publication . Article . Other literature type . Report . 2016

Neurokernel: An Open Source Platform for Emulating the Fruit Fly Brain

Givon, Lev E.; Lazar, Aurel A.;
Open Access
  • Published: 11 Jan 2016 Journal: PLOS ONE, volume 11, page e0146581 (eissn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science (PLoS)
Abstract
We have developed an open software platform called Neurokernel for collaborative development of comprehensive models of the brain of the fruit fly <em>Drosophila melanogaster</em> and their execution and testing on multiple Graphics Processing Units (GPUs). Neurokernel provides a programming model that capitalizes upon the structural organization of the fly brain into a fixed number of functional modules to distinguish between these modules' local information processing capabilities and the connectivity patterns that link them. By defining mandatory communication interfaces that specify how data is transmitted between models of each of these modules regardless o...
Subjects
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Programming paradigm, Information processing, Computer graphics, Connectomics, Bioinformatics, Emulation, Computer architecture, Computer science, CUDA, Software, business.industry, business, Graphics, Graphics processing units, Brain--Models, Drosophila melanogaster--Physiology, Neurosciences, Electrical engineering, Drosophila, GPU, Brain emulation, LPU, Medicine, R, Science, Q, Research Article
Related Organizations
Funded by
NSF| The Digital Fly Brain
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1544383
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72 references, page 1 of 5

1 Kandel ER, Markram H, Matthews PM, Yuste R, Koch C. Neuroscience thinks big (and collaboratively). Nature Reviews Neuroscience. 2013 9;14(9):659–664. 10.1038/nrn3578 23958663 [OpenAIRE] [PubMed] [DOI]

2 Sanes JR, Zipursky SL. Design Principles of Insect and Vertebrate Visual Systems. Neuron. 2010 4;66(1):15–36. Available from: http://linkinghub.elsevier.com/retrieve/pii/S0896627310000449. 10.1016/j.neuron.2010.01.018 20399726 [OpenAIRE] [PubMed] [DOI]

3 Armstrong JD, van Hemert JI. Towards a virtual fly brain. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2009 6;367(1896):2387–2397. Available from: http://rsta.royalsocietypublishing.org/content/367/1896/2387.abstract. 10.1098/rsta.2008.0308 [OpenAIRE] [DOI]

4 Chiang AS, Lin CY, Chuang CC, Chang HM, Hsieh CH, Yeh CW, et al Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution. Current Biology. 2011 1;21(1):1–11. Available from: http://www.cell.com/current-biology/abstract/S0960-9822(10)01522-8?switch=standard. 10.1016/j.cub.2010.11.056 21129968 [OpenAIRE] [PubMed] [DOI]

5 Duffy JB. GAL4 system in Drosophila: a fly geneticist’s Swiss Army knife. Genesis (New York, NY: 2000). 2002 10;34(1–2):1–15. PMID: 12324939. Available from: http://www.ncbi.nlm.nih.gov/pubmed/12324939. 10.1002/gene.10150 [OpenAIRE] [DOI]

6 Rister J, Pauls D, Schnell B, Ting CY, Lee CH, Sinakevitch I, et al Dissection of the Peripheral Motion Channel in the Visual System of Drosophila melanogaster. Neuron. 2007 10;56(1):155–170. Available from: http://www.cell.com/neuron/abstract/S0896-6273(07)00712-X. 10.1016/j.neuron.2007.09.014 17920022 [OpenAIRE] [PubMed] [DOI]

7 Song Z, Postma M, Billings SA, Coca D, Hardie RC, Juusola M. Stochastic, Adaptive Sampling of Information by Microvilli in Fly Photoreceptors. Current Biology. 2012 6;22(15):1371–1380. Available from: http://www.cell.com/current-biology/abstrac t/S0960-9822(12)00634-3. 10.1016/j.cub.2012.05.047 22704990 [OpenAIRE] [PubMed] [DOI]

8 Wardill TJ, List O, Li X, Dongre S, McCulloch M, Ting CY, et al Multiple Spectral Inputs Improve Motion Discrimination in the Drosophila Visual System. Science. 2012 5;336(6083):925–931. PMID: 22605779. Available from: http://www.sciencemag.org/content/336/6083/925. 10.1126/science.1215317 22605779 [OpenAIRE] [PubMed] [DOI]

9 Maisak MS, Haag J, Ammer G, Serbe E, Meier M, Leonhardt A, et al A directional tuning map of Drosophila elementary motion detectors. Nature. 2013 8;500(7461):212–216. Available from: http://www.nature.com/nature/journal/v500/n7461/abs/nature12320.html. 10.1038/nature12320 23925246 [OpenAIRE] [PubMed] [DOI]

