NeuroDataPub: NCCR-SYNAPSY Neuroimaging Dataset Publishing Tool

Latest released version: v0.4

This tool is developed by the Connectomics Lab at the University Hospital of Lausanne (CHUV) for use within the lab and within the National Centre of Competence in Research (NCCR) “SYNAPSY – Synaptic Bases of Mental Diseases” NCCR-SYNAPSY, as well as for open-source software distribution.

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Introduction

NeuroDataPub is a neuroimaging dataset publishing tool written in Python and built on top of Datalad and git-annex, that lowers the barriers, for the NCCR-SYNAPSY members, to adopt Datalad to manage and publish, privately or publicly, their dataset repository on GitHub and the annexed files on their SSH data server, in order to fully fulfill the implemented Neuroimaging Data Management Plan.

Since v0.3, you can use either (1) a server accessible via ssh or (2) the Open Science Foundation (OSF) platform, as a git-annex special remote, to host your annexed files.

Since v0.4, NeuroDataPub can handle datasets that do and do not follow the Brain Imaging Data Structure standard.

_images/neurodatapub_illustration.png

NeuroDataPub comes with its graphical user interface, aka the NeuroDataPub Assistant, created to facilitate:

  • the configuration of the siblings,

  • the creation of the JSON configuration files, as well as

  • the execution of NeuroDataPub in the three different modes, and

  • the creation of a Linux shell script for later execution where all commands are recorded.

Acknowledgment

If your are using NeuroDataPub in your work, please acknowledge this software and its dependencies. See Citing for more details.

License information

This software is distributed under the open-source Apache 2.0 license. See license for more details.

All trademarks referenced herein are property of their respective holders.

Help/Questions

If you run into any problems or have any code bugs or questions, please create a new GitHub Issue.

Eager to contribute?

See Contributing for more details.

Funding

Supported by the National Centre of Competence in Research (NCCR) “SYNAPSY – Synaptic Bases of Mental Diseases” NCCR-SYNAPSY (NCCR-SYNAPSY website / NCCR-SYNAPSY Swiss National Science Foundation Page) under SNF-185897 grant.

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