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PEPhub is a database, web interface, and API for sharing, retrieving, and validating sample metadata. PEPhub takes advantage of the Portable Encapsulated Projects (PEP) biological metadata standard to store, edit, and access your PEPs in one place. PEPhub consists of two components:

How to use this documentation

We have two types of documentation for PEPhub: user and developer documentation. The user documentation is intended for users who want to learn how to use PEPhub. The developer documentation is intended for developers who want to contribute to the PEPhub codebase or build on top of the PEPhub API and deploy their own instance.



  • Setup: Learn how to set up the PEPhub development environment.
  • Development: Learn about developing the PEPhub API and user interface.
  • Deployment: Learn how to deploy PEPhub.
  • Authentication: Learn about the authentication methods used in PEPhub.
  • Device authentication: Learn about the device authentication method used in PEPhub.
  • Semantic search: Learn about the semantic search functionality in PEPhub.
  • Server settings: Learn about the server settings in PEPhub.
  • PEPembed: Learn about pepembed, the PEP embedding tool for PEPhub.
  • pepdbagent: Learn about pepdbagent, the database driver for PEPhub.
  • PEPhubClient: Learn about PEPhubClient, the command-line tool and Python API for PEPhub.
  • geopephub: Learn about PEPhubs GEO namespace for the gene expression omnibus.