TheFourfront Metadata Database,or just "Fourfront", is an open-source platform developedat thePark Labin Harvard'sDepartment of Biomedical Informatics (DBMI)as part of our service in the role ofData Coordination and Integration Center (DCIC)for the4D Nucleome Network,one of theNIH Common Fund programs.

The4D Nucleome Network aims to understand the principles behind the three-dimensionalorganization of the nucleus in space and time (the 4th dimension), and the role nuclearorganization plays in gene expression and cellular function.The Network uses existing omics and imaging technologies, and develops new ones to generate dataand create resources to enable the study of the 4D Nucleome.

More information about the 4D Nucleome program can be obtained at:

• the4DN portal and
• theNIH program website,which also lists thefunded research centers.

Information about our implementation can be found at:

• ourGitHub repositories, detailed below, and

• ouronline documentation, detailed below, but including particularly:

  • Fourfront - metadata portal
  • Submit4DN - data submission tools

Please address all questions and comments tosupport@4dnucleome.org

Fourfront consists of multiple repositories which support a complex ecosystem ofapplications and tools that implementFourfront (the portal itself),Tibanna (the genomics pipeline),Foursight (tools for monitoring and service actions), andSubmit4DN (a command line tool to aid in metadata and data file submission).

Work on the Fourfront portal began in 2015 as a fork of earlier work onENCODE-DCC/encoded andENCODE-DCC/snovault,developed by theStanford ENCODE teamThe initial base and has been substantially developed and changed since then.However, the two teams stay in periodic touch and share ideas since thework is related.

In turn, our later work on theCGAP PortalandSMaHT Portal build on this work.Using a common codebase, especially based on our shareddcicutilsandsnovault repositories,we have refactored all three systems to no longer use AWS ElasticBeanstalk instances,and instead to use a more modern architecture based onDocker containers and AWS Fargate.

• tibanna - Core software that runs pipelines on Amazon Web Services (AWS).
• tibanna_ff - An extension of Tibanna that works with the 4DN data portal.

• fourfront - The primary codebase of the Fourfront portal.
• utils - A set of utility functions & scripts which are used in the Fourfront Portal and others.
• snovault - Contains abstractions for communicating with our databases, including PostgreSQL and ElasticSearch. A major dependency of CGAP Portal. Originally this was forked from ENCODE Project in ~2015.
• react-workflow-viz - A React component/library for visualizing workflow runs.

• foursight - Tools for monitoring and periodic service actions.
• foursight-core - Core software supporting Foursight.

• Submit4DN - Command-line tools for submitting and uploading metadata and data files to Fourfront.

• 4DN Policies - NIH Common Fund 4D Nucleome Network Policies.
• Governance - Repository of governance, legal and policy information for our projects.
• Legal Notices - Legal notices for portal users.

Repositories