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1		-XWiki.denker
	1	+XWiki.robing

Content

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75	75
76	76	* **Run the notebook**
77	77	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.
78		-Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake
	78	+Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
	79	+
	80	+* **Coming soon**
	81	+** Use of KnowledgeGraph API
	82	+** Provenance Tracking
	83	+** HPC support
79	79
80	80	=== ii) Local execution ===
81	81
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114	114
115	115	All results are stored in the path specified in the //settings.py// file. The folder structure reflects the structuring of the pipeline into stages and blocks. All intermediate results are stored as //.nix// files using the [[Neo data format>>https://neo.readthedocs.io/en/stable/]] and can be loaded with ##neo.NixIO('/path/to/file.nix').read_block()##. Additionally, most blocks produce a figure, and each stage a report file, to give an overview of the execution log, parameters, intermediate results, and to help with debugging. The final stage (//stage05_wave_characterization//) stores the results as[[ //pandas.DataFrames//>>https://pandas.pydata.org/]] in //.csv// files, separately for each measure as well as in a combined dataframe for all measures.
116	116
117		-== Outlook ==
118		-
119		-* 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.
120		-* Adding support for the pipeline to make use of **HPC** resources when running on the collab.
121		-* Further extending the available **methods** to address a wider variety of analysis objectives and support the processing of other datatypes. Additional documentation and guides should also make it easier for non-developers to contribute new method blocks.
122		-* Extending the **application** of the pipeline to the analysis of other types of activity waves and oscillations.
123		-* Integrating and co-developing new features of the underlying **software tools **[[Elephant>>https://elephant.readthedocs.io/en/latest/]], [[Neo>>https://neo.readthedocs.io/en/stable/]], [[Nix>>https://github.com/G-Node/nix]], [[Snakemake>>https://snakemake.readthedocs.io/en/stable/]].
124		-
125	125	== References ==
126	126
127	127	* [[Celotto, Marco, et al. "Analysis and Model of Cortical Slow Waves Acquired with Optical Techniques." //Methods and Protocols// 3.1 (2020): 14.>>https://doi.org/10.3390/mps3010014]]
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130	130	* [[Sanchez-Vives, M. (2020). "Propagation modes of slow waves in mouse cortex".  //EBRAINS//>>https://doi.org/10.25493/WKA8-Q4T]]
131	131	* [[Sanchez-Vives, M. (2019). "Cortical activity features in transgenic mouse models of cognitive deficits (Fragile X Syndrome).//" EBRAINS//>>https://doi.org/10.25493/ANF9-EG3]]
132	132
133		-== License ==
	130	+== License (to discuss) ==
134	134
135		-Text is licensed under the Creative Commons CC-BY 4.0 license. LENS data is licensed under the Creative Commons CC-BY-NC-ND 4.0 license. IDIBAPS data is licensed under the Creative Commons CC-BY-NC-SA 4.0 license. Software code is licensed under GNU General Public License v3.0.
	132	+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.
136	136
137	137	[[image:https://i.creativecommons.org/l/by/4.0/88x31.png||style="float:left"]]
138	138
139		- [[image:https://licensebuttons.net/l/by-nc-sa/4.0/88x31.png||alt="https://i.creativecommons.org/l/by/4.0/88x31.png" style="float:left"]]
	136	+== ==
140	140
141		-[[image:https://licensebuttons.net/l/by-nc-nd/4.0/88x31.png||alt="https://i.creativecommons.org/l/by/4.0/88x31.png" style="float:left"]]
142		-
143		-
144	144	== Acknowledgments ==
145	145
146	146	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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150	150	)))
151	151
152	152
153		-== ==
	147	+== Executing the pipeline ==
154	154
155	155	(% class="col-xs-12 col-sm-4" %)
156	156	(((
157	157	{{box title="**Contents**"}}
158		-{{toc depth="3"/}}
	152	+{{toc/}}
159	159	{{/box}}
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