Methods in Neuronal Modeling: From synapses to networks
Methods in Neuronal Modeling: From synapses to networks
An overview of the BlueGene/L Supercomputer
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IEEE Transactions on Information Technology in Biomedicine
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Proceedings of the 2013 ACM SIGMOD International Conference on Management of Data
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Simulating neural tissue requires the construction of models of the anatomical structure and physiological function of neural microcircuitry. The Blue Brain Project is simulating the microcircuitry of a neocortical column with very high structural and physiological precision. This paper describes how we model anatomical structure by identfying, tabulating, and analyzing contacts between 104 neurons in a morphologically precise model of a column. A contact occurs when one element touches another, providing the opportunity for the subsequent creation of a simulated synapse. The architecture of our application divides the problem of detecting and analyzing contacts among thousands of processors on the IBM Blue Gene/L™ supercomputer. Data required for contact tabulation is encoded with geometrical data for contact detection and is exchanged among processors. Each processor selects a subset of neurons and then iteratively 1) divides the number of points that represents each neuron among column subvolumes, 2) detects contacts in a subvolume, 3) tabulates arbitrary categories of local contacts, 4) aggregates and analyzes global contacts, and 5) revises the contents of a column to achieve a statistical objective. Computing, analyzing, and optimizing local data in parallel across distributed global data objects involve problems common to other domains (such as three-dimensional image processing and registration). Thus, we discuss the generic nature of the application architecture.