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cmadjar edited this page Jul 16, 2020 · 4 revisions

CONP portal documentation

Open neuroscience is a collective effort that requires extensive coordination between multiple organizations and across geographical boundaries to promote important discoveries and protect data value. The CONP Portal provides infrastructure that allows interoperability of neuroscience datasets across data modalities, timescales, and experimental models. In addition to dissemination and aggregation of research objects, the CONP Portal enhances and extends the data management lifecycle by providing access to analytical tools and pipelines, and interactive environments for scholarly communication and collaboration.

On the left side of the screen menu items divide the portal content by functionality:

Dashboard

The dashboard of the portal is the homepage of the portal. It contains several cards:

  • a brief introduction to the portal with a link to a more detailed page about the portal
  • a graphical representation of the number of datasets and pipelines present on the portal with a link to additional analytics of the portal
  • a study spotlight section highlighting some key datasets
  • a tutorial video with a link to the portal tutorial document

Data

The CONP portal provides a gateway to a diverse range of datasets, primarily neuroimaging but also transcriptomics, genomics, and other related data modalities. Many of these datasets have been made accessible by neuroscience research institutes across Canada, while others link to publicly available resources that may be of interest to neuroscientists. A full list can be found in the Data page of the portal.

The CONP portal was designed to parse existing datasets both externally and within the CONP context. As such, a variety of datasets are available for download within this portal. To access the data, the user will first go to the Data page and filter for data of interest. Clicking on an individual dataset will provide more detailed information and download instructions. There are a number of data download methodologies that will be available to match different user preferences. At the moment, access to datasets is available using the DataLad data management system. One-click data download functionality is under development and will be available in the future.

Tools & Pipelines

The Tools & Pipelines page shows the list of tools/pipelines available in CONP. Many of these tools/pipelines are well-established and have been provided by neuroscience or genomics research institutes.

Several mechanisms are available to run tools and pipelines found on the CONP portal:

  • Tools and pipelines can be run locally on any system using Boutiques and a container engine ( Docker or Singularity ) based on the Zenodo ID of the tool.
  • Some tools and pipelines can be run on HPCs via the CBRAIN infrastructure.

Share

The Share page contains detailed technical instructions on how to share tools or datasets on CONP.

Tools can be uploaded via Boutiques and Zenodo while data can be uploaded to CONP via the following mechanisms, using:

  • Zenodo by tagging your dataset with the keyword canadian-open-neuroscience-platform
  • The Open Science Framework ( OSF ) by tagging your dataset with canadian-open-neuroscience-platform and setting the dataset to Public
  • Using DataLad within the context of CONP

FAQ

The FAQ page contains a set of frequently asked questions organized in 5 categories:

  • CONP
  • Data Access & Download
  • Data Upload
  • Tools & Pipelines
  • DataLad
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