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1		-XWiki.robing
	1	+XWiki.denker

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.
79		-
80		-* **Coming soon**
81		-** Use of KnowledgeGraph API
82		-** Provenance Tracking
83		-** HPC support
	78	+Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake
84	84
85	85	=== ii) Local execution ===
86	86
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119	119
120	120	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.
121	121
	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	+
122	122	== References ==
123	123
124	124	* [[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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127	127	* [[Sanchez-Vives, M. (2020). "Propagation modes of slow waves in mouse cortex".  //EBRAINS//>>https://doi.org/10.25493/WKA8-Q4T]]
128	128	* [[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]]
129	129
130		-== License (to discuss) ==
	133	+== License ==
131	131
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.
	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.
133	133
134	134	[[image:https://i.creativecommons.org/l/by/4.0/88x31.png||style="float:left"]]
135	135
136		-== ==
	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"]]
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	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	+
138	138	== Acknowledgments ==
139	139
140	140	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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144	144	)))
145	145
146	146
147		-== Executing the pipeline ==
	153	+== ==
148	148
149	149	(% class="col-xs-12 col-sm-4" %)
150	150	(((
151	151	{{box title="**Contents**"}}
152		-{{toc/}}
	158	+{{toc depth="3"/}}
153	153	{{/box}}
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