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Publications of the Simulation Lab Neuroscience

Journal articles, Other contributions

Journal articles

Journal Article
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"Bernstein Network – Simulation Lab Neuroscience" HPC Workshop
Innovatives Supercomputing in Deutschland 12(2), 93-94 (2014)  GO

Journal Article
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JSC Guest Student Programme 2014 – Experience Scientific Computing
Innovatives Supercomputing in Deutschland 12(2), 86-87 (2014)  GO

Journal Article
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Spiking network simulation code for petascale computers
Frontiers in neuroinformatics 8, 78 (2014) [10.3389/fninf.2014.00078]  GO

Journal Article
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Domain and Interdomain Energetics Underlying Gating in Shaker-Type Kv Channels
Biophysical journal 107(8), 1841 - 1852 (2014) [10.1016/j.bpj.2014.08.015]  GO

Journal Article
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Homeostatic structural plasticity can account for topology changes following deafferentation and focal stroke
Frontiers in neuroanatomy 8, 115 (2014) [10.3389/fnana.2014.00115]  GO

Journal Article
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Homeostatic structural plasticity increases the efficiency of small-world networks
Frontiers in synaptic neuroscience 6(7), 14 (2014) [10.3389/fnsyn.2014.00007]  GO

Journal Article
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CyNEST: a maintainable Cython-based interface for the NEST simulator
Frontiers in neuroinformatics 8, 23 (2014) [10.3389/fninf.2014.00023]  GO

Journal Article
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Neural system prediction and identification challenge
Frontiers in neuroinformatics 7(43), 1-10 (2013) [10.3389/fninf.2013.00043]  GO

Journal Article
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Relating Polarized Light Imaging Data Across Scales
Imaging the brain at different scales: How to integrate multi-scale structural information?, Antwerp, Belgium, 09/02/2013 - 09/06/2013 Frontiers in neuroinformatics 7, 3 (2013) [10.3389/conf.fninf.2013.10.00029]  GO

Journal Article
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A Simple Rule for Dendritic Spine and Axonal Bouton Formation Can Account for Cortical Reorganization after Focal Retinal Lesions
PLoS Computational Biology 9(10), e1003259 (2013) [10.1371/journal.pcbi.1003259]  GO

Journal Article
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Increasing quality and managing complexity in neuroinformatics software development with continuous integration.
Frontiers in neuroinformatics 6(31), 1-16 (2013) [10.3389/fninf.2012.00031]  GO

Journal Article
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JSC Guest Student Programme on Scientific Computing 2013
Innovatives Supercomputing in Deutschland 11(2), 104-105 (2013)  GO

Other contributions

Contribution to a conference proceedings/Contribution to a book
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Integrating brain structure and dynamics on supercomputers
Brain-inspired Computing
1st International Workshop on Brain-inspired Computing, BrainComp 2013, Cetraro, Italy, 07/08/2013 - 07/11/2013
Lecture Notes in Computer Science 8603, 22-32 (2014) [10.1007/978-3-319-12084-3_3]  GO

Poster (After Call)
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Performance Model for Large-Scale Neural Simulations with NEST
Supercomputing 2014, SC14, New Orleans, USA, 11/16/2014 - 11/21/2014 (2014)

Talk (non-conference) (Other)
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Dry-Run Mode for the Simulation Phase of NEST
NEST 100k Meeting (INM-6), Jülich, Germany, 07/21/2014 - (2014)

Talk (non-conference) (Other)

Simple and hybrid parallelizations for GPU clusters in a nutshell
BrainScaleS CodeJam Workshop #6, Jülich, Germany, 01/27/2014 - 01/29/2014 (2014)

Poster
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Hybrid parallelization of a seeded region growing segmentation of brain images for a GPU cluster
1st HBP School, Alpbach, Austria, 09/08/2014 - 09/14/2014 (2014)

Poster
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Simulating structural plasticity of large scale networks in NEST
Twenty Third Annual Computational Neuroscience Meeting, CNS*2014, Quebec City, Canada, 07/26/2014 - 07/31/2014 (2014) [10.1186/1471-2202-15-S1-P194]  GO

Conference Presentation

Tools, Services and Workflows: A Short Story about Nearly Everything Else
"Bernstein Network - Simulation Lab Neuroscience" HPC Workshop, Jülich, Germany, 06/04/2014 - 06/05/2014 (2014)

Talk (non-conference)

Electrostatics of the Voltage Sensor of Ion Channels: Simulation as a science
Seminar at the Department of Mathematics, State College, PA, United States, 07/24/2014 - (2014)

Talk (non-conference)

