Merge pull request #82 from cpp-lln-lab/sid0309-patch-1

Update code_and_data_management.md

Author: fcerpe

doc/code_and_data_management.md

@@ -0,0 +1,89 @@
+# Code and data arrangement
+
+## Version control
+
+In the lab we (try) to stick to version control for code with git/github and data with datalad and gin. Somewhere else is already mentioned but repetita iuvant so 
+1. Install git on your computer 
+2. Create a GITHUB account and ask to be added to the lab organization [https://github.com/cpp-lln-lab]
+3. Make sure you have your SSH key for GITHUB following this tutorial 
+4. Have a look at this doc to have a first idea on how to contribute on github
+5. Have a look around cause we already have a lot of ready to use code ;)
+6. Make sure you are set up with the following tools having a look at this doc’s first section
+    1. Datalad (in a nutshell git for data but checkout more here https://handbook.datalad.org/en/latest/)
+    2. Gin (host server for data, good for “unlimited” and free cloud back and private and public data sharing)
+7. Ask to be added to the Gin organization of the lab to start storing your data there
+
+## Data management
+for MRI data the lab is moving towards using the BIDS data structure
+* bids starter kit
+* bids specification
+
+### Official GIN/DATALAD CPP dataset organization 
+
+
+[WIP] Checklist to make an official “raw” repo (bids, bids-validator checked, standard CPP data organization (eg group naming, task naming, readme with link to published/preprint, etc)) 
+
+[WIP - Just dropping useful links here for now]
+
+Data:
+
+Dataset summary (put together all the bidsified raw and derivatives repos of the lab and summarize metadata in a table)  https://cpp-lln-lab.github.io/Datasets/
+repo to edit it: https://github.com/cpp-lln-lab/Datasets
+
+main organization for "structured": data saving and conversion control and sharing with “raw” (bidsifield) and “derivatives” and “source” repos: https://gin.g-node.org/cpp-lln-lab
+
+
+Guidelines to maintain the CPP dataset https://github.com/cpp-lln-lab/dataset_maintenance
+
+Datalad superdataset to grab all the repo together:
+https://github.com/cpp-lln-lab/cpp-lln-lab_derivatives
+https://github.com/cpp-lln-lab/cpp-lln-lab_source
+
+Tools:
+https://github.com/cpp-lln-lab/template_datalad_bids-raw
+https://github.com/cpp-lln-lab/CPP_dcm2Bids
+https://github.com/cpp-lln-lab/letswave_bids_import
+https://github.com/cpp-lln-lab/eeg_bids_conversion
+
+
+
+## Other back ups
+
+
+### IONS cloud storage
+
+
+http://sss-intranet.icp.ucl.ac.be/wiki/index.php/Storage_access#Groups
+
+cooked step by step for MacOS users:
+
+1. Open Finder
+2. Go menu
+3. Element Connect to server
+4. Add address smb://sss-samba.icp.ucl.ac.be/cosy-oc 
+5. Use your UCLouvain credentials when asked
+6. Add the opened folder as a favorite (top of the right panel)
+
+
+Short guidelines:
+* not suitable for an “online” usage (eg running analyses within the folder), it is a cloud service so reading and writing is as fast as your internet connection
+* Long term storage
+* Please, be organized. Imagine that another person in the future will open that folder and make sense of the content in less than 2 minutes
+* Add README files to help the future user understand what’s inside that folder (e.g. dicoms from the study XXX published in XXX code for conversion/analyses here github.com/xxx, copy of this dataset is also on gin.g-node.org/xxx)
+
+What to put there? Should not become a data dump so not just a new space where a user can free up her/his hard disk
+
+
+
+## Get organised
+
+### Code style guides
+
+
+matlab
+https://www.mathworks.com/matlabcentral/fileexchange/46056-matlab-style-guidelines-2-0
+
+### Useful links
+
+A quick thread on how to organize your scripts:
+https://twitter.com/wmvanvliet/status/1240907591791886337