10 Kim AJ, Lazar AA, Slutskiy YB. System identification of Drosophila olfactory sensory neurons. Journal of Computational Neuroscience. 2011 8;30(1):143–161. Available from: http://www.springerlink.com/content/j046v670uj85v48v/. 10.1007/s10827-010-0265-0 20730480 [OpenAIRE] [PubMed] [DOI]

11 Wilson RI. Understanding the functional consequences of synaptic specialization: insight from the Drosophila antennal lobe. Current Opinion in Neurobiology. 2011 4;21(2):254–260. Available from: http://www.sciencedirect.com/science/article/pii/S095943881 1000420. 10.1016/j.conb.2011.03.002 21441021 [OpenAIRE] [PubMed] [DOI]

12 Kim AJ, Lazar AA, Slutskiy YB. Projection neurons in Drosophila antennal lobes signal the acceleration of odor concentrations. eLife. 2015 May;p. e06651. Available from: http://elifesciences.org/content/early/2015/05/14/eLife.06651.

13 Budick SA, Dickinson MH. Free-flight responses of Drosophila melanogaster to attractive odors. Journal of Experimental Biology. 2006;209(15):3001–3017. Available from: http://jeb.biologists.org/content/209/15/3001.abstract. 10.1242/jeb.02305 16857884 [OpenAIRE] [PubMed] [DOI]

14 Maimon G, Straw AD, Dickinson MH. A simple vision-based algorithm for decision making in flying Drosophila. Current Biology. 2008 3;18(6):464–470. Available from: http://www.sciencedirect.com/science/article/B6VRT-4S21J46-2/2/5ef5f08d7f9b78d3777a5e731d088567. 10.1016/j.cub.2008.02.054 18342508 [OpenAIRE] [PubMed] [DOI]

15 Chiappe ME, Seelig JD, Reiser MB, Jayaraman V. Walking Modulates Speed Sensitivity in Drosophila Motion Vision. Current Biology. 2010 8;20(16):1470–1475. Available from: http://www.sciencedirect.com/science/article/pii/S0960982210008614. 10.1016/j.cub.2010.06.072 20655222 [OpenAIRE] [PubMed] [DOI]

72 references, page 1 of 5
Abstract
We have developed an open software platform called Neurokernel for collaborative development of comprehensive models of the brain of the fruit fly <em>Drosophila melanogaster</em> and their execution and testing on multiple Graphics Processing Units (GPUs). Neurokernel provides a programming model that capitalizes upon the structural organization of the fly brain into a fixed number of functional modules to distinguish between these modules' local information processing capabilities and the connectivity patterns that link them. By defining mandatory communication interfaces that specify how data is transmitted between models of each of these modules regardless o...
Subjects
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Programming paradigm, Information processing, Computer graphics, Connectomics, Bioinformatics, Emulation, Computer architecture, Computer science, CUDA, Software, business.industry, business, Graphics, Graphics processing units, Brain--Models, Drosophila melanogaster--Physiology, Neurosciences, Electrical engineering, Drosophila, GPU, Brain emulation, LPU, Medicine, R, Science, Q, Research Article
Related Organizations
Funded by
NSF| The Digital Fly Brain
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1544383
Download fromView all 8 versions
PLoS ONE
Article . 2016
Provider: Crossref
PLoS ONE
Article
Provider: UnpayWall
Zenodo
Other literature type . 2015
Provider: Datacite
72 references, page 1 of 5

1 Kandel ER, Markram H, Matthews PM, Yuste R, Koch C. Neuroscience thinks big (and collaboratively). Nature Reviews Neuroscience. 2013 9;14(9):659–664. 10.1038/nrn3578 23958663 [OpenAIRE] [PubMed] [DOI]

2 Sanes JR, Zipursky SL. Design Principles of Insect and Vertebrate Visual Systems. Neuron. 2010 4;66(1):15–36. Available from: http://linkinghub.elsevier.com/retrieve/pii/S0896627310000449. 10.1016/j.neuron.2010.01.018 20399726 [OpenAIRE] [PubMed] [DOI]

3 Armstrong JD, van Hemert JI. Towards a virtual fly brain. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2009 6;367(1896):2387–2397. Available from: http://rsta.royalsocietypublishing.org/content/367/1896/2387.abstract. 10.1098/rsta.2008.0308 [OpenAIRE] [DOI]

