformatics 2013, INCF, Stockholm, Sweden, Aug 2013, Stockholm, Sweden. ⟨10.3389/conf.fninf.2013.09.00025⟩. ⟨hal-03047325⟩
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2008

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Olivier Marre, Pierre Yger, Andrew Davison, Yves Frégnac. Reliable recall of spontaneous activity patterns in chaotic cortical networks. Deuxième conférence française de Neurosciences Computationnelles, "Neurocomp08", Oct 2008, Marseille, France. ⟨hal-00331545⟩
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https://hal.archives-ouvertes.fr/hal-00331545/file/NEUROCOMP2008_0028.pdf BibTex
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Pierre Yger, Abigail Morrison, M. Diesmann, Andrew P. Davison, Yves Frégnac. STDP in topogra-phical neuronal networks.. Proceedings of the 44th Japan Workshop - ISTC-RIKEN BSI, 2008, Wako, Japan. pp.en cours. ⟨hal-00382367⟩
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2007

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Mathilde Badoual, Thierry Bal, Pierre Baudot, Andrew P. Davison, Alain Destexhe, et al.. Plasticité associative dépendante de l'ordre temporel entre activités pré- et post-synaptiques (Spike Timing Dependent Plasticity) : son implication dans l'adaptation fonctionnelle des réseaux sensoriels et l'apprentissage perceptif.. Colloque de l'ACI (Action Concertée Incitative) Neurosciences Intégratives et Computationnelles, 2007, Paris, France. pp.en cours. ⟨hal-00380905⟩
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Andrew P. Davison, Pierre Yger, Jens Kremkow, Laurent Perrinet, Eilif Muller. PyNN: Towards a universal neural simulator API in Python.. CNS 2007 Proceedings of the 16th Annual Computational Neuroscience Meeting, 2007, Toronto, Canada. pp.73. ⟨hal-00381688⟩
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2006

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Andrew P. Davison, Pierre Yger, Yves Frégnac, J. Chan, F. Newell. A combined pyschophysical--modelling investigation of the mechanisms of tactile picture perception.. Proceedings of the 15th Annual Computational Neuroscience Meeting, 2006, Edinburgh, United Kingdom. pp.170. ⟨hal-00380061⟩
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2004

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Andrew P. Davison, Yves Frégnac. Training a network of spiking neurons to perform coordinate transformations.. 34th Annual Meeting of the Society for Neuroscience, 2004, San Diego, United States. pp.4. ⟨hal-00379386⟩
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Andrew P. Davison. Learning simple computations in spiking basis function networks using spike time-dependent plasticity.. 4th Forum of European Neuroscience, 2004, Lisbon, Portugal. pp.A224. ⟨hal-00379381⟩
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2000

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Andrew P. Davison, Jf Feng, D. Brown. Spike synchronization in a biophysically-detailed model of the olfactory bulb. 9th Annual Computational Neuroscience Meeting, 2000, Brugge, Belgium. pp.515-521, ⟨10.1016/S0925-2312(01)00391-5⟩. ⟨hal-01055784⟩
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Chapitre d'ouvrage

2007

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Yves Frégnac, Michael Rudolph, Andrew P. Davison, Alain Destexhe. Complexity and level hierarchy in neural networks. François Képès. Biological networks, World Scientific Publishing Company, pp.1-52, 2007, Complex Systems and Interdisciplinary Science, vol. 3. ⟨hal-00211742⟩
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Yves Frégnac, Michael Rudolph, Andrew P. Davison, Alain Destexhe. Complexity in Neuronal Networks. François Képès. Biological Networks, World Scientific, pp.291-338, 2007, Complex Systems and Interdisciplinary Science vol.3, 9789812706959. ⟨hal-00739550⟩
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2004

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Andrew P. Davison. Biologically-Detailed Network Modelling. Jianfeng Feng. Computational Neuroscience. A Comprehensive Approach, Chapman & Hall / CRC Press, pp.287-304, 2004, Chapman & Hall/CRC Mathematical Biology and Medicine. ⟨hal-00377318⟩
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Pré-publication, Document de travail

2020

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Sára Sáray, Christian Rössert, Shailesh Appukuttan, Rosanna Migliore, Paola Vitale, et al.. HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data. 2020. ⟨hal-03063383⟩
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https://hal.archives-ouvertes.fr/hal-03063383/file/2020.07.02.184333v2.full.pdf BibTex

Livres et Thèses (1)

2001

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

Chapitres de livre (2)

2002

> 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)

> 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)

Présentations (27)

2010

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

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

> Andrew Davison, Challenges and solutions in replicability and provenance tracking, Poster At: CNS*2010, (San Antonio (Texas)) (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: Eighteenth Annual Computational Neuroscience Meeting, (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: BMC Neuroscience 10 , (Berlin (Germany)) (2009)

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)

> 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)

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)

> 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)

2006

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

> Andrew Davison, Simulator-independent network modelling with Python and XML. , Talk invité 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)

> 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)

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

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)

> Andrew Davison and Yves Frégnac, The Two-ring paradigm: a computational approach of multisensory code binding. , Talk invité 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. , Poster At: International SenseMaker Workshop on Life-Like Perception Systems, (Derry (U.K)) (2005)

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, 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]

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

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)

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)