Data Sharing#

Background#

Data is key to neuroscience, and it should be shared for maximal utility. There is increasing pressure from funders and publishers to share data alongside publications:

Wellcome:

“We expect our researchers to maximise the availability of research data, software and materials with as few restrictions as possible. As a minimum, the data underpinning research papers should be made available to other researchers at the time of publication, as well as any original software that is required to view datasets or to replicate analyses.”

Cell Press:

“All datasets that are composed of standardized datatypes and reported in Cell Press papers must be deposited in a datatype-specific, Cell-Press-recommended repository before a paper is accepted for publication.”

“All original code must be either deposited in a repository that mints DOIs or included in the supplemental information before a paper is accepted for publication.”

Requirements#

Currently, SWC does not have any specific code and data sharing requirements, but your funder or publisher may do.

Ideally, all data and code will be shared in such a way that any other researcher could easily reproduce key figures from a publication, and build on those data and software in their own research.

Code#

Original code can be hosted in a public GitHub/GitLab repository, hosted on an organisational account (i.e. not an individual account). This could be the SWC organisation, or that of a particular team, lab or collaboration. To enable reuse, code should include an appropriate license.

To ensure a permanent archive of the code associated with a publication a DOI should be created (e.g. using Zenodo).

Data#

Repository#

There are many repositories that will accept the types of data generated by SWC. They come into three categories, general, neuroscience-specific and modality-specific. If you do not have a preference, we recommended:

For small (<20GB) datasets: Use the existing SWC section of the UCL FigShare instance. This is easy to use, and is supported centrally by UCL

For larger datasets: Create a GIN repository, ideally within the SWC organisation. GIN uses Git and provides a versioning system, making it particularly well suited for ongoing research projects.

Specific modalities: In some cases, there may be a modality or field-specific repository that would be best suited for the data (or mandated by the publisher), some examples include:

In all cases, using a repository that can create a DOI will help increase citations.

Structure#

There is no single best way to structure your data, but it must be in a form that allows users to easily reuse it for their own purposes. This may be by adopting specific file formats (such as NeuroData Without Borders). Alternatively the data could be organised within a standardised project folder structure. Many labs have their own system, but those starting from scratch may wish to use the NeuroBlueprint data structure.

However the data is structured, all relevant metadata must be included with the raw data.

Assistance#

If you have any technical questions about sharing data or code, please contact adam.tyson@ucl.ac.uk.

Reference of potential repositories for neuroscience data#

Repository

URL

Domain

Globus

Anything

figshare

https://rdr.ucl.ac.uk/The_Sainsbury_Wellcome_Centre

Anything

Zenodo

https://zenodo.org/

Anything

Dryad

https://datadryad.org

Anything

GIN (German Neuroinformatics Node)

https://gin.g-node.org/

Neuroscience

EBRAINS

https://ebrains.eu/service/share-data

Neuroscience

Open Source Brain

https://www.v2.opensourcebrain.org/

Any neuroscience data (data must be hosted elsewhere)

Brain Image Library

http://www.brainimagelibrary.org/

Large brain image datasets

Image data resource

https://idr.openmicroscopy.org/

Reference image datasets

BioImage Archive

https://www.ebi.ac.uk/bioimage-archive/

Biological images

DANDI

https://dandiarchive.org/

Electrophysiology, optophysiology, behavioural time-series and images from immunostaining experiments

NeMO

https://nemoarchive.org/

Omic data from the BRAIN Initiative (& others)

Openneuro

https://openneuro.org/

BIDS-compliant MRI, PET, EEG etc

CRCNS

https://crcns.org/

Computational neuroscience

BrainGlobe

https://gin.g-node.org/BrainGlobe/atlases

Brain Atlases

NeuroMorpho

https://neuromorpho.org/

Neuronal morphologies

Cell Image Library

http://ccdb.ucsd.edu/home

Cell images

ModelDB

https://modeldb.science/

Computational neuroscience models