4 Chiang AS, Lin CY, Chuang CC, Chang HM, Hsieh CH, Yeh CW, et al Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution. Current Biology. 2011 1;21(1):1–11. Available from: http://www.cell.com/current-biology/abstract/S0960-9822(10)01522-8?switch=standard. 10.1016/j.cub.2010.11.056 21129968 [OpenAIRE] [PubMed] [DOI]

5 Duffy JB. GAL4 system in Drosophila: a fly geneticist’s Swiss Army knife. Genesis (New York, NY: 2000). 2002 10;34(1–2):1–15. PMID: 12324939. Available from: http://www.ncbi.nlm.nih.gov/pubmed/12324939. 10.1002/gene.10150 [OpenAIRE] [DOI]

6 Rister J, Pauls D, Schnell B, Ting CY, Lee CH, Sinakevitch I, et al Dissection of the Peripheral Motion Channel in the Visual System of Drosophila melanogaster. Neuron. 2007 10;56(1):155–170. Available from: http://www.cell.com/neuron/abstract/S0896-6273(07)00712-X. 10.1016/j.neuron.2007.09.014 17920022 [OpenAIRE] [PubMed] [DOI]

7 Song Z, Postma M, Billings SA, Coca D, Hardie RC, Juusola M. Stochastic, Adaptive Sampling of Information by Microvilli in Fly Photoreceptors. Current Biology. 2012 6;22(15):1371–1380. Available from: http://www.cell.com/current-biology/abstrac t/S0960-9822(12)00634-3. 10.1016/j.cub.2012.05.047 22704990 [OpenAIRE] [PubMed] [DOI]

8 Wardill TJ, List O, Li X, Dongre S, McCulloch M, Ting CY, et al Multiple Spectral Inputs Improve Motion Discrimination in the Drosophila Visual System. Science. 2012 5;336(6083):925–931. PMID: 22605779. Available from: http://www.sciencemag.org/content/336/6083/925. 10.1126/science.1215317 22605779 [OpenAIRE] [PubMed] [DOI]

9 Maisak MS, Haag J, Ammer G, Serbe E, Meier M, Leonhardt A, et al A directional tuning map of Drosophila elementary motion detectors. Nature. 2013 8;500(7461):212–216. Available from: http://www.nature.com/nature/journal/v500/n7461/abs/nature12320.html. 10.1038/nature12320 23925246 [OpenAIRE] [PubMed] [DOI]

10 Kim AJ, Lazar AA, Slutskiy YB. System identification of Drosophila olfactory sensory neurons. Journal of Computational Neuroscience. 2011 8;30(1):143–161. Available from: http://www.springerlink.com/content/j046v670uj85v48v/. 10.1007/s10827-010-0265-0 20730480 [OpenAIRE] [PubMed] [DOI]

11 Wilson RI. Understanding the functional consequences of synaptic specialization: insight from the Drosophila antennal lobe. Current Opinion in Neurobiology. 2011 4;21(2):254–260. Available from: http://www.sciencedirect.com/science/article/pii/S095943881 1000420. 10.1016/j.conb.2011.03.002 21441021 [OpenAIRE] [PubMed] [DOI]

12 Kim AJ, Lazar AA, Slutskiy YB. Projection neurons in Drosophila antennal lobes signal the acceleration of odor concentrations. eLife. 2015 May;p. e06651. Available from: http://elifesciences.org/content/early/2015/05/14/eLife.06651.

13 Budick SA, Dickinson MH. Free-flight responses of Drosophila melanogaster to attractive odors. Journal of Experimental Biology. 2006;209(15):3001–3017. Available from: http://jeb.biologists.org/content/209/15/3001.abstract. 10.1242/jeb.02305 16857884 [OpenAIRE] [PubMed] [DOI]

14 Maimon G, Straw AD, Dickinson MH. A simple vision-based algorithm for decision making in flying Drosophila. Current Biology. 2008 3;18(6):464–470. Available from: http://www.sciencedirect.com/science/article/B6VRT-4S21J46-2/2/5ef5f08d7f9b78d3777a5e731d088567. 10.1016/j.cub.2008.02.054 18342508 [OpenAIRE] [PubMed] [DOI]

15 Chiappe ME, Seelig JD, Reiser MB, Jayaraman V. Walking Modulates Speed Sensitivity in Drosophila Motion Vision. Current Biology. 2010 8;20(16):1470–1475. Available from: http://www.sciencedirect.com/science/article/pii/S0960982210008614. 10.1016/j.cub.2010.06.072 20655222 [OpenAIRE] [PubMed] [DOI]

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publication . Article . Other literature type . Report . 2016

Neurokernel: An Open Source Platform for Emulating the Fruit Fly Brain

Givon, Lev E.; Lazar, Aurel A.;