Gen3 Features

A list of Gen3 features

Gen3 is an open-source platform that enables the standing-up of data commons for managing, analyzing, and sharing research data. Below you can find an exhaustive list of Gen3 features.

Dictionary and structured data

  • Explore the graph in the dictionary page of Windmill:
    • Search keywords
    • Visualize possible paths between nodes
    • Download JSON or TSV format for node templates
  • Explore project graphs and nodes in Windmill:
    • Visualize graph model
    • Browse/download data for each node
  • Structured data submission (create, update, delete records) in JSON, TSV or CSV:
    • Submission page of Windmill
    • Gen3 SDK (Python, R)
  • Export structured data as a JSON, TSV or CSV file
  • Structured data is stored in Postgres databases
  • Flattened data:
    • Structured data can be flattened and stored in ElasticSearch by using our ETL tool
    • Explore the ElasticSearch structured data using Guppy
  • Generate fake data specific to a dictionary for testing
  • Import and export using the Portable Format for Biomedical Data (PFB): (Work in progress)
    • Import and export a dictionary
    • Import and export structured data

Data files

  • Data upload through the Gen3 Client
  • Indexing data files:
    • Create data file records and mint GUIDs
    • Index a new version of the same file
    • Get the most recent version of a file
    • Index data files that are stored outside of the Commons
  • GUID resolver
  • Data download:
  • Core metadata endpoint to get information about a data file

Data exploration and analysis

  • GraphQL endpoint and UI to explore structured data via Peregrine (graph data)
  • GraphQL endpoint and UI to explore flattened data via Guppy (in ElasticSearch)
  • Explorer page of Windmill
    • Filters to select a cohort
    • Charts and visualizations: count, pie charts, bar charts, stacked bar charts, heatmaps
    • Download clinical data for the selected cohort
    • Download a manifest for the selected cohort
    • Export the selected cohort to Workspace/PFB/Terra
  • Workspaces
    • Jupyter notebooks (Python, R)
    • RStudio
  • Run complex CWL analysis workflows (Work in progress)

Access management and security

Automation