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Image-based configuration and interaction for large neural network simulations


Large neural network simulations are becoming more complex to set up. They require modeling at multiple scales, include the effects of many interacting physical processes, encompass greater detail, and consume greater computational resources. The drive to solve problems that rely on increasingly complex codes will soon land us in the realm of petascale computing. How will we manage such simulations, configure them, and accurately aim them at the problems we're trying to solve? Simulation is an increasingly expensive process, with each run providing data to inform configuration and targeting of subsequent runs. Hence, it is vital to configure and execute simulations efficiently in order to minimize time spent on the computer cycles as well as time spent interpreting simulation results and designing follow-up experiments. We are developing a framework for interacting with and configuring large simulations using image-based interfaces generated automatically from the simulation source code.

Figure 1 shows a working prototype of some of the key components of the interactive framework. The diagram at the left is an automatically generated view of the probabilistic wiring diagram showing excitatory (*) and inhibitory connections between pyramidal, basket, and chandelier cell types. The central image is an automatically generated physical layout of a portion of the neurons in a larger patch of the neocortex simulation. Circles, triangles, pluses, and exes correspond to superficial and deep pyramidal, basket, and chandelier cells. The mouse has been used to select two cells in the subpatch, which caused the signal viewer shown on the right to launch (not wired to a live simulation in this prototype).

Figure 1
figure 1

Framework for interacting with large simulations.


The goal of the project is to create an interface to supercomputing platforms that will enable scientists to directly engage the live simulation during its critical setup and initial phases and at later times for monitoring and redirecting. This capability will enable rapid intuition building and will improve scientists' effectiveness in deploying productive, well-targeted experiments across research domains.


This work was supported in part by the Falk Foundation, the Linn family, and the U.S. Department of Energy under Contract DE-AC02-06CH11357.

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Correspondence to Mark Hereld.

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Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution 2.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Hereld, M., Lee, H.C., van Drongelen, W. et al. Image-based configuration and interaction for large neural network simulations. BMC Neurosci 8 (Suppl 2), P22 (2007).

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