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

  • {"files"=>["https://ndownloader.figshare.com/files/2625929"], "description"=>"<p>Independently developed LPUs and connectivity patterns may be composed into subsystems (red, green) which may in turn be connected to other subsystems to construct a model of the whole brain (yellow).</p>", "links"=>[], "tags"=>["module", "communication interfaces", "Drosophila melanogaster", "information processing capabilities", "lamina neuropils", "programming model", "Graphics Processing Units", "collaboratively model", "neuroinformation processing capability", "connectivity patterns", "Neurokernel", "gpu", "constituent processing units", "software platform", "Open Source Platform", "interface ports"], "article_id"=>1636480, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Lev E. Givon", "Aurel A. Lazar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146581.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Neurokernel_brain_modeling_architectural_hierarchy_/1636480", "title"=>"Neurokernel brain modeling architectural hierarchy.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 15:28:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/2625930"], "description"=>"<p>The hexagonal tiling depicts the array of ommatidia in the retina and the corresponding retinotopic cartridges in the lamina. Outputs of select photoreceptors in the retina (R1) that are fed to neurons in the lamina and outputs of specific neurons in the lamina (L1, L2) are also depicted.</p>", "links"=>[], "tags"=>["module", "communication interfaces", "Drosophila melanogaster", "information processing capabilities", "lamina neuropils", "programming model", "Graphics Processing Units", "collaboratively model", "neuroinformation processing capability", "connectivity patterns", "Neurokernel", "gpu", "constituent processing units", "software platform", "Open Source Platform", "interface ports"], "article_id"=>1636481, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Lev E. Givon", "Aurel A. Lazar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146581.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_of_natural_input_to_the_combined_retina_lamina_model_/1636481", "title"=>"Example of natural input to the combined retina/lamina model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 15:28:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/2625931"], "description"=>"<p>The number of output ports was varied over 25 equally spaced values between 50 and 15,000. The plot on the left depicts average synchronization time per execution step, while the plot on the right depicts average synchronization throughput (in number of ports per unit time) per execution step.</p>", "links"=>[], "tags"=>["module", "communication interfaces", "Drosophila melanogaster", "information processing capabilities", "lamina neuropils", "programming model", "Graphics Processing Units", "collaboratively model", "neuroinformation processing capability", "connectivity patterns", "Neurokernel", "gpu", "constituent processing units", "software platform", "Open Source Platform", "interface ports"], "article_id"=>1636482, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Lev E. Givon", "Aurel A. Lazar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146581.g007", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Synchronization_performance_for_an_emulation_comprising_2_interconnected_LPUs_accessing_2_different_GPUs_on_the_same_host_scaled_over_number_of_output_ports_exposed_by_each_LPU_/1636482", "title"=>"Synchronization performance for an emulation comprising 2 interconnected LPUs accessing 2 different GPUs on the same host scaled over number of output ports exposed by each LPU.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 15:28:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/2625933"], "description"=>"<p>The total number of output ports exposed by each LPU was varied between 250 and 10,000 at 250 port intervals.</p>", "links"=>[], "tags"=>["module", "communication interfaces", "Drosophila melanogaster", "information processing capabilities", "lamina neuropils", "programming model", "Graphics Processing Units", "collaboratively model", "neuroinformation processing capability", "connectivity patterns", "Neurokernel", "gpu", "constituent processing units", "software platform", "Open Source Platform", "interface ports"], "article_id"=>1636484, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Lev E. Givon", "Aurel A. Lazar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146581.g008", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Speedup_of_average_synchronization_time_per_execution_step_for_an_emulation_scaled_over_number_of_LPUs_where_each_LPU_is_mapped_to_a_single_GPU_/1636484", "title"=>"Speedup of average synchronization time per execution step for an emulation scaled over number of LPUs, where each LPU is mapped to a single GPU.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 15:28:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/2625934"], "description"=>"<p>Synchronization performance for an emulation comprising between 4 and 19 interconnected LPUs selected from the central complex, olfactory, and vision systems partitioned over 2 to 4 GPUs on the same host.</p>", "links"=>[], "tags"=>["module", "communication interfaces", "Drosophila melanogaster", "information processing capabilities", "lamina neuropils", "programming model", "Graphics Processing Units", "collaboratively model", "neuroinformation processing capability", "connectivity patterns", "Neurokernel", "gpu", "constituent processing units", "software platform", "Open Source Platform", "interface ports"], "article_id"=>1636485, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Lev E. Givon", "Aurel A. Lazar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146581.g009", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Synchronization_performance_for_an_emulation_comprising_between_4_and_19_interconnected_LPUs_selected_from_the_central_complex_olfactory_and_vision_systems_partitioned_over_2_to_4_GPUs_on_the_same_host_/1636485", "title"=>"Synchronization performance for an emulation comprising between 4 and 19 interconnected LPUs selected from the central complex, olfactory, and vision systems partitioned over 2 to 4 GPUs on the same host.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 15:28:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/2625936"], "description"=>"<p>Neural responses to sensory stimuli are recorded from the live fly brain in real time and compared to the computed responses of the corresponding components in a fly brain model executed on the same time scale. Discrepancies between these responses and new connectome data may be used to improve the model’s accuracy (fruit fly photograph adapted from Berger and fly robot image adapted from Vizcano, Benton, Gerber, and Louis, both reproduced with permission).</p>", "links"=>[], "tags"=>["module", "communication interfaces", "Drosophila melanogaster", "information processing capabilities", "lamina neuropils", "programming model", "Graphics Processing Units", "collaboratively model", "neuroinformation processing capability", "connectivity patterns", "Neurokernel", "gpu", "constituent processing units", "software platform", "Open Source Platform", "interface ports"], "article_id"=>1636487, "categories"=>["Uncategorised"], "users"=>["Lev E. Givon", "Aurel A. Lazar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146581.g010", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_vivo_validation_is_essential_to_the_development_of_accurate_fly_brain_models_/1636487", "title"=>"In vivo validation is essential to the development of accurate fly brain models.