Attention: Due to an upgrade beginning on Friday, the 22nd August 2025, any new collabs, groups and any changes to teams will not be kept beyond the weekend. User creation will also be disabled during this time. The actual upgrade will take place on Wednesday, 27th August. On that day, any service requiring a Keycloak login will be unavailable for the duration of the upgrade. Thank you for your understanding as we complete this important work.


Last modified by robing on 2022/03/25 09:55
From version 20.1
edited by robing
on 2020/01/21 00:34
Change comment: There is no comment for this version
To version 15.2
edited by epastorelli
on 2020/01/20 14:08
Change comment: There is no comment for this version

Summary

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26 26  
27 27  === in the collab (beta) ===
28 28  
29 -* **Copy the collab drive to your drive space**
30 -** Open the Drive from the left menu
31 -** Select the folders 'pipeline' and 'datasets'
32 -** Select 'Copy', and then 'My Library' from the dropdown 'Other Libraries'
33 -
34 -* **Start a Jupyter Hub instance **
35 -copy the URL to another browser page: 'jupyterhub-preview.apps-dev.hbp.eu'
36 -
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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42 42  ** stage04_wavefront_detection: [README.md](), [config.yaml]()
43 43  ** stage05_wave_characterization: [README.md](), [config.yaml]()
44 44  
45 -* **Run the notebook**
46 -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.
47 -* Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
37 +* **Start a Jupyter Hub instance (copy the URL below in a separate browser page)**
38 +[[jupyterhub-preview.apps-dev.hbp.eu>>jupyterhub-preview.apps-dev.hbp.eu]]
48 48  
40 +* **Follow the notebook**
41 +In the jupyter hub, navigate to `drive/Shared with groups/Slow Wave Analysis Pipeline/pipeline/showcase_notebooks/run_snakemake_in_collab.ipynb`.
42 +Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
49 49  * **Coming soon**
50 50  ** Use of KnowledgeGraph API
51 51  ** Provenance Tracking