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Template initialisation

julien colomb před 1 rokem
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63aa29b761

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.datalad/.gitattributes

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+config annex.largefiles=nothing

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.datalad/config

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+[datalad "dataset"]
+	id = 2b68d466-2b33-4776-ac2a-734ce365ec10

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.doc/information.md

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+# How to use this template
+
+## Origin
+
+This project provides a template structure for research projects within the CRC/TRR 135 according to the results of a joint work with CRC 1158 and CRC 1315 (see <https://genr.eu/wp/towards-a-standardized-research-folder-structure/> for details).
+
+Check <https://github.com/tonic-team/Tonic-Research-Project-Template> if you want to use your own.
+
+## License
+
+By default, we added a CC-BY license to the repository, meaning anyone who can access this can reuse it anywhere, as long as he is mentioning the original work. You may want to delete it for now, and put it back (or another license) when you are ready to share this repository.
+
+## Easier Collaboration
+
+- Make sure every collaborator got to understand what files to find where.
+- This template was meant to be used in a git based workflow. This would allow you to collaborate using issues and pull requests.
+- The use of git submodule technology may help you share and publish only part of this repository. 
+
+Refer to XXX for further information.
+
+## Cheat sheet about what goes where:
+
+- Prior to data acquisition
+    - Save all documents related to research planning in the 01-Project_management folder, and update material and methods information as soon as possible.
+      For instance, indicate all information about reagents at the time of purchase.
+      And put any code or variable files created for data acquisition in the 02_material_methods folder.
+
+- Data acquisition and analysis
+    - Data is organised first following experiments, make sure to describe every experiment in a readme file and link to the adequate files saved in 02_material_methods.
+    - All files coming directly from your hardware should go in the rawdata folder.
+    - Any file that you want to archive or publish should go in the derivateddata folder. This includes results from manual analysis of the raw data.
+    - Any file created automatically during the analysis and that is easy to recreate should be saved in the processed_data folder: it will not be included in the long term storage or publication of the data.
+    - The 04_data_analysis folder should only include code and documentation of the analysis. If you are using excel to analyse the data, put the files in the processed_data and only add some text describing the analysis in the analysis folder. If you are using notebooks in python or R for analysis, their place is here.
+    - The output of your analysis (figures, and reproducible reports -pdfs-) should be saved in the 05_figures or the 06_disseminations/01_report_conferences/01_textreports folders, to facilitates sharing with non-coders.
+
+- Manuscript preparation
+    - Put figures ready for publication in the 05_figures/shared_figures folder.
+    - Put the manuscript (or some important versions of it, if using an external tool for writing it) in the 06_disseminations/02_manuscripts folder. You may want to use full URL to embed figures in the manuscript if the repository is open.
+
+
+
+## How to create a new study
+
+
+### Github
+
+Creating a new study project according to the tonic template is really easy: Just use the button `Use this template`, specify the owner, name and privacy and select button `Create repository from template`. Here we go!
+
+### GIN, GOGS
+
+Click the create new repository button on GIN, choose import repository and use `https://github.com/tonic-team/Tonic-Research-Project-Template` as the clone address
+
+### Tonic
+
+Yet to come !
+
+## Notes
+  
+We have some forks of this repository made for specific communities with additional information.
+
+# Changing folder name
+
+It is advised not to change folder names, so it is kept a standard. Also some implementation of this standard uses submodules, and changing folder name there might break the synchronisation work (one needs to use specific git command to change submodule path).

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.gitattributes

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+* annex.backend=MD5E
+**/.git* annex.largefiles=nothing
+* annex.largefiles=((mimeencoding=binary)and(largerthan=0))

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.gitmodules

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+
+[submodule "06_dissemination"]
+	path = 06_dissemination
+	url = ../template_02-06_dissemination
+	datalad-id = 8154943d-b846-4f00-a6e1-f22068209ac6
+[submodule "03_data/001_rawdata"]
+	path = 03_data/001_rawdata
+	url = ../template_02-03_data-001_rawdata
+	datalad-id = da576025-282b-48c4-8b43-353fcbbdd4e1
+[submodule "03_data/001_deriveddata"]
+	path = 03_data/001_deriveddata
+	url = ../template_02-03_data-001_deriveddata
+	datalad-id = 844a1ad4-224b-4b6d-a003-e97809c2724e
+[submodule "04_data_analysis/001_analysiscode"]
+	path = 04_data_analysis/001_analysiscode
+	url = ../template_02-04_data_analysis-001_analysiscode
+	datalad-id = 1787bebf-e3df-47e5-a242-8ba596979903
+[submodule "05_figures/990_shared_figures"]
+	path = 05_figures/990_shared_figures
+	url = ../template_02-05_figures-990_shared_figures
+	datalad-id = 7e63a757-b7dd-40b9-a91a-3b8ad0b54bde

