Institut NeuroPSI - UMR9197
CNRS Université Paris-Saclay
Campus CEA Saclay
Saclay, FRANCE

Dr. Andrew Davison

Chargé de Recherche
Neuroinformatique

andrew.davison cnrs.fr
+33(0)1 69 82 34 51, bureau 3149
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.

Publications

Article dans une revue

2024

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Onur Ates, Shailesh Appukuttan, Hélissande Fragnaud, Corentin Fragnaud, Andrew P. Davison. NeoViewer: Facilitating reuse of electrophysiology data through browser-based interactive visualization. SoftwareX, 2024, 26, pp.101710. ⟨10.1016/j.softx.2024.101710⟩. ⟨hal-04551480⟩
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https://cnrs.hal.science/hal-04551480/file/PIIS2352711024000815.pdf BibTex

2023

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Shailesh Appukuttan, Luca L. Bologna, Felix Schürmann, Michele Migliore, Andrew P. Davison. EBRAINS Live Papers - Interactive Resource Sheets for Computational Studies in Neuroscience. Neuroinformatics, 2023, 21 (1), pp.101-113. ⟨10.1007/s12021-022-09598-z⟩. ⟨hal-03783756⟩
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https://cnrs.hal.science/hal-03783756/file/s12021-022-09598-z.pdf BibTex

2022

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Luca Leonardo Bologna, Roberto Smiriglia, Carmen Alina Lupascu, Shailesh Appukuttan, Andrew P. Davison, et al.. The EBRAINS Hodgkin-Huxley Neuron Builder: An online resource for building data-driven neuron models. Frontiers in Neuroinformatics, 2022, 16, pp.991609. ⟨10.3389/fninf.2022.991609⟩. ⟨hal-03788861⟩
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https://cnrs.hal.science/hal-03788861/file/fninf-16-991609.pdf BibTex
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Andrew P. Davison, Shailesh Appukuttan. A faster way to model neuronal circuitry. eLife, 2022, 11, pp.e84463. ⟨10.7554/eLife.84463⟩. ⟨hal-04304568⟩
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https://hal.science/hal-04304568/file/elife-84463-v1.pdf BibTex

2021

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Sára Sáray, Christian A 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. PLoS Computational Biology, 2021, 17 (1), pp.e1008114. ⟨10.1371/journal.pcbi.1008114⟩. ⟨hal-03063383⟩
Accès au texte intégral et bibtex
https://hal.science/hal-03063383/file/2020.07.02.184333v2.full.pdf BibTex

2020

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Sharon Crook, Andrew P. Davison, Robert Mcdougal, Hans Ekkehard Plesser. Editorial: Reproducibility and Rigour in Computational Neuroscience. Frontiers in Neuroinformatics, 2020, 14, pp.23. ⟨10.3389/fninf.2020.00023⟩. ⟨hal-02913122⟩
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https://hal.science/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, 2020, 16 (2), pp.e1007696. ⟨10.1371/journal.pcbi.1007696⟩. ⟨hal-02913116⟩
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https://hal.science/hal-02913116/file/journal.pcbi.1007696%20%281%29.pdf BibTex
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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.science/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, 2019, 103 (3), pp.395. ⟨10.1016/j.neuron.2019.05.019⟩. ⟨hal-02193259⟩
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https://hal.science/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, 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 A Cleland, Thomas G Close, Daniel Coca, et al.. Code Generation in Computational Neuroscience: A Review of Tools and Techniques. Frontiers in Neuroinformatics, 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, 2017, 20 (6), pp.770-773. ⟨10.1038/nn.4550⟩. ⟨hal-02064847⟩
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Padraig Gleeson, Andrew P. Davison, R Angus Silver, Giorgio Ascoli. A Commitment to Open Source in Neuroscience. Neuron, 2017, 96 (5), pp.964-965. ⟨10.1016/j.neuron.2017.10.013⟩. ⟨hal-02064834⟩
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Nicolas P. Rougier, Konrad Hinsen, Frédéric Alexandre, Thomas Arildsen, Lorena Barba, et al.. Sustainable computational science: the ReScience initiative. PeerJ Computer Science, 2017, 3, pp.e142. ⟨10.7717/peerj-cs.142⟩. ⟨hal-01592078⟩
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https://inria.hal.science/hal-01592078/file/peerj-cs-142.pdf 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, 2017, 18 (Suppl 1), pp.59. ⟨10.1186/s12868-017-0371-2⟩. ⟨hal-01580190⟩
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https://inria.hal.science/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, 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, 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.. Frontiers in Neuroinformatics, 2014, 8, pp.10. ⟨10.3389/fninf.2014.00010⟩. ⟨hal-01055571⟩
Accès au texte intégral et bibtex
https://hal.science/hal-01055571/file/fninf-08-00010.pdf BibTex
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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, 2012, 23 (4), pp.131-49. ⟨10.3109/0954898X.2012.722743⟩. ⟨hal-01055577⟩
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Andrew P. Davison. Collaborative modelling: the future of computational neuroscience?. Network: Computation in Neural Systems, 2012, 23 (4), pp.157-66. ⟨10.3109/0954898X.2012.718482⟩. ⟨hal-01055579⟩
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Andrew P. Davison. Automated Capture of Experiment Context for Easier Reproducibility in Computational Research. Computing in Science and Engineering, 2012, 14 (4), pp.48-56. ⟨10.1109/MCSE.2012.41⟩. ⟨hal-01055702⟩
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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), 2011, 104 (4-5), pp.263-96. ⟨10.1007/s00422-011-0435-9⟩. ⟨hal-00635967⟩
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https://arxiv.org/pdf/1011.2861 BibTex

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, 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, 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, 2009, 2, pp.11. ⟨10.3389/neuro.11.011.2008⟩. ⟨hal-00586786⟩
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https://hal.science/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, 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, 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, 2007, 23 (3), pp.349-98. ⟨10.1007/s10827-007-0038-6⟩. ⟨hal-00180662⟩
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https://arxiv.org/pdf/q-bio/0611089 BibTex

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.. International Journal of Neural Systems, 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, 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, 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, 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, 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, 2000, 51 (5), pp.393-9. ⟨hal-00635986⟩
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