Last modified by robing on 2022/03/25 09:55
From version 72.1
edited by denker
on 2020/05/07 14:22
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To version 64.1
edited by robing
on 2020/04/29 13:47
Change comment: There is no comment for this version

Summary

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1 -XWiki.denker
1 +XWiki.robing
Content
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39 39  (((
40 40  == Flexible workflows to generate multi-scale analysis scenarios ==
41 41  
42 -This collab illustrates the usage of the [[Neo>>https://neo.readthedocs.io/en/stable/]] and [[Elephant>>https://elephant.readthedocs.io/en/latest/]] tools in performing data analysis with regards to the SGA2-SP3-UC002 KR3.2, investigating sleep, anesthesia, and the transition to wakefulness: see Chapter 1 and Figure 2  of SGA2[[ Deliverable D3.2.1.>>https://drive.ebrains.eu/smart-link/17ac0d6e-e050-4a49-8ca2-e223b70a3121/]], for an overview of the scientific motivations and a description of the UseCase workflow; Chapter 2 (same document) for an introduction to KR3.2; Chapter 3, for a description of the mice ECoG data sets; Chapter 5, about the Slow Wave Analysis Pipeline and Chapter 6 for the mice wide-field GECI data). For details on the datasets used in this collab, please see the References below.
42 +This Collab is aimed at experimental and computational neuroscientists interested in the usage of the [[Neo>>https://neo.readthedocs.io/en/stable/]] and [[Elephant>>https://elephant.readthedocs.io/en/latest/]] tools in performing data analysis of spiking data.
43 +Here, the collab illustrates the tool usage with regards to the SGA2-SP3-UC002 KR3.2, investigating sleep, anesthesia, and the transition to wakefulness: see Chapter 1 and Figure 2  of SGA2[[ Deliverable D3.2.1.>>https://drive.ebrains.eu/smart-link/17ac0d6e-e050-4a49-8ca2-e223b70a3121/]], for an overview of the scientific motivations and a description of the UseCase workflow; Chapter 2 (same document) for an introduction to KR3.2; Chapter 3, for a description of the mice ECoG data sets; Chapter 5, about the Slow Wave Analysis Pipeline and Chapter 6 for the mice wide-field GECI data)
43 43  
45 +[[image:https://github.githubassets.com/images/modules/logos_page/GitHub-Mark.png||height="35" width="35"]][[INM-6/wavescalephant>>https://github.com/INM-6/wavescalephant]]
46 +
44 44  == How the pipeline works ==
45 45  
46 46  The design of the pipeline aims at interfacing a variety of general and specific analysis and processing steps in a flexible modular manner. Hence, it enables the pipeline to adapt to diverse types of data (e.g., electrical ECoG, or optical Calcium Imaging recordings) and to different analysis questions. This makes the analyses a) more reproducible and b) comparable amongst each other since they rely on the same stack of algorithms and any differences in the analysis are fully transparent.
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72 72  
73 73  * **Run the notebook**
74 74  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.
75 -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
76 76  
77 77  === ii) Local execution ===
78 78  
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111 111  
112 112  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.
113 113  
114 -== Outlook ==
115 -
116 -* 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.
117 -* Adding support for the pipeline to make use of **HPC** resources when running on the collab.
118 -* 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.
119 -* Extending the **application** of the pipeline to the analysis of other types of activity waves and oscillations.
120 -* 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/]].
121 -
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) ==
130 130  
131 -Code developed at:
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.
132 132  
133 -[[image:https://github.githubassets.com/images/modules/logos_page/GitHub-Mark.png||height="35" width="35"]][[INM-6/wavescalephant>>https://github.com/INM-6/wavescalephant]]
134 -
135 -== License ==
136 -
137 -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.
138 -
139 139  [[image:https://i.creativecommons.org/l/by/4.0/88x31.png||style="float:left"]]
140 140  
141 -[[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 +== ==
142 142  
143 -[[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"]]
144 -
145 -
146 146  == Acknowledgments ==
147 147  
148 148  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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152 152  )))
153 153  
154 154  
155 -== ==
147 +== Executing the pipeline ==
156 156  
157 157  (% class="col-xs-12 col-sm-4" %)
158 158  (((
159 159  {{box title="**Contents**"}}
160 -{{toc depth="3"/}}
152 +{{toc/}}
161 161  {{/box}}
162 162  
163 163  
Collaboratory.Apps.Collab.Code.CollabClass[0]
Description
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1 -Use Case SGA2-SP3-002 KR3.2: Integrating multi-scale data and the output of simulations in a reproducible and adaptable pipeline
1 +Space for developing and hosting a showcase pipeline for performing reproducible and adaptable analysis with the focus of slow cortical waves.