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 15:28:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/2625942"], "description"=>"<div><p>We have developed an open software platform called Neurokernel for collaborative development of comprehensive models of the brain of the fruit fly <i>Drosophila melanogaster</i> 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 of their internal design, Neurokernel explicitly enables multiple researchers to collaboratively model the fruit fly’s entire brain by integration of their independently developed models of its constituent processing units. We demonstrate the power of Neurokernel’s model integration by combining independently developed models of the retina and lamina neuropils in the fly’s visual system and by demonstrating their neuroinformation processing capability. We also illustrate Neurokernel’s ability to take advantage of direct GPU-to-GPU data transfers with benchmarks that demonstrate scaling of Neurokernel’s communication performance both over the number of interface ports exposed by an emulation’s constituent modules and the total number of modules comprised by an emulation.</p></div>", "links"=>[], "tags"=>["module", "communication interfaces", "Drosophila melanogaster", "information processing capabilities", "lamina neuropils", "programming model", "Graphics Processing Units", "collaboratively model", "neuroinformation processing capability", "connectivity patterns", "Neurokernel", "gpu", "constituent processing units", "software platform", "Open Source Platform", "interface ports"], "article_id"=>1636493, "categories"=>["Uncategorised"], "users"=>["Lev E. Givon", "Aurel A. Lazar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146581", "stats"=>{"downloads"=>3, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Neurokernel_An_Open_Source_Platform_for_Emulating_the_Fruit_Fly_Brain_/1636493", "title"=>"Neurokernel: An Open Source Platform for Emulating the Fruit Fly Brain", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2016-01-18 15:28:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/2625919"], "description"=>"<p>Individual neuropils are identified by different colors in the left-hand figure, with the names of several major neuropils listed. Most neuropils are paired across the fly’s two hemispheres. The right-hand figure depicts a tract of neuronal axons connecting neuropils across hemispheres highlighted in yellow (image created using data and software from [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146581#pone.0146581.ref026\" target=\"_blank\">26</a>–<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146581#pone.0146581.ref028\" target=\"_blank\">28</a>], reproduced with permission).</p>", "links"=>[], "tags"=>["module", "communication interfaces", "Drosophila melanogaster", "information processing capabilities", "lamina neuropils", "programming model", "Graphics Processing Units", "collaboratively model", "neuroinformation processing capability", "connectivity patterns", "Neurokernel", "gpu", "constituent processing units", "software platform", "Open Source Platform", "interface ports"], "article_id"=>1636470, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Lev E. Givon", "Aurel A. Lazar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146581.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Modular_structure_of_fruit_fly_brain_/1636470", "title"=>"Modular structure of fruit fly brain.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 15:28:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/2625921"], "description"=>"<p>The application plane provides support for hardware-independent specification of LPUs and their interconnects. Services that implement the neural primitives and computing methods required to execute neural circuit model instantiations on GPUs are provided by the compute plane. Translation or mapping of specified model components to the methods provided by the compute plane and management of multiple GPUs and communication resources is performed by the control plane operating on a cluster of CPUs.</p>", "links"=>[], "tags"=>["module", "communication interfaces", "Drosophila melanogaster", "information processing capabilities", "lamina neuropils", "programming model", "Graphics Processing Units", "collaboratively model", "neuroinformation processing capability", "connectivity patterns", "Neurokernel", "gpu", "constituent processing units", "software platform", "Open Source Platform", "interface ports"], "article_id"=>1636472, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Lev E. Givon", "Aurel A. Lazar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146581.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_three_plane_structure_of_the_Neurokernel_architecture_is_based_on_the_principle_of_separation_of_time_scales_/1636472", "title"=>"The three-plane structure of the Neurokernel architecture is based on the principle of separation of time scales.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 15:28:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/2625923"], "description"=>"<p>An LPU model’s internal components (cyan) are exposed via input and output ports (yellow and orange). Connections between LPUs are described by patterns (green) that link the ports of one LPU to those of another. Connections may only be defined between ports of the same transmission type.</p>", "links"=>[], "tags"=>["module", "communication interfaces", "Drosophila melanogaster", "information processing capabilities", "lamina neuropils", "programming model", "Graphics Processing Units", "collaboratively model", "neuroinformation processing capability", "connectivity patterns", "Neurokernel", "gpu", "constituent processing units", "software platform", "Open Source Platform", "interface ports"], "article_id"=>1636474, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Lev E. Givon", "Aurel A. Lazar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146581.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Neurokernel_programming_model_/1636474", "title"=>"Neurokernel programming model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 15:28:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/2625924"], "description"=>"<p>Each communication port must either receive input (yellow) or emit output (orange), and must either transmit spikes (diamonds) or graded potentials (circles).</p>", "links"=>[], "tags"=>["module", "communication interfaces", "Drosophila melanogaster", "information processing capabilities", "lamina neuropils", "programming model", "Graphics Processing Units", "collaboratively model", "neuroinformation processing capability", "connectivity patterns", "Neurokernel", "gpu", "constituent processing units", "software platform", "Open Source Platform", "interface ports"], "article_id"=>1636475, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Lev E. Givon", "Aurel A. Lazar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146581.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_LPU_interface_/1636475", "title"=>"LPU interface.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 15:28:32"}

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{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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