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Last modified by robing on 2022/03/25 09:55
From version 50.1
edited by debonisg
on 2020/04/24 12:58
Change comment: There is no comment for this version
To version 39.1
edited by robing
on 2020/04/17 12:14
Change comment: There is no comment for this version

Summary

Details

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1 -XWiki.debonisg
1 +XWiki.robing
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= (% style="--darkreader-inline-color:inherit; color:inherit" %)Slow Wave Analysis Pipeline (SWAP)(%%) =
5 += (% style="--darkreader-inline-color:inherit; color:inherit" %)Slow Wave Analysis Pipeline(%%) =
6 6  
7 7  (% class="wikigeneratedid" id="HUseCaseSGA2-SP3-002:IntegratingmultiscaledataA0inareproducibleandadaptablepipeline" %)
8 -(% style="--darkreader-inline-color:inherit; color:inherit; font-size:24px" %)**Use Case SGA2-SP3-002 KR3.2: Integrating multi-scale data and the output of simulations in a reproducible and adaptable pipeline**
8 +(% style="--darkreader-inline-color:inherit; color:inherit; font-size:24px" %)**Use Case SGA2-SP3-002: Integrating multi-scale data in a reproducible and adaptable pipeline**
9 9  
10 -Robin Gutzen^^1^^, Giulia De Bonis^^2^^, Elena Pastorelli^^2,3^^, Cristiano Capone^^2^^,
10 +To be discussed Author orders, contributions,...:
11 11  
12 -Chiara De Luca^^2,3^^, Michael Denker^^1^^, Sonja Grün^^1^^,
12 +Experiments: ...?
13 13  
14 -Pier Stanislao Paolucci^^2^^, Andrew Davison^^4^^
14 +Implementation: Robin Gutzen^^1^^, Elena Pastorelli^^2^^, ...
15 15  
16 -Experiments: Anna Letizia Allegra Mascaro^^5,6^^, Francesco Resta^^5^^, Francesco Saverio Pavone^^5^^, Maria-Victoria Sanchez-Vives^^7,8^^
16 +Lead: Michael Denker^^1^^, Sonja Grün^^1^^, Pier Stanislao Paolucci^^2^^, Andrew Davison?
17 17  
18 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 19  
20 -,,2) Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy,,
20 +,,2) Dipartimento di Fisica, Università di Cagliari and INFN Sezione di Roma, Italy,,
21 21  
22 -,,3) Ph.D. Program in Behavioural Neuroscience, “Sapienza” University of Rome, Rome, Italy,,
23 -
24 -,,4) Unité de Neurosciences, Information et Complexité, Neuroinformatics Group, CNRS FRE 3693, Gif-sur-Yvette, France,,
25 -
26 -,,5) European Laboratory for Non-linear Spectroscopy (LENS), (% style="color:inherit" %)University of Florence, Florence, Italy(%%),,
27 -
28 -,,6) Istituto di Neuroscienze, CNR, Pisa, Italy,,
29 -
30 -,,7) Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain,,
31 -
32 -,,8) Institució Catalana de Recerca i Estudis Avanc ̨ats (ICREA), Barcelona, Spain,,
22 +
33 33  )))
34 34  )))
35 35  
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60 60  **Copy the collab drive to your personal drive space**
61 61  
62 62  * Open the Drive from the left menu
63 -* Select the folders //pipeline// and //datasets,//
64 -and the notebook// run_snakemake_in_collab.ipynb//
53 +* Select the folders //pipeline// and //datasets//
65 65  * Select 'Copy', and then 'My Library' from the dropdown 'Other Libraries'
66 66  
67 67  )))
68 68  * **Start a Jupyter Hub instance **
69 69  In another browser tab, open [[https:~~/~~/lab.ebrains.eu>>https://lab.ebrains.eu]]
70 -
59 +
71 71  * **Edit the config files**
72 -Each stage has a config file (//pipeline/<stage_name>/config.yaml//) 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 of each stage. The default values are set for an example dataset (ECoG, anesthetized mouse, [[IDIBAPS>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset&q=sanchez-vives#Dataset/2ead029b-bba5-4611-b957-bb6feb631396]]]).
61 +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 of each stage. The default values are set for an example dataset (ECoG, anesthetized mouse, [[IDIBAPS>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset&q=sanchez-vives#Dataset/2ead029b-bba5-4611-b957-bb6feb631396]]]).
73 73  
74 74  * **Run the notebook**
75 75  In the jupyter hub, navigate to //drive/My Libraries/My Library/pipeline/showcase_notebooks/run_snakemake_in_collab.ipynb//, or where you copied the //pipeline// folder to.
76 -Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
65 +* Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
77 77  
78 78  * **Coming soon**
79 79  ** Use of KnowledgeGraph API