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	1	+XWiki.denker

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4	4	(((
5	5	= (% style="color:inherit" %)Slow Wave Analysis Pipeline(%%) =
6	6
7		-= (% style="color:inherit; font-size:24px" %)Integrating multiscale data in a reproducible and adaptable pipeline(%%) =
	7	+(% class="wikigeneratedid" id="HUseCaseSGA2-SP3-002:IntegratingmultiscaledataA0inareproducibleandadaptablepipeline" %)
	8	+(% style="color:inherit; font-size:24px" %)**Use Case SGA2-SP3-002: Integrating multi-scale data in a reproducible and adaptable pipeline**
	9	+
	10	+To be discussed Author order, contributions,...:
	11	+
	12	+Experiments: ...?
	13	+
	14	+Implementation: Robin Gutzen^^1,*^^, Elena Pastorelli^^2,*^^, ...
	15	+
	16	+Lead: Michael Denker^^1^^, Sonja Grün^^1^^, Pier Stanislao Paolucci^^2^^, Andrew Davison?
	17	+
	18	+,,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,,
	19	+
	20	+,,2) Dipartimento di Fisica, Università di Cagliari and INFN Sezione di Cagliari, Italy,,
	21	+
	22	+
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10	10
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13	13	(% class="col-xs-12 col-sm-8" %)
14	14	(((
15		-= What can I find here? =
	30	+== Flexible workflows to generate multi-scale analysis scenarios ==
16	16
17		-...
	32	+This Collab is aimed at experimental and computational neuroscientists interested in the usage of the Neo and Elephant tools in performing data analysis of spiking data.
18	18
19		-= Who has access? =
20		-
21		-Describe the audience of this collab.
22		-
23	23	== Executing the pipeline ==
24	24
25	25	[[image:pipeline_flowchart.png]]
26	26
27		-=== in the collab (beta) ===
	38	+=== In the collab (beta) ===
28	28
29	29	* **Copy the collab drive to your drive space**
30	30	** Open the Drive from the left menu
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32	32	** Select 'Copy', and then 'My Library' from the dropdown 'Other Libraries'
33	33
34	34	* **Start a Jupyter Hub instance **
35		-copy the URL to another browser page: 'jupyterhub-preview.apps-dev.hbp.eu'
36		-
	46	+In another browser, open [[https:~~/~~/lab.ebrains.eu>>https://lab.ebrains.eu]]
	47	+
37	37	* **Edit the config files**
38	38	Each stage has a config file to specify which analysis/processing blocks to execute and which parameters to use. General and specific information about the blocks and parameters can found in the README and config files. The default values are set for an example dataset (ECoG, anesthetized mouse, IDIBAPS [ref]).
39	39	** stage01_data_entry: [README.md](), [config.yaml]()
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51	51	** Provenance Tracking
52	52	** HPC support
53	53
54		-=== locally ===
	65	+=== Local execution ===
55	55
56	56	* **Get the code**
57	57	The source code of the pipeline is available via Github: [INM-6/wavescalephant]('https:~/~/github.com/INM-6/wavescalephant') and can be cloned to your machine ([how to use Github]()).
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82	82	== References ==
83	83
84	84
	96	+== License (to discuss) ==
	97	+
	98	+All text and example data in this collab is licensed under Creative Commons CC-BY 4.0 license. Software code is licensed under a modified BSD license.
	99	+
85	85	== Acknowledgments ==
86	86
87		-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
88		-under the Specific Grant Agreement No. 785907 (Human Brain Project SGA2).
	102	+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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