Dan Goodman
| I am a postdoctoral researcher in neuroscience. I'm currently working at the Eaton Peabody Laboratory in the Massachusetts Eye and Ear Infirmary, affiliated to Harvard Medical School, with Bertrand Delgutte, on complex responses in inferior colliculus. |  |
Research Interests
I am interested in neural mechanisms underlying computations performed by the brain. In particular, I'm interested in understanding spike-timing based codes and computation, especially in the auditory system.
Projects
Brian
"Brian" is a software package for simulating spiking neural networks. Specifically, it is a package for the Python programming language providing functions and classes designed to make writing simulations of neural networks as easy and flexible as possible. See Brian's web page.
The most recent release of Brian added the Brian.hears package, for auditory modelling. For the next major release, we will be focussing on running Brian on GPU chips (inexpensive massively parallel processors available in consumer graphics cards).
Sound localisation
Sound localisation is the ability of many animals to determine to a greater or lesser degree of accuracy the direction from which a sound is coming. I have worked on two main models relating to sound localisation: (1) a spike timing based model of sound localisation that is able to account for not only azimuthal localisation, but also elevation and disambiguating front/back responses. (2) a coding/decoding model of azimuth location that addresses which codes could realistically be supported given their behaviour in complex acoustic environments.
Spike sorting
I am working with Kenneth Harris to extend the KlustaKwik spike sorting algorithm to work on the next generation of multi-electrode recordings, and to create SpikeDeteKt, the spike detection software used with the new version of KlustaKwik.
Hearing loss
I am working with Alain de Cheveigné and Christian Lorenzi on computational models of hearing loss. Specifically, I am modelling the effects of hearing loss on cells in the cochlear nucleus of guinea pigs.
Complex responses in inferior colliculus
I am working with Bertrand Delgutte on recording and modelling inferior colliculus responses to complex stimuli.
Selected publications
- Kremer Y, Léger J-F, Goodman D, Brette R, Bourdieu L (2011).
Late emergence of the vibrissa direction selectivity map in the rat barrel cortex.
Journal of Neuroscience 31(29). doi:10.1523/JNEUROSCI.6541-10.2011 [preprint] - Goodman DFM, Brette R (2010).
Spike-timing-based computation in sound localization.
PLoS Comput. Biol. 6(11): e1000993. doi:10.1371/journal.pcbi.1000993 - Goodman DFM, Brette R (2009).
The Brian simulator.
Frontiers in Neuroscience 3(2), doi:10.3389/neuro.01.026.2009 - Goodman D, Brette R (2008).
Brian: a simulator for spiking neural networks in Python.
Frontiers in Neuroinformatics 2(5), doi:10.3389/neuro.11.005.2008.
Publications
2013- Goodman DFM, Brette R (2013).
Brian simulator.
Scholarpedia 8(1):10883 - Rossant C, Fontaine B, Goodman DFM (2013).
Playdoh: a lightweight Python package for distributed computing and optimisation.
Journal of Computational Science (in press) [preprint]
2012
- Brette R, Goodman DFM (2012).
Simulating spiking neural networks on GPU.
Network: Computation in Neural Systems 23(4) [preprint]
2011
- Kremer Y, Léger J-F, Goodman D, Brette R, Bourdieu L (2011).
Late emergence of the vibrissa direction selectivity map in the rat barrel cortex.
Journal of Neuroscience 31(29). doi:10.1523/JNEUROSCI.6541-10.2011 [preprint] - Fontaine B, Goodman DFM (joint first authors), Benichoux V, Brette R (2011).
Brian Hears: online auditory processing using vectorisation over channels.
Frontiers in Neuroinformatics 5:9. doi: 10.3389/fninf.2011.00009 [preprint] - Brette R, Goodman DFM (2011).
Vectorised algorithms for spiking neural network simulation.
Neural Computation 23:6 [preprint] - Rossant C, Goodman DFM, Fontaine B, Platkiewicz J, Magnusson AK, Brette R (2011).
Fitting neuron models to spike trains.
Frontiers in Neuroscience. 5:9. doi: 10.3389/fnins.2011.00009
- Goodman DFM, Brette R (2010).
Learning to localise sounds with spiking neural networks.