+ 0 - 0
01_project_management/01_administration_files/.gitkeep


+ 0 - 0
01_project_management/02_accepted_grants/.gitkeep


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01_project_management/03_meeting_minutes/.gitkeep


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01_project_management/04_related_literature/.gitkeep


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01_project_management/05_data_management_plans/.gitkeep


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01_project_management/06_notebook/.gitkeep


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02_material_and_methods/01_protocols/.gitkeep


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02_material_and_methods/02_code/.gitkeep


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02_material_and_methods/README_MM.md

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+# Content
+
+## Hardware details
+
+For self-built hardware, it is recommended to have a special repository for its description and link it with a URL or as a submodule here. For any hardware, you should provide a user guide with the following information:
+
+- How to check the hardware is working: calibration, validation
+- Troubleshooting guide, common issues
+- What was bought were?
+- What was custom-built, by whom and how ?
+- Critical hardware parts, what could be modified?
+- Schematics and/or photos (lots of photos)

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03_data/001_defaultexp/README.md

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+# Content
+
+Please provide a summary of the content of this section and update it properly.

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03_data/001_deriveddata

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+Subproject commit c8365472e087b6b3368d54a6169e73c40fdbc430

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03_data/001_rawdata

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+Subproject commit 189bbbe66ba6b40ee004e2484c8d22cd54ccd15f

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03_data/999_processed_data/001_defaultexp_processed_data/.gitkeep


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03_data/README_DATA_STORE.md

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+# Content
+
+This readme contains a summary of information you should provide about your data. This is mostly meant as a checklist, as the information should be best included in the readme of the data folders or in the data management plan. It is advised to draw the data flow to keep an overview.
+
+# 001
+
+## Hardware/tool used for acquisition
+
+## protocol
+
+- Standard procedure
+- Glossary/definition of terms (for categorical variables)
+- What changed, when and why
+- Techniques that were tested but not chosen, and why
+
+## raw data description
+
+- how does good/reliable data look like
+- exclusion criteria
+- data flow. What type of data is collected when
+- headers description, how to interpret the data
+
+## data analysis
+
+- analysis workflow
+- code versions

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04_data_analysis/001_analysiscode

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+Subproject commit 4c50665344c8a476ffd48c2acd62c4392fe18999

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04_data_analysis/001_defaultexp_analysis/.gitkeep


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04_data_analysis/990_code_libraries/.gitkeep


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04_data_analysis/991_preregistration/.gitkeep


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04_data_analysis/README_DATA_ANALYSIS.md

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+# Content
+
+Please provide a summary of the content of this section and update it properly.

+ 0 - 0
05_figures/001_defaultexp_figures/.gitkeep


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05_figures/990_shared_figures

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+Subproject commit c90f7b350b5ca70d64f1386b861c274e2896bb8c

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05_figures/README_FIGURES.md

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+# Content
+
+Please provide a summary of the content of this section and update it properly.

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06_dissemination

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+Subproject commit 6ba27fd16c220f802d8e0e71dd6c93fafb57c253

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07_misc/README_MISC.md

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+# Content
+
+Please provide a summary of the content of this section and update it properly.

+ 95 - 0
LICENSE-CC-BY

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+Creative Commons Attribution 4.0 International Public License
+
+By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution 4.0 International Public License ("Public License"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions.
+
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+    Nothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority.

+ 42 - 0
README.md

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+# FIXME:Project title
+
+## Abstract, vision and goals
+
+## Project status
+
+### Roadmap and Milestones
+
+### Successes and failures
+
+## Contributors
+
+- jane doe, jane.doe@example.com, https://orcid.org/XXXX-XXXX-XXXX-XXXX, role:, responsibilities: , special skills
+
+[Mention your contributors either by including a contributors list here, or by referring to another file that lists your contributors, see documentation for options and examples. It is good practice to set roles for each contributor at the start of the project and discuss author byline of a future paper early.]
+
+## Experiments
+
+### 001
+
+FIX: short description, 
+details at [03_data/README_DATA_STORE](03_data/README_DATA_STORE)
+and/or in the data management plan: [01_project_management/05_data_management_plans](01_project_management/05_data_management_plans).
+
+## Communication
+
+- todo list: [use issues](../../issues)
+- minutes: [01_project_management/03_meeting_minutes](01_project_management/03_meeting_minutes)
+- Communication tools and email archive:
+
+## Outreach and external links
+
+- Smartfigure tag: [YOURTAG](https://sdash.sourcedata.io/?q=YOURTAG) [FIXME:replace YOURTAG in the url and the text.]
+
+
+## Contribution
+
+If you are new to this project, get familiar with the vision, set your own role and responsibilities with the team, and read the data management plan. Make sure your contributions can be understood and reused by other members of the team.
+
+## Technical note
+
+**Note:** This repository follows the Research repository template, v.2.4, see [further information offline](.doc/information.md) or [the online documentation page](https://gin-tonic.netlify.app/). Do not modify folder name unless you are sure of what you are doing.