Last modified by robing on 2022/03/25 09:55
From version 81.1
edited by robing
on 2020/05/28 15:12
Change comment: There is no comment for this version
To version 83.1
edited by robing
on 2020/05/28 15:46
Change comment: There is no comment for this version

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73 73  Each stage has config files (//pipeline/<stage_name>/configs/config_<profile>.yaml//) to specify which analysis/processing blocks to execute and which parameters to use. General and specific information about the blocks and parameters can be found in the README and config files of each stage. There are preset configuration profiles for the benchmark datasets IDIBAPS ([[ECoG, anesthetized mouse>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset&q=sanchez-vives#Dataset/2ead029b-bba5-4611-b957-bb6feb631396]]) and LENS ([[Calcium Imaging, anesthetized mouse>>https://kg.ebrains.eu/search/instances/Dataset/71285966-8381-48f7-bd4d-f7a66afa9d79]]).
74 74  
75 75  * **Run the notebook**
76 -In the jupyter hub, navigate to //drive/My Libraries/My Library/run_snakemake_in_collab.ipynb//, or where you copied the //pipeline// folder to.
76 +In the jupyter hub, navigate to //drive/My Libraries/My Library/run_snakemake_in_collab.ipynb//, or where you copied the file to.
77 77  Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
78 78  
79 79  === ii) Local execution ===
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131 131  * Stage 05 - [[planar velocities>>https://drive.ebrains.eu/smart-link/f4de8073-cb40-47a7-bc82-f97d36dbae25/]]
132 132  * Stage 05 - [[directionality>>https://drive.ebrains.eu/smart-link/5485032d-0121-4cde-9ea2-3e0af3f12178/]]
133 133  
134 -=== Outlook ===
134 +== Outlook ==
135 135  
136 136  * Using the **KnowledgeGraph API **to insert data directly from the Knowledge Graph into the pipeline and also register and store the corresponding results as Analysis Objects. Such Analysis Objects are to incorporate **Provenance Tracking, **using [[fairgraph>>https://github.com/HumanBrainProject/fairgraph]],** **to record the details of the processing and analysis steps.
137 137  * Adding support for the pipeline to make use of **HPC** resources when running on the collab.