Advances in Neural Information Processing Systems 23 [bibtex, video abstract] - Fletcher A, Goodman DFM (2010).
Quasiregular mappings of polynomial type in R2.
Conformal Geometry and Dynamics 14. [preprint] - Goodman DFM, Brette R (2010).
Spike-timing-based computation in sound localization.
PLoS Comput. Biol. 6(11): e1000993. doi:10.1371/journal.pcbi.1000993 [code on ModelDB] - Goodman DFM (2010).
Code Generation: A Strategy for Neural Network Simulators.
Neuroinformatics 8, no. 3 (9). doi:10.1007/s12021-010-9082-x. [pdf] - Rossant C, Goodman DFM, Platkiewicz J, Brette R (2010).
Automatic fitting of spiking neuron models to electrophysiological recordings.
Frontiers in Neuroinformatics. doi:10.3389/neuro.11.002.2010
- Goodman DFM, Brette R (2009).
The Brian simulator.
Frontiers in Neuroscience 3(2), doi:10.3389/neuro.01.026.2009 - Brette R, Goodman D. (2009).
Brian: a simple and flexible simulator for spiking neural networks.
The Neuromorphic Engineer. doi: 10.2417/1200906.1659
2006
- Goodman D (2006).
Spirals in the boundaries of slices of quasifuchsian space.
Conformal Geometry and Dynamics 10. [pdf]
Presentations and Posters
- Invited talk on spike detection at the Spike Sorting Workshop, Janelia Farm (February 2013)
- Posters on "Spike sorting for large dense arrays" with Shabnam Kadir, John Schulman, Mariano Belluscio, György Buzsáki and Kenneth Harris, at the Society for Neuroscience meeting, New Orleans (October 2012) and Neuroinformatics 2012, Munich (September 2012)
- Invited talk on simulating neural networks with GPUs, at G-Node Workshop on Neuronal GPU Computing, Munich (April 2012)
- Co-author of talk given by Shabnam Kadir on "Spike sorting for large dense arrays" at UK Neuroinformatics Congress, Edinburgh (March 2012)
- Invited talk on "Computation with spikes" at Mathematical Neuroscience, Edinburgh (April 2010)
- Spotlight presentation of poster on "Learning to localise sounds with spiking neural networks" at NIPS, Vancouver (December 2010)
- Co-author of presentation given by Cyrille Rossant on “Playdoh: a lightweight Python library for distributed computation and optimisation” at EuroSciPy (July 2010)
- Tutorial on Brian (via Skype) at Telluride in Colorado (July 2010)
- Talk on "Computation with spikes" at Mathematical Neuroscience, Edinburgh (April 2010)
- Poster on sound localisation at Mathematical Neuroscience, Edinburgh (April 2010)
- Tutorial on Python and Brian at Neurocomp in Bordeaux, France (September 2009)
- Tutorial on Python and Brian at the Python in neuroscience workshop at CNS, Berlin (July 2009)
- Poster on sound localisation at CNS, Berlin (July 2009)
- Presentation on Brian at the Gatsby computational neuroscience unit, London (July 2009)
- Presentation on sound localisation at The Ear Institute, London (July 2009)
- Presentation on sound localisation at CerCo , Toulouse, France (Jan 2009)
- Presentation on Brian at software interoperability workshop at CNS, Portland OR, USA (July 2008)
- Poster on Brian at CNS, Portland OR, USA (July 2008)
- Tutorial on Brian at "Using Python in computational neuroscience" workshop in Freiburg, Germany (June 2008)
- Presentation on Brian at Visiontrain meeting in Malmo, Sweden (May 2008)
- Presentation on Brian at Facets CodeJam 2 in Gif-sur-Yvette, France (May 2008)
- Poster on Brian at the Mathematical Neuroscience Meeting in Edinburgh, Scotland (March 2008)
Other
- Reviewer for Frontiers in Neuroinformatics, Neural Computation, the Journal of Computational Neuroscience, the Journal of Neuroscience Methods, Network: Computation in Neural Systems and IEEE Transactions on Neural Networks and Learning Systems.
- Designed the front cover of the May 2010 issue of Neuron (right, click for higher resolution version), featuring Agus et al.'s "Rapid Formation of Robust Auditory Memories: Insights from Noise".