Multiscaling the Human Brian, from Ion Channels to Neural Networks
Seminar at the Department of Biophysics and Physiology of the Rush University Medical Center, Chicago, United States, 07/21/2014 - (2014)

Poster (Other)
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Theoretical predictions of gating behavior for mutants of Shaker-type Kv channels from inter-domain energetics
Bernstein Conference 2014, Göttingen, Germany, 09/03/2014 - 09/05/2014 (2014)

Conference Presentation (Invited)

Advanced Python profiling
EuroScipy 2014, Cambridge, United Kindgom, 08/27/2014 - 08/31/2014 (2014)

Conference Presentation (Other)

Python profiling for responsible performance optimization
BrainScaleS CodeJam 6, Jülich, Germany, 01/27/2014 - 01/29/2014 (2014)

Conference Presentation (After Call)

Hybrid parallelization of a seeded region growing segmentation of brain images for a GPU cluster
11th Workshop on Parallel Systems and Algorithms, PASA2014, Lübeck, Germany, 02/25/2014 - 02/26/2014 (2014)

Contribution to a conference proceedings/Contribution to a book

Hybrid parallelization of a seeded region growing segmentation of brain images for a GPU cluster
ARCS 2014: 27th International Conference on Architecture of Computing Systems - Workshop Proceedings
27th International Conference on Architecture of Computing Systems, ARCS2014, Lübeck, Germany, 02/25/2014 - 02/28/2014
190 (2014)  GO

Poster (After Call)
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20 years of NEST: a mature brain simulator
INM Retreat 2013, Jülich, Germany, 07/02/2013 - 07/03/2013 (2013)

Poster
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From laptops to supercomputers: a single highly scalable code base for spiking neuronal network simulations
Annual CNS Meeting 2013, Paris, France, 07/13/2013 - 07/18/2013 BMC neuroscience 14(Suppl 1), P163 - (2013) [10.1186/1471-2202-14-S1-P163]  GO

Conference Presentation (Invited)
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Simulation technology at cellular and synaptic resolution for the largest computers
EU - US workshop on Cortical Processors, Heidelberg, Germany, 10/14/2013 - 10/15/2013 (2013)

Talk (non-conference) (Other)

Weihnachtsdeko mal anders ‒ Segmentierung hochauflösender Hirnbilder auf JUDGE
JSC-Jahresabschlusskolloquium 2013, Jülich, Germany, 12/16/2013 - 12/16/2013 (2013)

Poster
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Relating PLI Data Across Scales
Imaging the brain at different scales: How to integrate multi-scale structural information?, Antwerp, Belgium, 09/02/2013 - 09/06/2013 (2013)

Poster (After Call)
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GPU-accelerated Segmentation of High-resolution Human Brain Images Acquired with Polarized Light Imaging
Bernstein Conference on Computational Neuroscience 2013, BCCN2013, Tübingen, Germany, 09/24/2013 - 09/27/2013 (2013)

Talk (non-conference) (Other)

GPU-accelerated Segmentation of high-resolution Human Brain Images acquired with Polarized Light Imaging
JSC-internal Seminar, Jülich, Germany, 07/19/2013 - 07/19/2013 (2013)

Master Thesis/Internal Report

GPU-accelerated Segmentation of high-resolution Human Brain Images acquired with Polarized Light Imaging
Berichte des Forschungszentrums Jülich 4365, 84 p. (2013)

Poster (Poster)
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Effect of Alzheimer’s disease on the dynamical and computational characteristics of recurrent neural networks
22nd Annual Computational Neuroscience Meeting, CNS*2013, Paris, France, 07/13/2013 - 07/18/2013 (2013)

Contribution to a book
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Supercomputers ready for use as discovery machines for neuroscience
Proceedings of the 10th Meeting of the German Neuroscience Society
10th Meeting of the German Neuroscience Society, NWG 2013, Goettingen, Germany, 03/13/2013 - 03/16/2013
T26-8B (2013)

Poster (After Call)
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Supercomputers ready for use as discovery machines for neuroscience
10th Meeting of the German Neuroscience Society, NWG 2013, Goettingen, Germany, 03/13/2013 - 03/18/2013 (2013)

Conference Presentation (Invited)
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Estimation of fiber orientation distribution functions in 3D-polarized light imaging
19th Annual Meeting of the Organization for Human Brain Mapping, Seattle, USA, 06/16/2013 - 06/20/2013 (2013)

Poster (Other)
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Estimation of fiber orientation distribution functions in 3D-polarized light imaging
19th Annual Meeting of the Organization for Human Brain Mapping, Seattle, USA, 06/16/2013 - 06/20/2013 (2013)


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