Wiki source code of SGA2 SP3 UC003 - Temporal Structure in Recorded Ensemble Activity

Version 66.1 by denker on 2020/04/21 15:47

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40.1	5	= Temporal Structure in Recorded Ensemble Activity =
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66.1	7	Contribution to Use Case SGA2-SP3-003: Pipeline for analyzing Temporal structure in recorded Ensemble Activity and related Systems Neuroscience data in association with behavior, cognitive processing and modeling
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33.1	9	Experiments: Julien Fiorilli^^2^^
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33.1	11	Implementation: Regimantas Jurkus^^1^^, Julien Fiorilli^^2^^, Pietro Marchesi^^2^^, Thijs Ruikes^^2^^
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45.1	13	Lead: Michael Denker^^1^^, Sonja Grün^^1^^, Cyriel Pennartz^^2^^
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	15	,,1) Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany,,
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	17	,,2) Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands,,
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66.1	25	== Analysis of temporal correlations in electrophysiological data using Neo and Elephant ==
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66.1	27	This notebook, aimed at experimental and computational neuroscientists, demonstrates the principles of performing analysis of activity data on a complex dataset using the Neo and Elephant tools. We demonstrate the advantage of a common and shared data representation format for a challenging and complex electrophysiology dataset. Also, we showcase the first part of a pipeline for analysing for population-level data, including parallel spiking activity, paired with and behavioural and cognitive state variables.
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66.1	29	A detailed description is found in the interactive Jupyter notebook.
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28.1	31	== Executing the analysis notebook ==
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	33	* Copy the collab drive to your drive space
	34	** Open the Drive from the left menu
29.1	35	** Select "Demonstrator_Use_Case_SGA2-SP3-003.ipynb", the "Figures" folder, and the "Data" folder
	36	** Copy the selected items, and select the destination 'My Library' from the dropdown 'Other Libraries'
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	38	* Start a Jupyter Hub instance
	39	In another browser, open [[https:~~/~~/lab.ebrains.eu>>url:https://lab.ebrains.eu]]
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	41	* Run the notebook
30.1	42	In the Jupyter Hub, navigate to `drive/My Libraries/My Library/Demonstrator_Use_Case_SGA2-SP3-003.ipynb`, and run the notebook.
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46.1	45	== License ==
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63.1	47	All text and example data in this collab is licensed under under a [[Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License>>url:https://creativecommons.org/licenses/by-nc-nd/4.0/]]. Software code is licensed under [[a modified BSD license>>https://opensource.org/licenses/BSD-3-Clause]].
51.1	48	Please note that the data in this Collab is preliminary and might therefore still contain inaccuracies in specific event timestamps.
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62.1	50	[[image:88x31.png]]
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65.1	53	== Acknowledgments ==
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20.1	55	This open source software code was developed in part or in whole in the Human Brain Project, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 785907 (Human Brain Project SGA2).
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44.1	58	[[image:logos_sga2_sp3_uc003.png\|\|alt="Logos SP3 Use Case 3"]]
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	64	{{box title="Contents"}}
	65	{{toc/}}
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