Book Chapter10.1007/978-3-319-53862-4_21
A Collaborative Simulation-Analysis Workflow for Computational Neuroscience Using HPC
Johanna Senk,Alper Yegenoglu,Olivier Amblet,Yury Brukau,Andrew P. Davison,David Lester,Anna Lührs,Pietro Quaglio,Vahid Rostami,Andrew Rowley,Bernd Schuller,Alan B. Stokes,Sacha J. van Albada,Daniel Zielasko,Markus Diesmann,Markus Diesmann,Benjamin Weyers,Michael Denker,Sonja Grün,Sonja Grün +19 more
- 04 Oct 2016
- pp 243-256
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TL;DR: It is argued for the need of software platforms integrating HPC systems that allow scientists to construct, comprehend and execute workflows composed of diverse data generation and processing steps using different tools.
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Abstract: Workflows for the acquisition and analysis of data in the natural sciences exhibit a growing degree of complexity and heterogeneity, are increasingly performed in large collaborative efforts, and often require the use of high-performance computing (HPC). Here, we explore the reasons for these new challenges and demands and discuss their impact with a focus on the scientific domain of computational neuroscience. We argue for the need of software platforms integrating HPC systems that allow scientists to construct, comprehend and execute workflows composed of diverse data generation and processing steps using different tools. As a use case we present a concrete implementation of such a complex workflow, covering diverse topics such as HPC-based simulation using the NEST software, access to the SpiNNaker neuromorphic hardware platform, complex data analysis using the Elephant library, and interactive visualization methods for facilitating further analysis. Tools are embedded into a web-based software platform under development by the Human Brain Project, called the Collaboratory. On the basis of this implementation, we discuss the state of the art and future challenges in constructing large, collaborative workflows with access to HPC resources.
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Citations
Performance Comparison of the Digital Neuromorphic Hardware SpiNNaker and the Neural Network Simulation Software NEST for a Full-Scale Cortical Microcircuit Model
Sacha J. van Albada,Andrew Rowley,Johanna Senk,Michael Hopkins,Maximilian Schmidt,Alan B. Stokes,David Lester,Markus Diesmann,Steve Furber +8 more
TL;DR: The first full-scale simulations of a cortical microcircuit with biological time scales on SpiNNaker is described, showing that further optimizations such as synapse-centric network representation are necessary to enable real-time simulation of large biological neural networks.
SpiNNTools: The Execution Engine for the SpiNNaker Platform.
Andrew Rowley,Christian Y. Brenninkmeijer,Simon Davidson,Donal Fellows,A. D. Gait,David Lester,Luis A. Plana,Oliver Rhodes,Alan B. Stokes,Steve Furber +9 more
TL;DR: This work introduces a software suite called SpiNNTools that can map a computational problem described as a graph into the required set of executables, application data and routing information necessary for simulation on this novel machine.
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Reconciliation of weak pairwise spike-train correlations and highly coherent local field potentials across space
TL;DR: Based on model predictions of spiking activity and LFPs, it is found that the upscaling procedure preserves the overall spiking statistics of the original model and reproduces asynchronous irregular spiking across populations and weak pairwise spike-train correlations observed in sensory cortex.
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Simulation, visualization and analysis tools for pattern recognition assessment with spiking neuronal networks
TL;DR: A systematic work-flow is presented for the configuration of spiking-neuronal-network-based learning systems including evolutionary algorithms for information transmission optimization, advanced visualization tools for the validation of the best suitable configuration and customized scripts for final quantitative evaluation of the learning capabilities.
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- 01 Jan 2008
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